Maximum Likelihood Analyses of 3,490 rbcL Sequences: Scalability of Comprehensive Inference versus Group-Specific Taxon Sampling
Identifieur interne : 000569 ( Pmc/Checkpoint ); précédent : 000568; suivant : 000570Maximum Likelihood Analyses of 3,490 rbcL Sequences: Scalability of Comprehensive Inference versus Group-Specific Taxon Sampling
Auteurs : Alexandros Stamatakis [Allemagne] ; Markus Göker [Allemagne] ; Guido W. Grimm [Suède]Source :
- Evolutionary Bioinformatics Online [ 1176-9343 ] ; 2010.
Abstract
The constant accumulation of sequence data poses new computational and methodological challenges for phylogenetic inference, since multiple sequence alignments grow both in the horizontal (number of base pairs, phylogenomic alignments) as well as vertical (number of taxa) dimension. Put aside the ongoing controversial discussion about appropriate models, partitioning schemes, and assembly methods for phylogenomic alignments, coupled with the high computational cost to infer these, for many organismic groups, a sufficient number of taxa is often exclusively available from one or just a few genes (e.g., rbcL, matK, rDNA). In this paper we address scalability of Maximum-Likelihood-based phylogeny reconstruction with respect to the number of taxa by example of several large nested single-gene
Url:
PubMed: 20535232
PubMed Central: 2880847
Affiliations:
- Allemagne, Suède
- Bavière, District de Haute-Bavière, Svealand
- Munich, Stockholm
- Université technique de Munich
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Maximum Likelihood Analyses of 3,490 rbcL Sequences: Scalability of Comprehensive Inference versus Group-Specific Taxon Sampling</title>
<author><name sortKey="Stamatakis, Alexandros" sort="Stamatakis, Alexandros" uniqKey="Stamatakis A" first="Alexandros" last="Stamatakis">Alexandros Stamatakis</name>
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<front><div type="abstract" xml:lang="en"><p>The constant accumulation of sequence data poses new computational and methodological challenges for phylogenetic inference, since multiple sequence alignments grow both in the horizontal (number of base pairs, phylogenomic alignments) as well as vertical (number of taxa) dimension. Put aside the ongoing controversial discussion about appropriate models, partitioning schemes, and assembly methods for phylogenomic alignments, coupled with the high computational cost to infer these, for many organismic groups, a sufficient number of taxa is often exclusively available from one or just a few genes (e.g., rbcL, matK, rDNA). In this paper we address scalability of Maximum-Likelihood-based phylogeny reconstruction with respect to the number of taxa by example of several large nested single-gene <italic>rbcL</italic>
alignments comprising 400 up to 3,491 taxa. In order to test the effect of taxon sampling, we employ an appropriately adapted taxon jackknifing approach. In contrast to standard jackknifing, this taxon subsampling procedure is not conducted entirely at random, but based on drawing subsamples from empirical taxon-groups which can either be user-defined or determined by using taxonomic information from databases. Our results indicate that, despite an unfavorable number of sequences to number of base pairs ratio, i.e., many relatively short sequences, Maximum Likelihood tree searches and bootstrap analyses scale well on single-gene <italic>rbcL</italic>
alignments with a dense taxon sampling up to several thousand sequences. Moreover, the newly implemented taxon subsampling procedure can be beneficial for inferring higher level relationships and interpreting bootstrap support from comprehensive analysis.</p>
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<author><name sortKey="Moulton, V" uniqKey="Moulton V">V Moulton</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Grimm, Gw" uniqKey="Grimm G">GW Grimm</name>
</author>
<author><name sortKey="Renner, Ss" uniqKey="Renner S">SS Renner</name>
</author>
<author><name sortKey="Stamatakis, A" uniqKey="Stamatakis A">A Stamatakis</name>
</author>
<author><name sortKey="Hemleben, V" uniqKey="Hemleben V">V Hemleben</name>
</author>
</analytic>
</biblStruct>
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</author>
<author><name sortKey="Huber, Kt" uniqKey="Huber K">KT Huber</name>
</author>
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</author>
<author><name sortKey="Lockhart, Pj" uniqKey="Lockhart P">PJ Lockhart</name>
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</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Nandi, Oi" uniqKey="Nandi O">OI Nandi</name>
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<author><name sortKey="Chase, Mw" uniqKey="Chase M">MW Chase</name>
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<author><name sortKey="Lee, Jh" uniqKey="Lee J">JH Lee</name>
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</listBibl>
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</TEI>
<pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Evol Bioinform Online</journal-id>
<journal-id journal-id-type="publisher-id">101256319</journal-id>
<journal-title-group><journal-title>Evolutionary Bioinformatics Online</journal-title>
</journal-title-group>
<issn pub-type="epub">1176-9343</issn>
<publisher><publisher-name>Libertas Academica</publisher-name>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">20535232</article-id>
<article-id pub-id-type="pmc">2880847</article-id>
<article-id pub-id-type="publisher-id">ebo-2010-073</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Original Research</subject>
</subj-group>
</article-categories>
<title-group><article-title>Maximum Likelihood Analyses of 3,490 rbcL Sequences: Scalability of Comprehensive Inference versus Group-Specific Taxon Sampling</article-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Stamatakis</surname>
<given-names>Alexandros</given-names>
</name>
<xref ref-type="aff" rid="af1-ebo-2010-073">1</xref>
<xref ref-type="corresp" rid="c1-ebo-2010-073"></xref>
</contrib>
<contrib contrib-type="author"><name><surname>Göker</surname>
<given-names>Markus</given-names>
</name>
<xref ref-type="aff" rid="af2-ebo-2010-073">2</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Grimm</surname>
<given-names>Guido W.</given-names>
</name>
<xref ref-type="aff" rid="af3-ebo-2010-073">3</xref>
</contrib>
</contrib-group>
<aff id="af1-ebo-2010-073"><label>1</label>
The Exelixis Lab, Dept. of Computer Science, Technische Universität München, Germany</aff>
<aff id="af2-ebo-2010-073"><label>2</label>
German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany</aff>
<aff id="af3-ebo-2010-073"><label>3</label>
Department of Palaeobotany, Swedish Museum of Natural History, Stockholm, Sweden</aff>
<author-notes><corresp id="c1-ebo-2010-073">Email:
<email>stamatak@cs.tum.edu</email>
</corresp>
</author-notes>
<pub-date pub-type="epub"><day>24</day>
<month>5</month>
<year>2010</year>
</pub-date>
<pub-date pub-type="collection"><year>2010</year>
</pub-date>
<volume>6</volume>
<fpage>73</fpage>
<lpage>90</lpage>
<permissions><copyright-statement>© 2010 the author(s), publisher and licensee Libertas Academica Ltd.</copyright-statement>
<copyright-year>2010</copyright-year>
<license license-type="open-access"><license-p>This is an open access article. Unrestricted non-commercial use is permitted provided the original work is properly cited.</license-p>
</license>
</permissions>
<abstract><p>The constant accumulation of sequence data poses new computational and methodological challenges for phylogenetic inference, since multiple sequence alignments grow both in the horizontal (number of base pairs, phylogenomic alignments) as well as vertical (number of taxa) dimension. Put aside the ongoing controversial discussion about appropriate models, partitioning schemes, and assembly methods for phylogenomic alignments, coupled with the high computational cost to infer these, for many organismic groups, a sufficient number of taxa is often exclusively available from one or just a few genes (e.g., rbcL, matK, rDNA). In this paper we address scalability of Maximum-Likelihood-based phylogeny reconstruction with respect to the number of taxa by example of several large nested single-gene <italic>rbcL</italic>
alignments comprising 400 up to 3,491 taxa. In order to test the effect of taxon sampling, we employ an appropriately adapted taxon jackknifing approach. In contrast to standard jackknifing, this taxon subsampling procedure is not conducted entirely at random, but based on drawing subsamples from empirical taxon-groups which can either be user-defined or determined by using taxonomic information from databases. Our results indicate that, despite an unfavorable number of sequences to number of base pairs ratio, i.e., many relatively short sequences, Maximum Likelihood tree searches and bootstrap analyses scale well on single-gene <italic>rbcL</italic>
alignments with a dense taxon sampling up to several thousand sequences. Moreover, the newly implemented taxon subsampling procedure can be beneficial for inferring higher level relationships and interpreting bootstrap support from comprehensive analysis.</p>
</abstract>
<kwd-group><kwd>RAxML</kwd>
<kwd>phylogenetic inference</kwd>
<kwd>many taxon analyses</kwd>
<kwd>taxon jackknifing</kwd>
</kwd-group>
</article-meta>
</front>
<floats-group><fig id="f1-ebo-2010-073" position="float"><label>Figure 1.</label>
<caption><p>Scheme illustrating the GRTS procedure (this study) in comparison to random taxon jackknifing.<xref ref-type="bibr" rid="b47-ebo-2010-073">47</xref>
In contrast to random jackknifing, GRTS assures that each replicate includes always members of all pre-defined TU (in the given example TU 3 is missing in the random jackknife replicate) and that each TU is sampled proportionally to its original size. For instance, TU 1 includes 16 accessions. Thus, using a reduction factor of 2 each GRTS replicate will include exactly 8 members of TU 1. The number in random jackknife replicates may vary, resulting in an over- (TU 1 in given example) or underrepresentation of TUs (TUs 4 and 5).</p>
</caption>
<graphic xlink:href="ebo-2010-073f1"></graphic>
</fig>
<fig id="f2-ebo-2010-073" position="float"><label>Figure 2.</label>
<caption><p>A family-level representation of the best-known ML tree inferred from the EUDIS matrix. The basic tree includes more than 3,500 leaves and has here been reduced to family-level TU (see Material and Methods); the latter have also been used for the GRTS analyses (following chapter).</p>
</caption>
<graphic xlink:href="ebo-2010-073f2"></graphic>
</fig>
<fig id="f3-ebo-2010-073" position="float"><label>Figure 3.</label>
<caption><p>A circle cladogram of the best-known ML tree inferred from the ROSI D matrix. By far the most sequences are placed according to well-known clades (occasional mislabeled sequences not addressed). Note that the <italic>CA-BS</italic>
support of these higher order clades is often low (<50; Tables S2, S3 in <xref ref-type="supplementary-material" rid="SD2">OS 2</xref>
).</p>
</caption>
<graphic xlink:href="ebo-2010-073f3"></graphic>
</fig>
<fig id="f4-ebo-2010-073" position="float"><label>Figure 4.</label>
<caption><p>Support values of second-level BS values over first-level BS support values on the best-scoring ML tree for the eudicots.</p>
</caption>
<graphic xlink:href="ebo-2010-073f4"></graphic>
</fig>
<fig id="f5-ebo-2010-073" position="float"><label>Figure 5.</label>
<caption><p>Potential of <italic>GRTS-ML</italic>
to recover ‘correct’ relationships. Top, ML phylogram based on EURO1 matrix. Bottom, bipartition network based on 100 <italic>GRTS-ML</italic>
replicates (family-level TU, reduction factor 1/4).</p>
</caption>
<graphic xlink:href="ebo-2010-073f5"></graphic>
</fig>
<fig id="f6-ebo-2010-073" position="float"><label>Figure 6.</label>
<caption><p>Competing topological alternatives in GRTS-ML and CA-BS replicates. Unlabeled circles represent ‘candidate’ common ancestors (topological alternatives); support indicated by intensity of gray tones.</p>
</caption>
<graphic xlink:href="ebo-2010-073f6"></graphic>
</fig>
<fig id="f7-ebo-2010-073" position="float"><label>Figure 7.</label>
<caption><p><italic>GRTS-ML-</italic>
based bipartition networks using different reduction factors and order-level TUs. Red, eurosid I clades, blue, eurosid II clades; important changes in the recognition of well-known groups are highlighted by arrows. The analyses were done based on the ROSID matrix. <bold>A</bold>
) Reduction factor of ¼. The nitrogen fixing clade is recovered in most replicate trees. <bold>B</bold>
) Reduction factor of 1/8. Sapindales are separated from Zygophyllales and Celastrales from Malpighiales. <bold>C</bold>
) Reduction factor of 1/16. Zygophyllales are placed with other eurosids I. <bold>D</bold>
) Reduction factor of 1/32. Eurosid 2 clades and Crossosomatales, respectively, are grouped.</p>
</caption>
<graphic xlink:href="ebo-2010-073f7"></graphic>
</fig>
<table-wrap id="t1-ebo-2010-073" position="float"><label>Table 1.</label>
<caption><p>Correlation between bootstrap support values for comprehensive analyses and number of bipartitions in the respective tree collections of nested <italic>rbcL</italic>
datasets.</p>
</caption>
<table frame="hsides" rules="groups"><thead><tr><th align="left" valign="top" rowspan="1" colspan="1"><bold>Data sets</bold>
</th>
<th align="left" valign="top" rowspan="1" colspan="1"><bold># taxa</bold>
</th>
<th align="left" valign="top" rowspan="1" colspan="1"><bold><italic>ρ</italic>
-all</bold>
</th>
<th align="left" valign="top" rowspan="1" colspan="1"><bold># bipartitions</bold>
</th>
<th align="left" valign="top" rowspan="1" colspan="1"><bold><italic>ρ</italic>
-best</bold>
</th>
<th align="left" valign="top" rowspan="1" colspan="1"><bold>WRF</bold>
</th>
</tr>
</thead>
<tbody><tr><td align="left" valign="top" rowspan="1" colspan="1">Eudicots ⊇</td>
<td align="left" valign="top" rowspan="1" colspan="1">3,490</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.989</td>
<td align="left" valign="top" rowspan="1" colspan="1">Eudicots: 31,124</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.986</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.021</td>
</tr>
<tr><td align="left" valign="top" rowspan="1" colspan="1">rosids</td>
<td align="left" valign="top" rowspan="1" colspan="1">2,259</td>
<td align="left" valign="top" rowspan="1" colspan="1"></td>
<td align="left" valign="top" rowspan="1" colspan="1">Rosids: 30,338</td>
<td align="left" valign="top" rowspan="1" colspan="1"></td>
<td align="left" valign="top" rowspan="1" colspan="1"></td>
</tr>
<tr><td align="left" valign="top" rowspan="1" colspan="1">Eudicots ⊇</td>
<td align="left" valign="top" rowspan="1" colspan="1">3,490</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.987</td>
<td align="left" valign="top" rowspan="1" colspan="1">Eudicots: 22,060</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.982</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.032</td>
</tr>
<tr><td align="left" valign="top" rowspan="1" colspan="1">eurosids I</td>
<td align="left" valign="top" rowspan="1" colspan="1">1,590</td>
<td align="left" valign="top" rowspan="1" colspan="1"></td>
<td align="left" valign="top" rowspan="1" colspan="1">Eurosids I: 21,688</td>
<td align="left" valign="top" rowspan="1" colspan="1"></td>
<td align="left" valign="top" rowspan="1" colspan="1"></td>
</tr>
<tr><td align="left" valign="top" rowspan="1" colspan="1">Eudicots ⊇</td>
<td align="left" valign="top" rowspan="1" colspan="1">3,490</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.988</td>
<td align="left" valign="top" rowspan="1" colspan="1">Eudicots: 6,110</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.983</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.048</td>
</tr>
<tr><td align="left" valign="top" rowspan="1" colspan="1">eurosids II</td>
<td align="left" valign="top" rowspan="1" colspan="1">436</td>
<td align="left" valign="top" rowspan="1" colspan="1"></td>
<td align="left" valign="top" rowspan="1" colspan="1">Eurosids II: 5,894</td>
<td align="left" valign="top" rowspan="1" colspan="1"></td>
<td align="left" valign="top" rowspan="1" colspan="1"></td>
</tr>
<tr><td align="left" valign="top" rowspan="1" colspan="1">Rosids ⊇</td>
<td align="left" valign="top" rowspan="1" colspan="1">2,259</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.993</td>
<td align="left" valign="top" rowspan="1" colspan="1">Rosids: 22,060</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.993</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.019</td>
</tr>
<tr><td align="left" valign="top" rowspan="1" colspan="1">eurosids I</td>
<td align="left" valign="top" rowspan="1" colspan="1">1,590</td>
<td align="left" valign="top" rowspan="1" colspan="1"></td>
<td align="left" valign="top" rowspan="1" colspan="1">Eurosids I: 21,983</td>
<td align="left" valign="top" rowspan="1" colspan="1"></td>
<td align="left" valign="top" rowspan="1" colspan="1"></td>
</tr>
<tr><td align="left" valign="top" rowspan="1" colspan="1">Rosids ⊇</td>
<td align="left" valign="top" rowspan="1" colspan="1">2,259</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.992</td>
<td align="left" valign="top" rowspan="1" colspan="1">Rosids: 6,110</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.990</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.053</td>
</tr>
<tr><td align="left" valign="top" rowspan="1" colspan="1">eurosids II</td>
<td align="left" valign="top" rowspan="1" colspan="1">436</td>
<td align="left" valign="top" rowspan="1" colspan="1"></td>
<td align="left" valign="top" rowspan="1" colspan="1">Eurosids II: 6,019</td>
<td align="left" valign="top" rowspan="1" colspan="1"></td>
<td align="left" valign="top" rowspan="1" colspan="1"></td>
</tr>
</tbody>
</table>
</table-wrap>
<table-wrap id="t2-ebo-2010-073" position="float"><label>Table 2.</label>
<caption><p>Correlation between family-level TU <italic>CA-BS</italic>
and family-level TU <italic>GRTS-ML</italic>
, using a reduction factor of 1/4, support values for the distinct datasets.</p>
</caption>
<table frame="hsides" rules="groups"><thead><tr><th align="left" valign="top" rowspan="1" colspan="1"><bold>Datatset</bold>
</th>
<th align="left" valign="top" rowspan="1" colspan="1"><bold># taxa</bold>
</th>
<th align="left" valign="top" rowspan="1" colspan="1"><bold><italic>ρ</italic>
-all</bold>
</th>
<th align="left" valign="top" rowspan="1" colspan="1"><bold># bipartitions</bold>
</th>
<th align="left" valign="top" rowspan="1" colspan="1"><bold><italic>ρ</italic>
-best</bold>
</th>
<th align="left" valign="top" rowspan="1" colspan="1"><bold>WRF</bold>
</th>
</tr>
</thead>
<tbody><tr><td align="left" valign="top" rowspan="2" colspan="1">Eudicots</td>
<td align="left" valign="top" rowspan="1" colspan="1">256</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.925</td>
<td align="left" valign="top" rowspan="1" colspan="1">CA-BS: 4,427</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.883</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.079</td>
</tr>
<tr><td align="left" valign="top" rowspan="1" colspan="1"></td>
<td align="left" valign="top" rowspan="1" colspan="1"></td>
<td align="left" valign="top" rowspan="1" colspan="1">GRTS-ML: 2,987</td>
<td align="left" valign="top" rowspan="1" colspan="1"></td>
<td align="left" valign="top" rowspan="1" colspan="1"></td>
</tr>
<tr><td align="left" valign="top" rowspan="2" colspan="1">Rosids</td>
<td align="left" valign="top" rowspan="1" colspan="1">153</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.915</td>
<td align="left" valign="top" rowspan="1" colspan="1">CA-BS: 2,587</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.889</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.092</td>
</tr>
<tr><td align="left" valign="top" rowspan="1" colspan="1"></td>
<td align="left" valign="top" rowspan="1" colspan="1"></td>
<td align="left" valign="top" rowspan="1" colspan="1">GRTS-ML: 1,390</td>
<td align="left" valign="top" rowspan="1" colspan="1"></td>
<td align="left" valign="top" rowspan="1" colspan="1"></td>
</tr>
<tr><td align="left" valign="top" rowspan="2" colspan="1">Eurosids I</td>
<td align="left" valign="top" rowspan="1" colspan="1">80</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.908</td>
<td align="left" valign="top" rowspan="1" colspan="1">CA-BS: 1,683</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.899</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.094</td>
</tr>
<tr><td align="left" valign="top" rowspan="1" colspan="1"></td>
<td align="left" valign="top" rowspan="1" colspan="1"></td>
<td align="left" valign="top" rowspan="1" colspan="1">GRTS-ML: 771</td>
<td align="left" valign="top" rowspan="1" colspan="1"></td>
<td align="left" valign="top" rowspan="1" colspan="1"></td>
</tr>
<tr><td align="left" valign="top" rowspan="2" colspan="1">Eurosids II</td>
<td align="left" valign="top" rowspan="1" colspan="1">43</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.924</td>
<td align="left" valign="top" rowspan="1" colspan="1">CA-BS: 322</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.824</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.229</td>
</tr>
<tr><td align="left" valign="top" rowspan="1" colspan="1"></td>
<td align="left" valign="top" rowspan="1" colspan="1"></td>
<td align="left" valign="top" rowspan="1" colspan="1">GRTS-ML: 139</td>
<td align="left" valign="top" rowspan="1" colspan="1"></td>
<td align="left" valign="top" rowspan="1" colspan="1"></td>
</tr>
</tbody>
</table>
</table-wrap>
<table-wrap id="t3-ebo-2010-073" position="float"><label>Table 3.</label>
<caption><p>Correlation between order-level TU <italic>CA-BS</italic>
and order-level TU <italic>GRTS-ML</italic>
support values for the distinct datasets and reduction factors.</p>
</caption>
<table frame="hsides" rules="groups"><thead><tr><th align="left" valign="top" rowspan="1" colspan="1"><bold>Dataset</bold>
</th>
<th align="left" valign="top" rowspan="1" colspan="1"><bold>Reduction factor</bold>
</th>
<th align="left" valign="top" rowspan="1" colspan="1"><bold># taxa</bold>
</th>
<th align="left" valign="top" rowspan="1" colspan="1"><bold><italic>ρ</italic>
-all</bold>
</th>
<th align="left" valign="top" rowspan="1" colspan="1"><bold><italic>ρ</italic>
-best</bold>
</th>
<th align="left" valign="top" rowspan="1" colspan="1"><bold>WRF</bold>
</th>
</tr>
</thead>
<tbody><tr><td align="left" valign="top" rowspan="4" colspan="1">Rosids</td>
<td align="left" valign="top" rowspan="1" colspan="1">1/4</td>
<td align="left" valign="top" rowspan="1" colspan="1">565</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.836</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.842</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.262</td>
</tr>
<tr><td align="left" valign="top" rowspan="1" colspan="1">1/8</td>
<td align="left" valign="top" rowspan="1" colspan="1">282</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.845</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.847</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.240</td>
</tr>
<tr><td align="left" valign="top" rowspan="1" colspan="1">1/16</td>
<td align="left" valign="top" rowspan="1" colspan="1">141</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.882</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.869</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.213</td>
</tr>
<tr><td align="left" valign="top" rowspan="1" colspan="1">1/32</td>
<td align="left" valign="top" rowspan="1" colspan="1">71</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.884</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.868</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.160</td>
</tr>
<tr><td align="left" valign="top" rowspan="4" colspan="1">Eurosids I</td>
<td align="left" valign="top" rowspan="1" colspan="1">1/4</td>
<td align="left" valign="top" rowspan="1" colspan="1">398</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.828</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.781</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.283</td>
</tr>
<tr><td align="left" valign="top" rowspan="1" colspan="1">1/8</td>
<td align="left" valign="top" rowspan="1" colspan="1">199</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.828</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.584</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.253</td>
</tr>
<tr><td align="left" valign="top" rowspan="1" colspan="1">1/16</td>
<td align="left" valign="top" rowspan="1" colspan="1">99</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.693</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.390</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.206</td>
</tr>
<tr><td align="left" valign="top" rowspan="1" colspan="1">1/32</td>
<td align="left" valign="top" rowspan="1" colspan="1">50</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.639</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.345</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.229</td>
</tr>
</tbody>
</table>
</table-wrap>
<table-wrap id="t4-ebo-2010-073" position="float"><label>Table 4.</label>
<caption><p>Correlation between order-level TU <italic>CA-BS</italic>
and order-level TU <italic>GRTS-BS</italic>
support values for the distinct datasets and reduction factors.</p>
</caption>
<table frame="hsides" rules="groups"><thead><tr><th align="left" valign="top" rowspan="1" colspan="1"><bold>Dataset</bold>
</th>
<th align="left" valign="top" rowspan="1" colspan="1"><bold>Reduction factor</bold>
</th>
<th align="left" valign="top" rowspan="1" colspan="1"><bold># taxa</bold>
</th>
<th align="left" valign="top" rowspan="1" colspan="1"><bold><italic>ρ</italic>
-all</bold>
</th>
<th align="left" valign="top" rowspan="1" colspan="1"><bold><italic>ρ</italic>
-best</bold>
</th>
<th align="left" valign="top" rowspan="1" colspan="1"><bold>WRF</bold>
</th>
</tr>
</thead>
<tbody><tr><td align="left" valign="top" rowspan="5" colspan="1">Rosids</td>
<td align="left" valign="top" rowspan="1" colspan="1">1/4</td>
<td align="left" valign="top" rowspan="1" colspan="1">565</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.977</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.974</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.162</td>
</tr>
<tr><td align="left" valign="top" rowspan="1" colspan="1">1/8</td>
<td align="left" valign="top" rowspan="1" colspan="1">282</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.966</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.959</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.120</td>
</tr>
<tr><td align="left" valign="top" rowspan="1" colspan="1">1/16</td>
<td align="left" valign="top" rowspan="1" colspan="1">141</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.946</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.940</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.119</td>
</tr>
<tr><td align="left" valign="top" rowspan="1" colspan="1">1/32</td>
<td align="left" valign="top" rowspan="1" colspan="1">71</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.950</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.938</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.123</td>
</tr>
<tr><td align="left" valign="top" rowspan="1" colspan="1">1/64</td>
<td align="left" valign="top" rowspan="1" colspan="1">35</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.891</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.875</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.055</td>
</tr>
<tr><td align="left" valign="top" rowspan="5" colspan="1">Eurosids I</td>
<td align="left" valign="top" rowspan="1" colspan="1">1/4</td>
<td align="left" valign="top" rowspan="1" colspan="1">398</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.977</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.878</td>
<td align="left" valign="top" rowspan="1" colspan="1">0</td>
</tr>
<tr><td align="left" valign="top" rowspan="1" colspan="1">1/8</td>
<td align="left" valign="top" rowspan="1" colspan="1">199</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.932</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.714</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.136</td>
</tr>
<tr><td align="left" valign="top" rowspan="1" colspan="1">1/16</td>
<td align="left" valign="top" rowspan="1" colspan="1">99</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.918</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.640</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.097</td>
</tr>
<tr><td align="left" valign="top" rowspan="1" colspan="1">1/32</td>
<td align="left" valign="top" rowspan="1" colspan="1">50</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.865</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.500</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.053</td>
</tr>
<tr><td align="left" valign="top" rowspan="1" colspan="1">1/64</td>
<td align="left" valign="top" rowspan="1" colspan="1">25</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.836</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.522</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.146</td>
</tr>
<tr><td align="left" valign="top" rowspan="5" colspan="1">Eurosids II</td>
<td align="left" valign="top" rowspan="1" colspan="1">1/4</td>
<td align="left" valign="top" rowspan="1" colspan="1">109</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.999</td>
<td align="left" valign="top" rowspan="1" colspan="1">∼</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.517</td>
</tr>
<tr><td align="left" valign="top" rowspan="1" colspan="1">1/8</td>
<td align="left" valign="top" rowspan="1" colspan="1">55</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.999</td>
<td align="left" valign="top" rowspan="1" colspan="1">∼</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.517</td>
</tr>
<tr><td align="left" valign="top" rowspan="1" colspan="1">1/16</td>
<td align="left" valign="top" rowspan="1" colspan="1">28</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.999</td>
<td align="left" valign="top" rowspan="1" colspan="1">∼</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.513</td>
</tr>
<tr><td align="left" valign="top" rowspan="1" colspan="1">1/32</td>
<td align="left" valign="top" rowspan="1" colspan="1">14</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.993</td>
<td align="left" valign="top" rowspan="1" colspan="1">∼</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.485</td>
</tr>
<tr><td align="left" valign="top" rowspan="1" colspan="1">1/64</td>
<td align="left" valign="top" rowspan="1" colspan="1">7</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.970</td>
<td align="left" valign="top" rowspan="1" colspan="1">∼</td>
<td align="left" valign="top" rowspan="1" colspan="1">0.467</td>
</tr>
</tbody>
</table>
</table-wrap>
</floats-group>
</pmc>
<affiliations><list><country><li>Allemagne</li>
<li>Suède</li>
</country>
<region><li>Bavière</li>
<li>District de Haute-Bavière</li>
<li>Svealand</li>
</region>
<settlement><li>Munich</li>
<li>Stockholm</li>
</settlement>
<orgName><li>Université technique de Munich</li>
</orgName>
</list>
<tree><country name="Allemagne"><region name="Bavière"><name sortKey="Stamatakis, Alexandros" sort="Stamatakis, Alexandros" uniqKey="Stamatakis A" first="Alexandros" last="Stamatakis">Alexandros Stamatakis</name>
</region>
<name sortKey="Goker, Markus" sort="Goker, Markus" uniqKey="Goker M" first="Markus" last="Göker">Markus Göker</name>
</country>
<country name="Suède"><region name="Svealand"><name sortKey="Grimm, Guido W" sort="Grimm, Guido W" uniqKey="Grimm G" first="Guido W." last="Grimm">Guido W. Grimm</name>
</region>
</country>
</tree>
</affiliations>
</record>
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