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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Revisiting the taxonomy of the Rattini tribe: a phylogeny-based delimitation of species boundaries</title><author><name sortKey="Pages, Marie" sort="Pages, Marie" uniqKey="Pages M" first="Marie" last="Pagès">Marie Pagès</name><affiliation><nlm:aff id="I1">INRA, UMR CBGP (INRA/IRD/Cirad/Montpellier SupAgro), Campus International de Baillarguet, CS 30016, 34988 Montferrier-sur-Lez cedex, France</nlm:aff></affiliation></author><author><name sortKey="Chaval, Yannick" sort="Chaval, Yannick" uniqKey="Chaval Y" first="Yannick" last="Chaval">Yannick Chaval</name><affiliation><nlm:aff id="I1">INRA, UMR CBGP (INRA/IRD/Cirad/Montpellier SupAgro), Campus International de Baillarguet, CS 30016, 34988 Montferrier-sur-Lez cedex, France</nlm:aff></affiliation></author><author><name sortKey="Herbreteau, Vincent" sort="Herbreteau, Vincent" uniqKey="Herbreteau V" first="Vincent" last="Herbreteau">Vincent Herbreteau</name><affiliation><nlm:aff id="I2">Cemagref, Territories, Environment, Remote Sensing and Spatial Information Joint Research Unit (UMR TETIS), Maison de la Télédétection, 500 rue J-F Breton, 34093 Montpellier Cedex 5, France</nlm:aff></affiliation><affiliation><nlm:aff id="I3">Institut de Recherche pour le Développement (IRD), Research Unit UR178, Center for Vectors and Vector-borne Diseases (CVVD), Faculty of Sciences, Mahidol University, Bangkok 10400, Thailand</nlm:aff></affiliation></author><author><name sortKey="Waengsothorn, Surachit" sort="Waengsothorn, Surachit" uniqKey="Waengsothorn S" first="Surachit" last="Waengsothorn">Surachit Waengsothorn</name><affiliation><nlm:aff id="I4">Thailand Institute of Scientific and Technological Research, Bangkok, Thailand</nlm:aff></affiliation></author><author><name sortKey="Cosson, Jean Francois" sort="Cosson, Jean Francois" uniqKey="Cosson J" first="Jean-François" last="Cosson">Jean-François Cosson</name><affiliation><nlm:aff id="I1">INRA, UMR CBGP (INRA/IRD/Cirad/Montpellier SupAgro), Campus International de Baillarguet, CS 30016, 34988 Montferrier-sur-Lez cedex, France</nlm:aff></affiliation></author><author><name sortKey="Hugot, Jean Pierre" sort="Hugot, Jean Pierre" uniqKey="Hugot J" first="Jean-Pierre" last="Hugot">Jean-Pierre Hugot</name><affiliation><nlm:aff id="I5">Muséum National d'Histoire Naturelle, Origine, Structure et Evolution de la Biodiversité, Paris, France</nlm:aff></affiliation></author><author><name sortKey="Morand, Serge" sort="Morand, Serge" uniqKey="Morand S" first="Serge" last="Morand">Serge Morand</name><affiliation><nlm:aff id="I6">Institut des Sciences de l'Evolution, CNRS-UM2, Université Montpellier 2, 34095 Montpellier, France</nlm:aff></affiliation><affiliation><nlm:aff id="I7">UR AGIRs, CIRAD, Campus International de Baillarguet 34398 Montpellier, France</nlm:aff></affiliation></author><author><name sortKey="Michaux, Johan" sort="Michaux, Johan" uniqKey="Michaux J" first="Johan" last="Michaux">Johan Michaux</name><affiliation><nlm:aff id="I1">INRA, UMR CBGP (INRA/IRD/Cirad/Montpellier SupAgro), Campus International de Baillarguet, CS 30016, 34988 Montferrier-sur-Lez cedex, France</nlm:aff></affiliation><affiliation><nlm:aff id="I8">Laboratoire de génétique des microorganismes, Institut de Botanique, Université de Liège, 4000 Liège (Sart Tilman), Belgique</nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">20565819</idno><idno type="pmc">2906473</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2906473</idno><idno type="RBID">PMC:2906473</idno><idno type="doi">10.1186/1471-2148-10-184</idno><date when="2010">2010</date><idno type="wicri:Area/Pmc/Corpus">000036</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000036</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Revisiting the taxonomy of the Rattini tribe: a phylogeny-based delimitation of species boundaries</title><author><name sortKey="Pages, Marie" sort="Pages, Marie" uniqKey="Pages M" first="Marie" last="Pagès">Marie Pagès</name><affiliation><nlm:aff id="I1">INRA, UMR CBGP (INRA/IRD/Cirad/Montpellier SupAgro), Campus International de Baillarguet, CS 30016, 34988 Montferrier-sur-Lez cedex, France</nlm:aff></affiliation></author><author><name sortKey="Chaval, Yannick" sort="Chaval, Yannick" uniqKey="Chaval Y" first="Yannick" last="Chaval">Yannick Chaval</name><affiliation><nlm:aff id="I1">INRA, UMR CBGP (INRA/IRD/Cirad/Montpellier SupAgro), Campus International de Baillarguet, CS 30016, 34988 Montferrier-sur-Lez cedex, France</nlm:aff></affiliation></author><author><name sortKey="Herbreteau, Vincent" sort="Herbreteau, Vincent" uniqKey="Herbreteau V" first="Vincent" last="Herbreteau">Vincent Herbreteau</name><affiliation><nlm:aff id="I2">Cemagref, Territories, Environment, Remote Sensing and Spatial Information Joint Research Unit (UMR TETIS), Maison de la Télédétection, 500 rue J-F Breton, 34093 Montpellier Cedex 5, France</nlm:aff></affiliation><affiliation><nlm:aff id="I3">Institut de Recherche pour le Développement (IRD), Research Unit UR178, Center for Vectors and Vector-borne Diseases (CVVD), Faculty of Sciences, Mahidol University, Bangkok 10400, Thailand</nlm:aff></affiliation></author><author><name sortKey="Waengsothorn, Surachit" sort="Waengsothorn, Surachit" uniqKey="Waengsothorn S" first="Surachit" last="Waengsothorn">Surachit Waengsothorn</name><affiliation><nlm:aff id="I4">Thailand Institute of Scientific and Technological Research, Bangkok, Thailand</nlm:aff></affiliation></author><author><name sortKey="Cosson, Jean Francois" sort="Cosson, Jean Francois" uniqKey="Cosson J" first="Jean-François" last="Cosson">Jean-François Cosson</name><affiliation><nlm:aff id="I1">INRA, UMR CBGP (INRA/IRD/Cirad/Montpellier SupAgro), Campus International de Baillarguet, CS 30016, 34988 Montferrier-sur-Lez cedex, France</nlm:aff></affiliation></author><author><name sortKey="Hugot, Jean Pierre" sort="Hugot, Jean Pierre" uniqKey="Hugot J" first="Jean-Pierre" last="Hugot">Jean-Pierre Hugot</name><affiliation><nlm:aff id="I5">Muséum National d'Histoire Naturelle, Origine, Structure et Evolution de la Biodiversité, Paris, France</nlm:aff></affiliation></author><author><name sortKey="Morand, Serge" sort="Morand, Serge" uniqKey="Morand S" first="Serge" last="Morand">Serge Morand</name><affiliation><nlm:aff id="I6">Institut des Sciences de l'Evolution, CNRS-UM2, Université Montpellier 2, 34095 Montpellier, France</nlm:aff></affiliation><affiliation><nlm:aff id="I7">UR AGIRs, CIRAD, Campus International de Baillarguet 34398 Montpellier, France</nlm:aff></affiliation></author><author><name sortKey="Michaux, Johan" sort="Michaux, Johan" uniqKey="Michaux J" first="Johan" last="Michaux">Johan Michaux</name><affiliation><nlm:aff id="I1">INRA, UMR CBGP (INRA/IRD/Cirad/Montpellier SupAgro), Campus International de Baillarguet, CS 30016, 34988 Montferrier-sur-Lez cedex, France</nlm:aff></affiliation><affiliation><nlm:aff id="I8">Laboratoire de génétique des microorganismes, Institut de Botanique, Université de Liège, 4000 Liège (Sart Tilman), Belgique</nlm:aff></affiliation></author></analytic><series><title level="j">BMC Evolutionary Biology</title><idno type="eISSN">1471-2148</idno><imprint><date when="2010">2010</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>Rodents are recognized as hosts for at least 60 zoonotic diseases and may represent a serious threat for human health. In the context of global environmental changes and increasing mobility of humans and animals, contacts between pathogens and potential animal hosts and vectors are modified, amplifying the risk of disease emergence. An accurate identification of each rodent at a specific level is needed in order to understand their implications in the transmission of diseases. Among the Muridae, the Rattini tribe encompasses 167 species inhabiting South East Asia, a hotspot of both biodiversity and emerging and re-emerging diseases. The region faces growing economical development that affects habitats, biodiversity and health. Rat species have been demonstrated as significant hosts of pathogens but are still difficult to recognize at a specific level using morphological criteria. DNA-barcoding methods appear as accurate tools for rat species identification but their use is hampered by the need of reliable identification of reference specimens. In this study, we explore and highlight the limits of the current taxonomy of the Rattini tribe.</p></sec><sec><title>Results</title><p>We used the DNA sequence information itself as the primary information source to establish group membership and estimate putative species boundaries. We sequenced two mitochondrial and one nuclear genes from 122 rat samples to perform phylogenetic reconstructions. The method of Pons and colleagues (2006) that determines, with no prior expectations, the locations of ancestral nodes defining putative species was then applied to our dataset. To give an appropriate name to each cluster recognized as a putative species, we reviewed information from the literature and obtained sequences from a museum holotype specimen following the ancient DNA criteria.</p></sec><sec><title>Conclusions</title><p>Using a recently developed methodology, this study succeeds in refining the taxonomy of one of the most difficult groups of mammals. Most of the species expected within the area were retrieved but new putative species limits were also indicated, in particular within <italic>Berylmys </italic>and <italic>Rattus </italic>genera, where future taxonomic studies should be directed. Our study lays the foundations to better investigate rodent-born diseases in South East Asia and illustrates the relevance of evolutionary studies for health and medical sciences.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Morand, S" uniqKey="Morand S">S Morand</name></author><author><name sortKey="Krasnov, Br" uniqKey="Krasnov B">BR Krasnov</name></author><author><name sortKey="Poulin, R" uniqKey="Poulin R">R Poulin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Herbreteau, V" uniqKey="Herbreteau V">V Herbreteau</name></author><author><name sortKey="Henttonen, H" uniqKey="Henttonen H">H Henttonen</name></author><author><name sortKey="Yoshimatsu, K" uniqKey="Yoshimatsu K">K Yoshimatsu</name></author><author><name sortKey="Gonzalez, Jp" uniqKey="Gonzalez J">JP Gonzalez</name></author><author><name sortKey="Suputtamongkol" 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<front><journal-meta><journal-id journal-id-type="nlm-ta">BMC Evol Biol</journal-id><journal-title-group><journal-title>BMC Evolutionary Biology</journal-title></journal-title-group><issn pub-type="epub">1471-2148</issn><publisher><publisher-name>BioMed Central</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">20565819</article-id><article-id pub-id-type="pmc">2906473</article-id><article-id pub-id-type="publisher-id">1471-2148-10-184</article-id><article-id pub-id-type="doi">10.1186/1471-2148-10-184</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group></article-categories><title-group><article-title>Revisiting the taxonomy of the Rattini tribe: a phylogeny-based delimitation of species boundaries</article-title></title-group><contrib-group><contrib contrib-type="author" corresp="yes" id="A1"><name><surname>Pagès</surname><given-names>Marie</given-names></name><xref ref-type="aff" rid="I1">1</xref><email>marie.pages@supagro.inra.fr</email></contrib><contrib contrib-type="author" id="A2"><name><surname>Chaval</surname><given-names>Yannick</given-names></name><xref ref-type="aff" rid="I1">1</xref><email>chaval@supagro.inra.fr</email></contrib><contrib contrib-type="author" id="A3"><name><surname>Herbreteau</surname><given-names>Vincent</given-names></name><xref ref-type="aff" rid="I2">2</xref><xref ref-type="aff" rid="I3">3</xref><email>vincent.herbreteau@teledetection.fr</email></contrib><contrib contrib-type="author" id="A4"><name><surname>Waengsothorn</surname><given-names>Surachit</given-names></name><xref ref-type="aff" rid="I4">4</xref><email>swaengso@gmail.com</email></contrib><contrib contrib-type="author" id="A5"><name><surname>Cosson</surname><given-names>Jean-François</given-names></name><xref ref-type="aff" rid="I1">1</xref><email>cosson@supagro.inra.fr</email></contrib><contrib contrib-type="author" id="A6"><name><surname>Hugot</surname><given-names>Jean-Pierre</given-names></name><xref ref-type="aff" rid="I5">5</xref><email>Jean-Pierre.Hugot@ird.fr</email></contrib><contrib contrib-type="author" id="A7"><name><surname>Morand</surname><given-names>Serge</given-names></name><xref ref-type="aff" rid="I6">6</xref><xref ref-type="aff" rid="I7">7</xref><email>serge.morand@univ-montp2.fr</email></contrib><contrib contrib-type="author" id="A8"><name><surname>Michaux</surname><given-names>Johan</given-names></name><xref ref-type="aff" rid="I1">1</xref><xref ref-type="aff" rid="I8">8</xref><email>michaux@supagro.inra.fr</email></contrib></contrib-group><aff id="I1"><label>1</label>INRA, UMR CBGP (INRA/IRD/Cirad/Montpellier SupAgro), Campus International de Baillarguet, CS 30016, 34988 Montferrier-sur-Lez cedex, France</aff><aff id="I2"><label>2</label>Cemagref, Territories, Environment, Remote Sensing and Spatial Information Joint Research Unit (UMR TETIS), Maison de la Télédétection, 500 rue J-F Breton, 34093 Montpellier Cedex 5, France</aff><aff id="I3"><label>3</label>Institut de Recherche pour le Développement (IRD), Research Unit UR178, Center for Vectors and Vector-borne Diseases (CVVD), Faculty of Sciences, Mahidol University, Bangkok 10400, Thailand</aff><aff id="I4"><label>4</label>Thailand Institute of Scientific and Technological Research, Bangkok, Thailand</aff><aff id="I5"><label>5</label>Muséum National d'Histoire Naturelle, Origine, Structure et Evolution de la Biodiversité, Paris, France</aff><aff id="I6"><label>6</label>Institut des Sciences de l'Evolution, CNRS-UM2, Université Montpellier 2, 34095 Montpellier, France</aff><aff id="I7"><label>7</label>UR AGIRs, CIRAD, Campus International de Baillarguet 34398 Montpellier, France</aff><aff id="I8"><label>8</label>Laboratoire de génétique des microorganismes, Institut de Botanique, Université de Liège, 4000 Liège (Sart Tilman), Belgique</aff><pub-date pub-type="collection"><year>2010</year></pub-date><pub-date pub-type="epub"><day>18</day><month>6</month><year>2010</year></pub-date><volume>10</volume><fpage>184</fpage><lpage>184</lpage><history><date date-type="received"><day>21</day><month>7</month><year>2009</year></date><date date-type="accepted"><day>18</day><month>6</month><year>2010</year></date></history><permissions><copyright-statement>Copyright ©2010 Pagès et al; licensee BioMed Central Ltd.</copyright-statement><copyright-year>2010</copyright-year><copyright-holder>Pagès et al; licensee BioMed Central Ltd.</copyright-holder><license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/2.0"><license-p>This is an Open Access article distributed under the terms of the Creative Commons Attribution License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/2.0">http://creativecommons.org/licenses/by/2.0</ext-link>), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p></license></permissions><self-uri xlink:href="http://www.biomedcentral.com/1471-2148/10/184"></self-uri><abstract><sec><title>Background</title><p>Rodents are recognized as hosts for at least 60 zoonotic diseases and may represent a serious threat for human health. In the context of global environmental changes and increasing mobility of humans and animals, contacts between pathogens and potential animal hosts and vectors are modified, amplifying the risk of disease emergence. An accurate identification of each rodent at a specific level is needed in order to understand their implications in the transmission of diseases. Among the Muridae, the Rattini tribe encompasses 167 species inhabiting South East Asia, a hotspot of both biodiversity and emerging and re-emerging diseases. The region faces growing economical development that affects habitats, biodiversity and health. Rat species have been demonstrated as significant hosts of pathogens but are still difficult to recognize at a specific level using morphological criteria. DNA-barcoding methods appear as accurate tools for rat species identification but their use is hampered by the need of reliable identification of reference specimens. In this study, we explore and highlight the limits of the current taxonomy of the Rattini tribe.</p></sec><sec><title>Results</title><p>We used the DNA sequence information itself as the primary information source to establish group membership and estimate putative species boundaries. We sequenced two mitochondrial and one nuclear genes from 122 rat samples to perform phylogenetic reconstructions. The method of Pons and colleagues (2006) that determines, with no prior expectations, the locations of ancestral nodes defining putative species was then applied to our dataset. To give an appropriate name to each cluster recognized as a putative species, we reviewed information from the literature and obtained sequences from a museum holotype specimen following the ancient DNA criteria.</p></sec><sec><title>Conclusions</title><p>Using a recently developed methodology, this study succeeds in refining the taxonomy of one of the most difficult groups of mammals. Most of the species expected within the area were retrieved but new putative species limits were also indicated, in particular within <italic>Berylmys </italic>and <italic>Rattus </italic>genera, where future taxonomic studies should be directed. Our study lays the foundations to better investigate rodent-born diseases in South East Asia and illustrates the relevance of evolutionary studies for health and medical sciences.</p></sec></abstract></article-meta></front><body><sec><title>Background</title><p>Among mammals, rodents are recognized as major hosts and vectors of parasites and pathogens, some of them causing important zoonoses and representing a serious threat for human health [<xref ref-type="bibr" rid="B1">1</xref>-<xref ref-type="bibr" rid="B5">5</xref>]. Most epidemiological studies have focused on the most common rodents with emphasis on commensal species such as the laboratory rat, <italic>Rattus norvegicus</italic>. A common assumption is that the rodent species responsible for disease transmission are those living close to humans, but since wild species distant from human settlements have been proven to play a key role in maintaining, spreading and transmitting pathogens and parasites (e.g. [<xref ref-type="bibr" rid="B4">4</xref>]), this point of view is being questionned. Specific diversity within the host community has also been shown to play an important function in the maintenance of a disease and in the probability of its transmission to humans [<xref ref-type="bibr" rid="B6">6</xref>,<xref ref-type="bibr" rid="B7">7</xref>]. Consequently, researchers are now focusing not on a single particular host species but on the whole host community and are endeavouring to understand the role of each rodent species in the context of the entire host-pathogen community.</p><p>Today this knowledge is more urgent than ever since biodiversity in many areas is being altered rapidly by the ongoing global change. Because of anthropogenic disturbances, the host-pathogen interactions are being dramatically modified leading to new and unexpected disease risks and the emergence and/or re-emergence of infectious diseases [<xref ref-type="bibr" rid="B6">6</xref>-<xref ref-type="bibr" rid="B10">10</xref>]. To be able to predict and to anticipate some of these risks, one should be able in the case of rodent host communities, to identify first and foremost each rodent at a specific level, a real challenge when considering that rodents represent 40% of mammalian species [<xref ref-type="bibr" rid="B11">11</xref>] including many cryptic species, and that new genera and species are yearly described (<italic>e.g. Laonastes aenigmamus</italic>, [<xref ref-type="bibr" rid="B12">12</xref>]; <italic>Saxatilomys paulinae</italic>, [<xref ref-type="bibr" rid="B13">13</xref>]; <italic>Mayermys germani</italic>, [<xref ref-type="bibr" rid="B14">14</xref>]; <italic>Tonkinomys daovantieni</italic>, [<xref ref-type="bibr" rid="B15">15</xref>]).</p><p>Among Muridae rodents, the Rattini tribe encompasses 35 genera corresponding to 167 rat species [<xref ref-type="bibr" rid="B16">16</xref>] following the tribal arrangement of the Murinae proposed by Lecompte <italic>et al. </italic>[<xref ref-type="bibr" rid="B17">17</xref>]. Nearly all representatives of this tribe inhabit South East Asia, a major hotspot of biodiversity [<xref ref-type="bibr" rid="B18">18</xref>] faced with a runaway economic growth damaging habitats, biodiversity and health but also a hotspot of emerging and re-emerging diseases [<xref ref-type="bibr" rid="B19">19</xref>,<xref ref-type="bibr" rid="B20">20</xref>]. If the partition of the tribe among five divisions (<italic>i.e. </italic><italic>Crunomys, Dacnomys, Maxomys, Micromys </italic>and <italic>Rattus </italic>divisions) [<xref ref-type="bibr" rid="B16">16</xref>,<xref ref-type="bibr" rid="B17">17</xref>] is widely accepted, its taxonomy remains however largely untested phylogenetically and its delimitations are not yet secured. <italic>Chiropodomys</italic>, <italic>Vandeleuria, Hapalomys, Haeromys </italic>and <italic>Vernaya </italic>genera were included in the <italic>Micromys </italic>division by Musser and Carleton [<xref ref-type="bibr" rid="B16">16</xref>]. As the Eurasian harvest mouse, <italic>Micromys </italic>was proven to belong to the Rattini tribe ([<xref ref-type="bibr" rid="B17">17</xref>,<xref ref-type="bibr" rid="B21">21</xref>]), the whole <italic>Micromys </italic>division should belong to the Rattini tribe if Musser and Carleton's assumption is right. However, some of these genera (<italic>i.e. </italic><italic>Chiropodomys </italic>and <italic>Vandeleuria</italic>) were recently shown to be unaffiliated to <italic>Micromys </italic>according to molecular evidences [<xref ref-type="bibr" rid="B21">21</xref>], while putative representatives of the Rattini tribe (<italic>i.e. Tonkinomys daovantieni, Saxatilomys paulinae, Srilankamys sp., Hapalomys sp., Haeromys sp., Vernaya sp.</italic>) have not been investigated using molecular data and are currently considered as Murinae <italic>incertae sedis </italic>[<xref ref-type="bibr" rid="B17">17</xref>]. Numerous rat species have been demonstrated or postulated as major hosts of pathogens (<italic>e.g. </italic>Hantaviruses described from bandicoot rat, <italic>Bandicota indica </italic>in Thailand, [<xref ref-type="bibr" rid="B22">22</xref>,<xref ref-type="bibr" rid="B23">23</xref>]; <italic>Bandicota indica</italic>, <italic>B. savilei</italic>, <italic>Berylmys berdmorei</italic>, <italic>Niviventer sp.</italic>, and <italic>Rattus sp</italic>. serologically tested positive for <italic>Rickettsia tsutsugamushi</italic>, the agent responsible for scrub typhus [<xref ref-type="bibr" rid="B24">24</xref>]; etc.). Although easily identified at a generic level by an expert, Asian rats are often difficult to discriminate at a specific level using morphological or cytological criteria. The wide range of intra-specific morphological variation makes morphological criteria unsuitable for accurate rat species identification and has led to an over-description of species and to a confusing taxonomy, hampered by an overabundance of synonyms. It is particularly true concerning the <italic>Rattus </italic>genus (<italic>e.g. </italic>41 synonyms for <italic>R. norvegicus</italic>, 83 for <italic>R. rattus</italic>, etc. [<xref ref-type="bibr" rid="B16">16</xref>] and see also [<xref ref-type="bibr" rid="B25">25</xref>]) that consists of a heterogeneous accumulation of species and of several monophyletic clusters that may or may not prove to be grouped in a single genus [<xref ref-type="bibr" rid="B16">16</xref>]. This polyphyletic pattern is highlighted by the six species groups proposed by Musser and Carleton [<xref ref-type="bibr" rid="B16">16</xref>] (<italic>i.e. </italic>the <italic>Rattus rattus</italic>, <italic>Rattus exulans</italic>, <italic>Rattus norvegicus</italic>, <italic>Rattus fuscipes</italic>, <italic>Rattus leucopus </italic>and <italic>Rattus xanthurus </italic>species groups) and a seventh assemblage containing unaffiliated species (<italic>i.e. </italic>the <italic>Rattus </italic>species group unresolved) for which phylogenetic affinities are uncertain; some representatives will eventually be removed from the genus. Even karyotypic criteria, which previously claimed to be species diagnostic tools, were recently revealed to be unsuitable to discriminate between Asian rat species [<xref ref-type="bibr" rid="B26">26</xref>]. DNA-based methods, however, appear to be promising tools for easy and accurate rat species-specific identifications [<xref ref-type="bibr" rid="B26">26</xref>].</p><p>Robins <italic>et al. </italic>[<xref ref-type="bibr" rid="B25">25</xref>] were the first to attempt to identify <italic>Rattus </italic>species using mitochondrial DNA sequences mostly obtained from museum tissue samples. Nevertheless, their conclusions based on DNA-barcoding and tree based methods were limited because these methods need reliably identified specimens as reference. Specimens and tissues offered by museums to scientists are collected by many different people and it seems likely, given the extent of some misidentifications, that rat species identification is not an easy task even for mammal specialists. Moreover, the taxonomy of the tribe Rattini is complex and changing and often different to that in use when samples were first described and listed in museums [<xref ref-type="bibr" rid="B25">25</xref>].</p><p>Level of variation in cytochrome <italic>b </italic>sequences was also proposed as a reference point in making decisions concerning species-level distinctions [<xref ref-type="bibr" rid="B27">27</xref>]. Based on the analysis of 4 genera of rodents, Bradley and Baker [<xref ref-type="bibr" rid="B27">27</xref>] suggested that genetic distance values lesser than 2% were indicative of intraspecific variation and values higher than 11% of species recognition. But how to conclude between 2 and 11% ? The DNA-based species delimitation approach proposed by Pons <italic>et al. </italic>[<xref ref-type="bibr" rid="B28">28</xref>] relies on DNA sequence information itself as the primary information source for establishing group membership and defining putative species and does not require defining entities as priors. This method was shown to be useful for identifying meaningful entities among groups whose current taxonomy is incomplete (<italic>e.g</italic>. tiger beetles of the genus <italic>Rivacindela</italic>, [<xref ref-type="bibr" rid="B28">28</xref>]) or uncertain (<italic>e.g</italic>. aphids of the genus <italic>Brachycaudus</italic>) and has already been successfully applied when species are difficult to conceptualize (<italic>e.g. </italic>bacteria [<xref ref-type="bibr" rid="B29">29</xref>] or for asexual animals, [<xref ref-type="bibr" rid="B30">30</xref>,<xref ref-type="bibr" rid="B31">31</xref>]). Using a likelihood framework, this new procedure detects the point of transition in the rate of lineage branching of a tree from interspecific long branches to intraspecific short burgeoning branching and identifies clusters of specimens corresponding to putative species.</p><p>In our study, we used molecular data to test the limits of the current taxonomy of the Rattini tribe. We aimed at identifying where species boundaries are unclear and where further investigations need to be carried out to provide a more rigorous systematic framework for epidemiological surveys. As molecular data are useful to detect and distinguish morphologically similar species, this study investigated the existence of putative cryptic species among the Rattini tribe (<italic>i.e</italic>. two or more species that are classified as a single nominal species because they are at least superficially morphologically indistinguishable [<xref ref-type="bibr" rid="B32">32</xref>]). To these aims, we first sequenced two mitochondrial and one nuclear genes from rat specimens coming from Southeast Asia (Thailand, Cambodia and Lao People's Democratic Republic) to perform phylogenetic reconstructions. Then, as morphological characters are often misleading, we applied the method developed by Pons <italic>et al. </italic>[<xref ref-type="bibr" rid="B28">28</xref>] that determines, with no prior expectations, the locations of ancestral nodes to define putative species. Finally, we endeavoured to give a name to each cluster recognized as a putative species using information from the literature and also sequences obtained from a museum holotype specimen following all the ancient DNA guidelines.</p></sec><sec sec-type="methods"><title>Methods</title><sec><title>1. Sampling</title><p>116 specimens of Rattini were selected among the 3,000 trapped by our team in the fields mostly in Thailand and punctually in Cambodia and in Lao PDR. Specimens selected were chosen in order to maximise the number of species and geographic locations analysed. Field specimen identifications and locality information are listed in Table <xref ref-type="table" rid="T1">1</xref> and indicated in Figure <xref ref-type="fig" rid="F1">1</xref>. Field identifications were made based on morphological criteria according to [<xref ref-type="bibr" rid="B11">11</xref>,<xref ref-type="bibr" rid="B33">33</xref>-<xref ref-type="bibr" rid="B35">35</xref>]. Based on morphological and cytological evidences, no specimen was identified by us as a representative of the cosmopolitan <italic>Rattus rattus </italic>species. Considering their preponderant place in epidemiological surveys, 4 worldwide black rat specimens (identified in [<xref ref-type="bibr" rid="B36">36</xref>]) were added to the sample set. To provide an appropriate outgroup, we included specimens of the Eurasian harvest mouse, <italic>Micromys </italic>belonging to the Rattini tribe and previously recognized as the sister lineage to the <italic>Rattus </italic>group sensu lato of Verneau <italic>et al.</italic>, [<xref ref-type="bibr" rid="B37">37</xref>,<xref ref-type="bibr" rid="B38">38</xref>,<xref ref-type="bibr" rid="B17">17</xref>,<xref ref-type="bibr" rid="B21">21</xref>]. In total, our taxa sampling consisted of 122 rats.</p><table-wrap id="T1" position="float"><label>Table 1</label><caption><p>Samples used in this study.</p></caption><table frame="hsides" rules="groups"><thead><tr><th align="left" colspan="2"><italic>Sample information</italic></th><th></th><th></th><th></th><th align="left" colspan="3"><italic>GenBank Accession Number</italic></th></tr><tr><th align="left">Laboratory sample number</th><th align="left">Field Identification</th><th align="left">Locality</th><th align="left">Voucher localisation</th><th align="left">Phylogenetic species</th><th align="left">Cyt b</th><th align="left">COI</th><th align="left">IRBP</th></tr></thead><tbody><tr><td align="left">MDZ10Mada</td><td align="left"><italic>Rattus rattus</italic></td><td align="left">Madagascar</td><td></td><td align="left">R1</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217368">HM217368</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217495">HM217495</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217603">HM217603</ext-link></td></tr><tr><td align="left">ratcosT820</td><td align="left"><italic>Rattus rattus</italic></td><td align="left">India</td><td></td><td align="left">R1</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217367">HM217367</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217498">HM217498</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217606">HM217606</ext-link></td></tr><tr><td align="left">ratcosR12</td><td align="left"><italic>Rattus rattus</italic></td><td align="left">Oman</td><td></td><td align="left">R1</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217366">HM217366</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217496">HM217496</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217604">HM217604</ext-link></td></tr><tr><td align="left">ratcosTE4264</td><td align="left"><italic>Rattus rattus</italic></td><td align="left">Tanzania</td><td></td><td align="left">R1</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217365">HM217365</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217497">HM217497</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217605">HM217605</ext-link></td></tr><tr><td colspan="8"><hr></hr></td></tr><tr><td align="left">R4003</td><td align="left"><italic>Rattus tanezumi</italic></td><td align="left">Kalasin (Thailand)</td><td align="left">MahaU</td><td align="left">R2</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217436">HM217436</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217563">HM217563</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217673">HM217673</ext-link></td></tr><tr><td align="left"><bold>R2953</bold></td><td align="left"><bold><italic>Rattus tanezumi</italic></bold></td><td align="left"><bold>Kanchanaburi (Thailand)</bold></td><td></td><td align="left">R7</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217396">HM217396</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217525">HM217525</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217634">HM217634</ext-link></td></tr><tr><td align="left">R2996</td><td align="left"><italic>Rattus tanezumi</italic></td><td align="left">Kanchanaburi (Thailand)</td><td></td><td align="left">R2</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217398">HM217398</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217529">HM217529</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217636">HM217636</ext-link></td></tr><tr><td align="left">R3122</td><td align="left"><italic>Rattus tanezumi</italic></td><td align="left">Kanchanaburi (Thailand)</td><td></td><td align="left">R2</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217407">HM217407</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217537">HM217537</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217645">HM217645</ext-link></td></tr><tr><td align="left">R3214</td><td align="left"><italic>Rattus tanezumi</italic></td><td align="left">Kanchanaburi (Thailand)</td><td></td><td align="left">R2</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217410">HM217410</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217540">HM217540</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217648">HM217648</ext-link></td></tr><tr><td align="left">R3573</td><td align="left"><italic>Rattus tanezumi</italic></td><td align="left">Nakhon Pathom (Thailand)</td><td align="left">KU</td><td align="left">R2</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217430">HM217430</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217558">HM217558</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217667">HM217667</ext-link></td></tr><tr><td align="left">R4016</td><td align="left"><italic>Rattus tanezumi</italic></td><td align="left">Phrae (Thailand)</td><td align="left">CBGP</td><td align="left">R2</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217438">HM217438</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217565">HM217565</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217675">HM217675</ext-link></td></tr><tr><td align="left">R4424</td><td align="left"><italic>Rattus tanezumi</italic></td><td align="left">Phrae (Thailand)</td><td align="left">MahaU</td><td align="left">R2</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217456">HM217456</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217582">HM217582</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217693">HM217693</ext-link></td></tr><tr><td align="left">R4436</td><td align="left"><italic>Rattus tanezumi</italic></td><td align="left">Phrae (Thailand)</td><td align="left">MahaU</td><td align="left">R2</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217457">HM217457</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217583">HM217583</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217694">HM217694</ext-link></td></tr><tr><td align="left">R5294</td><td align="left"><italic>Rattus tanezumi</italic></td><td align="left">Nan (Thailand)</td><td align="left">MahaU</td><td align="left">R2</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217466">HM217466</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217592">HM217592</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217704">HM217704</ext-link></td></tr><tr><td align="left">R5296</td><td align="left"><italic>Rattus tanezumi</italic></td><td align="left">Nan (Thailand)</td><td align="left">CBGP</td><td align="left">R2</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217467">HM217467</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217593">HM217593</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217705">HM217705</ext-link></td></tr><tr><td align="left">L0100</td><td align="left"><italic>Rattus tanezumi</italic></td><td align="left">Luang Prabang (LPDR)</td><td align="left">MahaU</td><td align="left">R2</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217475">HM217475</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217489">HM217489</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217712">HM217712</ext-link></td></tr><tr><td align="left">L0194</td><td align="left"><italic>Rattus tanezumi</italic></td><td align="left">Luang Prabang (LPDR)</td><td align="left">MahaU</td><td align="left">R2</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217480">HM217480</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217494">HM217494</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217717">HM217717</ext-link></td></tr><tr><td align="left"><bold>R3029</bold></td><td align="left"><bold><italic>Rattus tanezumi</italic></bold></td><td align="left"><bold>Bangkok (Thailand)</bold></td><td></td><td align="left"><bold>R3</bold></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217399">HM217399</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217530">HM217530</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217637">HM217637</ext-link></td></tr><tr><td align="left"><bold>R1843</bold></td><td align="left"><bold><italic>Rattus tanezumi</italic></bold></td><td align="left"><bold>Krabi (Thailand)</bold></td><td></td><td align="left"><bold>R3</bold></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217393">HM217393</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217524">HM217524</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217631">HM217631</ext-link></td></tr><tr><td align="left"><bold>R1147</bold></td><td align="left"><bold><italic>Rattus tanezumi</italic></bold></td><td align="left"><bold>Nakhon Ratchasima (Thailand)</bold></td><td></td><td align="left"><bold>R3</bold></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217384">HM217384</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217515">HM217515</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217622">HM217622</ext-link></td></tr><tr><td align="left"><bold>R1016</bold></td><td align="left"><bold><italic>Rattus tanezumi</italic></bold></td><td align="left"><bold>Nakhon Ratchasima (Thailand)</bold></td><td></td><td align="left"><bold>R3</bold></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217382">HM217382</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217513">HM217513</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217620">HM217620</ext-link></td></tr><tr><td align="left"><bold>R1818</bold></td><td align="left"><bold><italic>Rattus tanezumi</italic></bold></td><td align="left"><bold>Prachinburi (Thailand)</bold></td><td></td><td align="left"><bold>R3</bold></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217389">HM217389</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217520">HM217520</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217627">HM217627</ext-link></td></tr><tr><td align="left"><bold>R2794</bold></td><td align="left"><bold><italic>Rattus tanezumi</italic></bold></td><td align="left"><bold>Ratchaburi (Thailand)</bold></td><td></td><td align="left"><bold>R3</bold></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217394">HM217394</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217526">HM217526</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217632">HM217632</ext-link></td></tr><tr><td align="left"><bold>R0169</bold></td><td align="left"><bold><italic>Rattus tanezumi</italic></bold></td><td align="left"><bold>Ratchaburi (Thailand)</bold></td><td></td><td align="left"><bold>R3</bold></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217372">HM217372</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217503">HM217503</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217610">HM217610</ext-link></td></tr><tr><td align="left"><bold>CB0028</bold></td><td align="left"><bold><italic>Rattus tanezumi</italic></bold></td><td align="left"><bold>Veal Renh (Cambodia)</bold></td><td align="left">MahaU</td><td align="left"><bold>R3</bold></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217363">HM217363</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217485">HM217485</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217601">HM217601</ext-link></td></tr><tr><td align="left"><bold>R1833</bold></td><td align="left"><bold><italic>Rattus tanezumi</italic></bold></td><td align="left"><bold>Nakhon Sri Thammarat (Thailand)</bold></td><td></td><td align="left">R5</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217391">HM217391</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217522">HM217522</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217629">HM217629</ext-link></td></tr><tr><td colspan="8"><hr></hr></td></tr><tr><td align="left">R4402</td><td align="left"><italic>Rattus losea</italic></td><td align="left">Loei (Thailand)</td><td align="left">MahaU</td><td align="left">R4</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217454">HM217454</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217581">HM217581</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217691">HM217691</ext-link></td></tr><tr><td align="left">R3484</td><td align="left"><italic>Rattus losea</italic></td><td align="left">Loei (Thailand)</td><td></td><td align="left">R4</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217421">HM217421</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217550">HM217550</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217659">HM217659</ext-link></td></tr><tr><td align="left">R4230</td><td align="left"><italic>Rattus losea</italic></td><td align="left">Loei (Thailand)</td><td align="left">CBGP</td><td align="left">R4</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217446">HM217446</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217573">HM217573</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217683">HM217683</ext-link></td></tr><tr><td align="left">R1015</td><td align="left"><italic>Rattus losea</italic></td><td align="left">Nakhon Ratchasima (Thailand)</td><td></td><td align="left">R4</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217381">HM217381</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217512">HM217512</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217619">HM217619</ext-link></td></tr><tr><td align="left">R4203</td><td align="left"><italic>Rattus losea</italic></td><td align="left">Phrae (Thailand)</td><td align="left">CBGP</td><td align="left">R4</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217443">HM217443</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217570">HM217570</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217680">HM217680</ext-link></td></tr><tr><td align="left">R3510</td><td align="left"><italic>Rattus losea</italic></td><td align="left">Phrae (Thailand)</td><td></td><td align="left">R4</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217423">HM217423</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217552">HM217552</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217661">HM217661</ext-link></td></tr><tr><td align="left">R0237</td><td align="left"><italic>Rattus losea</italic></td><td align="left">Ratchaburi (Thailand)</td><td></td><td align="left">R4</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217374">HM217374</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217505">HM217505</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217612">HM217612</ext-link></td></tr><tr><td align="left">R0238</td><td align="left"><italic>Rattus losea</italic></td><td align="left">Ratchaburi (Thailand)</td><td></td><td align="left">R4</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217375">HM217375</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217506">HM217506</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217613">HM217613</ext-link></td></tr><tr><td colspan="8"><hr></hr></td></tr><tr><td align="left">R1805</td><td align="left"><italic>Rattus exulans</italic></td><td align="left">Bangkok (Thailand)</td><td></td><td align="left">R8</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217388">HM217388</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217519">HM217519</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217626">HM217626</ext-link></td></tr><tr><td align="left">R4004</td><td align="left"><italic>Rattus exulans</italic></td><td align="left">Kalasin (Thailand)</td><td align="left">MahaU</td><td align="left">R8</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217437">HM217437</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217564">HM217564</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217674">HM217674</ext-link></td></tr><tr><td align="left">R3224</td><td align="left"><italic>Rattus exulans</italic></td><td align="left">Kanchanaburi (Thailand)</td><td></td><td align="left">R8</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217411">HM217411</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217541">HM217541</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217649">HM217649</ext-link></td></tr><tr><td align="left">R4103</td><td align="left"><italic>Rattus exulans</italic></td><td align="left">Loei (Thailand)</td><td align="left">MahaU</td><td align="left">R8</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217440">HM217440</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217567">HM217567</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217677">HM217677</ext-link></td></tr><tr><td align="left">R1055</td><td align="left"><italic>Rattus exulans</italic></td><td align="left">Nakhon Ratchasima (Thailand)</td><td></td><td align="left">R8</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217383">HM217383</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217514">HM217514</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217621">HM217621</ext-link></td></tr><tr><td align="left">R1836</td><td align="left"><italic>Rattus exulans</italic></td><td align="left">Nakhon Sri Thammarat (Thailand)</td><td></td><td align="left">R8</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217392">HM217392</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217523">HM217523</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217630">HM217630</ext-link></td></tr><tr><td align="left">R4140</td><td align="left"><italic>Rattus exulans</italic></td><td align="left">Phrae (Thailand)</td><td align="left">MahaU</td><td align="left">R8</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217441">HM217441</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217568">HM217568</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217678">HM217678</ext-link></td></tr><tr><td align="left">R0284</td><td align="left"><italic>Rattus exulans</italic></td><td align="left">Ratchaburi (Thailand)</td><td></td><td align="left">R8</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217377">HM217377</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217508">HM217508</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217615">HM217615</ext-link></td></tr><tr><td align="left">R2795</td><td align="left"><italic>Rattus exulans</italic></td><td align="left">Ratchaburi (Thailand)</td><td></td><td align="left">R8</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217395">HM217395</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217527">HM217527</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217633">HM217633</ext-link></td></tr><tr><td align="left">R3520</td><td align="left"><italic>Rattus exulans</italic></td><td align="left">Sakhon Nakhon (Thailand)</td><td align="left">MahiU</td><td align="left">R8</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217424">HM217424</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217553">HM217553</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217662">HM217662</ext-link></td></tr><tr><td align="left">R3563</td><td align="left"><italic>Rattus exulans</italic></td><td align="left">Surat Thani (Thailand)</td><td align="left">KU</td><td align="left">R8</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217428">HM217428</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217557">HM217557</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217666">HM217666</ext-link></td></tr><tr><td align="left">R5349</td><td align="left"><italic>Rattus exulans</italic></td><td align="left">Nan (Thailand)</td><td align="left">CBGP</td><td align="left">R8</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217470">HM217470</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217595">HM217595</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217703">HM217703</ext-link></td></tr><tr><td align="left">R5447</td><td align="left"><italic>Rattus exulans</italic></td><td align="left">Nan (Thailand)</td><td align="left">CBGP</td><td align="left">R8</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217472">HM217472</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217596">HM217596</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217708">HM217708</ext-link></td></tr><tr><td colspan="8"><hr></hr></td></tr><tr><td align="left">CB0001</td><td align="left"><italic>Rattus argentiventer</italic></td><td align="left">Veal Renh (Cambodia)</td><td align="left">MahaU</td><td align="left">R6</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217362">HM217362</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217484">HM217484</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217600">HM217600</ext-link></td></tr><tr><td align="left">CB0104</td><td align="left"><italic>Rattus argentiventer</italic></td><td align="left">Veal Renh (Cambodia)</td><td align="left">MahaU</td><td align="left">R6</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217364">HM217364</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217486">HM217486</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217602">HM217602</ext-link></td></tr><tr><td colspan="8"><hr></hr></td></tr><tr><td align="left">R3087</td><td align="left"><italic>Rattus andamanensis</italic></td><td align="left">Kanchanaburi (Thailand)</td><td></td><td align="left">R7</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217403">HM217403</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217533">HM217533</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217641">HM217641</ext-link></td></tr><tr><td align="left"><bold>R4377</bold></td><td align="left"><bold><italic>Rattus andamanensis</italic></bold></td><td align="left"><bold>Loei (Thailand)</bold></td><td align="left">MahaU</td><td align="left">R2</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217452">HM217452</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217579">HM217579</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217689">HM217689</ext-link></td></tr><tr><td align="left"><bold>R3548</bold></td><td align="left"><bold><italic>Rattus andamanensis</italic></bold></td><td align="left"><bold>Phrae (Thailand)</bold></td><td align="left">KU</td><td align="left">R2</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217426">HM217426</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217555">HM217555</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217664">HM217664</ext-link></td></tr><tr><td align="left"><bold>R4481</bold></td><td align="left"><bold><italic>Rattus andamanensis</italic></bold></td><td align="left"><bold>Phrae (Thailand)</bold></td><td align="left">MahaU</td><td align="left">R2</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217458">HM217458</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217584">HM217584</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217695">HM217695</ext-link></td></tr><tr><td align="left"><bold>R0130</bold></td><td align="left"><bold><italic>Rattus andamanensis</italic></bold></td><td align="left"><bold>Ratchaburi (Thailand)</bold></td><td></td><td align="left">R2</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217371">HM217371</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217502">HM217502</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217608">HM217608</ext-link></td></tr><tr><td align="left"><bold>R2976</bold></td><td align="left"><bold><italic>Rattus andamanensis</italic></bold></td><td align="left"><bold>Nakhon Pathom (Thailand)</bold></td><td></td><td align="left"><bold>R3</bold></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217397">HM217397</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217528">HM217528</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217635">HM217635</ext-link></td></tr><tr><td colspan="8"><hr></hr></td></tr><tr><td align="left">R3565</td><td align="left"><italic>Rattus norvegicus</italic></td><td align="left">Nakhon Pathom (Thailand)</td><td align="left">MahiU</td><td align="left">R9</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217429">HM217429</ext-link></td><td align="left">-</td><td align="left">-</td></tr><tr><td align="left">R0223</td><td align="left"><italic>Rattus norvegicus</italic></td><td align="left">Ratchaburi (Thailand)</td><td></td><td align="left">R9</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217373">HM217373</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217504">HM217504</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217611">HM217611</ext-link></td></tr><tr><td align="left">R0115</td><td align="left"><italic>Rattus norvegicus</italic></td><td align="left">Ratchaburi (Thailand)</td><td></td><td align="left">R9</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217370">HM217370</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217501">HM217501</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217609">HM217609</ext-link></td></tr><tr><td align="left">RNO 032</td><td align="left"><italic>Rattus norvegicus</italic></td><td align="left">Cambodia</td><td></td><td align="left">R9</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217481">HM217481</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217499">HM217499</ext-link></td><td align="left">-</td></tr><tr><td colspan="8"><hr></hr></td></tr><tr><td align="left">L0180</td><td align="left"><italic>Rattus nitidus</italic></td><td align="left">Luang Prabang (LPDR)</td><td align="left">MahaU</td><td align="left">R10</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217478">HM217478</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217492">HM217492</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217715">HM217715</ext-link></td></tr><tr><td align="left">L0192</td><td align="left"><italic>Rattus nitidus</italic></td><td align="left">Luang Prabang (LPDR)</td><td align="left">MahaU</td><td align="left">R10</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217479">HM217479</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217493">HM217493</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217716">HM217716</ext-link></td></tr><tr><td colspan="8"><hr></hr></td></tr><tr><td align="left">R4188</td><td align="left"><italic>Rattus sp.</italic></td><td align="left">Phrae (Thailand)</td><td align="left">CBGP</td><td align="left"><bold>R3</bold></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217442">HM217442</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217569">HM217569</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217679">HM217679</ext-link></td></tr><tr><td align="left">L0010</td><td align="left"><italic>Rattus sp.</italic></td><td align="left">Luang Prabang (LPDR)</td><td align="left">MahaU</td><td align="left">R10</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217474">HM217474</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217488">HM217488</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217711">HM217711</ext-link></td></tr><tr><td align="left"><bold>R0856</bold></td><td align="left"><bold><italic>Bandicota indica</italic></bold></td><td align="left"><bold>Nakhon Pathom (Thailand)</bold></td><td></td><td align="left">R8</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217379">HM217379</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217510">HM217510</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217617">HM217617</ext-link></td></tr><tr><td align="left">R4001</td><td align="left"><italic>Bandicota indica</italic></td><td align="left">Kalasin (Thailand)</td><td align="left">MahaU</td><td align="left">B1</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217435">HM217435</ext-link></td><td align="left">-</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217672">HM217672</ext-link></td></tr><tr><td align="left">R3189</td><td align="left"><italic>Bandicota indica</italic></td><td align="left">Kanchanaburi (Thailand)</td><td></td><td align="left">B1</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217408">HM217408</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217538">HM217538</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217646">HM217646</ext-link></td></tr><tr><td align="left">R4265</td><td align="left"><italic>Bandicota indica</italic></td><td align="left">Loei (Thailand)</td><td align="left">CBGP</td><td align="left">B1</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217447">HM217447</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217574">HM217574</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217684">HM217684</ext-link></td></tr><tr><td align="left">R1006</td><td align="left"><italic>Bandicota indica</italic></td><td align="left">Nakhon Ratchasima (Thailand)</td><td></td><td align="left">B1</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217380">HM217380</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217511">HM217511</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217618">HM217618</ext-link></td></tr><tr><td align="left">R3521</td><td align="left"><italic>Bandicota indica</italic></td><td align="left">Phrae (Thailand)</td><td align="left">KU</td><td align="left">B1</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217425">HM217425</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217554">HM217554</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217663">HM217663</ext-link></td></tr><tr><td align="left">R0269</td><td align="left"><italic>Bandicota indica</italic></td><td align="left">Ratchaburi (Thailand)</td><td></td><td align="left">B1</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217376">HM217376</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217507">HM217507</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217614">HM217614</ext-link></td></tr><tr><td align="left">R0304</td><td align="left"><italic>Bandicota indica</italic></td><td align="left">Ratchaburi (Thailand)</td><td></td><td align="left">B1</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217378">HM217378</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217509">HM217509</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217616">HM217616</ext-link></td></tr><tr><td align="left">R5313</td><td align="left"><italic>Bandicota indica</italic></td><td align="left">Nan (Thailand)</td><td align="left">MahaU</td><td align="left">B1</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217469">HM217469</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217594">HM217594</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217706">HM217706</ext-link></td></tr><tr><td align="left">L0142</td><td align="left"><italic>Bandicota indica</italic></td><td align="left">Luang Prabang (LPDR)</td><td align="left">MahaU</td><td align="left">B1</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217476">HM217476</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217490">HM217490</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217713">HM217713</ext-link></td></tr><tr><td align="left"><bold>R4408</bold></td><td align="left"><bold><italic>Bandicota indica</italic></bold></td><td align="left"><bold>Loei (Thailand)</bold></td><td align="left">CBGP</td><td align="left">B2</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217455">HM217455</ext-link></td><td align="left">-</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217692">HM217692</ext-link></td></tr><tr><td colspan="8"><hr></hr></td></tr><tr><td align="left"><bold>R1284</bold></td><td align="left"><bold><italic>Bandicota savilei</italic></bold></td><td align="left"><bold>Nakhon Ratchasima (Thailand)</bold></td><td></td><td align="left">B1</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217386">HM217386</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217517">HM217517</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217624">HM217624</ext-link></td></tr><tr><td align="left"><bold>R1822</bold></td><td align="left"><bold><italic>Bandicota savilei</italic></bold></td><td align="left"><bold>Nakhon Pathom (Thailand)</bold></td><td></td><td align="left">B1</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217390">HM217390</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217521">HM217521</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217628">HM217628</ext-link></td></tr><tr><td align="left">R1797</td><td align="left"><italic>Bandicota savilei</italic></td><td align="left">Kanchanaburi (Thailand)</td><td></td><td align="left">B2</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217387">HM217387</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217518">HM217518</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217625">HM217625</ext-link></td></tr><tr><td align="left">R1191</td><td align="left"><italic>Bandicota savilei</italic></td><td align="left">Nakhon Ratchasima (Thailand)</td><td></td><td align="left">B2</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217385">HM217385</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217516">HM217516</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217623">HM217623</ext-link></td></tr><tr><td align="left">R3550</td><td align="left"><italic>Bandicota savilei</italic></td><td align="left">Phrae (Thailand)</td><td align="left">KU</td><td align="left">B2</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217427">HM217427</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217556">HM217556</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217665">HM217665</ext-link></td></tr><tr><td colspan="8"><hr></hr></td></tr><tr><td align="left">R0093</td><td align="left"><italic>Bandicota sp.</italic></td><td align="left">Ratchaburi (Thailand)</td><td></td><td align="left">B2</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217369">HM217369</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217500">HM217500</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217607">HM217607</ext-link></td></tr><tr><td colspan="8"><hr></hr></td></tr><tr><td align="left">R3050</td><td align="left"><italic>Berylmys berdmorei</italic></td><td align="left">Kanchanaburi (Thailand)</td><td></td><td align="left">Be1</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217401">HM217401</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217532">HM217532</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217639">HM217639</ext-link></td></tr><tr><td align="left">R4266</td><td align="left"><italic>Berylmys berdmorei</italic></td><td align="left">Loei (Thailand)</td><td align="left">CBGP</td><td align="left">Be1</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217448">HM217448</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217575">HM217575</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217685">HM217685</ext-link></td></tr><tr><td align="left">R3441</td><td align="left"><italic>Berylmys berdmorei</italic></td><td align="left">Loei (Thailand)</td><td align="left">MahiU</td><td align="left">Be1</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217418">HM217418</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217547">HM217547</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217656">HM217656</ext-link></td></tr><tr><td align="left">R5310</td><td align="left"><italic>Berylmys berdmorei</italic></td><td align="left">Nan (Thailand)</td><td align="left">MahaU</td><td align="left">Be1</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217468">HM217468</ext-link></td><td align="left">-</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217709">HM217709</ext-link></td></tr><tr><td align="left">L0006</td><td align="left"><italic>Berylmys berdmorei</italic></td><td align="left">Luang Prabang (LPDR)</td><td align="left">MahaU</td><td align="left">Be1</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217473">HM217473</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217487">HM217487</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217710">HM217710</ext-link></td></tr><tr><td align="left">R3618</td><td align="left"><italic>Berylmys berdmorei</italic></td><td align="left">Phrae (Thailand)</td><td align="left">KU</td><td align="left">Be1</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217432">HM217432</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217560">HM217560</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217669">HM217669</ext-link></td></tr><tr><td align="left">R3603</td><td align="left"><italic>Berylmys berdmorei</italic></td><td align="left">Phrae (Thailand)</td><td align="left">KU</td><td align="left">Be1</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217431">HM217431</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217559">HM217559</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217668">HM217668</ext-link></td></tr><tr><td colspan="8"><hr></hr></td></tr><tr><td align="left">R4400</td><td align="left"><italic>Berylmys bowersi</italic></td><td align="left">Loei (Thailand)</td><td align="left">MahaU</td><td align="left">Be2, a</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217453">HM217453</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217580">HM217580</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217690">HM217690</ext-link></td></tr><tr><td align="left">R3425</td><td align="left"><italic>Berylmys bowersi</italic></td><td align="left">Loei (Thailand)</td><td align="left">KU</td><td align="left">Be2, a</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217415">HM217415</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217544">HM217544</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217653">HM217653</ext-link></td></tr><tr><td align="left">R3415</td><td align="left"><italic>Berylmys bowersi</italic></td><td align="left">Loei (Thailand)</td><td align="left">KU</td><td align="left">Be2, a</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217413">HM217413</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217542">HM217542</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217651">HM217651</ext-link></td></tr><tr><td align="left">R5410</td><td align="left"><italic>Berylmys bowersi</italic></td><td align="left">Nan (Thailand)</td><td align="left">MahaU</td><td align="left">Be2, a</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217471">HM217471</ext-link></td><td align="left">-</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217707">HM217707</ext-link></td></tr><tr><td align="left">L0151</td><td align="left"><italic>Berylmys bowersi</italic></td><td align="left">Luang Prabang (LPDR)</td><td align="left">MahaU</td><td align="left">Be2, a</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217477">HM217477</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217491">HM217491</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217714">HM217714</ext-link></td></tr><tr><td align="left"><bold>R3268</bold></td><td align="left"><bold><italic>Berylmys bowersi</italic></bold></td><td align="left"><bold>Kanchanaburi (Thailand)</bold></td><td align="left">KU</td><td align="left">Be2, b</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217412">HM217412</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217597">HM217597</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217650">HM217650</ext-link></td></tr><tr><td colspan="8"><hr></hr></td></tr><tr><td align="left"><bold>R4098</bold></td><td align="left"><bold><italic>Leopoldamys sabanus</italic></bold></td><td align="left"><bold>Loei (Thailand)</bold></td><td align="left">CBGP</td><td align="left">L1</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217439">HM217439</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217566">HM217566</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217676">HM217676</ext-link></td></tr><tr><td align="left"><bold>R4222</bold></td><td align="left"><bold><italic>Leopoldamys sabanus</italic></bold></td><td align="left"><bold>Loei (Thailand)</bold></td><td align="left">MahaU</td><td align="left">L1</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217444">HM217444</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217571">HM217571</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217681">HM217681</ext-link></td></tr><tr><td align="left"><bold>R4296</bold></td><td align="left"><bold><italic>Leopoldamys sabanus</italic></bold></td><td align="left"><bold>Phrae (Thailand)</bold></td><td align="left">MahaU</td><td align="left">L1</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217450">HM217450</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217577">HM217577</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217687">HM217687</ext-link></td></tr><tr><td align="left"><bold>R4276</bold></td><td align="left"><bold><italic>Leopoldamys sabanus</italic></bold></td><td align="left"><bold>Phrae (Thailand)</bold></td><td align="left">CBGP</td><td align="left">L1</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217449">HM217449</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217576">HM217576</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217686">HM217686</ext-link></td></tr><tr><td align="left"><bold>R4370</bold></td><td align="left"><bold><italic>Leopoldamys sabanus</italic></bold></td><td align="left"><bold>Phrae (Thailand)</bold></td><td align="left">CBGP</td><td align="left">L1</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217451">HM217451</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217578">HM217578</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217688">HM217688</ext-link></td></tr><tr><td align="left">R3111</td><td align="left"><italic>Leopoldamys sabanus</italic></td><td align="left">Kanchanaburi (Thailand)</td><td></td><td align="left">L3</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217404">HM217404</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217534">HM217534</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217642">HM217642</ext-link></td></tr><tr><td align="left">R3033</td><td align="left"><italic>Leopoldamys sabanus</italic></td><td align="left">Kanchanaburi (Thailand)</td><td></td><td align="left">L3</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217400">HM217400</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217531">HM217531</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217638">HM217638</ext-link></td></tr><tr><td colspan="8"><hr></hr></td></tr><tr><td align="left">R4517</td><td align="left"><italic>Leopoldamys neilli</italic></td><td align="left">Loei (Thailand)</td><td align="left">MahaU</td><td align="left">L2</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217462">HM217462</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217588">HM217588</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217699">HM217699</ext-link></td></tr><tr><td align="left">R4527</td><td align="left"><italic>Leopoldamys neilli</italic></td><td align="left">Loei (Thailand)</td><td align="left">MahaU</td><td align="left">L2</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217463">HM217463</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217590">HM217590</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217701">HM217701</ext-link></td></tr><tr><td align="left">R4486</td><td align="left"><italic>Leopoldamys neilli</italic></td><td align="left">Phrae (Thailand)</td><td align="left">MahaU</td><td align="left">L2</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217460">HM217460</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217586">HM217586</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217697">HM217697</ext-link></td></tr><tr><td align="left">R4485</td><td align="left"><italic>Leopoldamys neilli</italic></td><td align="left">Phrae (Thailand)</td><td align="left">MahaU</td><td align="left">L2</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217459">HM217459</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217585">HM217585</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217696">HM217696</ext-link></td></tr><tr><td colspan="8"><hr></hr></td></tr><tr><td align="left">R3419</td><td align="left"><italic>Leopoldamys sp.</italic></td><td align="left">Loei (Thailand)</td><td align="left">KU</td><td align="left">L1</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217414">HM217414</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217543">HM217543</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217652">HM217652</ext-link></td></tr><tr><td colspan="8"><hr></hr></td></tr><tr><td align="left">R4723</td><td align="left"><italic>Niviventer fulvescens</italic></td><td align="left">Loei (Thailand)</td><td align="left">MahaU</td><td align="left">N1</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217465">HM217465</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217591">HM217591</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217702">HM217702</ext-link></td></tr><tr><td align="left"><bold>R3212</bold></td><td align="left"><bold><italic>Niviventer fulvescens</italic></bold></td><td align="left"><bold>Kanchanaburi (Thailand)</bold></td><td align="left">KU</td><td align="left">N2</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217409">HM217409</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217539">HM217539</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217647">HM217647</ext-link></td></tr><tr><td colspan="8"><hr></hr></td></tr><tr><td align="left">R4525</td><td align="left"><italic>Niviventer sp.</italic></td><td align="left">Loei (Thailand)</td><td align="left">MahaU</td><td align="left">N1</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217464">HM217464</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217589">HM217589</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217700">HM217700</ext-link></td></tr><tr><td align="left">R3427</td><td align="left"><italic>Niviventer sp.</italic></td><td align="left">Loei (Thailand)</td><td align="left">KU</td><td align="left">N1</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217416">HM217416</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217545">HM217545</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217654">HM217654</ext-link></td></tr><tr><td align="left">R3429</td><td align="left"><italic>Niviventer sp.</italic></td><td align="left">Loei (Thailand)</td><td align="left">KU</td><td align="left">N1</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217417">HM217417</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217546">HM217546</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217655">HM217655</ext-link></td></tr><tr><td align="left">R3459</td><td align="left"><italic>Niviventer sp.</italic></td><td align="left">Loei (Thailand)</td><td align="left">KU</td><td align="left">N1</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217419">HM217419</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217548">HM217548</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217657">HM217657</ext-link></td></tr><tr><td align="left">R4497</td><td align="left"><italic>Niviventer sp.</italic></td><td align="left">Phrae (Thailand)</td><td align="left">MahaU</td><td align="left">N1</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217461">HM217461</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217587">HM217587</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217698">HM217698</ext-link></td></tr><tr><td align="left">R3492</td><td align="left"><italic>Niviventer sp.</italic></td><td align="left">Loei (Thailand)</td><td align="left">KU</td><td align="left">N1</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217422">HM217422</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217551">HM217551</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217660">HM217660</ext-link></td></tr><tr><td align="left">R3077</td><td align="left"><italic>Niviventer sp.</italic></td><td align="left">Kanchanaburi (Thailand)</td><td align="left">MahiU</td><td align="left">N3</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217402">HM217402</ext-link></td><td align="left">-</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217640">HM217640</ext-link></td></tr><tr><td colspan="8"><hr></hr></td></tr><tr><td align="left">R3795</td><td align="left">Nu Deng*</td><td align="left">Khammouane (LPDR)</td><td align="left">MahiU</td><td align="left">N4</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217433">HM217433</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217561">HM217561</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217670">HM217670</ext-link></td></tr><tr><td align="left">R3796</td><td align="left">Nu Deng*</td><td align="left">Khammouane (LPDR)</td><td align="left">MahiU</td><td align="left">N4</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217434">HM217434</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217562">HM217562</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217671">HM217671</ext-link></td></tr><tr><td colspan="8"><hr></hr></td></tr><tr><td align="left">R3118</td><td align="left"><italic>Maxomys surifer</italic></td><td align="left">Kanchanaburi (Thailand)</td><td></td><td align="left">M1</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217406">HM217406</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217536">HM217536</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217644">HM217644</ext-link></td></tr><tr><td align="left">R3116</td><td align="left"><italic>Maxomys surifer</italic></td><td align="left">Kanchanaburi (Thailand)</td><td></td><td align="left">M1</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217405">HM217405</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217535">HM217535</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217643">HM217643</ext-link></td></tr><tr><td align="left"><bold>R4223</bold></td><td align="left"><bold><italic>Maxomys surifer</italic></bold></td><td align="left"><bold>Loei (Thailand)</bold></td><td align="left">CBGP</td><td align="left">M2</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217445">HM217445</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217572">HM217572</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217682">HM217682</ext-link></td></tr><tr><td align="left"><bold>R3464</bold></td><td align="left"><bold><italic>Maxomys surifer</italic></bold></td><td align="left"><bold>Loei (Thailand)</bold></td><td align="left">KU</td><td align="left">M2</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217420">HM217420</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217549">HM217549</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217658">HM217658</ext-link></td></tr><tr><td colspan="8"><hr></hr></td></tr><tr><td align="left">MK0509 BZ02</td><td align="left"><italic>Micromys minutus</italic></td><td align="left">China</td><td align="left">CBGP</td><td align="left">Outgroup</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217360">HM217360</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217482">HM217482</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217598">HM217598</ext-link></td></tr><tr><td align="left">MK0509 BZ07</td><td align="left"><italic>Micromys minutus</italic></td><td align="left">China</td><td align="left">CBGP</td><td align="left">Outgroup</td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217361">HM217361</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217483">HM217483</ext-link></td><td align="left"><ext-link ext-link-type="gen" xlink:href="HM217599">HM217599</ext-link></td></tr></tbody></table><table-wrap-foot><p>Field identifications were achieved based on morphological criteria according to [<xref ref-type="bibr" rid="B33">33</xref>-<xref ref-type="bibr" rid="B35">35</xref>] and [<xref ref-type="bibr" rid="B11">11</xref>].</p><p>"Phylogenetic species" relies on the DNA-based species delimitation method (see also Figure 3).</p><p>Mismatches between field identifications and phylogenetic species are highlighted in bold and reflect the difficulty to identify rat species even for experts.</p><p>"<italic>Nu deng</italic>*" was assigned to animal identified but impossible to assigned to a particular species; in Thai language, "red rat".</p><p>"-" corresponds to missing data in the phylogenetic analyses.</p><p>Voucher locations:</p><p>CBGP: Centre de Biologie et de Gestion des Populations, Montpellier, France - curator of the collections, Y. Chaval, <email>chaval@supagro.inra.fr</email>/KU: Kasetsart University, Bangkok, Thailand - curator: W. Rerkamnuaychoke/MahiU: Mahidol University, Nakhon Pathom, Thailand - curator: V. Herbreteau, <email>vincent.herbreteau@cirad.fr</email>/MahaU: Mahasarakham University, Mahasarakham, Thailand - curator: S. Soonchan</p><p>See Figure 1 for additional information about sample locations.</p></table-wrap-foot></table-wrap><fig id="F1" position="float"><label>Figure 1</label><caption><p><bold>Sample locations of the Rattini specimens caught in the field and included in this study</bold>. See Table 1 for more sample information.</p></caption><graphic xlink:href="1471-2148-10-184-1"></graphic></fig><p>For nomenclatural prospects, a small piece of skin from the holotype specimen of <italic>Leopoldamys neilli </italic>was also analysed in this study. The type specimen is the male n°54-4330 from the Centre for Thai National Reference collections, collected by W.A. Neill in 1973 at Wat Tham Prapothisat, in the Saraburi Province (Kaengkhoi District, Thailand, 14°35'N X 101°8'E) (see [<xref ref-type="bibr" rid="B33">33</xref>] for further details).</p></sec><sec><title>2. Sequence acquisition</title><p>Three genes proven valuable for rodent systematics were considered for the phylogenetic analyses [<xref ref-type="bibr" rid="B39">39</xref>,<xref ref-type="bibr" rid="B40">40</xref>,<xref ref-type="bibr" rid="B25">25</xref>,<xref ref-type="bibr" rid="B17">17</xref>]. We targeted two mitochondrial markers, the cytochrome <italic>b </italic>(cytb) and the cytochrome c oxydase I (COI) genes and the first exon of the nuclear gene encoding the interphotoreceptor retinoid binding protein (IRBP).</p><p>To avoid contamination, pre-amplification procedures and post-amplification analyses were performed in independent rooms in the laboratory. DNA was extracted from tissue with DNEasy Tissue Kit (Qiagen) in accordance with the manufacturer's instructions. Primer sets used to amplify the cytb, COI and IRBP genes are listed in Table <xref ref-type="table" rid="T2">2</xref>. All amplifications were carried out in 25 μL reactions containing about 30 ng of extracted DNA, 0.2 mg/mL BSA (Roche, 1 mg/mL), 300 μM of each dNTP, 0.2 μM of each primer, 1 unit of Taq polymerase (Qiagen), 2.5 μL of 10X buffer, 0.5 mM of extra MgCl2. Cycling conditions were as follows: one activation step at 94°C for 4 min followed by 40 cycles of denaturation at 94°C for 30 s, annealing at 48°C-58°C depending on the primers (Table <xref ref-type="table" rid="T2">2</xref>) for 30 s, elongation at 72°C for 45 s-1'30 min depending on the length of the target (1 minute per kb), and a final extension at 72°C for 10 min. PCR products were sequenced by Macrogen (Seoul, South Korea).</p><table-wrap id="T2" position="float"><label>Table 2</label><caption><p>Primers and PCR cycling conditions used in this study.</p></caption><table frame="hsides" rules="groups"><thead><tr><th align="left">Designation</th><th align="left">Gene Name</th><th align="left">Nucleotide sequence 5' → 3'</th><th align="left">Annealing Temperature</th><th align="left">Fragment Length (bp)</th><th align="left">Original Publication</th></tr></thead><tbody><tr><td align="left"><bold>Cytb</bold></td><td align="left"><bold>cytochrome <italic>b</italic></bold></td><td></td><td></td><td></td><td></td></tr><tr><td align="left">L14723</td><td></td><td align="left">ACCAATGACATGAAAAATCATCGTT</td><td align="left">50°C</td><td align="left">1213</td><td align="left">[<xref ref-type="bibr" rid="B69">69</xref>]</td></tr><tr><td align="left">H15915</td><td></td><td align="left">TCTCCATTTCTGGTTTACAAGAC</td><td></td><td></td><td></td></tr><tr><td align="left"><bold>COI</bold></td><td align="left"><bold>Cytochrome c oxydase I</bold></td><td></td><td></td><td></td><td></td></tr><tr><td align="left">BatL5310</td><td></td><td align="left">CCTACTCRGCCATTTTACCTATG</td><td align="left">48°C</td><td align="left">750</td><td align="left">[<xref ref-type="bibr" rid="B25">25</xref>]</td></tr><tr><td align="left">R6036R</td><td></td><td align="left">ACTTCTGGGTGTCCAAAGAATCA</td><td></td><td></td><td></td></tr><tr><td align="left"><bold>IRBP1</bold></td><td align="left" colspan="2"><bold>Interphotoreceptor retinoid binding protein (fragment 1)</bold></td><td></td><td></td><td></td></tr><tr><td align="left">I1-Rattus</td><td></td><td align="left">ATTGAGCAGGCTATGAAGAG</td><td align="left">58°C</td><td align="left">785</td><td align="left">this study</td></tr><tr><td align="left">J2-Rattus</td><td></td><td align="left">TAGGGCTTGCTCYGCAGG</td><td></td><td></td><td></td></tr><tr><td align="left"><bold>IRBP2</bold></td><td align="left" colspan="2"><bold>Interphotoreceptor retinoid binding protein (fragment 2)</bold></td><td></td><td></td><td></td></tr><tr><td align="left">I2</td><td></td><td align="left">ATCCCCTATGTCATCTCCTACYTG</td><td align="left">52°C</td><td align="left">892</td><td align="left">[<xref ref-type="bibr" rid="B70">70</xref>]</td></tr><tr><td align="left">J1</td><td></td><td align="left">CGCAGGTCCATGATGAGGTGCTCCGTGTCCTG</td><td></td><td></td><td></td></tr><tr><td align="left"><bold>cytb barcode</bold></td><td align="left" colspan="2"><bold>Cytochrome <italic>b </italic>(museum specimens)</bold></td><td></td><td></td><td></td></tr><tr><td align="left">MPLeopol-fw MPRattusSL-Rev</td><td></td><td align="left">GAYAAAATYCCATTCCACCC TARTTRTCYGGGTCTCC</td><td align="left">48°C</td><td align="left">122</td><td align="left">this study</td></tr></tbody></table><table-wrap-foot><p>The IRBP gene was amplified into two overlapping fragments, IRBP1 and IRBP2.</p></table-wrap-foot></table-wrap></sec><sec><title>3. Phylogenetic analyses</title><p>Sequences were aligned by eye using SEAVIEW [<xref ref-type="bibr" rid="B41">41</xref>] and translated into peptide sequences using the Transeq EMBOSS tool [<xref ref-type="bibr" rid="B42">42</xref>] to exclude putative NUMt copies and to ensure sequence orthology. As the risk of homoplasy by convergence and reversal is reduced by considering a large number of characters [<xref ref-type="bibr" rid="B43">43</xref>], we combined the three genes into a single dataset using the DAMBE software [<xref ref-type="bibr" rid="B44">44</xref>]. Thus, a total of 3,068 bp were considered in the subsequent phylogenetic analyses.</p><p>Base composition bias was evaluated using PAUP* v4.0b10 [<xref ref-type="bibr" rid="B45">45</xref>], and a chi-square test was performed to check for taxa with deviations of nucleotide composition. Substitutional saturation was assessed via saturation plots. Using DAMBE [<xref ref-type="bibr" rid="B44">44</xref>], the absolute number of transitions was plotted against MLComposite TN93 (Tamura-Nei Model) distance for all pairwise comparisons of taxa. For the three genes, the curve did not reach a plateau when subtracting the third codon position, but did reach a plateau when considering the entire sequences (data not shown). To discard fast evolving transitions and improve inferences without drastically compromising the resolution, we decided to recode the third codon position nucleotides to two state categories, R (purine) and Y (pyrimidine), (RY-coding strategy; [<xref ref-type="bibr" rid="B46">46</xref>]).</p><p>Phylogenetic trees were reconstructed using two probabilistic approaches: maximum likelihood (ML) and Bayesian inferences (BI). The appropriate model of evolution was first determined for each gene and for the concatenated dataset (with and without RY-coding) using corrected Akaike information criterion (AICc) and MrAIC [<xref ref-type="bibr" rid="B47">47</xref>]. The HKY+I+Γ model was selected for both the cytb and COI genes while the GTR+ Γ was selected for the IRBP gene and the combined dataset (with and without RY-coding). ML analyses were performed with PhyML-v2.4.4 [<xref ref-type="bibr" rid="B48">48</xref>]. For each analysis, the transition/transversion ratio, the proportion of invariable sites as well as the gamma distribution parameter (if necessary) were estimated and the starting tree was determined by BioNJ analysis of the dataset (default settings). Using optimization options, 500 bootstrap (Bp) replicates were performed. PhyML analyses were first run independently on each locus and then on the combined dataset (with and without RY-coding). Taking into account that PhyML does not allow data-partitioning, partitioned ML analysis was also performed using RAxML 7.0.4 [<xref ref-type="bibr" rid="B49">49</xref>]. As the model choice is limited in RAxML, the general time-reversible (GTR) + Γ model (option -m GTRGAMMA) was selected for the three partitions (option -q multipleModelFileName), and individual α-shape parameters, GTR-rates and base frequencies were estimated and optimized for each partition. Robustness of the tree was assessed using the rapid bootstrap procedure (option -f a) with 100 replications (option -# numberOfRuns) [<xref ref-type="bibr" rid="B50">50</xref>].</p><p>Bayesian analyses were performed using MrBayes v3.1 [<xref ref-type="bibr" rid="B51">51</xref>]. Four independent runs of 5,000,000 generations each were performed applying appropriate independent models of evolution to each gene. A burn-in period of 1,000,000 generations was determined graphically using Tracer1.2 [<xref ref-type="bibr" rid="B52">52</xref>]. For each dataset, all runs gave similar tree topologies and posterior probability (pp) values.</p><p>Alternative topologies were finally tested for significance using the Shimodaira-Hasegawa test (SH test) [<xref ref-type="bibr" rid="B53">53</xref>] (RELL option, 1000 Bp replicates) in PAUP* v4.0b10 [<xref ref-type="bibr" rid="B45">45</xref>].</p></sec><sec><title>4. Species delimitation: DNA-based species delimitation method</title><p>We used the DNA-based approach proposed by Pons <italic>et al. </italic>[<xref ref-type="bibr" rid="B28">28</xref>]. Using a likelihood framework, this new procedure detects the switch in the rate of lineage branching of a tree from interspecific long branches to intraspecific short budding branching and identifies clusters of specimens corresponding to putative species. Two models are implemented to account for the branching process of the entire tree. Under the null model, the whole sample derives from a single population obeying a coalescent process. The alternative model, called general mixed Yule coalescent (GMYC) model combines equations that separately describe branching within populations (coalescent process) and branching between species (a Yule model including speciation and extinction rates). Under the GMYC model, a threshold (T) is optimized such that nodes before the threshold are considered as species diversification events, whereas branches crossing the threshold define clusters following a coalescent process. A standard likelihood ratio test (LRT) is used to assess whether the alternative model provides a better fit than the null model. If the GMYC model is favoured over the null model, the T parameter of the maximum likelihood solution allows the number of species to be estimated. This test was achieved using the R code provided by T. G. Barraclough. This latest version outputs the estimates of the number of species, of the threshold time and their 95% confidence limits (<italic>i.e. </italic>solutions with 2-log likelihood units of the maximum).</p><p>Because a pre-requisite of the method is an ultrametric tree, we used the relaxed Bayesian dating method implemented in Multidivtime [<xref ref-type="bibr" rid="B54">54</xref>] to convert our optimal phylogram tree (estimated from the Bayesian analysis of the combined dataset) in a rooted additive tree with terminal nodes equally distant to the root. In this aim, we followed the documentation files written by Rutschmann [<xref ref-type="bibr" rid="B55">55</xref>] and the procedure detailed in [<xref ref-type="bibr" rid="B29">29</xref>]. The settings for the Markov chain Monte Carlo analyses were slightly modified (200,000 cycles in which the Markov chain was sampled 20,000 times every 10<sup>th </sup>cycle following a burnin period of 100,000 cycles). No fossil is described to calibrate our Rattini phylogeny. As our aim was simply to obtain an ultrametric tree, prior ages to lineages were arbitrarily assigned to 1 (rttm = 1; rttmsd = 0). The mean of the prior distribution for the rate of molecular evolution at the ingroup root node (rtrate) was computed as the mean of the median of the amount of evolution for the different tips of the three independent gene trees (rtrate = 0.735; rtratesd = 0.367).</p></sec><sec><title>5. Species identification</title><sec><title>5.1. Within the Rattus genus</title><p><italic>Rattus </italic>cytb (663 bp) and COI (655 bp) sequences obtained by Robins <italic>et al. </italic>[<xref ref-type="bibr" rid="B25">25</xref>] were extracted from GenBank and added to our mitochondrial (<italic>mt</italic>) dataset (see Table <xref ref-type="table" rid="T3">3</xref>). As our study focuses on rodents from the Indochinese region, sequences of species belonging to the <italic>Rattus fuscipes </italic>species group (<italic>i.e. </italic>native Australian species) and to the <italic>Rattus leucopus </italic>species group (<italic>i.e. </italic>species indigenous to New Guinea and adjacent archipelagos) were not incorporated in this dataset. Two other unpublished cytb sequences of <italic>R. argentiventer </italic>and <italic>R. sikkimensis </italic>(synonym of <italic>R. andamanensis</italic>) provided by O. Verneau and F. Catzeflis were also included in the subsequent analysis. Sequences of a single representative of <italic>Berylmys, Niviventer, Leopoldamys, Maxomys </italic>and <italic>Micromys </italic>were used to root our mitochondrial phylogeny. Therefore, the <italic>mt </italic>dataset included 129 sequences corresponding to 1,318 bp of <italic>mt </italic>DNA. Partitioned ML analysis was performed using RAxML 7.0.4 [<xref ref-type="bibr" rid="B49">49</xref>] and the same options as before.</p><table-wrap id="T3" position="float"><label>Table 3</label><caption><p>Sequences from previous studies included in the <italic>mt </italic>dataset.</p></caption><table frame="hsides" rules="groups"><thead><tr><th align="left">Voucher</th><th align="left">Nominal species</th><th align="left">Origin of specimen</th><th align="left">Cytb</th><th align="left">COI</th><th align="left">Phylogenetic species</th></tr></thead><tbody><tr><td align="left">RrHu1</td><td align="left"><italic>R. rattus</italic></td><td align="left">Huahine, Society Islands</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186469">EF186469</ext-link>]</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186584">EF186584</ext-link>]</td><td align="left">R1</td></tr><tr><td align="left">RrSamoa2</td><td align="left"><italic>R. rattus</italic></td><td align="left">Samoa</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186475">EF186475</ext-link>]</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186590">EF186590</ext-link>]</td><td align="left">R1</td></tr><tr><td align="left">RrRa18</td><td align="left"><italic>R. rattus</italic></td><td align="left">Raiatea, Society Islands</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186474">EF186474</ext-link>]</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186589">EF186589</ext-link>]</td><td align="left">R1</td></tr><tr><td align="left">ABTC50177</td><td align="left"><italic>R. rattus</italic></td><td align="left">Sideia Is., Papua New Guinea</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186472">EF186472</ext-link>]</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186587">EF186587</ext-link>]</td><td align="left">R1</td></tr><tr><td colspan="6"><hr></hr></td></tr><tr><td align="left"><bold>ABTC64906</bold></td><td align="left"><bold><italic>R. rattus diardi </italic>(1)</bold></td><td align="left"><bold>Kuala Lumpur, Malaysia</bold></td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186413">EF186413</ext-link>]</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186528">EF186528</ext-link>]</td><td align="left"><bold>R3</bold></td></tr><tr><td align="left"><bold>ABTC64907</bold></td><td align="left"><bold><italic>R. rattus diardi</italic></bold></td><td align="left"><bold>Kuala Lumpur, Malaysia</bold></td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186409">EF186409</ext-link>]</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186524">EF186524</ext-link>]</td><td align="left"><bold>R3</bold></td></tr><tr><td align="left"><bold>ABTC64908</bold></td><td align="left"><bold><italic>R. rattus diardi</italic></bold></td><td align="left"><bold>Kuala Lumpur, Malaysia</bold></td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186410">EF186410</ext-link>]</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186525">EF186525</ext-link>]</td><td align="left"><bold>R3</bold></td></tr><tr><td align="left"><bold>ABTC64909</bold></td><td align="left"><bold><italic>R. rattus diardi</italic></bold></td><td align="left"><bold>Kuala Lumpur, Malaysia</bold></td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186411">EF186411</ext-link>]</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186526">EF186526</ext-link>]</td><td align="left"><bold>R3</bold></td></tr><tr><td align="left"><bold>ABTC64910</bold></td><td align="left"><bold><italic>R. rattus diardi</italic></bold></td><td align="left"><bold>Kuala Lumpur, Malaysia</bold></td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186412">EF186412</ext-link>]</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186527">EF186527</ext-link>]</td><td align="left"><bold>R3</bold></td></tr><tr><td colspan="6"><hr></hr></td></tr><tr><td align="left"><bold>ABTC 8529</bold></td><td align="left"><bold><italic>R. kandianus </italic>(2)</bold></td><td align="left"><bold>Sri Lanka</bold></td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186444">EF186444</ext-link>]</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF18655">EF18655</ext-link>]</td><td align="left"><bold>R3</bold></td></tr><tr><td align="left"><bold>ABTC 8536</bold></td><td align="left"><bold><italic>R. kandianus</italic></bold></td><td align="left"><bold>Sri Lanka</bold></td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186445">EF186445</ext-link>]</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186560">EF186560</ext-link>]</td><td align="left"><bold>R3</bold></td></tr><tr><td align="left"><bold>ABTC 8540</bold></td><td align="left"><bold><italic>R. kandianus</italic></bold></td><td align="left"><bold>Sri Lanka</bold></td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186446">EF186446</ext-link>]</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186561">EF186561</ext-link>]</td><td align="left"><bold>R3</bold></td></tr><tr><td colspan="6"><hr></hr></td></tr><tr><td align="left">ABTC 8487</td><td align="left"><italic>R. tanezumi</italic></td><td align="left">Amami Island, Japan</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186508">EF186508</ext-link>]</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186623">EF186623</ext-link>]</td><td align="left">R2</td></tr><tr><td align="left">ABTC 8562</td><td align="left"><italic>R. tanezumi</italic></td><td align="left">Amami Island, Japan</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186510">EF186510</ext-link>]</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186625">EF186625</ext-link>]</td><td align="left">R2</td></tr><tr><td align="left">ABTC47981</td><td align="left"><italic>R. tanezumi</italic></td><td align="left">Yogyakarta, Indonesia</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186493">EF186493</ext-link>]</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186608">EF186608</ext-link>]</td><td align="left">R2</td></tr><tr><td align="left">ABTC47982</td><td align="left"><italic>R. tanezumi</italic></td><td align="left">Yogyakarta, Indonesia</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186494">EF186494</ext-link>]</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186609">EF186609</ext-link>]</td><td align="left">R2</td></tr><tr><td align="left">ABTC47983</td><td align="left"><italic>R. tanezumi</italic></td><td align="left">Yogyakarta, Indonesia</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186495">EF186495</ext-link>]</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186610">EF186610</ext-link>]</td><td align="left">R2</td></tr><tr><td align="left">ABTC47984</td><td align="left"><italic>R. tanezumi</italic></td><td align="left">Yogyakarta, Indonesia</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186502">EF186502</ext-link>]</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186617">EF186617</ext-link>]</td><td align="left">R2</td></tr><tr><td align="left">ABTC47985</td><td align="left"><italic>R. tanezumi</italic></td><td align="left">Yogyakarta, Indonesia</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186503">EF186503</ext-link>]</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186618">EF186618</ext-link>]</td><td align="left">R2</td></tr><tr><td align="left">ABTC47986</td><td align="left"><italic>R. tanezumi</italic></td><td align="left">Yogyakarta, Indonesia</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186504">EF186504</ext-link>]</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186619">EF186619</ext-link>]</td><td align="left">R2</td></tr><tr><td align="left">ABTC47987</td><td align="left"><italic>R. tanezumi</italic></td><td align="left">Yogyakarta, Indonesia</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186505">EF186505</ext-link>]</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186620">EF186620</ext-link>]</td><td align="left">R2</td></tr><tr><td align="left"><bold>ABTC47988</bold></td><td align="left"><bold><italic>R. tanezumi</italic></bold></td><td align="left"><bold>Yogyakarta, Indonesia</bold></td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186506">EF186506</ext-link>]</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186621">EF186621</ext-link>]</td><td align="left"><bold>R3</bold></td></tr><tr><td align="left">ABTC47989</td><td align="left"><italic>R. tanezumi</italic></td><td align="left">Yogyakarta, Indonesia</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186507">EF186507</ext-link>]</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186622">EF186622</ext-link>]</td><td align="left">R2</td></tr><tr><td align="left"><bold>ABTC47992</bold></td><td align="left"><bold><italic>R. tanezumi</italic></bold></td><td align="left"><bold>Jakarta, Indonesia</bold></td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186490">EF186490</ext-link>]</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186605">EF186605</ext-link>]</td><td align="left"><bold>R3</bold></td></tr><tr><td align="left">ABTC47993</td><td align="left"><italic>R. tanezumi</italic></td><td align="left">Jakarta, Indonesia</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186491">EF186491</ext-link>]</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186606">EF186606</ext-link>]</td><td align="left">R2</td></tr><tr><td align="left"><bold>ABTC47994</bold></td><td align="left"><bold><italic>R. tanezumi</italic></bold></td><td align="left"><bold>Jakarta, Indonesia</bold></td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186492">EF186492</ext-link>]</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186607">EF186607</ext-link>]</td><td align="left"><bold>R5</bold></td></tr><tr><td align="left"><bold>ABTC47995</bold></td><td align="left"><bold><italic>R. tanezumi</italic></bold></td><td align="left"><bold>Jakarta, Indonesia</bold></td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186496">EF186496</ext-link>]</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186611">EF186611</ext-link>]</td><td align="left"><bold>R3</bold></td></tr><tr><td align="left"><bold>ABTC47996</bold></td><td align="left"><bold><italic>R. tanezumi</italic></bold></td><td align="left"><bold>Jakarta, Indonesia</bold></td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186497">EF186497</ext-link>]</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186612">EF186612</ext-link>]</td><td align="left"><bold>R3</bold></td></tr><tr><td align="left"><bold>ABTC47997</bold></td><td align="left"><bold><italic>R. tanezumi</italic></bold></td><td align="left"><bold>Jakarta, Indonesia</bold></td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186498">EF186498</ext-link>]</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186613">EF186613</ext-link>]</td><td align="left"><bold>R3</bold></td></tr><tr><td align="left"><bold>ABTC47998</bold></td><td align="left"><bold><italic>R. tanezumi</italic></bold></td><td align="left"><bold>Jakarta, Indonesia</bold></td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186499">EF186499</ext-link>]</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186614">EF186614</ext-link>]</td><td align="left"><bold>R3</bold></td></tr><tr><td align="left"><bold>ABTC47999</bold></td><td align="left"><bold><italic>R. tanezumi</italic></bold></td><td align="left"><bold>Jakarta, Indonesia</bold></td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186500">EF186500</ext-link>]</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186615">EF186615</ext-link>]</td><td align="left"><bold>R3</bold></td></tr><tr><td align="left"><bold>ABTC48000</bold></td><td align="left"><bold><italic>R. tanezumi</italic></bold></td><td align="left"><bold>Jakarta, Indonesia</bold></td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186501">EF186501</ext-link>]</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186616">EF186616</ext-link>]</td><td align="left"><bold>R3</bold></td></tr><tr><td align="left"><bold>ABTC48004</bold></td><td align="left"><bold><italic>R. tanezumi</italic></bold></td><td align="left"><bold>Northern Sulawesi, Indonesia</bold></td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186511">EF186511</ext-link>]</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186626">EF186626</ext-link>]</td><td align="left"><bold>R3</bold></td></tr><tr><td align="left"><bold>ABTC48005</bold></td><td align="left"><bold><italic>R. tanezumi</italic></bold></td><td align="left"><bold>Northern Sulawesi, Indonesia</bold></td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186512">EF186512</ext-link>]</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186627">EF186627</ext-link>]</td><td align="left"><bold>R3</bold></td></tr><tr><td align="left">ABTC 8489</td><td align="left"><italic>R. flavipectus </italic><bold>(3)</bold></td><td align="left">Hong Kong, China</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186440">EF186440</ext-link>]</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186555">EF186555</ext-link>]</td><td align="left">R2</td></tr><tr><td colspan="6"><hr></hr></td></tr><tr><td align="left">Chat2</td><td align="left"><italic>R. exulans</italic></td><td align="left">Chatham Islands, New Zealand</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186426">EF186426</ext-link>]</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186541">EF186541</ext-link>]</td><td align="left">R8</td></tr><tr><td align="left">CI 6</td><td align="left"><italic>R. exulans</italic></td><td align="left">Aitutaki, Cook Islands</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186414">EF186414</ext-link>]</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186529">EF186529</ext-link>]</td><td align="left">R8</td></tr><tr><td align="left">Fiji1</td><td align="left"><italic>R. exulans</italic></td><td align="left">Fiji</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186417">EF186417</ext-link>]</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186532">EF186532</ext-link>]</td><td align="left">R8</td></tr><tr><td align="left">Hawaii3</td><td align="left"><italic>R. exulans</italic></td><td align="left">Hawaii</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186418">EF186418</ext-link>]</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186533">EF186533</ext-link>]</td><td align="left">R8</td></tr><tr><td align="left">Hu38</td><td align="left"><italic>R. exulans</italic></td><td align="left">Huahine, Society Islands</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186420">EF186420</ext-link>]</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186535">EF186535</ext-link>]</td><td align="left">R8</td></tr><tr><td align="left">Kap6</td><td align="left"><italic>R. exulans</italic></td><td align="left">Kapiti Island, New Zealand</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186425">EF186425</ext-link>]</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186540">EF186540</ext-link>]</td><td align="left">R8</td></tr><tr><td align="left">Ra22</td><td align="left"><italic>R. exulans</italic></td><td align="left">Raiatea, Society Islands</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186429">EF186429</ext-link>]</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186544">EF186544</ext-link>]</td><td align="left">R8</td></tr><tr><td align="left">RNZAwa01</td><td align="left"><italic>R. exulans</italic></td><td align="left">Great Barrier Island, New Zealand</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186424">EF186424</ext-link>]</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186539">EF186539</ext-link>]</td><td align="left">R8</td></tr><tr><td align="left">Samoa 3</td><td align="left"><italic>R. exulans</italic></td><td align="left">Manua, Samoa</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186430">EF186430</ext-link>]</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186545">EF186545</ext-link>]</td><td align="left">R8</td></tr><tr><td align="left">Taku5</td><td align="left"><italic>R. exulans</italic></td><td align="left">Takutea, Cook Islands</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186416">EF186416</ext-link>]</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186531">EF186531</ext-link>]</td><td align="left">R8</td></tr><tr><td align="left">UaHuka4</td><td align="left"><italic>R. exulans</italic></td><td align="left">UaHuka, Marquesas Islands</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186422">EF186422</ext-link>]</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186537">EF186537</ext-link>]</td><td align="left">R8</td></tr><tr><td align="left">ABTC 8480</td><td align="left"><italic>R. exulans</italic></td><td align="left">Thailand</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186434">EF186434</ext-link>]</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186549">EF186549</ext-link>]</td><td align="left">R8</td></tr><tr><td align="left">ABTC 8553</td><td align="left"><italic>R. exulans</italic></td><td align="left">Thailand</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186432">EF186432</ext-link>]</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186547">EF186547</ext-link>]</td><td align="left">R8</td></tr><tr><td align="left">ABTC 8559</td><td align="left"><italic>R. exulans</italic></td><td align="left">Thailand</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186433">EF186433</ext-link>]</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186548">EF186548</ext-link>]</td><td align="left">R8</td></tr><tr><td align="left">ABTC43078</td><td align="left"><italic>R. exulans</italic></td><td align="left">Yuro, Papua New Guinea</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186427">EF186427</ext-link>]</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186542">EF186542</ext-link>]</td><td align="left">R8</td></tr><tr><td align="left">ABTC48011</td><td align="left"><italic>R. exulans</italic></td><td align="left">Cibodas Forest, Java, Indonesia</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186421">EF186421</ext-link>]</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186536">EF186536</ext-link>]</td><td align="left">R8</td></tr><tr><td align="left">ABTC48895</td><td align="left"><italic>R. exulans</italic></td><td align="left">Nagada Harbour, Papua New Guinea</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186428">EF186428</ext-link>]</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186543">EF186543</ext-link>]</td><td align="left">R8</td></tr><tr><td align="left">ABTC65753</td><td align="left"><italic>R. hoffmanni</italic></td><td align="left">Tangoa, Sulawesi, Indonesia</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186443">EF186443</ext-link>]</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186558">EF186558</ext-link>]</td><td align="left">-</td></tr><tr><td align="left">ABTC65754</td><td align="left"><italic>R. hoffmanni</italic></td><td align="left">Tangoa, Sulawesi, Indonesia</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186441">EF186441</ext-link>]</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186556">EF186556</ext-link>]</td><td align="left">-</td></tr><tr><td align="left">ABTC65809</td><td align="left"><italic>R. hoffmanni</italic></td><td align="left">Mt Nokilalaki, Sulawesi, Indonesia</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186442">EF186442</ext-link>]</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186557">EF186557</ext-link>]</td><td align="left">-</td></tr><tr><td colspan="6"><hr></hr></td></tr><tr><td align="left">Rargen_1266</td><td align="left"><italic>R. argentiventer**</italic></td><td align="left">Bangkok, Thailand</td><td align="left">O.Verneau, unpublished</td><td align="left">-</td><td align="left">R6</td></tr><tr><td colspan="6"><hr></hr></td></tr><tr><td align="left">Rsikki_866</td><td align="left"><italic>R. sikkimensis </italic><bold>**(4)</bold></td><td align="left">Mocchan, Vietnam</td><td align="left">O.Verneau, unpublished</td><td align="left">-</td><td align="left">R7</td></tr><tr><td colspan="6"><hr></hr></td></tr><tr><td align="left">ABTC48025</td><td align="left"><italic>R. tiomanicus</italic></td><td align="left">Cibodas Forest, Java, Indonesia</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186514">EF186514</ext-link>]</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186629">EF186629</ext-link>]</td><td align="left">R5</td></tr><tr><td align="left">ABTC48026</td><td align="left"><italic>R. tiomanicus</italic></td><td align="left">Cibodas Forest, Java, Indonesia</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186513">EF186513</ext-link>]</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186628">EF186628</ext-link>]</td><td align="left">R5</td></tr><tr><td colspan="6"><hr></hr></td></tr><tr><td align="left">Rn Ra 15</td><td align="left"><italic>R. norvegicus</italic></td><td align="left">Raiatea, Society Islands</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186462">EF186462</ext-link>]</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186577">EF186577</ext-link>]</td><td align="left">R9</td></tr><tr><td align="left">Rn Hu 21</td><td align="left"><italic>R. norvegicus</italic></td><td align="left">Huahine, Society Islands</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186461">EF186461</ext-link>]</td><td align="left">[GenBank: <ext-link ext-link-type="gen" xlink:href="EF186576">EF186576</ext-link>]</td><td align="left">R9</td></tr></tbody></table><table-wrap-foot><p>"Nominal species" stands for the identification given to the specimen by the curator or the collector ([<xref ref-type="bibr" rid="B25">25</xref>] and F. Catzeflis, pers. comm.).</p><p>"Phylogenetic species" relies on the DNA-based species delimitation method (see also Figure 3).</p><p>(1) <italic>Rattus rattus diardi</italic>: Robins et al [<xref ref-type="bibr" rid="B25">25</xref>] reports that the specimens ABTC64906-64910 are identified by the South Australian Museum as the subspecies <italic>Rattus rattus </italic><italic>diardi </italic>(not <italic>diardii</italic>) as listed by Ellerman [<xref ref-type="bibr" rid="B71">71</xref>] on the basis on <italic>R. r. diardi </italic>after Jentink [<xref ref-type="bibr" rid="B72">72</xref>]. As already mentioned by Robins et al., [<xref ref-type="bibr" rid="B25">25</xref>], <italic>R. diardii </italic>(after Jentink 1880) is however considered as a synonym for <italic>R. tanezumi </italic>by Musser and Carleton [<xref ref-type="bibr" rid="B16">16</xref>] but there is no 1880 reference in their bibliography.</p><p>(2) <italic>R. kandianus </italic>is listed as a synonym of <italic>R. rattus </italic>[<xref ref-type="bibr" rid="B16">16</xref>], (3) <italic>R. flavipectus </italic>of <italic>R. tanezumi </italic>[<xref ref-type="bibr" rid="B16">16</xref>], (4) <italic>R. sikkimensis </italic>of <italic>R. andamanensis </italic>[<xref ref-type="bibr" rid="B16">16</xref>].</p><p>** indicates that specimens are no more available in the mammal tissue collection housed at the Institut des Sciences de l'Evolution de Montpellier [<xref ref-type="bibr" rid="B73">73</xref>].</p><p>Mismatches between nominal species and phylogenetic species are highlighted in bold.</p></table-wrap-foot></table-wrap></sec><sec><title>5.2. Ancient DNA analysis of a holotype specimen</title><p>For species assignment, we tested the relevance of DNA sequences obtained from a holotype specimen. As museum samples contain tiny amounts of poorly preserved DNA, we selected a 85 bp fragment of the cytb gene, corresponding to positions from 666 to 750 of the gene sequence of <italic>Rattus norvegicus </italic>(NCBI accession number [GenBank NC_001665]). This fragment was chosen for the following reasons: i) it corresponds to an highly variable region of the gene that allows the discrimination of most vertebrate species including the closest related ones [<xref ref-type="bibr" rid="B56">56</xref>] ii) its short length is suited for the PCR amplification of degraded DNA [<xref ref-type="bibr" rid="B56">56</xref>] and iii) it has proved valuable for species assignment based on degraded DNA extracted from archaeological samples [<xref ref-type="bibr" rid="B57">57</xref>].</p><p>To check if it provides adequate discrimination for rat species, the whole cytb sequences of the 122 specimens were reduced to the 85 bp fragment following the groups evidenced by the DNA-based species delimitation method. Based on our sampling, rat species could be easily discriminated with this small sequence (except the two entities hereafter named Be2a and Be2b but see discussion) (see the 85 bp alignment in additional file <xref ref-type="supplementary-material" rid="S1">1</xref>). So, we decided to target this DNA barcode from the holotype of <italic>Leopoldamys neilli</italic>.</p><p>As we used a museum specimen, the difficulties associated with ancient DNA studies are relevant to this analysis. Hence, ancient DNA work was performed at the PALGENE national platform (CNRS, ENS Lyon, France) dedicated to ancient DNA analysis, following the standard procedures and using specific equipment and personal protections [<xref ref-type="bibr" rid="B58">58</xref>,<xref ref-type="bibr" rid="B59">59</xref>].</p><p>DNA was extracted from the holotype of <italic>Leopoldamys neilli </italic>following the protocol detailed by Rohland and Hofreiter [<xref ref-type="bibr" rid="B60">60</xref>]. Primer sets declined from Télétchéa <italic>et al.</italic>, [<xref ref-type="bibr" rid="B56">56</xref>] were used for PCR attempts (Table <xref ref-type="table" rid="T2">2</xref>). At least two independent PCR amplifications were performed in 25 μL reaction volumes containing 2.5 units of Perkin Elmer Gold <italic>Taq </italic>polymerase (Applied Biosystems), 1 mg/mL BSA (Roche, 20 mg/mL), 2 mM MgCl<sub>2</sub>, 250 μM of each dNTP, 0.5 μM of primers. For each independent PCR attempt, a range of dilutions was performed to find the best compromise between inhibitor's concentration and targeted DNA molecule concentration. DNA was amplified with a 5 min activation step at 95°C followed by 55 cycles of denaturation (94°C, 30 s), annealing (48°C, 30 s) and elongation (72°C, 45 s). Amplification products were systematically cloned using Topo TA Cloning for sequencing kit (Invitrogen). 16 clones of independent amplifications were sequenced to determine the consensus sequence (Macrogen, Seoul, South Korea).</p><p>The CAOS software, a two step character-based DNA barcoding method [<xref ref-type="bibr" rid="B61">61</xref>] was then used to determine if the <italic>Leopoldamys neilli </italic>holotype consensus sequence could be assigned to one of the clusters recognized as a putative species by the method of Pons <italic>et al.</italic>, [<xref ref-type="bibr" rid="B28">28</xref>]. First, a diagnostic rules generator, P-Gnome, was used to search DNA changes through the 85 bp cytb matrix (122 sequences) and to establish diagnostic rule sets for each of the previously described entities (outputs of the DNA-based species delimitation method). Then, the P-Elf program was run to classify as a query the holotype sequence according to the rules generated by P-Gnome.</p></sec></sec></sec><sec><title>Results</title><sec><title>1. Sequence analyses and phylogenetic reconstructions</title><p>Cytb, IRBP and COI sequences were generated for 122, 120 and 116 rat specimens respectively. All sequences were deposited in GenBank under the accession numbers HM217360 to HM217717 (Table <xref ref-type="table" rid="T1">1</xref>). No significant difference in nucleotide composition among taxa was detected which indicated that no artificial grouping could occur due to a misleading compositional signal in the dataset. PhyML analyses were first carried out on each locus independently (data not shown). Each gene considered separately does not result in a robust Rattini phylogeny: mitochondrial markers help to resolve terminal nodes, while IRBP lends support to deepest ones. But, since the 3 genes yielded consistent, compatible topologies, sequences were concatenated and phylogenetic analyses were then carried out using the combined dataset.</p><p>Identical topologies were obtained with and without a RY-coding of the 3<sup>rd </sup>codon position (data not shown). However, better resolution and stronger topological supports (Bp and pp) were reached without an RY recoding strategy. It seems that our dataset was not informative enough for a RY recoding strategy resulting in this case in an over-depletion of the phylogenetic signal.</p><p>BI, partitioned and unpartitioned ML analyses (without RY recoding strategy) yielded the identical topology given in Figure <xref ref-type="fig" rid="F2">2</xref>. Most relationships among the Rattini tribe were well resolved (supports 61-100 for Bp, 0.82-1.00 for pp). Monophyletic groups corresponding to the Rattini divisions proposed by Musser and Carleton [<xref ref-type="bibr" rid="B16">16</xref>] are sustained with the highest values of Bp or pp. The <italic>Maxomys </italic>division clearly appears as the first division to diverge followed by the <italic>Dacnomys </italic>division, here represented by <italic>Leopoldamys </italic>and <italic>Niviventer </italic>genera, and the <italic>Rattus division</italic>. <italic>Berylmys </italic>appears with maximum support values as the earliest lineage to diverge among the <italic>Rattus </italic>division. A sister grouping is indicated between the genera <italic>Bandicota </italic>and <italic>Rattus</italic>, but this association is weakly supported. In fact, the monophyly of the <italic>Rattus </italic>genus received moderate pp (0.82) to weak Bp supports (61 for unpartitioned, 63 for partitioned ML analyses). To test the reliability of these findings, we considered an alternative hypothesis concerning the position of <italic>Bandicota </italic>within the <italic>Rattus </italic>division (<italic>i.e. </italic><italic>Bandicota </italic>was placed inside the <italic>Rattus sp. </italic>cluster). SH-test failed to find significant differences between these hypotheses and the alternative branching orders of <italic>Bandicota </italic>inside the <italic>Rattus </italic>division could not be excluded (P > 0.05). Inside the <italic>Rattus sp. </italic>clade, the 3 <italic>Rattus </italic>species groups proposed by Musser and Carleton [<xref ref-type="bibr" rid="B16">16</xref>] could be distinguished. The <italic>R. exulans </italic>monotypic group (<italic>Re</italic>, Figure <xref ref-type="fig" rid="F2">2</xref>) clustered with the <italic>R. rattus </italic>species group (<italic>Rr</italic>, Figure <xref ref-type="fig" rid="F2">2</xref>) with high branch supports (Bp = 94/96 for the unpartitioned/partitioned ML analyses; pp = 1) and the <italic>R. norvegicus </italic>species group (<italic>Rn</italic>, Figure <xref ref-type="fig" rid="F2">2</xref>) is placed as sister taxa to the <italic>R. exulans </italic>species group/<italic>R. rattus </italic>species group cluster.</p><fig id="F2" position="float"><label>Figure 2</label><caption><p><bold>Phylogenetic tree depicting relationships of the Indochinese Rattini based on the analyses of the combined cytb, COI and IRBP genes and reconstructed following Bayesian method</bold>. BI and ML analyses of the dataset gave an identical topology. Numbers above the branches reflect support obtained from the analysis of the dataset following 3 different reconstruction methods: BI/unpartitioned ML/partitioned ML. Support values are not shown for very short branches. The symbol "**" indicates that phylogenetic relationships are not supported by the partitioned ML analysis. <bold>Rr </bold>stands for <italic>Rattus rattus </italic>species group, <bold>Re </bold>for <italic>Rattus exulans </italic>species group, <bold>Rn </bold>for <italic>Rattus norvegicus </italic>species group, following Musser and Carleton's denominations [<xref ref-type="bibr" rid="B16">16</xref>]. At the right hand of the tree, lineages are labelled according to the genus to which they belong.</p></caption><graphic xlink:href="1471-2148-10-184-2"></graphic></fig><p>At this point in the analysis, 23 lineages (labelled R1 to M2 in the Figure <xref ref-type="fig" rid="F2">2</xref>) are identified within our taxon sampling. As their specific status are still questioned, intra-generic relationships are problematic to describe and will not be discussed in this section.</p></sec><sec><title>2. Species delimitation</title><p>The existence of distinct phylogenetic lineages was corroborated by the analysis of the branching rate pattern. A lineage-through-time plot based on the Multidivtime ultrametric tree evidenced a sudden increase in branching rate towards the present, likely corresponding to the switch from interspecies to intraspecies branching events (see additional file <xref ref-type="supplementary-material" rid="S2">2</xref>). To fit the position of the switch, the method of Pons <italic>et al. </italic>[<xref ref-type="bibr" rid="B28">28</xref>] was applied to the time calibrated tree (Figure <xref ref-type="fig" rid="F3">3</xref>). The GMYC model was preferred over the null model of uniform branching rates (<italic>log</italic>L = 700.133, compared to null model <italic>log</italic>L = 687.218; 2ΔL= 25.83, χ2 test, d.f. = 3, p < 0.0001). The model fitted the switch in the branching pattern occurring at -0.07084 (<italic>i.e. </italic>T of the ML solution/it is worth reminding that the time separating the ingroup root from the present was arbitrarily assigned to 1), leading to an estimate of 24 putative species, 4 of which containing a single individual (labelled R5, Be2b, N2 and N3 respectively in Figure <xref ref-type="fig" rid="F3">3</xref>). Two <italic>Maxomys </italic>(M1 and M2), 4 <italic>Niviventer </italic>(N1 to N4), 3 <italic>Leopoldamys </italic>(L1 to L3), 2 <italic>Bandicota </italic>(B1 and B2), 3 <italic>Berylmys </italic>(Be1, Be2a, Be2b) and 10 <italic>Rattus </italic>species (R1 to R10) could be numbered as indicated in Figure <xref ref-type="fig" rid="F3">3</xref>. It is worth noting that the <italic>Berylmys </italic>lineage (labelled Be2 in Figure <xref ref-type="fig" rid="F2">2</xref>) actually seems to correspond to two putative species following Pons et al's approach (therefore labelled Be2a and Be2b in Figure <xref ref-type="fig" rid="F3">3</xref>). Confidence interval for the threshold ranged from -0.09439 to -0.04189 and the estimated number of species ranged from 22 to 32 (<italic>i.e. </italic>estimates falling within 2 log-likelihood units of the ML solution).</p><fig id="F3" position="float"><label>Figure 3</label><caption><p><bold>Rattini ultrametric tree obtained with Multidivtime and clusters of specimens recognized as putative species by the method of Pons <italic>et al. </italic></bold>[<xref ref-type="bibr" rid="B28">28</xref>]. Genetic clusters recognized as a putative species are highlighted in red and separated by longer black branches. The vertical bars group all sequences within each significant cluster, labelled R1 to M2 according to the genus to which they belong. <bold>Rr </bold>for <italic>Rattus rattus </italic>species group, <bold>Re </bold>for <italic>Rattus exulans </italic>species group, <bold>Rn </bold>for <italic>Rattus norvegicus </italic>species group.</p></caption><graphic xlink:href="1471-2148-10-184-3"></graphic></fig></sec><sec><title>3. Species identification</title><sec><title>3.1. Within the Rattus genus</title><p>The partitioned ML analysis of the <italic>mt </italic>dataset including 64 new <italic>Rattus </italic>sequences (this study) plus 61 from previous studies [<xref ref-type="bibr" rid="B25">25</xref>] gave the highly resolved and robust tree represented in Figure <xref ref-type="fig" rid="F4">4</xref>. This has allowed us to name some clusters identified as putative species by the DNA-based species delimitation method. Because the monophyly of each cluster embracing the supplementary published sequences is supported with the highest Bp value, the level of confidence of these identifications could be considered as maximal if the voucher identification beforehand is correct.</p><fig id="F4" position="float"><label>Figure 4</label><caption><p><bold>ML tree depicting relationships within the <italic>Rattus </italic>division on the basis of <italic>mt </italic>dataset and estimated using partitioned ML analysis</bold>. Bp values are shown above branches. Bp values equal to 100% are not indicated. Robins' sequences are highlighted in blue when nominal and phylogenetic species are congruent, in red on the contrary (see also Table 3). <italic>Rattus hoffmanni </italic>sequences are indicated in grey; sequences provided by Verneau and Catzeflis in green. <bold>Rr </bold>for <italic>Rattus rattus </italic>species group, <bold>Re </bold>for <italic>Rattus exulans </italic>species group, <bold>Rn </bold>for <italic>Rattus norvegicus </italic>species group. At the right hand of the tree, cluster denomination is the same as in the Figure 3.</p></caption><graphic xlink:href="1471-2148-10-184-4"></graphic></fig><p>Robins' sequences identified as <italic>Rattus rattus </italic>cluster with 100% Bp support with sequences assigned to <italic>R. rattus </italic>specimens in [<xref ref-type="bibr" rid="B36">36</xref>]. Specific identification of group R1 as <italic>Rattus rattus </italic>is thus convincingly confirmed. According to the <italic>mt </italic>tree, none of our samples from Thailand, Cambodia or Lao PDR could be assigned to this species. Following the same approach, R2 seems to correspond to <italic>Rattus tanezumi</italic>, R5 to <italic>Rattus tiomanicus</italic>, R8 to <italic>Rattus exulans </italic>and R9 to <italic>Rattus norvegicus</italic>. Sequences provided by O. Verneau and F. Catzeflis allow us identifying R6 as <italic>R. argentiventer </italic>and R7 as <italic>R. andamanensis</italic>. As expected, since its distribution is restricted to Sulawesi, sequences of <italic>Rattus hoffmanni </italic>group with none of our specimens. <italic>R. hoffmanni </italic>whose phylogenetic affinities among the <italic>Rattus rattus </italic>group need to be elucidated [<xref ref-type="bibr" rid="B16">16</xref>] appears as the sister taxa to <italic>R. argentiventer </italic>with strong support (88 Bp). The situation appears more complex for the species R3. This group corresponds to a mix of specimens identified as <italic>R. rattus diardi </italic>in [<xref ref-type="bibr" rid="B25">25</xref>], <italic>Rattus kandianus </italic>(considered as a synonym of <italic>R. rattus</italic>, [<xref ref-type="bibr" rid="B16">16</xref>]) in [<xref ref-type="bibr" rid="B25">25</xref>], <italic>R. tanezumi </italic>from Indonesia [<xref ref-type="bibr" rid="B25">25</xref>] and <italic>R. tanezumi</italic>, <italic>R. andamanensis </italic>or <italic>R. argentiventer </italic>according to the field names we assigned during our sampling. Consequently, no nominal species could be reliably assigned to R3.</p><p>According to morphological criteria and because its sistership with <italic>Rattus norvegicus </italic>[<xref ref-type="bibr" rid="B16">16</xref>] (see Table <xref ref-type="table" rid="T4">4</xref> in discussion), R10 could be convincingly assigned to <italic>Rattus nitidus</italic>.</p><table-wrap id="T4" position="float"><label>Table 4</label><caption><p>Species names proposed for each species recognized as putative ones by the method of Pons <italic>et al</italic>., [<xref ref-type="bibr" rid="B28">28</xref>].</p></caption><table frame="hsides" rules="groups"><thead><tr><th align="left">Phylogenetic species</th><th align="left">Species name proposed</th><th align="left">Phylogenetic evidences</th><th align="left">Morphological, geographical and ecological evidences</th></tr></thead><tbody><tr><td align="left"><bold>R1</bold></td><td align="left"><bold><italic>Rattus rattus</italic></bold></td><td align="left">R1 specimens identified in [<xref ref-type="bibr" rid="B36">36</xref>] cluster unambiguously with <italic>R. rattus </italic>specimens identified by Robins <italic>et al. </italic>[<xref ref-type="bibr" rid="B25">25</xref>] (see Figure 4). It is worth noting that, during this study, this species was never sampled in the fields in Thailand, Laos and Cambodia.</td><td></td></tr><tr><td colspan="4"><hr></hr></td></tr><tr><td align="left"><bold>R2</bold></td><td align="left"><bold><italic>Rattus tanezumi</italic></bold></td><td align="left">R2 specimens cluster unambiguously with <italic>R. tanezumi </italic>specimens identified in [<xref ref-type="bibr" rid="B25">25</xref>] (see Figure 4).</td><td align="left">Medium-sized rat; fur light brown to reddish brown above, white below; dark tail, equal or longer than head and body length; caught in a large range of habitats, from houses, gardens, crops and rice fields to the edge of secondary forests.</td></tr><tr><td colspan="4"><hr></hr></td></tr><tr><td align="left"><bold>R3</bold></td><td align="left"><bold><italic>Rattus sp.(to be named)</italic></bold></td><td align="left">R3 includes specimens identified as <italic>Rattus diardii </italic>in the study of Robins <italic>et al</italic>., [<xref ref-type="bibr" rid="B25">25</xref>] and rats referred to Malaysian house rat (<italic>i.e. </italic><italic>Rattus diardii</italic>) by local populations in Indonesia (Andru, J., <italic>pers. comm</italic>.). Today, <italic>Rattus diardii </italic>has been placed as a synonym of <italic>Rattus tanezumi </italic>according to morphological criteria.</td><td align="left">Urban rat or rat living near human habitations. Misidentified by us as <italic>Rattus tanezumi</italic>, <italic>R argentiventer </italic>and <italic>R. andamanensis </italic>in the <italic>Rattus rattus </italic>species group.</td></tr><tr><td colspan="4"><hr></hr></td></tr><tr><td align="left"><bold>R4</bold></td><td align="left"><bold><italic>Rattus losea or "losea-like"</italic></bold></td><td></td><td align="left">Medium-sized rat; shaggy fur brownish grey above, white to geyish below; dark tail, shorter than head and body length; caught mostly in rice fields and sometimes in dry agricultural fields. According to Aplin [<xref ref-type="bibr" rid="B35">35</xref>] two distinct forms of <italic>R. losea </italic>may exist. True <italic>R. losea </italic>(described from Taiwan) would be distributed from Southern China to central Vietnam. The second form "losea-like" would inhabit the Mekong Delta region from Southern Vietnam, Cambodia, Thailand, to the North of Vientiane Province in Laos. Since our analyses did not include samples from the two putative groups, it was not possible to determine if they are genetically distinct. Until this taxonomic issue is resolved, we prefer to name R4 "<italic>losea</italic>-like".</td></tr><tr><td colspan="4"><hr></hr></td></tr><tr><td align="left"><bold>R5</bold></td><td align="left"><bold><italic>Rattus tiomanicus</italic></bold></td><td align="left">R5 specimens cluster unambiguously with <italic>R. tiomanicus </italic>specimens identified in [<xref ref-type="bibr" rid="B25">25</xref>] (see Figure 4).</td><td align="left">Medium-sized rat; fur brown above, white below; dark tail, slightly longer than head and body length; arboreal; caught in palm plantations. Morphologically very similar to <italic>Rattus tanezumi </italic>but with shorter guard hairs.</td></tr><tr><td colspan="4"><hr></hr></td></tr><tr><td align="left"><bold>R6</bold></td><td align="left"><bold><italic>Rattus argentiventer</italic></bold></td><td align="left">R6 sequences cluster unambiguously with <italic>R. argentiventer </italic>sequences provided by O. Verneau and F. Catzeflis (see Figure 4)/identification of Verneau's specimen confirmed by G. Musser [<xref ref-type="bibr" rid="B64">64</xref>].</td><td align="left">Medium-sized rat; fur yellowish brown above, grey-white below, with developed guard hair on the back, distinct orange fringe of fur just forward of the ear; dark tail, shorter than head and body length; caught in rice fields and plantations.</td></tr><tr><td colspan="4"><hr></hr></td></tr><tr><td align="left"><bold>R7</bold></td><td align="left"><bold><italic>Rattus andamanensis</italic></bold></td><td align="left">R7 sequences cluster unambiguously with <italic>R. sikkimensis </italic>sequences provided by O. Verneau and F. Catzeflis (see Figure 4).</td><td align="left">Medium-sized rat; fur orange brown above, white-creamy below, with very elongated guard hairs; dark tail, longer than head and body length; caught in evergreen forests.</td></tr><tr><td colspan="4"><hr></hr></td></tr><tr><td align="left"><bold>R8</bold></td><td align="left"><bold><italic>Rattus exulans</italic></bold></td><td align="left">R8 specimens cluster unambiguously with <italic>R. exulans </italic>specimens identified in [<xref ref-type="bibr" rid="B25">25</xref>] (see Figure 4).</td><td align="left">Small-sized rat; fur grey-brown above, pale grey below; dark tail, longer than head and body length; domestic species found in houses.</td></tr><tr><td colspan="4"><hr></hr></td></tr><tr><td align="left"><bold>R9</bold></td><td align="left"><bold><italic>Rattus norvegicus</italic></bold></td><td align="left">R9 specimens cluster unambiguously with <italic>R. norvegicus </italic>specimens identified in [<xref ref-type="bibr" rid="B25">25</xref>] (see Figure 4).</td><td align="left">Large-sized rat; fur dark-grey above, pale grey below; tail shorter than head and body length, dark above and paler beneath but not clearly separated; occurs in major ports and neighbouring cities.</td></tr><tr><td colspan="4"><hr></hr></td></tr><tr><td align="left"><bold>R10</bold></td><td align="left"><bold><italic>Rattus nitidus</italic></bold></td><td align="left">Sister relationship with <italic>Rattus norvegicus </italic>evidenced by molecular data (see Figure 2) .</td><td align="left">Medium-size rat with a soft woolly fur, dorsally brown and grey-based cream on belly. Pearly white feet. A <italic>nitidus/norvegicus </italic>sistership was proposed by morphologists. According to Musser and Carleton [<xref ref-type="bibr" rid="B11">11</xref>], both have "dense and soft fur, six pairs of teats, and an upper M1 in which the anterolabial cusp on the anterior lamina is missing or undetectable due to its coalesence with the adjacent central cusp".</td></tr><tr><td colspan="4"><hr></hr></td></tr><tr><td align="left"><bold>B1</bold></td><td align="left"><bold><italic>Bandicota indica</italic></bold></td><td align="left">Only two <italic>Bandicota </italic>species have been described in the Indochinese region. Usually, <italic>B. indica </italic>specimens are unambiguously larger than <italic>B. savilei. </italic>Adult <italic>B. savilei </italic>and juvenile or immature <italic>B. indica </italic>may be confounded. A molecular test based on PCR amplifications with specific primers allowing discriminating between the 2 species (Chaval <italic>et al.</italic>, in prep.) was used in such cases (data not shown).</td><td align="left">Large-sized rat; fur dark above, grey below; tail shorter than head and body; aggressive and stocky; inhabits agricultural fields. The ratio of pes length to head+body length is used to distinguish <italic>B.indica </italic>from <italic>B.savilei </italic>[<xref ref-type="bibr" rid="B74">74</xref>].</td></tr><tr><td colspan="4"><hr></hr></td></tr><tr><td align="left"><bold>B2</bold></td><td align="left"><bold><italic>Bandicota savilei</italic></bold></td><td></td><td align="left">Medium-sized rat; fur dark above, grey below; tail shorter than head and body; inhabits dry lands, grasslands, clearings in forest.</td></tr><tr><td colspan="4"><hr></hr></td></tr><tr><td align="left"><bold>Be1</bold></td><td align="left"><bold><italic>Berylmys berdmorei</italic></bold></td><td></td><td align="left">Medium-sized rat; fur grey above, white below; tail shorter than head and body; inhabits secondary forests and fields close to forests.</td></tr><tr><td colspan="4"><hr></hr></td></tr><tr><td align="left"><bold>Be2a</bold></td><td align="left"><bold><italic>Berylmys bowersi</italic></bold></td><td></td><td align="left">Large-sized rat; fur grey above, white below; tail slightly longer than head and body; inhabits secondary forests and fields close to forests.</td></tr><tr><td colspan="4"><hr></hr></td></tr><tr><td align="left"><bold>Be2b</bold></td><td align="left"><bold><italic>Berylmys sp.</italic></bold></td><td></td><td align="left"><italic>Berylmys mackensiei </italic>has been described in the Indochinese region by Marshall [<xref ref-type="bibr" rid="B33">33</xref>]. However the skull of <italic>B. mackenziei </italic>he studied was identified by Musser and Newcomb [<xref ref-type="bibr" rid="B75">75</xref>] as <italic>B. bowersi</italic>. Populations of <italic>Berylmys bowersi </italic>in peninsular Thailand were reported to be geographically isolated and to differ in some ways from those elsewhere (here speculated as to be Be2,a) [<xref ref-type="bibr" rid="B67">67</xref>]. Be2b specimen came from the Kanchanaburi locality, North to the isthmus of Kra and could consequently belong to this former particular population. Because of the lack of additional information about this specimen, no species name could be convincingly assigned to Be2b.</td></tr><tr><td colspan="4"><hr></hr></td></tr><tr><td align="left"><bold>L1</bold></td><td align="left"><bold><italic>Leopoldamys edwardsi</italic></bold></td><td></td><td align="left">Large-sized rat; fur red-brown above, white-cream below; very long tail, longer than head and body; inhabits secondary forests.</td></tr><tr><td colspan="4"><hr></hr></td></tr><tr><td align="left"><bold>L2</bold></td><td align="left"><bold><italic>Leopoldamys neilli</italic></bold></td><td align="left">Genuine sequence obtained from the holotype specimen of <italic>L. neilli </italic>was assigned to L2 without ambiguities.</td><td align="left">Large-sized rat (but the smallest <italic>Leopoldamys </italic>species); fur greyish -brown above, white-cream below; tail longer than head and body. Until now, the species has been recorded from a few locations in limestone areas of northern and South western Thailand, North of the peninsular region [<xref ref-type="bibr" rid="B76">76</xref>]. Our specimens were also trapped on tower karst in northern and northeastern Thailand (Phrae and Loei provinces).</td></tr><tr><td colspan="4"><hr></hr></td></tr><tr><td align="left"><bold>L3</bold></td><td align="left"><bold><italic>Leopoldamys sabanus</italic></bold></td><td></td><td align="left">Large-sized rat; fur red-brown above, white-cream below; very long tail, longer than head and body; inhabits secondary forests. Caught in secondary forests. Often misidentified as <italic>Leopoldamys edwardsi</italic>. The two species of <italic>Leopoldamys sabanus </italic>and <italic>Leopoldamys edwardsi </italic>are indeed morphologically very similar. The species name we proposed for L3 is based on geographical evidences from Marshall (1977). Based on his work, the only <italic>Leopoldamys </italic>species that has been described in Kanchanaburi province is <italic>Leopoldamys </italic><italic>sabanus</italic>. The L3 specimens were caught in this province.</td></tr><tr><td colspan="4"><hr></hr></td></tr><tr><td align="left"><bold>N1</bold></td><td align="left"><bold><italic>Niviventer fulvescens</italic></bold></td><td></td><td align="left">Medium-sized rat; spiny fur red-brown above, white-cream below; tail longer than head and body, sharply bicoloured from base to tip; absence of terminal pencil and smallest length of bulla make us exclude <italic>Niviventer confucianus </italic>as species name.</td></tr><tr><td colspan="4"><hr></hr></td></tr><tr><td align="left"><bold>N2</bold></td><td align="left"><bold><italic>Niviventer sp. 1</italic></bold></td><td></td><td align="left">Marshall [<xref ref-type="bibr" rid="B67">67</xref>], Musser [<xref ref-type="bibr" rid="B77">77</xref>] and Corbet [<xref ref-type="bibr" rid="B34">34</xref>] documented the occurrence of <italic>Niviventer bukit </italic>in Kanchanaburi, where representatives of N2 and N3 species were caught. One of the two could be <italic>N. bukit</italic>. However, <italic>bukit </italic>is today considered as conspecific with <italic>Niviventer fulvescens </italic>[<xref ref-type="bibr" rid="B16">16</xref>]. Consequently, we prefer to refrain from giving a species name to these 2 species.</td></tr><tr><td colspan="4"><hr></hr></td></tr><tr><td align="left"><bold>N3</bold></td><td align="left"><bold><italic>Niviventer sp. 2</italic></bold></td><td></td><td></td></tr><tr><td colspan="4"><hr></hr></td></tr><tr><td align="left"><bold>N4</bold></td><td align="left"><bold><italic>Niviventer langbianis or Chiromyscus chiropus</italic></bold></td><td align="left">N4 is placed at the base of the <italic>Niviventer </italic>group. It could thus belong to the genus <italic>Niviventer </italic>or to a sister genus to <italic>Niviventer. </italic>According to Musser and Carleton [<xref ref-type="bibr" rid="B16">16</xref>], <italic>Chiromyscus </italic>is presumed to be one of the closest phylogenetic relatives of <italic>Niviventer. </italic>Based on morphological criteria, this specimen could be a <italic>Chiromyscus chiropus </italic>representative. However, <italic>Chiromyscus chiropus </italic>is morphologically very closed to <italic>N. langbianis</italic>. Thus, N4 could be one of these two species. At the end of this work, we have just received <italic>N. langbianis </italic>samples from the AMCC. Our preliminary work based on mitochondrial DNA suggests that N4 may be <italic>N. langbianis </italic>rather than <italic>C. chiropus</italic>.</td><td align="left">Identified in the field as Nu-deng because of its reddish fur (in Lao, "red rat"). Further considerations of pictures of one of the two specimens included in this study show that legs, feet and head are buffy orange as described by Musser [<xref ref-type="bibr" rid="B77">77</xref>] regarding <italic>Chiromyscus chiropus</italic>. However, the wide dark brown rings around the eyes are not visible and the tail is not bicoloured as expected for <italic>Chiromyscus. </italic><italic>Chiromyscus </italic>is morphologically very close to <italic>Niviventer langbianis </italic>[<xref ref-type="bibr" rid="B77">77</xref>] and easily confused with it. Other criteria to discriminate between the two species such as the presence of a nail on each hallux instead of a claw for <italic>Chiromyscus </italic>are not obvious on our pictures. Morphological identification is thus questionable. However, molecular data are tipping the balance for <italic>N. langbianis </italic>assignation.</td></tr><tr><td colspan="4"><hr></hr></td></tr><tr><td align="left"><bold>M1</bold></td><td align="left"><bold><italic>Maxomys sp.</italic></bold></td><td></td><td align="left">Identified by us as <italic>Maxomys surifer </italic>in the field. Could be assigned to <italic>Maxomys rajah </italic>but this species has never been reported in this area. This result could be to a bias of the branching-length method that could have some difficulties to deal with strong phylogeographic pattern. The phylogeography of <italic>Maxomys surifer </italic>was investigated using <italic>mt </italic>DNA but focusing on the large Sunda shelf area [<xref ref-type="bibr" rid="B78">78</xref>]. A structuration between the North-eastern Vietnam and the Southern Vietnam seems to exist but this finding is based on only four sampled (for which sequences are not available in databanks). As a greater sampling and more additional data are needed to assess the phylogeographic pattern of this species, we prefer to refrain from giving a species name to this cluster.</td></tr><tr><td colspan="4"><hr></hr></td></tr><tr><td align="left"><bold>M2</bold></td><td align="left"><bold><italic>Maxomys surifer.</italic></bold></td><td></td><td align="left">Medium-sized rat; spiny fur red-brown above, white-cream below; tail slightly longer but nearly equal to head and body length, sharply bicoloured with a white tip. This is the only <italic>Maxomys </italic>species described in this area</td></tr></tbody></table><table-wrap-foot><p>The congruence between geographical, morphological and phylogenetic data allows us proposing species names. Waiting for a complete taxonomic revision of the Rattini tribe, these propositions are not definitive but are revisable ones.</p></table-wrap-foot></table-wrap></sec><sec><title>3.2 Ancient DNA analysis of a holotype specimen</title><sec><title>Sequences obtained from holotype specimen</title><p>We successfully obtained 85 bp cytb sequences from the <italic>Leopoldamys neilli </italic>holotype. At least two independent PCR runs were performed, positive PCR products were cloned and consensus sequences were determined using clone sequences of independent PCR amplifications. Analysis of the differences observed between the clone sequences and consensus sequence shows that 75% of the degradation was due to deamination of cytosines, as expected from ancient DNA substrates [<xref ref-type="bibr" rid="B62">62</xref>,<xref ref-type="bibr" rid="B63">63</xref>].</p></sec><sec><title>Holotype sequence authentication</title><p>The consensus sequence was identified as a rat cytochrome <italic>b </italic>sequence using a BLAST program (no <italic>Leopoldamys neilli </italic>cytochrome <italic>b </italic>sequence was available in databanks such as EMBL or GenBank before this study). This sequence is a genuine holotype sequence for the following reasons: (i) Rattini samples were never introduced in the ancient DNA facilities before the analysis of this specimen was performed; (ii) all the 16 clones analysed were identified as rat; (iii) the errors induced by DNA damage are perfectly consistent with the pattern generally observed for ancient DNA sequences (strong bias toward type 2 transitions caused by deamination of cytosine [<xref ref-type="bibr" rid="B62">62</xref>,<xref ref-type="bibr" rid="B63">63</xref>]); (iv) for each amplification, all three PCR blanks remained negative [<xref ref-type="bibr" rid="B58">58</xref>]; (v) independent PCRs were performed and furnished the same conclusions. All in all, these points satisfy criteria of authentication for the ancient DNA work [<xref ref-type="bibr" rid="B59">59</xref>].</p></sec><sec><title>Assignment of the holotype sequence to a cluster</title><p>The genuine holotype sequence was deposited in GenBank under the accession number HM235947. It was assigned using the CAOS software to the monophyletic cluster corresponding to the <italic>Leopoldamys </italic>species, L2, in our tree (Figures <xref ref-type="fig" rid="F2">2</xref> and <xref ref-type="fig" rid="F3">3</xref>). Consequently, this monophyletic cluster recognized as a putative species by the method of Pons <italic>et al. </italic>[<xref ref-type="bibr" rid="B28">28</xref>] could be without ambiguity named as <italic>Leopoldamys neilli</italic>.</p></sec></sec></sec></sec><sec><title>Discussion</title><sec><title>1. Phylogenetic relationships within the Rattini tribe</title><sec><title>1.1. Division-level relationships</title><p>Our phylogenetic analyses of Indochinese Rattini based on the combination of cytb, COI and the first exon of the IRBP genes is compatible with the revised taxonomy of Rattini divisions proposed by Musser and Carleton [<xref ref-type="bibr" rid="B16">16</xref>]. The <italic>Maxomys </italic>division, the <italic>Dacnomys </italic>division (here consisting of <italic>Leopoldamys </italic>and <italic>Niviventer </italic>as sister taxa) and the <italic>Rattus </italic>division (here including the genera <italic>Rattus</italic>, <italic>Bandicota </italic>and <italic>Berylmys</italic>) are sustained with the highest support values (Figure <xref ref-type="fig" rid="F2">2</xref>). These results are congruent with the Murinae phylogeny obtained by Lecompte <italic>et al. </italic>[<xref ref-type="bibr" rid="B17">17</xref>] based on the analysis of the combined cytb, IRBP and GHR genes. In this latter analysis, the 3 divisions are well supported and the <italic>Maxomys </italic>division is also the first to diverge followed by the <italic>Dacnomys </italic>one and the <italic>Rattus </italic>group sensu stricto of Verneau [<xref ref-type="bibr" rid="B64">64</xref>].</p></sec><sec><title>1.2. Relationships among the <italic>Rattus</italic> division: is the genus <italic>Rattus</italic> paraphyletic?</title><p>In our analyses, the position of <italic>Bandicota </italic>still remains uncertain. The monophyly of the genus <italic>Rattus </italic>is in reality weakly supported (0.82 for pp and 61/63 for Bp) and SH-test failed to reject the hypothesis of a paraphyletic <italic>Rattus </italic>genus (<italic>i.e. </italic><italic>Bandicota </italic>is placed within <italic>Rattus</italic>). Verneau and collaborators [<xref ref-type="bibr" rid="B64">64</xref>,<xref ref-type="bibr" rid="B37">37</xref>] attempted to determine the evolutionary relationships in <italic>Rattus </italic>sensu lato using LINE-1 (L1) amplification events. In their study [<xref ref-type="bibr" rid="B37">37</xref>], two LINE subfamilies were identified in the <italic>Bandicota </italic>and the other <italic>Rattus </italic>species except in <italic>Rattus fuscipes</italic>. Since L1 subfamily absence from a particular taxa reflects an ancestral state rather than a derived state [<xref ref-type="bibr" rid="B64">64</xref>], these findings excluded <italic>Rattus fuscipes </italic>from a <italic>Bandicota/Rattus </italic>clade and placed <italic>Bandicota </italic>inside the genus <italic>Rattus </italic>leading to its paraphyly. Our study is in agreement with the multi-locus phylogeny of Lecompte <italic>et al.</italic>, [<xref ref-type="bibr" rid="B17">17</xref>] which shows <italic>Bandicota </italic>and the genus <italic>Diplothrix </italic>diverging together prior to the <italic>Rattus </italic>clade. In the Lecompte's study, the monophyly of the genus <italic>Rattus </italic>is highly supported (98 Bp, 1 pp) but, as in our study, no specimen of the <italic>Rattus fuscipes </italic>species group was included. To draw conclusions about paraphyly in <italic>Rattus </italic>genus, it would be judicious to complete the taxa sampling among the genus <italic>Rattus </italic>and to include representatives of each <italic>Rattus </italic>species group defined by Musser and Carleton [<xref ref-type="bibr" rid="B16">16</xref>] particularly representatives of the <italic>Rattus fuscipes </italic>species group.</p></sec><sec><title>1.3. Relationships within the genus <italic>Rattus</italic></title><p>The genus <italic>Rattus</italic>, with a total of 66 species currently recognised [<xref ref-type="bibr" rid="B16">16</xref>] "is not only the single largest mammalian genus of all, but also arguably among the most complex and least understood" [<xref ref-type="bibr" rid="B65">65</xref>].</p><p>Within this genus, <italic>7 </italic>species groups have been defined by Musser and Carleton [<xref ref-type="bibr" rid="B16">16</xref>], of which 3 inhabit the Indochinese region and are relevant to this study (Rr, Re and Rn in Figures <xref ref-type="fig" rid="F2">2</xref> and <xref ref-type="fig" rid="F3">3</xref>). The <italic>Rattus rattus </italic>species group as described by Musser and Carleton [<xref ref-type="bibr" rid="B16">16</xref>] comprises 21 species of which 5 may be found in Thailand, Cambodia and Lao PDR. In our phylogenetic analysis, this cluster appears unambiguously to be monophyletic (1.00 for pp; 93/97 for Bp) and was placed undoubtedly as the sister group of the monotypic <italic>exulans </italic>species group (pp = 1.00; Bp = 94/96). This association was also found in recent molecular studies [<xref ref-type="bibr" rid="B25">25</xref>,<xref ref-type="bibr" rid="B17">17</xref>] but encompassing fewer representatives of the <italic>Rattus rattus </italic>species group. According to Musser and Carleton [<xref ref-type="bibr" rid="B16">16</xref>], the <italic>R. norvegicus </italic>species group includes 3 species (<italic>Rattus norvegicus</italic>, <italic>R. nitidus </italic>and <italic>R. pyctoris</italic>) of which only 2 may occur in the Indochinese region (<italic>Rattus norvegicus </italic>and <italic>R. nitidus</italic>). This group appears in our study as the sister taxa to the "<italic>R. exulans species </italic>group/<italic>R. rattus </italic>species group" cluster as found in [<xref ref-type="bibr" rid="B25">25</xref>] and [<xref ref-type="bibr" rid="B17">17</xref>].</p><p>Robins and colleagues [<xref ref-type="bibr" rid="B25">25</xref>] focusing on rats inhabiting islands in Southeast Asia, included in their sampling specimens from Australia (<italic>i.e. </italic>belonging to the <italic>Rattus fuscipes </italic>species group as defined by [<xref ref-type="bibr" rid="B16">16</xref>]) and from New Guinea and adjacent archipelagos (i.e. belonging to the <italic>Rattus leucopus </italic>group). Based on the analysis of nearly 2 kb of <italic>mt </italic>DNA, they recovered 5 of the 7 groups proposed by Musser and Carleton [<xref ref-type="bibr" rid="B16">16</xref>]. Our study, even if focusing on a different region of South East Asia, is perfectly congruent with Robins' study, and both studies are compatible with the revised taxonomy of the <italic>Rattus </italic>genus recently proposed by Musser and Carleton [<xref ref-type="bibr" rid="B16">16</xref>]. The sixth group defined by the authors [<xref ref-type="bibr" rid="B16">16</xref>] corresponds to the <italic>xanthurus </italic>species group encompassing species native to Sulawesi and adjacent islands. According to preliminary phylogenetic analyses of cytb sequences cited in [<xref ref-type="bibr" rid="B16">16</xref>], this assemblage could be placed as the sister-group to the <italic>R. leucopus </italic>and <italic>R. fuscipes </italic>groups. The last group defined by Musser and Carleton [<xref ref-type="bibr" rid="B16">16</xref>] does not correspond to a natural cluster but was formed for practical reasons since it includes species whose phylogenetic affinities have to be clarified; some may need to be excised from <italic>Rattus</italic>.</p></sec></sec><sec><title>2. Toward a deep taxonomic revision of the Rattini tribe</title><p>At a specific level, we realized that phylogenetic relationships were difficult to discuss. Species misidentifications are indeed plentiful and recurrent both in our sampling (see Table <xref ref-type="table" rid="T1">1</xref>) and in the literature. <italic>Mt </italic>sequences from Robins <italic>et al. </italic>[<xref ref-type="bibr" rid="B25">25</xref>] or provided by O. Verneau and F. Catzeflis were included in our dataset but questions about the reliability of the identification of vouchers were rapidly raised. To cite a few examples, the <italic>Rattus tanezumi </italic>sample occurring in the <italic>tiomanicus </italic>cluster in [<xref ref-type="bibr" rid="B25">25</xref>] (see Figure <xref ref-type="fig" rid="F4">4</xref>) was proposed by the authors to represent a misidentification. Similarly, the <italic>R. rattus cf. moluccarius </italic>specimen in [<xref ref-type="bibr" rid="B64">64</xref>] and [<xref ref-type="bibr" rid="B37">37</xref>] was, according to Musser and Carleton [<xref ref-type="bibr" rid="B16">16</xref>], an example of <italic>R. nitidus </italic>whereas their specimen assigned to <italic>Niviventer niviventer </italic>was probably improperly identified since <italic>N. niviventer </italic>has never been described in the locality where the specimen was caught [<xref ref-type="bibr" rid="B64">64</xref>]. We observed that the situation was worse regarding the <italic>Niviventer </italic>genus. When including sequences available in the databanks (<italic>i.e. </italic>cytochrome <italic>b </italic>sequences from [<xref ref-type="bibr" rid="B66">66</xref>]), numerous species appeared to be paraphyletic (data not shown). These results are presumably the consequence of species misidentifications and this explains why we decided to exclude these sequences from our analyses. All in all, these reports ([<xref ref-type="bibr" rid="B25">25</xref>,<xref ref-type="bibr" rid="B64">64</xref>] and this study) stressed the necessity of a sound taxonomic revision of the Rattini tribe. Consequently one must first determine valid species boundaries and then assign an appropriate name in accordance with the rules of the International Code of the Nomenclature.</p><sec><title>2.1. How many rat species in the Indochinese area we investigated?</title><p>According to Musser and Carleton [<xref ref-type="bibr" rid="B16">16</xref>], 9 genera corresponding to the following 27 species of Rattini may occur in our sampling area (Figure <xref ref-type="fig" rid="F1">1</xref>): <italic>Hapalomys delacouri </italic>(see <italic>Background </italic>for justification of its inclusion into the Rattini tribe), <italic>Sundamys muelleri</italic>, <italic>Chiromyscus chiropus</italic>, 3 <italic>Maxomys </italic>species (<italic>rajah, surifer, whiteheadi</italic>), 6 <italic>Niviventer </italic>species (<italic>fulvescens, hinpoon, langbianis, tenaster, cremoriventer, confucianus</italic>), 3 <italic>Leopoldamys </italic>species (<italic>neilli, edwardsi, sabanus</italic>), 2 <italic>Bandicota </italic>species (<italic>indica </italic>and <italic>savilei</italic>), 2 <italic>Berylmys </italic>species (<italic>bowersi </italic>and <italic>berdmorei</italic>) and 8 <italic>Rattus </italic>species (<italic>andamanensis, argentiventer, exulans, tanezumi, losea, tiomanicus, norvegicus, nitidus)</italic>. According to our phylogeny (Figure <xref ref-type="fig" rid="F2">2</xref>), 23 lineages exist within our sampling and 24 putative species were suggested by the method of Pons <italic>et al. </italic>[<xref ref-type="bibr" rid="B28">28</xref>]. Confidence interval for the estimated number of species ranged from 22 to 32 (<italic>i.e. </italic>estimates falling within 2 log-likelihood units of the ML solution). An inadequate population sampling is one of the potential limitations of the branch length method as identified by Pons et al. [<xref ref-type="bibr" rid="B28">28</xref>]. However, the GMYC model was preferred over the null model of uniform branching rates indicated that the intraspecific sampling effort is satisfactory in our dataset (failure to reject the null model over the GMYC model could be an incomplete sampling per species; [<xref ref-type="bibr" rid="B28">28</xref>]). Moreover, among the 24 estimated species, 4 species (labelled R5, Be2b, N2 and N3 respectively in Figure <xref ref-type="fig" rid="F3">3</xref>) contain a single individual. In accordance with Pons et al, it seems that the GMYC method correctly deals with the inclusion of some rare species represented by only one single individual [<xref ref-type="bibr" rid="B28">28</xref>].</p><p>The estimated number of species fit well with the number of species described in the literature for this area, although there are some exceptions, in particular within the <italic>Berylmys </italic>and the <italic>Rattus </italic>genera. Our study suggests 3 putative species of <italic>Berylmys </italic>in our sampling whereas only 2 are mentioned in the literature within the geographic area sampled (<italic>Berylmys bowersi </italic>and <italic>B. berdmorei</italic>) (see Table <xref ref-type="table" rid="T4">4</xref>). This outcome was supported by all the solutions included in the 95% confidence interval of the estimate of the number of species (Figure <xref ref-type="fig" rid="F3">3</xref>). This finding may be an artefact of the species delimitation method which could have difficulty in dealing with high level of population differentiation and strong phylogeographic patterns. As acknowledged by Pons <italic>et al.</italic>, [<xref ref-type="bibr" rid="B28">28</xref>], a limitation of this method is that populations with partial gene flow risk being recognized as separate entities. A marked phylogeographic structuring within <italic>Berylmys bowersi </italic>could explain the distinction of Be2a and Be2b as two putative species by the branch-length method. Be2b specimen came from the Kanchanaburi locality (Table <xref ref-type="table" rid="T1">1</xref>, Figure <xref ref-type="fig" rid="F1">1</xref>), North to the Isthmus of Kra corresponding to the limit of the peninsular Thailand whereas the specimens of the Be2b group came from the Northern Thailand (Loei and Nan provinces, Figure <xref ref-type="fig" rid="F1">1</xref>) and Northern Lao PDR (Luang Prabang province, Figure <xref ref-type="fig" rid="F1">1</xref>). Populations of <italic>Berylmys bowersi </italic>in peninsular Thailand were reported to be geographically isolated and to differ in some ways from other populations [<xref ref-type="bibr" rid="B67">67</xref>]. Our findings are congruent with this report. Further investigations are needed to determine if Be2a and Be2b are two phylogenetic lineages of a same species exhibiting a strong phylogeographical pattern or if they have two be considered as two closely related but separate species.</p><p>In a similar way, five species belonging to the <italic>Rattus rattus </italic>species group have been described in this area (<italic>i.e. </italic><italic>R. andamanensis, argentiventer, tanezumi, losea</italic>, and <italic>tiomanicus</italic>). Marshall [<xref ref-type="bibr" rid="B33">33</xref>] reported also the presence of <italic>R. rattus </italic>in all provinces of Thailand and considered the roof rat as the most abundant mammal in the country. Interestingly, since 1998, no specimen among the 3,000 caught during our successive field surveys in rural or urban areas of Thailand, Lao PDR and Cambodia could be identified as a representative of <italic>R. rattus</italic>, according to morphological, cytological and molecular evidences. Our findings offer no support for the presence of <italic>R. rattus </italic>in the area and are in conflict with previous claims of <italic>R. rattus </italic>in the Indochinese region [<xref ref-type="bibr" rid="B33">33</xref>]. However, this inconsistancy is probably due to a difference in the usage of "<italic>Rattus </italic><italic>rattus</italic>" in place of "<italic>Rattus tanezumi</italic>" rather than a problem of identification or occurrence.</p><p>Finally, our analysis corroborates the presence of an additional <italic>Rattus </italic>species (labelled R3 in Figure <xref ref-type="fig" rid="F3">3</xref>) already identified as the <italic>diardii </italic>clade in the mitochondrial phylogeny of Robins et al. [<xref ref-type="bibr" rid="B25">25</xref>]. R3 could be a cryptic species. This statement yet needs further investigation using independent data (morphology, nuclear genes). Then, if this hypothesis proved to be correct, the R3 species would have to be carefully named (<italic>R. diardii </italic>is indeed considered at present as a synonym of <italic>R. tanezumi </italic>[<xref ref-type="bibr" rid="B16">16</xref>]). In agreement with our result, Aplin in his preliminary study of the cytb [<xref ref-type="bibr" rid="B65">65</xref>] observed that the taxonomy of the <italic>Rattus rattus </italic>species group might be rather thornier than suggested by previous studies mostly based on karyotypic or electrophoretic evidences. Indeed, his ongoing study reports two distinct phylogenetic clades in the Asian region. The first one would correspond to an endemic Southeast Asian taxon (recorded in Vietnam, Cambodia and Southern Laos) and might correspond to our R3 according to geographical evidence. Our study and Robins' work reveal that the distribution of this Southeast group spreads far into the South as it occurs in Thailand and in Sri Lanka and also in Malaysia, in Indonesia and Northern Sulawesi (Figures <xref ref-type="fig" rid="F4">4</xref> and <xref ref-type="fig" rid="F5">5</xref>). The second clade proposed by Aplin [<xref ref-type="bibr" rid="B65">65</xref>] would be a northern and South Asian taxon (found in Japan, Hong Kong, northern Vietnam, northern Laos, and Bangladesh) and might correspond to R2 (here also found in Thailand and Indonesia, Figure <xref ref-type="fig" rid="F4">4</xref>, Table <xref ref-type="table" rid="T3">3</xref>/see also Table <xref ref-type="table" rid="T4">4</xref> for species name). Indeed when including Robins' sequences, R2 includes specimens from Japan and Hong Kong (Figures <xref ref-type="fig" rid="F4">4</xref> and <xref ref-type="fig" rid="F5">5</xref>). As mentioned by Aplin [<xref ref-type="bibr" rid="B65">65</xref>], the latter group (R2) is more closely related to <italic>Rattus rattus </italic>rather than the former group (R3). In our trees (Figures <xref ref-type="fig" rid="F2">2</xref> and <xref ref-type="fig" rid="F4">4</xref>), R2 is clearly placed as the sister taxa of <italic>R. rattus </italic>(R1). Our study reinforces Aplin's assumption [<xref ref-type="bibr" rid="B65">65</xref>] that the two Asian clades (<italic>i.e. </italic>R2 and R3) are sympatric in some part of their distribution by increasing greatly the area where the two taxa co-occur in continental Southeast Asia. Both are found in Northern and Central Thailand (Phrae, Nakhon Pathom and Ratchaburi provinces; this study). Since some specimens of both taxa were trapped in exactly the same location and time, at least in Phrae, they probably also share similar habitats and are likely syntopic.</p><fig id="F5" position="float"><label>Figure 5</label><caption><p><bold>Map of the distribution of the two Asian species of the <italic>Rattus rattus </italic>species group, according to the samples identified as belonging to R2 and R3 in our study</bold>. (Figures 3 and 4).</p></caption><graphic xlink:href="1471-2148-10-184-5"></graphic></fig></sec><sec><title>2.2. How to give a name?</title><p>By integrating phylogenetic, morphological and geographical evidence, we proposed to attribute the names summarized in Table <xref ref-type="table" rid="T4">4</xref> to the 24 species highlighted herein. Our propositions are not definitive but are revisable ones. Indeed, once species boundaries are delimitated, assigning the appropriate name to each species is not an easy task particularly for the Rattini species whose taxonomy is complicated by a large number of synonym names. Even for a rodent specialist, morphological characters are sometimes misleading (see aforementioned misidentification examples) and intraspecific morphological polymorphism makes the problem more difficult. To alleviate this last difficulty, morphological studies have to consider a large number of specimens, a process that may be difficult and time-consuming to perform.</p><p>These inconveniences highlighted the great interest in obtaining molecular data from a holotype. Indeed, the holotype is by definition the element to which the name of a taxon is permanently attached. Consequently, including holotype specimens in molecular phylogenies would be very suitable to name each cluster recognized as a valid species providing that a rigorous and sound taxonomy is already set up. Indeed, holotype specimens may correspond to problematic taxa (<italic>e.g</italic>. problems of synonymy not yet revealed), and the use of type specimens could be misleading in such context. Including holotype specimens in molecular phylogenies is however totally infeasible for the two following reasons. Firstly, holotype specimens are unique and are difficult to obtain for genetic research purposes. Sampling authorisations are very scarce and destructive sampling is generally not possible. To achieve our study, no more than 24 holotypes would be damaged if our assumptions are correct. Faced with the understandable reluctance of museum curators, non-destructive extraction procedure [<xref ref-type="bibr" rid="B68">68</xref>] would be an elegant suggestion. Secondly, ancient materials contain tiny amounts of poorly preserved and highly fragmented DNA. As required for this study, getting 3 kb corresponding to 3 different genes (including one nuclear one) for more than 24 holotype specimens, and following the ancient DNA guidelines would be too expensive and much too time-consuming. To circumvent this problem it is fortunately possible to target small DNA fragments as barcodes. Our study proved that this strategy is a powerful one. Following all the ancient DNA requirements, we succeeded in amplifying a genuine small cytb fragment from the <italic>Leopoldamys neilli </italic>holotype. This barcode was used to assign a name without ambiguity to one of the clusters (<italic>i.e. </italic>L2) recognized as a valid species in our analyses. Even if more holotype specimens have to be investigated to achieve a steady revision of the Rattini tribe, our work illustrates the huge opportunities ancient DNA analysis may offer to taxonomists.</p></sec></sec></sec><sec><title>Conclusions</title><p>This study represents the first step of a long-term project aiming at a deep taxonomic revision of the Rattini. Putative species delimitations have been determined here without prior assumptions and we propose a suitable methodology using molecular data from holotypes to assign the right name to each delineated species. Ancient DNA analysis of holotypes should be considered by taxonomists as a promising tool opening up new realms of possibilities (<italic>e.g. </italic>testing synonymy of names of unclear taxonomies such as the synonymy of <italic>R. tanezumi </italic>and <italic>R. diardii</italic>; see Table <xref ref-type="table" rid="T4">4</xref>). Although DNA data alone are not a panacea for species description and delimitation, we are confident that future investigations combined with other types of information will clarify the taxonomy of this confusing group. Indeed, integrative approaches merging independent data such as morphology, karyology, mitochondrial and nuclear markers are the only means to understand the diversification among, and interactions between, evolutionary lineages. Our molecular study revealed that at least 7 putative different species, including a cryptic one (R3), could exist among the <italic>Rattus rattus </italic>species group (among which six were sampled within the area we investigated). As each of these species is expected to have specific ecological traits and to carry its own set of diseases, the recognition of cryptic species within Rattini could have serious implications for human health in Southeast Asia. However, this result has to be carefully considered. Indeed, it is worth noticing that the terminal nodes of our multilocus phylogeny are mostly supported by mitochondrial data (cytb and COI genes) while the deepest nodes are sustained by nuclear data (IRPB). Other kinds of markers have thus to be checked for congruence. Such clarifications for the Rattini tribe are today urgently required to achieve meaningful epidemiological research in South East Asia.</p></sec><sec><title>List of Abbreviations</title><p>bp: base pairs; kb: kilo base pairs.</p></sec><sec><title>Authors' contributions</title><p>Conceived and designed the experiments: JM, JFC, MP. Performed the experiments: MP, YC, VH, SW. Analyzed the data: MP. Wrote the paper: MP, YC. Senior epidemiologists and supervisors responsible for all scientific output of the program: SM, JM, JPH. All authors read and approved the final manuscript.</p></sec><sec sec-type="supplementary-material"><title>Supplementary Material</title><supplementary-material content-type="local-data" id="S1"><caption><title>Additional file 1</title><p><bold>Rat 85 pb cytb alignment</bold>. The whole cytb sequences obtained from the 122 specimens selected in this study were reduced to the 85 bp DNA marker already used to discriminate closely related species from degraded DNA [<xref ref-type="bibr" rid="B56">56</xref>,<xref ref-type="bibr" rid="B57">57</xref>]. Small sequences were sorted following the results of the DNA-based species delimitation method. Dots indicate identical positions as those of the reference sequence of <italic>Rattus rattus </italic>R12. Sites allowing discrimination between species are those shared by all the specimens of a same entitie but different for all the specimens of another one. Each rat species could be distinguished from each other based on this fragment except the two <italic>Berylmys </italic>species Be2a and Be2b (but see discussion). We tried to maximize the geographic diversity of the specimens, however, our sampling was achieved without prior expectation and some entities determined by the DNA-based species delimitation method encompass few specimens coming from the same locality (e.g. R5, R6, R7, Be2b, L3, etc.). In this case, intra-polymorphism is not taken into account and substitutions allowing discriminatation between species are thus overestimated. However, closely related rat species (such as R1 and R2 or R3 and R4, see phylogeny in Figure <xref ref-type="fig" rid="F2">2</xref>) could be easily discriminated. We thus considered that this fragment is reliable for an adequate discrimination for rat species.</p></caption><media xlink:href="1471-2148-10-184-S1.DOC" mimetype="application" mime-subtype="msword"><caption><p>Click here for file</p></caption></media></supplementary-material><supplementary-material content-type="local-data" id="S2"><caption><title>Additional file 2</title><p><bold>Lineage-through-time plot based on the Multidivtime ultrametric tree</bold>. The sudden increase in branching rate, indicated by a red line, corresponds to the shift from interspecific to intraspecific lineage branching.</p></caption><media xlink:href="1471-2148-10-184-S2.DOC" mimetype="application" mime-subtype="msword"><caption><p>Click here for file</p></caption></media></supplementary-material></sec></body><back><sec><title>Acknowledgements</title><p>Firstly, we would like to thank the two anonymous reviewers for their comments that helped us to greatly improve the manuscript. We thank K. Blasdell for English corrections. We are particularly grateful to the people who have made this work possible in the field: S. Jittapalapong from the Faculty of Veterinary Medicine, W. Rerkamnuaychoke from the Faculty of Veterinary Technology at Kasetsart University in Thailand, B. Douangboupha from the National Agricultural and Forestry Research Institute in Lao PDR and P. Buchy from the Pasteur Institute in Cambodia. We also warmly thank all the people that worked hard with us in the field to collect samples used in this study, and especially K. Chaisiri and K. Satchasataporn. Thanks to C. Tollenaere and F. Catzeflis who provided us rat sequences or samples. We would like to acknowledge the Ambrose Monell Cryo Collection (AMCC) at the American Museum of Natural History, New York, for their support in our research. We are indebted to all the people of the ancient DNA platform PALGENE (directed by C. Hänni) and more particularly to B. Gillet. Thanks to L. Missa and S. Sutjarit for help in the lab and to C. Corbisier who started this work during her master study. Thanks to A. Cruaud, JY. Rasplus, E. Jousselin and G. Kergoat for helpful discussions, to G. Dobigny for constant support. We express gratitude to PH. Fabre who offered us judicious advice to use the Multidivtime software and help us to obtain the ultrametric tree needed in this study. Many thanks from Asia to T. Barraclough for help for the R code.</p><p>This work was supported by the French GIPANR, Programme Santé Environnement - Santé Travail (Program 00121 05), by the PHC Franco-Thai Cooperation in Higher Education and Research (Program No.16601PK). 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