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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Diversity and Genetic Variation among <italic>Brevipalpus</italic> Populations from Brazil and Mexico</title><author><name sortKey="Sanchez Velazquez, E J" sort="Sanchez Velazquez, E J" uniqKey="Sanchez Velazquez E" first="E. J." last="Sánchez-Velázquez">E. J. Sánchez-Velázquez</name><affiliation><nlm:aff id="aff001"><addr-line>Postgrado en Fitosanidad-Entomología y Acarología. Colegio de Postgraduados, Montecillo, Edo. de Mexico, Mexico</addr-line></nlm:aff></affiliation></author><author><name sortKey="Santillan Galicia, M T" sort="Santillan Galicia, M T" uniqKey="Santillan Galicia M" first="M. T." last="Santillán-Galicia">M. T. Santillán-Galicia</name><affiliation><nlm:aff id="aff001"><addr-line>Postgrado en Fitosanidad-Entomología y Acarología. Colegio de Postgraduados, Montecillo, Edo. de Mexico, Mexico</addr-line></nlm:aff></affiliation></author><author><name sortKey="Novelli, V M" sort="Novelli, V M" uniqKey="Novelli V" first="V. M." last="Novelli">V. M. Novelli</name><affiliation><nlm:aff id="aff002"><addr-line>Centro APTA Citros Sylvio Moreira-IAC, Cordeirópolis, Sao Paulo, Brazil</addr-line></nlm:aff></affiliation></author><author><name sortKey="Nunes, M A" sort="Nunes, M A" uniqKey="Nunes M" first="M. A." last="Nunes">M. A. Nunes</name><affiliation><nlm:aff id="aff002"><addr-line>Centro APTA Citros Sylvio Moreira-IAC, Cordeirópolis, Sao Paulo, Brazil</addr-line></nlm:aff></affiliation></author><author><name sortKey="Mora Aguilera, G" sort="Mora Aguilera, G" uniqKey="Mora Aguilera G" first="G." last="Mora-Aguilera">G. Mora-Aguilera</name><affiliation><nlm:aff id="aff003"><addr-line>Postgrado en Fitosanidad-Fitopatología. Colegio de Postgraduados, Montecillo, Edo. de Mexico, Mexico</addr-line></nlm:aff></affiliation></author><author><name sortKey="Valdez Carrasco, J M" sort="Valdez Carrasco, J M" uniqKey="Valdez Carrasco J" first="J. M." last="Valdez-Carrasco">J. M. Valdez-Carrasco</name><affiliation><nlm:aff id="aff001"><addr-line>Postgrado en Fitosanidad-Entomología y Acarología. Colegio de Postgraduados, Montecillo, Edo. de Mexico, Mexico</addr-line></nlm:aff></affiliation></author><author><name sortKey="Otero Colina, G" sort="Otero Colina, G" uniqKey="Otero Colina G" first="G." last="Otero-Colina">G. Otero-Colina</name><affiliation><nlm:aff id="aff001"><addr-line>Postgrado en Fitosanidad-Entomología y Acarología. Colegio de Postgraduados, Montecillo, Edo. de Mexico, Mexico</addr-line></nlm:aff></affiliation></author><author><name sortKey="Freitas Astua, J" sort="Freitas Astua, J" uniqKey="Freitas Astua J" first="J." last="Freitas-Astúa">J. Freitas-Astúa</name><affiliation><nlm:aff id="aff002"><addr-line>Centro APTA Citros Sylvio Moreira-IAC, Cordeirópolis, Sao Paulo, Brazil</addr-line></nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">26207373</idno><idno type="pmc">4514743</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4514743</idno><idno type="RBID">PMC:4514743</idno><idno type="doi">10.1371/journal.pone.0133861</idno><date when="2015">2015</date><idno type="wicri:Area/Pmc/Corpus">000168</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Diversity and Genetic Variation among <italic>Brevipalpus</italic> Populations from Brazil and Mexico</title><author><name sortKey="Sanchez Velazquez, E J" sort="Sanchez Velazquez, E J" uniqKey="Sanchez Velazquez E" first="E. J." last="Sánchez-Velázquez">E. J. Sánchez-Velázquez</name><affiliation><nlm:aff id="aff001"><addr-line>Postgrado en Fitosanidad-Entomología y Acarología. Colegio de Postgraduados, Montecillo, Edo. de Mexico, Mexico</addr-line></nlm:aff></affiliation></author><author><name sortKey="Santillan Galicia, M T" sort="Santillan Galicia, M T" uniqKey="Santillan Galicia M" first="M. T." last="Santillán-Galicia">M. T. Santillán-Galicia</name><affiliation><nlm:aff id="aff001"><addr-line>Postgrado en Fitosanidad-Entomología y Acarología. Colegio de Postgraduados, Montecillo, Edo. de Mexico, Mexico</addr-line></nlm:aff></affiliation></author><author><name sortKey="Novelli, V M" sort="Novelli, V M" uniqKey="Novelli V" first="V. M." last="Novelli">V. M. Novelli</name><affiliation><nlm:aff id="aff002"><addr-line>Centro APTA Citros Sylvio Moreira-IAC, Cordeirópolis, Sao Paulo, Brazil</addr-line></nlm:aff></affiliation></author><author><name sortKey="Nunes, M A" sort="Nunes, M A" uniqKey="Nunes M" first="M. A." last="Nunes">M. A. Nunes</name><affiliation><nlm:aff id="aff002"><addr-line>Centro APTA Citros Sylvio Moreira-IAC, Cordeirópolis, Sao Paulo, Brazil</addr-line></nlm:aff></affiliation></author><author><name sortKey="Mora Aguilera, G" sort="Mora Aguilera, G" uniqKey="Mora Aguilera G" first="G." last="Mora-Aguilera">G. Mora-Aguilera</name><affiliation><nlm:aff id="aff003"><addr-line>Postgrado en Fitosanidad-Fitopatología. Colegio de Postgraduados, Montecillo, Edo. de Mexico, Mexico</addr-line></nlm:aff></affiliation></author><author><name sortKey="Valdez Carrasco, J M" sort="Valdez Carrasco, J M" uniqKey="Valdez Carrasco J" first="J. M." last="Valdez-Carrasco">J. M. Valdez-Carrasco</name><affiliation><nlm:aff id="aff001"><addr-line>Postgrado en Fitosanidad-Entomología y Acarología. Colegio de Postgraduados, Montecillo, Edo. de Mexico, Mexico</addr-line></nlm:aff></affiliation></author><author><name sortKey="Otero Colina, G" sort="Otero Colina, G" uniqKey="Otero Colina G" first="G." last="Otero-Colina">G. Otero-Colina</name><affiliation><nlm:aff id="aff001"><addr-line>Postgrado en Fitosanidad-Entomología y Acarología. Colegio de Postgraduados, Montecillo, Edo. de Mexico, Mexico</addr-line></nlm:aff></affiliation></author><author><name sortKey="Freitas Astua, J" sort="Freitas Astua, J" uniqKey="Freitas Astua J" first="J." last="Freitas-Astúa">J. Freitas-Astúa</name><affiliation><nlm:aff id="aff002"><addr-line>Centro APTA Citros Sylvio Moreira-IAC, Cordeirópolis, Sao Paulo, Brazil</addr-line></nlm:aff></affiliation></author></analytic><series><title level="j">PLoS ONE</title><idno type="eISSN">1932-6203</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><italic>Brevipalpus phoenicis</italic> s.l. is an economically important vector of the <italic>Citrus leprosis virus</italic>-C (CiLV-C), one of the most severe diseases attacking citrus orchards worldwide. Effective control strategies for this mite should be designed based on basic information including its population structure, and particularly the factors that influence its dynamics. We sampled sweet orange orchards extensively in eight locations in Brazil and 12 in Mexico. Population genetic structure and genetic variation between both countries, among locations and among sampling sites within locations were evaluated by analysing nucleotide sequence data from fragments of the mitochondrial cytochrome oxidase subunit I (COI). In both countries, <italic>B</italic>. <italic>yothersi</italic> was the most common species and was found in almost all locations. Individuals from <italic>B</italic>. <italic>papayensis</italic> were found in two locations in Brazil. <italic>Brevipalpus yothersi</italic> populations collected in Brazil were more genetically diverse (14 haplotypes) than Mexican populations (four haplotypes). Although geographical origin had a low but significant effect (ca. 25%) on the population structure, the greatest effect was from the within location comparison (37.02 %). 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<front><journal-meta><journal-id journal-id-type="nlm-ta">PLoS One</journal-id><journal-id journal-id-type="iso-abbrev">PLoS ONE</journal-id><journal-id journal-id-type="publisher-id">plos</journal-id><journal-id journal-id-type="pmc">plosone</journal-id><journal-title-group><journal-title>PLoS ONE</journal-title></journal-title-group><issn pub-type="epub">1932-6203</issn><publisher><publisher-name>Public Library of Science</publisher-name><publisher-loc>San Francisco, CA USA</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">26207373</article-id><article-id pub-id-type="pmc">4514743</article-id><article-id pub-id-type="doi">10.1371/journal.pone.0133861</article-id><article-id pub-id-type="publisher-id">PONE-D-15-14427</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group></article-categories><title-group><article-title>Diversity and Genetic Variation among <italic>Brevipalpus</italic> Populations from Brazil and Mexico</article-title><alt-title alt-title-type="running-head">Diversity and Genetic Variation in <italic>Brevipalpus</italic> Populations</alt-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Sánchez-Velázquez</surname><given-names>E. J.</given-names></name><xref ref-type="aff" rid="aff001"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Santillán-Galicia</surname><given-names>M. T.</given-names></name><xref ref-type="aff" rid="aff001"><sup>1</sup></xref><xref rid="cor001" ref-type="corresp">*</xref></contrib><contrib contrib-type="author"><name><surname>Novelli</surname><given-names>V. M.</given-names></name><xref ref-type="aff" rid="aff002"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Nunes</surname><given-names>M. A.</given-names></name><xref ref-type="aff" rid="aff002"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Mora-Aguilera</surname><given-names>G.</given-names></name><xref ref-type="aff" rid="aff003"><sup>3</sup></xref></contrib><contrib contrib-type="author"><name><surname>Valdez-Carrasco</surname><given-names>J. M.</given-names></name><xref ref-type="aff" rid="aff001"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Otero-Colina</surname><given-names>G.</given-names></name><xref ref-type="aff" rid="aff001"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Freitas-Astúa</surname><given-names>J.</given-names></name><xref ref-type="aff" rid="aff002"><sup>2</sup></xref></contrib></contrib-group><aff id="aff001"><label>1</label><addr-line>Postgrado en Fitosanidad-Entomología y Acarología. Colegio de Postgraduados, Montecillo, Edo. de Mexico, Mexico</addr-line></aff><aff id="aff002"><label>2</label><addr-line>Centro APTA Citros Sylvio Moreira-IAC, Cordeirópolis, Sao Paulo, Brazil</addr-line></aff><aff id="aff003"><label>3</label><addr-line>Postgrado en Fitosanidad-Fitopatología. Colegio de Postgraduados, Montecillo, Edo. de Mexico, Mexico</addr-line></aff><contrib-group><contrib contrib-type="editor"><name><surname>Etges</surname><given-names>William J.</given-names></name><role>Editor</role><xref ref-type="aff" rid="edit1"></xref></contrib></contrib-group><aff id="edit1"><addr-line>University of Arkansas, UNITED STATES</addr-line></aff><author-notes><fn fn-type="conflict" id="coi001"><p><bold>Competing Interests: </bold>The authors have declared that no competing interests exist.</p></fn><fn fn-type="con" id="contrib001"><p>Conceived and designed the experiments: EJSV MTSG VMN GMA JFA. Performed the experiments: EJSV VMN MAN JFA. Analyzed the data: EJSV MTSG VMN JFA. Contributed reagents/materials/analysis tools: MTSG MAN GMA JMVC GOC JFA. Wrote the paper: EJSV MTSG VMN JFA MAN.</p></fn><corresp id="cor001">* E-mail: <email>tgalicia@colpos.mx</email></corresp></author-notes><pub-date pub-type="epub"><day>24</day><month>7</month><year>2015</year></pub-date><pub-date pub-type="collection"><year>2015</year></pub-date><volume>10</volume><issue>7</issue><elocation-id>e0133861</elocation-id><history><date date-type="received"><day>6</day><month>4</month><year>2015</year></date><date date-type="accepted"><day>2</day><month>7</month><year>2015</year></date></history><permissions><copyright-year>2015</copyright-year><copyright-holder>Sánchez-Velázquez et al</copyright-holder><license xlink:href="http://creativecommons.org/licenses/by/4.0/"><license-p>This is an open access article distributed under the terms of the <ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution License</ext-link>, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited</license-p></license></permissions><self-uri content-type="pdf" xlink:type="simple" xlink:href="pone.0133861.pdf"></self-uri><abstract><p><italic>Brevipalpus phoenicis</italic> s.l. is an economically important vector of the <italic>Citrus leprosis virus</italic>-C (CiLV-C), one of the most severe diseases attacking citrus orchards worldwide. Effective control strategies for this mite should be designed based on basic information including its population structure, and particularly the factors that influence its dynamics. We sampled sweet orange orchards extensively in eight locations in Brazil and 12 in Mexico. Population genetic structure and genetic variation between both countries, among locations and among sampling sites within locations were evaluated by analysing nucleotide sequence data from fragments of the mitochondrial cytochrome oxidase subunit I (COI). In both countries, <italic>B</italic>. <italic>yothersi</italic> was the most common species and was found in almost all locations. Individuals from <italic>B</italic>. <italic>papayensis</italic> were found in two locations in Brazil. <italic>Brevipalpus yothersi</italic> populations collected in Brazil were more genetically diverse (14 haplotypes) than Mexican populations (four haplotypes). Although geographical origin had a low but significant effect (ca. 25%) on the population structure, the greatest effect was from the within location comparison (37.02 %). Potential factors driving our results were discussed.</p></abstract><funding-group><funding-statement>ESV received a scholarship from Consejo Nacional de Ciencia y Tecnología (CONACYT) Mexico. This research was done under the project ‘Implicaciones epidemiológicas del CTV en el sistema vector – planta: bases epidemiológicas y cuantitativas para la aplicación de la campaña en México’ funded by the Servicio Nacional de Sanidad, Inocuidad y Calidad Agroalimentaria (SENASICA), Mexico and Fundação de Amparo à Pesquisa do Estado de São Paulo, Brazil.</funding-statement></funding-group><counts><fig-count count="4"></fig-count><table-count count="3"></table-count><page-count count="16"></page-count></counts><custom-meta-group><custom-meta id="data-availability"><meta-name>Data Availability</meta-name><meta-value>All sequences files are available from the GenBank database. Accession numbers are provided in the paper.</meta-value></custom-meta></custom-meta-group></article-meta><notes><title>Data Availability</title><p>All sequences files are available from the GenBank database. Accession numbers are provided in the paper.</p></notes></front><body><sec sec-type="intro" id="sec001"><title>Introduction</title><p>Citrus crops are important worldwide and sweet orange, <italic>Citrus sinensis</italic> (L.) Osbeck (Sapindales: Rutaceae), is the most economically important species produced [<xref rid="pone.0133861.ref001" ref-type="bibr">1</xref>]. Currently, Brazil is the world's largest producer of oranges followed by the United States, China, India and Mexico [<xref rid="pone.0133861.ref001" ref-type="bibr">1</xref>]. Currently, one of the most important viral diseases affecting citrus production in Brazil is leprosis, caused by <italic>Citrus leprosis virus</italic> C (CiLV-C) [<xref rid="pone.0133861.ref002" ref-type="bibr">2</xref>]. Transmission of this virus has been related to mite species in the genus <italic>Brevipalpus</italic>, specifically <italic>B</italic>. <italic>phoenicis</italic> (Geijskes) [<xref rid="pone.0133861.ref003" ref-type="bibr">3</xref>–<xref rid="pone.0133861.ref005" ref-type="bibr">5</xref>]. However, the existence of a species complex within <italic>B</italic>. <italic>phoenicis</italic> [<xref rid="pone.0133861.ref006" ref-type="bibr">6</xref>] makes it more difficult to assess the true role of each species in the transmission of CiLV-C. Previously, this species complex has been referred to as <italic>B</italic>. <italic>phoenicis</italic> group species A-G [<xref rid="pone.0133861.ref006" ref-type="bibr">6</xref>], but recently the species status of <italic>B</italic>. <italic>phoenicis</italic> has been revised and the putative species referred to as species groups within <italic>B</italic>. <italic>phoenicis</italic> have been elevated to separate species, specifically: <italic>B</italic>. <italic>azores</italic> Beard & Ochoa, <italic>B</italic>. <italic>feresi</italic> Ochoa & Beard, <italic>B</italic>. <italic>ferraguti</italic> Ochoa & Beard and <italic>B</italic>. <italic>tucuman</italic> Beard & Ochoa. Furthermore, four species previously considered as synonyms of <italic>B</italic>. <italic>phoenicis</italic> have been confirmed as separate species, specifically: <italic>B</italic>. <italic>hondurani</italic> Evans, <italic>B</italic>. <italic>papayensis</italic> Baker, <italic>B</italic>. <italic>phoenicis</italic> s.s. (Geijskes) and <italic>B</italic>. <italic>yothersi</italic> Baker [<xref rid="pone.0133861.ref007" ref-type="bibr">7</xref>]. All the information reported so far regarding <italic>B</italic>. <italic>phoenicis</italic> has been done without considering the existence of a species complex. Therefore, we will consider this species as <italic>B</italic>. <italic>phoenicis sensu lato</italic>, and wherever possible we will refer to the new species description made by Beard et al. [<xref rid="pone.0133861.ref007" ref-type="bibr">7</xref>].</p><p><italic>Brevipalpus phoenicis</italic> s.l. is a tropical and subtropical species that feeds on at least 486 host plants including agricultural, ornamental and weed species [<xref rid="pone.0133861.ref008" ref-type="bibr">8</xref>–<xref rid="pone.0133861.ref010" ref-type="bibr">10</xref>]. Reproduction of <italic>Brevipalpus</italic> mite species is by thelytokous parthenogenesis with females producing females that are genetically similar [<xref rid="pone.0133861.ref011" ref-type="bibr">11</xref>]. Females are haploid with two chromosomes and males are rarely found [<xref rid="pone.0133861.ref012" ref-type="bibr">12</xref>]. Interestingly, asexuality in this species complex is due to the presence of bacteria from the genus <italic>Cardinium</italic> [<xref rid="pone.0133861.ref013" ref-type="bibr">13</xref>]. When these bacteria were removed from mite populations, some males were produced [<xref rid="pone.0133861.ref014" ref-type="bibr">14</xref>], although they appeared to be unable to reproduce [<xref rid="pone.0133861.ref015" ref-type="bibr">15</xref>]. Although some males can be produced, perhaps by an inefficient transmission of the bacteria, as suggested by Groot et al. [<xref rid="pone.0133861.ref013" ref-type="bibr">13</xref>], the lack of functional males induces parthenogenesis as the main mode of reproduction in this species [<xref rid="pone.0133861.ref014" ref-type="bibr">14</xref>]. The fact that this species is polyphagous contradicts the hypothesis that asexual species are unsuccessful colonizers of different environments [<xref rid="pone.0133861.ref016" ref-type="bibr">16</xref>]. However, it has also been reported that successful colonization of new host plants depends on the original host plant. For example, <italic>B</italic>. <italic>phoencisis</italic> s.l originating from acerola (<italic>Malpighia glabra</italic> L. Malpighiales: Malpighiaceae) did not adapt to two new host plants tested—sweet orange and hibiscus (<italic>Hibiscus rosa-sinensis</italic>, L. Malvales: Malvaceae). However, populations originating from sweet orange adapted well to the other two host plant species [<xref rid="pone.0133861.ref017" ref-type="bibr">17</xref>]. It is not known whether these results may be explained by the recent description of cryptic species within <italic>B</italic>. <italic>phoenicis</italic> s.l. [<xref rid="pone.0133861.ref007" ref-type="bibr">7</xref>] where each new species might be associated with different host ranges.</p><p>In Brazil, only <italic>B</italic>. <italic>phoenicis</italic> has been reported causing damage on citrus, mainly due to the transmission of CiLV-C [<xref rid="pone.0133861.ref002" ref-type="bibr">2</xref>, <xref rid="pone.0133861.ref018" ref-type="bibr">18</xref>]. However, in Mexico <italic>B</italic>. <italic>phoenicis</italic> s.l. is part of a community of mites on citrus that also include <italic>Brevipalpus obovatus</italic> (Donnadieu) and <italic>Brevipalpus californicus</italic> (Banks) [<xref rid="pone.0133861.ref019" ref-type="bibr">19</xref>–<xref rid="pone.0133861.ref023" ref-type="bibr">23</xref>]. In both countries, the presence of <italic>B</italic>. <italic>phoenicis</italic> s.l. is consistent with damage, suggesting the effect of CiLV-C in Mexico may become as severe as in Brazil if no new control strategies are designed and implemented. Currently, the most common strategy to control CiLV-C is by controlling mite populations [<xref rid="pone.0133861.ref024" ref-type="bibr">24</xref>–<xref rid="pone.0133861.ref025" ref-type="bibr">25</xref>]. In Brazil, the citrus industry spends $US 62 million per year on the control of <italic>B</italic>. <italic>phoenicis</italic> [<xref rid="pone.0133861.ref026" ref-type="bibr">26</xref>]. Effective control strategies for this mite should be based on an understanding of its population structure, and particularly the factors that influence its dynamics [<xref rid="pone.0133861.ref027" ref-type="bibr">27</xref>]. In Mexico, to our knowledge, there have only been two studies on the population dynamics and distribution of <italic>B</italic>. <italic>phoenicis</italic> on different citrus species and in different regions of Mexico [<xref rid="pone.0133861.ref023" ref-type="bibr">23</xref>–<xref rid="pone.0133861.ref028" ref-type="bibr">28</xref>].</p><p><italic>Brevipalpus yothersi</italic> (formerly <italic>B</italic>. <italic>phoenicis</italic> morphotype B) has been reported in both Brazil and Mexico, but <italic>B</italic>. <italic>papayensis</italic> (formerly <italic>B</italic>. <italic>phoenicis</italic> morphotype C) has only been reported from Brazil [<xref rid="pone.0133861.ref029" ref-type="bibr">29</xref>]. Despite studies determining genetic population structure and genetic variation [<xref rid="pone.0133861.ref030" ref-type="bibr">30</xref>], and the recent publication of Beard et al. [<xref rid="pone.0133861.ref007" ref-type="bibr">7</xref>], studies of different species within the <italic>B</italic>. <italic>phoenicis</italic> s.l. species complex in Brazilian and Mexican populations are practically non-existent and therefore urgently needed. There are several molecular markers used to resolve taxonomic relationships and quantify genetic variation within the same population of a particular mite species [<xref rid="pone.0133861.ref031" ref-type="bibr">31</xref>, <xref rid="pone.0133861.ref032" ref-type="bibr">32</xref>]. DNA sequence information of the mitochondrial cytochrome oxidase subunit I (COI) has also been used previously to quantify genetic variation and population structure of other mite pests on citrus [<xref rid="pone.0133861.ref033" ref-type="bibr">33</xref>] and to aid taxonomic identification of mites within Tetranychidae and Tenuipalpidae [<xref rid="pone.0133861.ref034" ref-type="bibr">34</xref>]. Improved analyses of genetic diversity and population structure over both large and local geographic scales are important to understand the factors affecting population dynamics and to design effective control strategies [<xref rid="pone.0133861.ref027" ref-type="bibr">27</xref>, <xref rid="pone.0133861.ref035" ref-type="bibr">35</xref>].</p><p>With this aim in mind, we took extensive samples of mites from different locations in Mexico and Brazil and compared the species diversity, genetic diversity and population structure of the <italic>B</italic>. <italic>phoenicis</italic> s.l. species complex using COI sequence information to infer relationships between haplotypes and evaluate genetic differentiation among different populations.</p></sec><sec id="sec002"><title>Material and Methods</title><sec id="sec003"><title>Sampling of mites</title><p><italic>Brevipalpus</italic> mites were collected from sweet orange orchards. In total, we sampled 35 orchards that were distributed as follows: one orchard at each of 11 locations in Brazil (<xref rid="pone.0133861.t001" ref-type="table">Table 1</xref>) from five states, and one orchard at each of 24 locations in Mexico (<xref rid="pone.0133861.t001" ref-type="table">Table 1</xref>) from three states. Collections were made from September to November 2012 in Brazil, and from February to July 2013 in Mexico. At each location in Mexico, samples of leaves, branches and fruits were taken from each of five trees within the orchard (each tree represented one sample) and returned to the laboratory. The trees were selected based on their position in the orchard, one from each of the four corners and one from the centre. In the laboratory the plant material from each tree was searched for mites using a binocular stereomicroscope. Adult mites were collected using a fine brush and deposited into microtubes containing absolute ethanol. Where possible up to 100 individuals were collected from each tree. When only very few mites were found, they were allowed to reproduce on sweet orange fruits under laboratory conditions, following the methods proposed by Chiavegato-Gonzaga [<xref rid="pone.0133861.ref036" ref-type="bibr">36</xref>], to acquire sufficient numbers for identification and analysis. Although five samples were always taken from each location, some had no mites at all and therefore, the final number of trees sampled differed among locations. In Brazil, mite samples were collected and processed in a similar way except from the localities of Gurupi, Sao José Castanhal and Capitao Poco, where mites were stored in 70% ethanol. Before processing, these mites were lyophilized for 20 min to remove the alcohol. The study was conducted in private orchards with the permission of the landowners. The field studies did not involve endangered or protected species. In total 59 samples of mites were collected (<xref rid="pone.0133861.t001" ref-type="table">Table 1</xref>).</p><table-wrap id="pone.0133861.t001" orientation="portrait" position="float"><object-id pub-id-type="doi">10.1371/journal.pone.0133861.t001</object-id><label>Table 1</label><caption><title>Details of the <italic>Brevipalpus</italic> species sampled in this study.</title><p>These include those collected from different sites in Brazil and Mexico and also reference DNA material used for genetic comparisons.</p></caption><alternatives><graphic id="pone.0133861.t001g" xlink:href="pone.0133861.t001"></graphic><table frame="hsides" rules="groups"><colgroup span="1"><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col></colgroup><tbody><tr><td align="left" rowspan="1" colspan="1"><bold>Location (city, state, country)</bold></td><td align="left" rowspan="1" colspan="1"><bold>Code</bold></td><td align="left" rowspan="1" colspan="1"><bold>Orange variety</bold></td><td align="left" rowspan="1" colspan="1"><bold>Haplotype</bold><xref rid="t001fn002" ref-type="table-fn"><bold>‡</bold></xref></td><td align="left" rowspan="1" colspan="1"><bold>GenBank accesion number</bold></td><td align="left" rowspan="1" colspan="1"><bold>Geographical coordinates</bold></td></tr><tr><td rowspan="4" align="left" colspan="1">Pouso Alegre, Minas Gerais, Brazil</td><td align="left" rowspan="1" colspan="1">POA-1</td><td align="left" rowspan="1" colspan="1">Pêra</td><td align="left" rowspan="1" colspan="1">H1</td><td align="left" rowspan="1" colspan="1">KF954950**</td><td align="left" rowspan="1" colspan="1">22.266181S, 46.008686W</td></tr><tr><td align="left" rowspan="1" colspan="1">POA-2</td><td align="left" rowspan="1" colspan="1">Pêra</td><td align="left" rowspan="1" colspan="1">H2</td><td align="left" rowspan="1" colspan="1">KF954951**</td><td align="left" rowspan="1" colspan="1">22.266181S, 46.008686W</td></tr><tr><td align="left" rowspan="1" colspan="1">POA-3</td><td align="left" rowspan="1" colspan="1">Pêra</td><td align="left" rowspan="1" colspan="1">H1</td><td align="left" rowspan="1" colspan="1">KF954952**</td><td align="left" rowspan="1" colspan="1">22.266181S, 46.008686W</td></tr><tr><td align="left" rowspan="1" colspan="1">POA-4</td><td align="left" rowspan="1" colspan="1">Pêra</td><td align="left" rowspan="1" colspan="1">H3</td><td align="left" rowspan="1" colspan="1">KF954953**</td><td align="left" rowspan="1" colspan="1">22.266181S, 46.008686W</td></tr><tr><td rowspan="2" align="left" colspan="1">Lavras, Minas Gerais, Brazil</td><td align="left" rowspan="1" colspan="1">LAV-1</td><td align="left" rowspan="1" colspan="1">Pêra</td><td align="left" rowspan="1" colspan="1">H1</td><td align="left" rowspan="1" colspan="1">KF954956**</td><td align="left" rowspan="1" colspan="1">21.287306S, 44.988942W</td></tr><tr><td align="left" rowspan="1" colspan="1">LAV-2</td><td align="left" rowspan="1" colspan="1">Pêra</td><td align="left" rowspan="1" colspan="1">H2</td><td align="left" rowspan="1" colspan="1">KF954957**</td><td align="left" rowspan="1" colspan="1">21.287306S, 44.988942W</td></tr><tr><td rowspan="7" align="left" colspan="1">São José do Rio Preto, São Paulo, Brazil</td><td align="left" rowspan="1" colspan="1">SJRPB-1</td><td align="left" rowspan="1" colspan="1">Bahia</td><td align="left" rowspan="1" colspan="1">H12</td><td align="left" rowspan="1" colspan="1">KF954964</td><td align="left" rowspan="1" colspan="1">20.867119S, 49.357336W</td></tr><tr><td align="left" rowspan="1" colspan="1">SJRPB-2</td><td align="left" rowspan="1" colspan="1">Bahia</td><td align="left" rowspan="1" colspan="1">H8</td><td align="left" rowspan="1" colspan="1">KF954965</td><td align="left" rowspan="1" colspan="1">20.867119S, 49.357336W</td></tr><tr><td align="left" rowspan="1" colspan="1">SJRPB-3</td><td align="left" rowspan="1" colspan="1">Bahia</td><td align="left" rowspan="1" colspan="1">H13</td><td align="left" rowspan="1" colspan="1">KF954966</td><td align="left" rowspan="1" colspan="1">20.867119S, 49.357336W</td></tr><tr><td align="left" rowspan="1" colspan="1">SJRPL-1</td><td align="left" rowspan="1" colspan="1">Lima</td><td align="left" rowspan="1" colspan="1">H14</td><td align="left" rowspan="1" colspan="1">KF954967</td><td align="left" rowspan="1" colspan="1">20.867119S, 49.357336W</td></tr><tr><td align="left" rowspan="1" colspan="1">SJRPL-2</td><td align="left" rowspan="1" colspan="1">Lima</td><td align="left" rowspan="1" colspan="1">H15</td><td align="left" rowspan="1" colspan="1">KF954968</td><td align="left" rowspan="1" colspan="1">20.867119S, 49.357336W</td></tr><tr><td align="left" rowspan="1" colspan="1">SJRPL-3</td><td align="left" rowspan="1" colspan="1">Lima</td><td align="left" rowspan="1" colspan="1">H16</td><td align="left" rowspan="1" colspan="1">KF954969</td><td align="left" rowspan="1" colspan="1">20.867119S, 49.357336W</td></tr><tr><td align="left" rowspan="1" colspan="1">SJRPP-3</td><td align="left" rowspan="1" colspan="1">Pêra</td><td align="left" rowspan="1" colspan="1">H17</td><td align="left" rowspan="1" colspan="1">KF954970</td><td align="left" rowspan="1" colspan="1">20.867119S, 49.357336W</td></tr><tr><td align="left" rowspan="1" colspan="1">Terenos, Mato Grosso do Sul, Brazil</td><td align="left" rowspan="1" colspan="1">MS-1</td><td align="left" rowspan="1" colspan="1">Pêra</td><td align="left" rowspan="1" colspan="1">H6</td><td align="left" rowspan="1" colspan="1">KF954958</td><td align="left" rowspan="1" colspan="1">20.428611S, 55.008889W</td></tr><tr><td rowspan="2" align="left" colspan="1">Gurupi, Tocantins, Brazil</td><td align="left" rowspan="1" colspan="1">GUR-1</td><td align="left" rowspan="1" colspan="1">No commercial</td><td align="left" rowspan="1" colspan="1">H5</td><td align="left" rowspan="1" colspan="1">KF954954</td><td align="left" rowspan="1" colspan="1">11.746844S, 49.049178W</td></tr><tr><td align="left" rowspan="1" colspan="1">GUR-3</td><td align="left" rowspan="1" colspan="1">No commercial</td><td align="left" rowspan="1" colspan="1">H5</td><td align="left" rowspan="1" colspan="1">KF954955</td><td align="left" rowspan="1" colspan="1">11.746844S, 49.049178W</td></tr><tr><td rowspan="3" align="left" colspan="1">Palmas, Tocantins, Brazil</td><td align="left" rowspan="1" colspan="1">PAP3-3</td><td align="left" rowspan="1" colspan="1">No commercial</td><td align="left" rowspan="1" colspan="1">H7</td><td align="left" rowspan="1" colspan="1">KF954959</td><td align="left" rowspan="1" colspan="1">10.291125S, 48.2909W</td></tr><tr><td align="left" rowspan="1" colspan="1">PAP4-1</td><td align="left" rowspan="1" colspan="1">No commercial</td><td align="left" rowspan="1" colspan="1">H8</td><td align="left" rowspan="1" colspan="1">KF954960</td><td align="left" rowspan="1" colspan="1">10.291125S, 48.2909W</td></tr><tr><td align="left" rowspan="1" colspan="1">PAP4-3</td><td align="left" rowspan="1" colspan="1">No commercial</td><td align="left" rowspan="1" colspan="1">H9</td><td align="left" rowspan="1" colspan="1">KF954961</td><td align="left" rowspan="1" colspan="1">10.291125S, 48.2909W</td></tr><tr><td rowspan="2" align="left" colspan="1">São José Castanhal, Pará, Brazil</td><td align="left" rowspan="1" colspan="1">SJC-1</td><td align="left" rowspan="1" colspan="1">Pêra</td><td align="left" rowspan="1" colspan="1">H10</td><td align="left" rowspan="1" colspan="1">KF954962</td><td align="left" rowspan="1" colspan="1">1.43325S, 53.14735W</td></tr><tr><td align="left" rowspan="1" colspan="1">SJC-3</td><td align="left" rowspan="1" colspan="1">Pêra</td><td align="left" rowspan="1" colspan="1">H11</td><td align="left" rowspan="1" colspan="1">KF954963</td><td align="left" rowspan="1" colspan="1">1.43325S, 53.14735W</td></tr><tr><td align="left" rowspan="1" colspan="1">Capitão Poço, Pará, Brazil</td><td align="left" rowspan="1" colspan="1">CP2-1</td><td align="left" rowspan="1" colspan="1">Pêra</td><td align="left" rowspan="1" colspan="1">H4</td><td align="left" rowspan="1" colspan="1">KF954971</td><td align="left" rowspan="1" colspan="1">1.825639S, 53.10225W</td></tr><tr><td rowspan="6" align="left" colspan="1">Ocozocoautla de Espinosa, Chiapas, Mexico</td><td align="left" rowspan="1" colspan="1">O1a-1</td><td align="left" rowspan="1" colspan="1">Valencia</td><td align="left" rowspan="1" colspan="1">H8</td><td align="left" rowspan="1" colspan="1">KF954987</td><td align="left" rowspan="1" colspan="1">16.972417N, 93.503778W</td></tr><tr><td align="left" rowspan="1" colspan="1">O1a-2</td><td align="left" rowspan="1" colspan="1">Valencia</td><td align="left" rowspan="1" colspan="1">H8</td><td align="left" rowspan="1" colspan="1">KF954988</td><td align="left" rowspan="1" colspan="1">16.972417N, 93.503778W</td></tr><tr><td align="left" rowspan="1" colspan="1">O2-1</td><td align="left" rowspan="1" colspan="1">Valencia</td><td align="left" rowspan="1" colspan="1">H8</td><td align="left" rowspan="1" colspan="1">KF954989</td><td align="left" rowspan="1" colspan="1">17.007528N, 93.468111W</td></tr><tr><td align="left" rowspan="1" colspan="1">O2-2</td><td align="left" rowspan="1" colspan="1">Valencia</td><td align="left" rowspan="1" colspan="1">H8</td><td align="left" rowspan="1" colspan="1">KF954990</td><td align="left" rowspan="1" colspan="1">17.007528N, 93.468111W</td></tr><tr><td align="left" rowspan="1" colspan="1">O4-2</td><td align="left" rowspan="1" colspan="1">Valencia</td><td align="left" rowspan="1" colspan="1">H8</td><td align="left" rowspan="1" colspan="1">KF954991</td><td align="left" rowspan="1" colspan="1">17.134611N, 93.294472W</td></tr><tr><td align="left" rowspan="1" colspan="1">O5</td><td align="left" rowspan="1" colspan="1">No commercial</td><td align="left" rowspan="1" colspan="1">H19</td><td align="left" rowspan="1" colspan="1">KF954992</td><td align="left" rowspan="1" colspan="1">17.033861N, 93.544472W</td></tr><tr><td rowspan="2" align="left" colspan="1">Tecpatán, Chiapas, Mexico</td><td align="left" rowspan="1" colspan="1">T6-1</td><td align="left" rowspan="1" colspan="1">Valencia</td><td align="left" rowspan="1" colspan="1">H8</td><td align="left" rowspan="1" colspan="1">KF954998</td><td align="left" rowspan="1" colspan="1">17.217194N, 93.400667W</td></tr><tr><td align="left" rowspan="1" colspan="1">T6-2</td><td align="left" rowspan="1" colspan="1">Valencia</td><td align="left" rowspan="1" colspan="1">H8</td><td align="left" rowspan="1" colspan="1">KF954999</td><td align="left" rowspan="1" colspan="1">17.217194N, 93.400667W</td></tr><tr><td rowspan="2" align="left" colspan="1">Copainalá, Chiapas, Mexico</td><td align="left" rowspan="1" colspan="1">C9</td><td align="left" rowspan="1" colspan="1">Valencia</td><td align="left" rowspan="1" colspan="1">H8</td><td align="left" rowspan="1" colspan="1">KF954972</td><td align="left" rowspan="1" colspan="1">17.033861N, 93.515W</td></tr><tr><td align="left" rowspan="1" colspan="1">C10</td><td align="left" rowspan="1" colspan="1">Valencia</td><td align="left" rowspan="1" colspan="1">H8</td><td align="left" rowspan="1" colspan="1">KF954973</td><td align="left" rowspan="1" colspan="1">17.135583N, 93.293722W</td></tr><tr><td align="left" rowspan="1" colspan="1">Ángel Albino Corzo, Chiapas, Mexico</td><td align="left" rowspan="1" colspan="1">JAL15</td><td align="left" rowspan="1" colspan="1">Valencia</td><td align="left" rowspan="1" colspan="1">H8</td><td align="left" rowspan="1" colspan="1">KF954977</td><td align="left" rowspan="1" colspan="1">15.878583N, 93.729417W</td></tr><tr><td rowspan="6" align="left" colspan="1">La Concordia, Chiapas, Mexico</td><td align="left" rowspan="1" colspan="1">LC16-1</td><td align="left" rowspan="1" colspan="1">Valencia</td><td align="left" rowspan="1" colspan="1">H8</td><td align="left" rowspan="1" colspan="1">KF954978</td><td align="left" rowspan="1" colspan="1">15.888389N, 93.7235W</td></tr><tr><td align="left" rowspan="1" colspan="1">LC16-2</td><td align="left" rowspan="1" colspan="1">Valencia</td><td align="left" rowspan="1" colspan="1">H8</td><td align="left" rowspan="1" colspan="1">KF954979</td><td align="left" rowspan="1" colspan="1">15.888389N, 93.7235W</td></tr><tr><td align="left" rowspan="1" colspan="1">LC17-1</td><td align="left" rowspan="1" colspan="1">Valencia</td><td align="left" rowspan="1" colspan="1">H8</td><td align="left" rowspan="1" colspan="1">KF954980</td><td align="left" rowspan="1" colspan="1">16.097472N, 92.812361W</td></tr><tr><td align="left" rowspan="1" colspan="1">LC17-2</td><td align="left" rowspan="1" colspan="1">Valencia</td><td align="left" rowspan="1" colspan="1">H8</td><td align="left" rowspan="1" colspan="1">KF954981</td><td align="left" rowspan="1" colspan="1">16.097472N, 92.812361W</td></tr><tr><td align="left" rowspan="1" colspan="1">LC18-1</td><td align="left" rowspan="1" colspan="1">Valencia</td><td align="left" rowspan="1" colspan="1">H8</td><td align="left" rowspan="1" colspan="1">KF954982</td><td align="left" rowspan="1" colspan="1">16.097472N, 92.812361W</td></tr><tr><td align="left" rowspan="1" colspan="1">LC18-2</td><td align="left" rowspan="1" colspan="1">Valencia</td><td align="left" rowspan="1" colspan="1">H8</td><td align="left" rowspan="1" colspan="1">KF954983</td><td align="left" rowspan="1" colspan="1">16.097472N, 92.812361W</td></tr><tr><td rowspan="5" align="left" colspan="1">Villa Corzo, Chiapas, Mexico</td><td align="left" rowspan="1" colspan="1">VC19</td><td align="left" rowspan="1" colspan="1">Valencia</td><td align="left" rowspan="1" colspan="1">H8</td><td align="left" rowspan="1" colspan="1">KF955002</td><td align="left" rowspan="1" colspan="1">16.145472N, 93.016222W</td></tr><tr><td align="left" rowspan="1" colspan="1">VC20-1</td><td align="left" rowspan="1" colspan="1">Valencia</td><td align="left" rowspan="1" colspan="1">H8</td><td align="left" rowspan="1" colspan="1">KF955003</td><td align="left" rowspan="1" colspan="1">16.129639N, 93.031139W</td></tr><tr><td align="left" rowspan="1" colspan="1">VC20-2</td><td align="left" rowspan="1" colspan="1">Valencia</td><td align="left" rowspan="1" colspan="1">H8</td><td align="left" rowspan="1" colspan="1">KF955004</td><td align="left" rowspan="1" colspan="1">16.129639N, 93.031139W</td></tr><tr><td align="left" rowspan="1" colspan="1">VC21-1</td><td align="left" rowspan="1" colspan="1">Valencia</td><td align="left" rowspan="1" colspan="1">H8</td><td align="left" rowspan="1" colspan="1">KF955005</td><td align="left" rowspan="1" colspan="1">16.18625N, 93.064111W</td></tr><tr><td align="left" rowspan="1" colspan="1">VC21-2</td><td align="left" rowspan="1" colspan="1">Valencia</td><td align="left" rowspan="1" colspan="1">H8</td><td align="left" rowspan="1" colspan="1">KF955006</td><td align="left" rowspan="1" colspan="1">16.18625N, 93.064111W</td></tr><tr><td rowspan="2" align="left" colspan="1">Villa Flores, Chiapas, Mexico</td><td align="left" rowspan="1" colspan="1">VF22-1</td><td align="left" rowspan="1" colspan="1">Valencia</td><td align="left" rowspan="1" colspan="1">H20</td><td align="left" rowspan="1" colspan="1">KF955007</td><td align="left" rowspan="1" colspan="1">16.268778N, 93.268528W</td></tr><tr><td align="left" rowspan="1" colspan="1">VF22-2</td><td align="left" rowspan="1" colspan="1">Valencia</td><td align="left" rowspan="1" colspan="1">H8</td><td align="left" rowspan="1" colspan="1">KF955008</td><td align="left" rowspan="1" colspan="1">16.268778N, 93.268528W</td></tr><tr><td rowspan="5" align="left" colspan="1">Salto de Agua, Chiapas, Mexico</td><td align="left" rowspan="1" colspan="1">SA23-1</td><td align="left" rowspan="1" colspan="1">Valencia</td><td align="left" rowspan="1" colspan="1">H8</td><td align="left" rowspan="1" colspan="1">KF954993</td><td align="left" rowspan="1" colspan="1">17.321581N, 92.06575W</td></tr><tr><td align="left" rowspan="1" colspan="1">SA24-1</td><td align="left" rowspan="1" colspan="1">Valencia</td><td align="left" rowspan="1" colspan="1">H8</td><td align="left" rowspan="1" colspan="1">KF954994</td><td align="left" rowspan="1" colspan="1">17.338561N, 92.083811W</td></tr><tr><td align="left" rowspan="1" colspan="1">SA24-2</td><td align="left" rowspan="1" colspan="1">Valencia</td><td align="left" rowspan="1" colspan="1">H8</td><td align="left" rowspan="1" colspan="1">KF954995</td><td align="left" rowspan="1" colspan="1">17.338561N, 92.083811W</td></tr><tr><td align="left" rowspan="1" colspan="1">SA25-1</td><td align="left" rowspan="1" colspan="1">Valencia</td><td align="left" rowspan="1" colspan="1">H8</td><td align="left" rowspan="1" colspan="1">KF954996</td><td align="left" rowspan="1" colspan="1">17.33765N, 92.097989W</td></tr><tr><td align="left" rowspan="1" colspan="1">SA25-2</td><td align="left" rowspan="1" colspan="1">Valencia</td><td align="left" rowspan="1" colspan="1">H8</td><td align="left" rowspan="1" colspan="1">KF954997</td><td align="left" rowspan="1" colspan="1">17.33765N, 92.097989W</td></tr><tr><td rowspan="2" align="left" colspan="1">Uxpanapa, Veracruz, Mexico</td><td align="left" rowspan="1" colspan="1">UX26-1</td><td align="left" rowspan="1" colspan="1">Valencia</td><td align="left" rowspan="1" colspan="1">H8</td><td align="left" rowspan="1" colspan="1">KF955000</td><td align="left" rowspan="1" colspan="1">17.225931N, 94.64535W</td></tr><tr><td align="left" rowspan="1" colspan="1">UX26-2</td><td align="left" rowspan="1" colspan="1">Valencia</td><td align="left" rowspan="1" colspan="1">H8</td><td align="left" rowspan="1" colspan="1">KF955001</td><td align="left" rowspan="1" colspan="1">17.225931N, 94.64535W</td></tr><tr><td rowspan="3" align="left" colspan="1">Las Choapas, Veracruz, Mexico</td><td align="left" rowspan="1" colspan="1">LCH27-1</td><td align="left" rowspan="1" colspan="1">Valencia</td><td align="left" rowspan="1" colspan="1">H18</td><td align="left" rowspan="1" colspan="1">KF954984</td><td align="left" rowspan="1" colspan="1">17.599639N, 93.796519W</td></tr><tr><td align="left" rowspan="1" colspan="1">LCH27-2</td><td align="left" rowspan="1" colspan="1">Valencia</td><td align="left" rowspan="1" colspan="1">H8</td><td align="left" rowspan="1" colspan="1">KF954985</td><td align="left" rowspan="1" colspan="1">17.599639N, 93.796519W</td></tr><tr><td align="left" rowspan="1" colspan="1">LCH30</td><td align="left" rowspan="1" colspan="1">Valencia</td><td align="left" rowspan="1" colspan="1">H8</td><td align="left" rowspan="1" colspan="1">KF954986</td><td align="left" rowspan="1" colspan="1">17.555511N, 93.785331W</td></tr><tr><td rowspan="2" align="left" colspan="1">Cárdenas, Tabasco, Mexico</td><td align="left" rowspan="1" colspan="1">CAR28-1</td><td align="left" rowspan="1" colspan="1">Valencia</td><td align="left" rowspan="1" colspan="1">H8</td><td align="left" rowspan="1" colspan="1">KF954974</td><td align="left" rowspan="1" colspan="1">17.967194N, 93.332361W</td></tr><tr><td align="left" rowspan="1" colspan="1">CAR28-2</td><td align="left" rowspan="1" colspan="1">Valencia</td><td align="left" rowspan="1" colspan="1">H8</td><td align="left" rowspan="1" colspan="1">KF954975</td><td align="left" rowspan="1" colspan="1">17.967194N, 93.332361W</td></tr><tr><td align="left" rowspan="1" colspan="1">Comalcalco, Tabasco, Mexico</td><td align="left" rowspan="1" colspan="1">COM29</td><td align="left" rowspan="1" colspan="1">Valencia</td><td align="left" rowspan="1" colspan="1">H8</td><td align="left" rowspan="1" colspan="1">KF954976</td><td align="left" rowspan="1" colspan="1">18.191419N, 93.4054W</td></tr><tr><td colspan="6" align="center" rowspan="1"><bold>Sequences retrieved from GenBank used for comparison</bold></td></tr><tr><td align="left" rowspan="1" colspan="1"><bold>Species</bold></td><td colspan="3" align="center" rowspan="1"><bold>GenBank accession number</bold></td><td colspan="2" align="center" rowspan="1"><bold>Reference</bold></td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>Brevipalpus phoenicis</italic> Type 2</td><td colspan="3" align="left" rowspan="1">KC291373</td><td colspan="2" align="left" rowspan="1">Navia et al. [<xref rid="pone.0133861.ref030" ref-type="bibr">30</xref>]</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>B</italic>. <italic>phoenicis</italic> Type 2</td><td colspan="3" align="left" rowspan="1">KC291372</td><td colspan="2" align="left" rowspan="1">Navia et al. [<xref rid="pone.0133861.ref030" ref-type="bibr">30</xref>]</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>B</italic>. <italic>phoenicis</italic> Type 1</td><td colspan="3" align="left" rowspan="1">KC291388</td><td colspan="2" align="left" rowspan="1">Navia et al. [<xref rid="pone.0133861.ref030" ref-type="bibr">30</xref>]</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>B</italic>. <italic>phoenicis</italic> Type 1</td><td colspan="3" align="left" rowspan="1">KC291389</td><td colspan="2" align="left" rowspan="1">Navia et al. [<xref rid="pone.0133861.ref030" ref-type="bibr">30</xref>]</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>Brevipalpus obovatus</italic></td><td colspan="3" align="left" rowspan="1">KC291383</td><td colspan="2" align="left" rowspan="1">Navia et al. [<xref rid="pone.0133861.ref030" ref-type="bibr">30</xref>]</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>B</italic>. <italic>obovatus</italic></td><td colspan="3" align="left" rowspan="1">KC291384</td><td colspan="2" align="left" rowspan="1">Navia et al. [<xref rid="pone.0133861.ref030" ref-type="bibr">30</xref>]</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>Brevipalpus chilensis</italic></td><td colspan="3" align="left" rowspan="1">KC291398</td><td colspan="2" align="left" rowspan="1">Navia et al. [<xref rid="pone.0133861.ref030" ref-type="bibr">30</xref>]</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>B</italic>. <italic>chilensis</italic></td><td colspan="3" align="left" rowspan="1">KC291399</td><td colspan="2" align="left" rowspan="1">Navia et al. [<xref rid="pone.0133861.ref030" ref-type="bibr">30</xref>]</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>Brevipalpus californicus</italic></td><td colspan="3" align="left" rowspan="1">DQ789591</td><td colspan="2" align="left" rowspan="1">Groot and Breeuwer [<xref rid="pone.0133861.ref013" ref-type="bibr">13</xref>]</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>B</italic>. <italic>californicus</italic></td><td colspan="3" align="left" rowspan="1">KC291402</td><td colspan="2" align="left" rowspan="1">Navia et al. [<xref rid="pone.0133861.ref030" ref-type="bibr">30</xref>]</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>Cenopalpus pulcher</italic></td><td colspan="3" align="left" rowspan="1">AY320029</td><td colspan="2" align="left" rowspan="1">Rodriguez et al. [<xref rid="pone.0133861.ref049" ref-type="bibr">49</xref>]</td></tr></tbody></table></alternatives><table-wrap-foot><fn id="t001fn001"><p>All living samples from Brazil and Mexico were identified morphologically and DNA extracted for sequencing and phylogenetic analysis: Samples from Brazil and Mexico samples were identified as <italic>B</italic>. <italic>yothersi</italic> or <italic>B</italic>. <italic>papayensis</italic> (**),</p></fn><fn id="t001fn002"><p><sup>‡</sup> = Haplotypes obtained by a maximum parsimony network using TCS 1.21.</p></fn></table-wrap-foot></table-wrap></sec><sec id="sec004"><title>Morphological identification</title><p>Only adult females were used for morphological identification. From each sample, 30 mites were separated and processed for microscopy. Mites were deposited in Hoyer mounting liquid on a glass slide and covered with a coverslip [<xref rid="pone.0133861.ref037" ref-type="bibr">37</xref>]. The glass slides were maintained at 45°C for 15 days. All slides were cleaned using 70% ethanol and cotton swabs. The coverslip was sealed using transparent nail polish. Species identifications were made according to dichotomous keys [<xref rid="pone.0133861.ref019" ref-type="bibr">19</xref>, <xref rid="pone.0133861.ref020" ref-type="bibr">20</xref>, <xref rid="pone.0133861.ref022" ref-type="bibr">22</xref>]. Species determination within the <italic>B</italic>. <italic>phoenicis</italic> s.l. species complex was done using the descriptions of Beard et al [<xref rid="pone.0133861.ref007" ref-type="bibr">7</xref>]. All specimens were examined by phase and differential interference contrast (DIC) microscopy.</p></sec><sec id="sec005"><title>Analysis of genetic variation among populations of identified <italic>Brevipalpus</italic> species</title><p>DNA was extracted from ten adults per sample using the DNA extraction kit DNeasy Blood & Tissue (Qiagen, Germantown, MD, USA) following the manufacturer’s instructions. Partial sequences of the COI gene were obtained using the primers DNF- 5’ TGA TTT TTT GGT CAC CCA GAA G 3’ and DNR- 5’ TAC AGC TCC TAT AGA TAA AAC 3’ [<xref rid="pone.0133861.ref034" ref-type="bibr">34</xref>]. PCR was performed in a 25 μL reaction volume containing 2.5 μL of buffer 10X (600 mM Tris-SO4 (pH 8.9), 180 mM ammonium sulphate), 1 mM of MgSO<sub>4</sub>, 0.2 μM of each primer, 0.2 mM of dNTP′s, 0.5 μL of Platinum Taq High Fidelity DNA Polymerase (Invitrogen, Life Technologies, Carlsbad, California, USA) and 5 μL (approx. 20 ng) of DNA.</p><p>PCR amplifications were performed with an Applied Biosystems thermocycler (Life Technologies Corporation, Foster, CA, USA) in Brazil and a MyCycler (BIO-RAD Laboratories Inc., Hercules, CA, USA) thermocycler in Mexico, using the same thermal conditions: one cycle of 4 min at 94°C, followed by 35 cycles of 60 s at 94°C, 60 s at 54°C and 60 s at 72°C with a final extension at 72°C for 4 min. PCR products were visualised on 1.2% agarose gels in 1X TAE. GelPilot 100 bp Plus (QIAGEN, GmbH, Hilden, Germany) size markers were used. The gels were stained with ethidium bromide (0.1μg/mL) and photographed.</p><p>Sequencing of the Brazilian samples was done at the Centro APTA Citros ‘Sylvio Moreira’ IAC, Brazil. Sequencing reactions were performed using the BigDye Terminator 3.1 kit (Perkin Elmer, Foster City, CA) following the manufacturer’s instructions. Mexican samples were sent to Macrogen Inc. (South Korea) for direct sequencing.</p></sec><sec id="sec006"><title>Data analysis</title><p>Sequence traces were assembled using BioEdit [<xref rid="pone.0133861.ref038" ref-type="bibr">38</xref>]. For this, clear and unambiguous peaks representing each base were located in each raw sequence trace. Data beyond this point at both ends of the sequence were discarded. The same was done for forward and reverse sequences for each sample and, by combining both sequences (forward and reverse) we were able to generate only one sequence for each sample. All sequences were truncated to the same length (352 bp) to eliminate missing data. Multiple sequence alignments were made using Clustal W [<xref rid="pone.0133861.ref039" ref-type="bibr">39</xref>]. Maximum parsimony, maximum likelihood and neighbour joining analyses were done using Molecular Evolutionary Genetic Analysis (MEGA) software ver. 5.0 for Windows [<xref rid="pone.0133861.ref040" ref-type="bibr">40</xref>], using the Close-Neighbour-Interchange algorithm. The robustness of branches was estimated by bootstrap analysis with 1000 repeated samplings of the data [<xref rid="pone.0133861.ref041" ref-type="bibr">41</xref>]. Tree reconstructions were made excluding non-synonymous substitutions, without any effect on tree topology. We show the tree including all sites. Sequences from related species within the genus <italic>Brevipalpus</italic> were retrieved from GenBank and used for comparison (<xref rid="pone.0133861.t001" ref-type="table">Table 1</xref>). A <italic>Cenopalpus pulcher</italic> (Canestrini and Fanzago) (Acari: Tenuipalpidae) sequence was used as the outgroup for this analysis. In addition, the Nei-Gojobori method [<xref rid="pone.0133861.ref042" ref-type="bibr">42</xref>], as implemented in the Z test in the program MEGA 5.0 [<xref rid="pone.0133861.ref040" ref-type="bibr">40</xref>], was used to compute the synonymous and nonsynonymous distances at a 5% significance level. Genetic differences among haplotypes were represented in a maximum parsimony network [<xref rid="pone.0133861.ref043" ref-type="bibr">43</xref>] using TCS 1.21 [<xref rid="pone.0133861.ref044" ref-type="bibr">44</xref>] with 95% confidence in the connection limit (limits of parsimony) and where gaps were treated as a 5th state. Haplotype and nucleotide diversity [<xref rid="pone.0133861.ref045" ref-type="bibr">45</xref>] were calculated using DnaSP v5 [<xref rid="pone.0133861.ref046" ref-type="bibr">46</xref>]. Finally, the partition of genetic variation between countries, among populations (locations) within each country and amongst all populations regardless of country or location of origin was estimated only for <italic>B</italic>. <italic>yothersi</italic> populations using analysis of molecular variance (AMOVA) and by computing F-statistics using Arlequin v. 3.5 [<xref rid="pone.0133861.ref047" ref-type="bibr">47</xref>] with 10000 permutations. No AMOVA analysis was attempted for <italic>B</italic>. <italic>papayensis</italic> as there were only sufficient samples from Brazil for molecular study.</p></sec></sec><sec sec-type="results" id="sec007"><title>Results</title><p>All specimens were identified morphologically from Brazilian and Mexican samples, and the majority were from <italic>Brevipalpus yothersi</italic> and <italic>B</italic>. <italic>papayensis</italic>. In only three samples (O2, O4 and O5, <xref rid="pone.0133861.t001" ref-type="table">Table 1</xref>), <italic>B</italic>. <italic>californicus</italic> was also found. When two species were found, single adults were placed on oranges (one mite per orange and maintained separately to avoid any cross-contamination), and allowed to reproduce parthenogenetically. When a significant number of mites were produced (more than 100), ca. five mites per orange were mounted, identified, and only the sample oranges containing <italic>B</italic>. <italic>yothersi</italic> or <italic>B</italic>. <italic>papayensis</italic> were used in the genetic analysis. Those sample oranges with <italic>B</italic>. <italic>californicus</italic> were discarded because they were in such low numbers that any meaningful molecular analysis of <italic>B</italic>. <italic>californicus</italic> was not possible.</p><p>In both countries, <italic>B</italic>. <italic>yothersi</italic> (<xref rid="pone.0133861.g001" ref-type="fig">Fig 1</xref>) was the most common species and was found in almost all locations. Individuals from <italic>B</italic>. <italic>papayensis</italic> (<xref rid="pone.0133861.g002" ref-type="fig">Fig 2</xref>) were found in two locations in Brazil (Pouse Alegre and Lavras, Minas Gerais, <xref rid="pone.0133861.t001" ref-type="table">Table 1</xref>), and in only one location in Mexico (O1: Ocozocoautla de Espinosa) (<xref rid="pone.0133861.t001" ref-type="table">Table 1</xref>), where <italic>B</italic>. <italic>yothersi</italic> was also found. As very low numbers of mites (less than ten mites) from both <italic>B</italic>. <italic>yothersi</italic> and <italic>B</italic>. <italic>papayensis</italic> were found in location O1, increasing their population by rearing them on sweet oranges was attempted in the laboratory. However, successful reproduction was only achieved for <italic>B</italic>. <italic>yothersi</italic> meaning there were insufficient Mexican <italic>B</italic>. <italic>papayensis</italic> for genetic analysis. The morphological characteristics used to separate <italic>B</italic>. <italic>yothersi</italic> and <italic>B</italic>. <italic>papayensis</italic>, are listed in <xref rid="pone.0133861.t002" ref-type="table">Table 2</xref>, and illustrated in Figs <xref rid="pone.0133861.g001" ref-type="fig">1</xref> and <xref rid="pone.0133861.g002" ref-type="fig">2</xref>.</p><fig id="pone.0133861.g001" orientation="portrait" position="float"><object-id pub-id-type="doi">10.1371/journal.pone.0133861.g001</object-id><label>Fig 1</label><caption><title>Morphological characteristics of <italic>B</italic>. <italic>yothersi</italic>.</title><p>A) Palp femur with barbed, setiform dorsal seta. B) Cuticle of the propodosoma, sc1 = scapular seta, v2 = vertical seta, white arrows show anterior and posterior reticulation. C) Dorsal cuticle of the opisthosoma, dorsal opisthosomal setae: c1, c3, d1, d3, e1, e3, f3, h1, h2; white arrow shows ‘V’ shaped reticulated area. D) Ventral view of the cuticle between aggential setae 3a and 4a, white arrow shows rounded reticulations. E) White arrow shows spermatheca. Black line represents 50 μM.</p></caption><graphic xlink:href="pone.0133861.g001"></graphic></fig><fig id="pone.0133861.g002" orientation="portrait" position="float"><object-id pub-id-type="doi">10.1371/journal.pone.0133861.g002</object-id><label>Fig 2</label><caption><title>Morphological characteristics of <italic>B</italic>. <italic>papayensis</italic>.</title><p>A) Palp femur with barbed, setiform dorsal seta. B) Cuticle of the propodosoma, sc1 = scapular seta, v2 = vertical seta, white arrow shows anterior and posterior reticulation. C) Dorsal cuticle of the opisthosoma, dorsal opisthosomal setae: c1, c3, d1, d3, e1, e3, f3, h1, h2; white arrow shows reticulation between setae e1 and h1 starting as transverse folds and becoming longitudinal towards h1. D) Ventral view of the cuticle between aggential setae 3a and 4a, white arrow shows reticulations forming transverse bands. E) White arrow shows spermatheca. The black line represents 50 μM.</p></caption><graphic xlink:href="pone.0133861.g002"></graphic></fig><table-wrap id="pone.0133861.t002" orientation="portrait" position="float"><object-id pub-id-type="doi">10.1371/journal.pone.0133861.t002</object-id><label>Table 2</label><caption><title>Morphological characteristics used to separate <italic>B</italic>. <italic>yothersi and B</italic>. <italic>papayensis</italic> (Beard et al. [<xref rid="pone.0133861.ref007" ref-type="bibr">7</xref>]).</title></caption><alternatives><graphic id="pone.0133861.t002g" xlink:href="pone.0133861.t002"></graphic><table frame="hsides" rules="groups"><colgroup span="1"><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col></colgroup><thead><tr><th align="left" rowspan="1" colspan="1">Morphological characteristic</th><th align="left" rowspan="1" colspan="1"><italic>B</italic>. <italic>yothersi</italic></th><th align="left" rowspan="1" colspan="1"><italic>B</italic>. <italic>papayensis</italic></th></tr></thead><tbody><tr><td align="left" rowspan="1" colspan="1">Dorsal palp femur seta</td><td align="left" rowspan="1" colspan="1">Setiform and barbed (<xref rid="pone.0133861.g001" ref-type="fig">Fig 1A</xref>)</td><td align="left" rowspan="1" colspan="1">Broadly setiform and barbed (<xref rid="pone.0133861.g002" ref-type="fig">Fig 2A</xref>)</td></tr><tr><td align="left" rowspan="1" colspan="1">Sublateral region of propodosoma</td><td align="left" rowspan="1" colspan="1">Posterior region forming large cells, anterior region minus reticulate (<xref rid="pone.0133861.g001" ref-type="fig">Fig 1B</xref>)</td><td align="left" rowspan="1" colspan="1">Reticulations like large cells only in the posterior end (<xref rid="pone.0133861.g002" ref-type="fig">Fig 2B</xref>)</td></tr><tr><td align="left" rowspan="1" colspan="1">Opisthosoma</td><td align="left" rowspan="1" colspan="1">Reticulation between setae e1 and h1 with “V” shaped folds (<xref rid="pone.0133861.g001" ref-type="fig">Fig 1C</xref>)</td><td align="left" rowspan="1" colspan="1">Reticulation between setae e1 and h1 starting with transverse folds abruptly becoming longitudinal folds towards h1 (<xref rid="pone.0133861.g002" ref-type="fig">Fig 2C</xref>)</td></tr><tr><td align="left" rowspan="1" colspan="1">Ventral region posterior to setae 4a</td><td align="left" rowspan="1" colspan="1">Rounded reticulations (<xref rid="pone.0133861.g001" ref-type="fig">Fig 1D</xref>)</td><td align="left" rowspan="1" colspan="1">Elongate reticulations forming transverse bands (<xref rid="pone.0133861.g002" ref-type="fig">Fig 2D</xref>)</td></tr><tr><td align="left" rowspan="1" colspan="1">Spermatheca</td><td align="left" rowspan="1" colspan="1">With a long narrow duct, which merges to an oval vesicle with small distal stipe (<xref rid="pone.0133861.g001" ref-type="fig">Fig 1E</xref>)</td><td align="left" rowspan="1" colspan="1">With a long moderately thick duct, which ends in a spherical vesicle with a crown of small projections (<xref rid="pone.0133861.g002" ref-type="fig">Fig 2E</xref>)</td></tr></tbody></table></alternatives></table-wrap><sec id="sec008"><title>Genetic variation among <italic>B</italic>. <italic>yothersi</italic> and <italic>B</italic>. <italic>papayensis</italic> populations</title><p>Fifty-nine partial COI sequences were obtained which, after alignment and trimming, resulted in a final sequence length of 352 bp. The number of non-synonymous substitutions was greater than the number of synonymous substitutions per site (Z = 2.271, P = 0.012). These sequences contained 266 non-variable sites, 86 variable sites and 48 parsimony-informative sites. GenBank accession numbers are shown in <xref rid="pone.0133861.t001" ref-type="table">Table 1</xref>. Phylogenetic analyses showed a clear separation among species within the genus <italic>Brevipalpus</italic> with all bootstrap values above 90% (<xref rid="pone.0133861.g003" ref-type="fig">Fig 3</xref>). All samples morphologically identified as <italic>B</italic>. <italic>yothersi</italic> were grouped together with the <italic>B</italic>. <italic>phoenicis</italic> type 2 [<xref rid="pone.0133861.ref032" ref-type="bibr">32</xref>] (now considered as <italic>B</italic>. <italic>yothersi</italic>) sequences retrieved from GenBank that were used as a reference. Samples morphologically identified as <italic>B</italic>. <italic>papayensis</italic> were grouped together with the <italic>B</italic>. <italic>phoenicis</italic> type 1 [<xref rid="pone.0133861.ref032" ref-type="bibr">32</xref>] (now considered as <italic>B</italic>. <italic>papayensis</italic>) sequences (<xref rid="pone.0133861.g003" ref-type="fig">Fig 3</xref>). All samples of <italic>B</italic>. <italic>papayensis</italic> evaluated were from Brazil only, while the samples of <italic>B</italic>. <italic>yothersi</italic> evaluated were collected from both Brazil and Mexico. The <italic>B</italic>. <italic>yothersi</italic> samples could be further separated into two distinct groups, G1 and G2 (<xref rid="pone.0133861.g003" ref-type="fig">Fig 3</xref>). Group G1 contained 48 samples, with samples SJRPB-1 and SJRPP-3 forming a distinct group separated from the other samples with a bootstrap value above 90%. Group G2 contained five samples, all from Brazil, with samples SJRPL-2 and SJRPL-3 forming a distinct group, followed by sample SJRPL-1 with bootstrap values above 90% (<xref rid="pone.0133861.g003" ref-type="fig">Fig 3</xref>).</p><fig id="pone.0133861.g003" orientation="portrait" position="float"><object-id pub-id-type="doi">10.1371/journal.pone.0133861.g003</object-id><label>Fig 3</label><caption><title>Dendrogram inferred from maximum likelihood, maximum parsimony and neighbour joining analyses of COI data from <italic>B</italic>. <italic>yothersi</italic> and <italic>B</italic>. <italic>papayensis</italic>.</title><p>Samples in bold were collected in Brazil. Other <italic>Brevipalpus</italic> species used as reference species and <italic>Cenopalpus pulcher</italic> (Canestrini and Fanzago) (Acari: Tenuipalpidae) used as the outgroup, are labelled according to their GenBank accession numbers. Only bootstrap values above 90% with the three analyses were considered. Significance of values obtained with the three analyses are represented by asterisks (* ≥ 90%, ** ≥ 95%). G1 = group 1, G2 = group 2. Scale bar represents the number of nucleotide substitutions after maximum likelihood analysis.</p></caption><graphic xlink:href="pone.0133861.g003"></graphic></fig><p>Haplotype Network analysis showed the existence of 20 haplotypes from 35 sampled trees at 20 orchard localities in Mexico and Brazil (<xref rid="pone.0133861.t001" ref-type="table">Table 1</xref>; <xref rid="pone.0133861.g004" ref-type="fig">Fig 4</xref>). There were three discreet networks, network N1 contained only samples identified as <italic>B</italic>. <italic>papayensis</italic>, and networks N2 and N3 contained only samples identified as <italic>B</italic>. <italic>yothersi</italic>. Network N1 contained three haplotypes: H01, H02 and H03. H02 and H03 were each found in only one sample but H01 was found in four samples; all six samples were collected in Brazil. The second network (N2) contained four haplotypes, each found in only one sample and all from Brazil. The third and largest network (N3) contained 11 haplotypes that were found in 47 samples. The most common haplotype was H08, which was found in 36 samples, all from Mexico except PAP4-1 and SJRPB-2, which were from Brazil. Finally, there were two independent haplotypes from Brazil that did not belong to any network (H07 and H17) and were each found in only one sample (<xref rid="pone.0133861.g004" ref-type="fig">Fig 4</xref>). There was greater haplotype (0.966±0.028) and nucleotide (0.06248±0.00710) diversity in <italic>B</italic>. <italic>yothersi</italic> populations from Brazil, where 17 haplotypes were recorded from 22 samples analysed, compared with the haplotype (0.158±0.080) and nucleotide (0.000092±0.00152) diversity found in Mexico with only four haplotypes from 37 samples analysed.</p><fig id="pone.0133861.g004" orientation="portrait" position="float"><object-id pub-id-type="doi">10.1371/journal.pone.0133861.g004</object-id><label>Fig 4</label><caption><title>The most parsimonious haplotype network for the 20 haplotypes found in <italic>B</italic>. <italic>yothersi and B</italic>. <italic>papayensis</italic>.</title><p>Colours indicate different sampling locations where each haplotype is present in Brazil and Mexico (<xref rid="pone.0133861.t001" ref-type="table">Table 1</xref>). Haplotypes are connected with a 95% confidence limit. Each line in the network represents a single mutational change. Small circles indicate missing haplotypes. Numbers of samples per haplotype are shown in parentheses. N1-3 = network 1–3.</p></caption><graphic xlink:href="pone.0133861.g004"></graphic></fig><p>AMOVA analysis (<xref rid="pone.0133861.t003" ref-type="table">Table 3</xref>) revealed that the greatest amount of variation among <italic>B</italic>. <italic>yothersi</italic> populations could be accounted for by differences between individuals within each population (81.15%), followed by differences between Brazil and Mexico (16.33%) and finally by differences among populations within each country (2.52%). Although the figure for the difference between Brazil and Mexico was not the greatest, it showed a highly significant P value (P<0.0001) suggesting a geographically structured population (<xref rid="pone.0133861.t003" ref-type="table">Table 3</xref>).</p><table-wrap id="pone.0133861.t003" orientation="portrait" position="float"><object-id pub-id-type="doi">10.1371/journal.pone.0133861.t003</object-id><label>Table 3</label><caption><title>Results of AMOVA analysis of COI sequences from <italic>B</italic>. <italic>yothersi</italic> populations.</title></caption><alternatives><graphic id="pone.0133861.t003g" xlink:href="pone.0133861.t003"></graphic><table frame="hsides" rules="groups"><colgroup span="1"><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col></colgroup><thead><tr><th align="left" rowspan="1" colspan="1">Source of variation</th><th align="left" rowspan="1" colspan="1">d.f.</th><th align="left" rowspan="1" colspan="1">Sum of squares</th><th align="left" rowspan="1" colspan="1">Variance components</th><th align="left" rowspan="1" colspan="1">% of variation explained</th></tr></thead><tbody><tr><td align="left" rowspan="1" colspan="1">Between groups (Brazil and Mexico)</td><td align="left" rowspan="1" colspan="1">1</td><td align="char" char="." rowspan="1" colspan="1">30.384</td><td align="char" char="." rowspan="1" colspan="1">0.84</td><td align="char" char="." rowspan="1" colspan="1">16.33<xref rid="t003fn002" ref-type="table-fn">***</xref></td></tr><tr><td align="left" rowspan="1" colspan="1">Among populations within groups</td><td align="left" rowspan="1" colspan="1">16</td><td align="char" char="." rowspan="1" colspan="1">73.874</td><td align="char" char="." rowspan="1" colspan="1">0.12</td><td align="char" char="." rowspan="1" colspan="1">2.52<xref rid="t003fn001" ref-type="table-fn">**</xref></td></tr><tr><td align="left" rowspan="1" colspan="1">Within populations</td><td align="left" rowspan="1" colspan="1">46</td><td align="char" char="." rowspan="1" colspan="1">192.024</td><td align="char" char="." rowspan="1" colspan="1">4.17</td><td align="char" char="." rowspan="1" colspan="1">81.15<xref rid="t003fn001" ref-type="table-fn">**</xref></td></tr></tbody></table></alternatives><table-wrap-foot><fn id="t003fn001"><p>**P<0.04,</p></fn><fn id="t003fn002"><p>***P<0.0001</p></fn></table-wrap-foot></table-wrap></sec></sec><sec sec-type="conclusions" id="sec009"><title>Discussion</title><p>Combining morphological and genetic analyses is a powerful way to obtain the maximum information on taxonomic and genetic variation in any species [<xref rid="pone.0133861.ref048" ref-type="bibr">48</xref>]. Considerable taxonomic and genetic information is available for <italic>B</italic>. <italic>phoenicis</italic> s.l. [<xref rid="pone.0133861.ref029" ref-type="bibr">29</xref>, <xref rid="pone.0133861.ref030" ref-type="bibr">30</xref>, <xref rid="pone.0133861.ref049" ref-type="bibr">49</xref>–<xref rid="pone.0133861.ref051" ref-type="bibr">51</xref>], but there remain many gaps in understanding genetic variation within and between populations and species. For example, the recent report raising many morphotypes within the <italic>B</italic>. <italic>phoenicis</italic> species complex to species level [<xref rid="pone.0133861.ref007" ref-type="bibr">7</xref>], and the fact that specific relationships between virus and host have been reported [<xref rid="pone.0133861.ref052" ref-type="bibr">52</xref>], suggests the necessity for assessing the ability of each of these new species to transmit CiLV-C. Currently, only the relationship between CiLV-C and <italic>B</italic>. <italic>yothersi</italic> has been reported [<xref rid="pone.0133861.ref053" ref-type="bibr">53</xref>], so the relationship between CiLV-C and <italic>B</italic>. <italic>papayensis</italic> remains to be investigated. In addition, the factors that drive genetic variation within these new species, and how this might vary between their geographical origins are poorly understood.</p><p>Morphological identification showed the existence of two main species, <italic>B</italic>. <italic>yothersi</italic> and <italic>B</italic>. <italic>papayensis</italic>. Mites from <italic>B</italic>. <italic>papayensis</italic> were only found in Lavras and Pouso Alegre (Minas Gerais), Brazil and Ocozocoautla de Espinosa (Chiapas), Mexico, the latter representing the first report of this species from Mexico. Unfortunately, there were insufficient numbers of mites for DNA extraction to evaluate genetic variation as was done with the samples from Brazil. <italic>Brevipalpus papayensis</italic> specimens in this study were all collected from citrus orchards located in coffee growing regions, which was consistent with previous studies in Brazil [<xref rid="pone.0133861.ref030" ref-type="bibr">30</xref>]. More sampling near coffee plantations must be done to confirm this association.</p><p>The use of COI sequencing has been used previously to study <italic>B</italic>. <italic>phoenicis</italic> s.l. populations from Brazil, Chile, The Netherlands and USA [<xref rid="pone.0133861.ref052" ref-type="bibr">52</xref>]. Using the same marker, Groot and Breeuwer [<xref rid="pone.0133861.ref013" ref-type="bibr">13</xref>] found conflicts between genetic analysis and morphological identification. Navia et al. [<xref rid="pone.0133861.ref030" ref-type="bibr">30</xref>] suggested that these conflicts were due to the existence of cryptic species within the genus <italic>Brevipalpus</italic>, which was later confirmed by Beard et al. [<xref rid="pone.0133861.ref007" ref-type="bibr">7</xref>]. Our study confirms the existence of a species complex within <italic>B</italic>. <italic>phoenicis</italic> s.l. (Figs <xref rid="pone.0133861.g001" ref-type="fig">1</xref> and <xref rid="pone.0133861.g002" ref-type="fig">2</xref>), which corresponds to the species <italic>B</italic>. <italic>yothersi</italic> and <italic>B</italic>. <italic>papayensis</italic> reported by Beard et al. [<xref rid="pone.0133861.ref007" ref-type="bibr">7</xref>]. Our data showed that populations from both species were indeed genetically different (Figs <xref rid="pone.0133861.g003" ref-type="fig">3</xref> and <xref rid="pone.0133861.g004" ref-type="fig">4</xref>), which was clearly demonstrated in the Brazilian populations. Unfortunately, insufficient individuals from <italic>B</italic>. <italic>papayensis</italic> were collected in Mexico to allow us to confirm this genetic separation in Mexican populations. Although Beard et al. [<xref rid="pone.0133861.ref007" ref-type="bibr">7</xref>] have raised all of these morphotypes to species level, we still suggest that their study should be complemented with molecular data from more than one gene [<xref rid="pone.0133861.ref054" ref-type="bibr">54</xref>].</p><p>The haplotype network (<xref rid="pone.0133861.g004" ref-type="fig">Fig 4</xref>) showed the existence of three discrete networks where network 1 (<xref rid="pone.0133861.g004" ref-type="fig">Fig 4</xref>) contained only samples from <italic>B</italic>. <italic>papayensis</italic>. The existence of the other networks (2 and 3) including haplotypes 7 and 17 can be considered as a consequence of the genetic variation within <italic>B</italic>. <italic>yothersi</italic>. The majority of the specimens collected in both countries, corresponded to <italic>B</italic>. <italic>yothersi</italic>, and within this species, greater genetic variation was observed in populations from Brazil than in populations from Mexico (<xref rid="pone.0133861.g004" ref-type="fig">Fig 4</xref>). In fact, the majority of the Mexican populations were clustered in one group following phylogenetic analyses (<xref rid="pone.0133861.g003" ref-type="fig">Fig 3</xref>) and there were only four haplotypes (<xref rid="pone.0133861.g004" ref-type="fig">Fig 4</xref>). Although, thelytokous parthenogenesis may be responsible, it is also likely that selection pressures on <italic>B</italic>. <italic>yothersi</italic> populations, such as the number and type of acaricide applications made, are greater in Brazil compared to Mexico, resulting in genetically more diverse populations in Brazil, This mechanism has also been suggested to account for variability in genetic diversity in <italic>Panonychus citri</italic> (Acari: Tetranychidae), another important mite pest in citrus orchards worldwide. ITS1 sequence analysis revealed greatest genetic diversity among <italic>P</italic>. <italic>citri</italic> populations from different locations in China, where the control of this mite relied most heavily on acaricides [<xref rid="pone.0133861.ref055" ref-type="bibr">55</xref>].</p><p>Additionally, it is possible that the host plant may also be playing a significant role in the greater genetic diversity found in the Brazilian samples of <italic>B</italic>. <italic>yothersi</italic>. Although all Brazilian mites were collected from sweet orange (<italic>C</italic>. <italic>sinensis</italic>) orchards, samples were collected from four different varieties, Pêra, Lima, Bahia and a non-commercial variety. With the exception of one sample (O5) all samples from Mexico were from the same variety, Valencia (<xref rid="pone.0133861.t001" ref-type="table">Table 1</xref>). This may contribute to a lack of genetic diversity within <italic>B</italic>. <italic>yothersi</italic> populations in Mexico. Host-association differentiation (HAD) has been described for mites previously. For example the existence of a large number of genetically distinct lineages of the mite <italic>Aceria tosichella</italic> Keifer (Prostigmata: Eriophyidae) were associated with specific plant hosts, regardless of geographic origin [<xref rid="pone.0133861.ref056" ref-type="bibr">56</xref>]. Based on this, we propose that sampling different varieties of <italic>C</italic>. <italic>sinensis</italic> may have contributed to the existence of more haplotypes within <italic>B</italic>. <italic>yothersi</italic> populations in Brazil compared with Mexico where only one orange variety is normally grown by producers. Although they reproduce clonally, genetically distinct lineages or haplotypes of <italic>B</italic>. <italic>yothersi</italic> may be related to the orange variety on which they were collected suggesting some level of host-plant specialisation, a process described as the Frozen Niche Variation model (FNV) as previously reported for <italic>B</italic>. <italic>phoenicis</italic> s.l. by Groot et al. [<xref rid="pone.0133861.ref017" ref-type="bibr">17</xref>]. Currently, we are performing more studies to assess the role of the host plant in shaping patterns of genetic variation in <italic>B</italic>. <italic>yothersi</italic> and <italic>B</italic>. <italic>papayensis</italic> populations.</p><p>In summary, morphological and genetic analysis has demonstrated the existence of <italic>B</italic>. <italic>yothersi</italic> and <italic>B</italic>. <italic>papayensis</italic> populations collected in Brazil and Mexico, although genetic variation between these two species was only confirmed for Brazilian populations. In both countries, <italic>B</italic>. <italic>yothersi</italic> was the most abundant species and was more genetically diverse in Brazil than in Mexico. The existence of these two species in Mexico and Brazil requires research, including behavioural and ecological studies, as it is likely that one species may be more efficient in transmitting CiLV-V. Such information should be included in the design of monitoring and control programs, especially for <italic>B</italic>. <italic>yothersi</italic>, which was the most abundant species compared to <italic>B</italic>. <italic>papayensis</italic>.</p></sec></body><back><ack><p>We are most grateful to the Centro APTA Citros Sylvio Moreira-IAC, for allowing us to use its facilities for this research. We thank our Brazilian colleagues who kindly sent all mite samples. In Mexico, we thank the Crop Protection Committees from the states of Chiapas, Tabasco and Veracruz, for their valuable help during mite collection in the field. 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