Natural Selection for Nucleotide Usage at Synonymous and Nonsynonymous Sites in Influenza A Virus Genes▿
Identifieur interne : 000359 ( Pmc/Curation ); précédent : 000358; suivant : 000360Natural Selection for Nucleotide Usage at Synonymous and Nonsynonymous Sites in Influenza A Virus Genes▿
Auteurs : Sergey Kryazhimskiy ; Georgii A. Bazykin ; Jonathan DushoffSource :
- Journal of Virology [ 0022-538X ] ; 2008.
Abstract
Influenza A virus is one of the best-studied viruses and a model organism for the study of molecular evolution; in particular, much research has focused on detecting natural selection on influenza virus proteins. Here, we study the dynamics of the synonymous and nonsynonymous nucleotide composition of influenza A virus genes. In several genes, the nucleotide frequencies at synonymous positions drift away from the equilibria predicted from the synonymous substitution matrices. We investigate possible reasons for this unexpected behavior by fitting several regression models. Relaxation toward a mutation-selection equilibrium following a host jump fails to explain the dynamics of the synonymous nucleotide composition, even if we allow for slow temporal changes in the substitution matrix. Instead, we find that deep internal branches of the phylogeny show distinct patterns of nucleotide substitution and that these branches strongly influence the dynamics of nucleotide composition, suggesting that the observed trends are at least in part a result of natural selection acting on synonymous sites. Moreover, we find that the dynamics of the nucleotide composition at synonymous and nonsynonymous sites are highly correlated, providing evidence that even nonsynonymous sites can be influenced by selection pressure for nucleotide composition.
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DOI: 10.1128/JVI.02415-07
PubMed: 18321967
PubMed Central: 2346729
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Natural Selection for Nucleotide Usage at Synonymous and Nonsynonymous Sites in Influenza A Virus Genes<xref ref-type="fn" rid="fn1">▿</xref> </title><author><name sortKey="Kryazhimskiy, Sergey" sort="Kryazhimskiy, Sergey" uniqKey="Kryazhimskiy S" first="Sergey" last="Kryazhimskiy">Sergey Kryazhimskiy</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Bazykin, Georgii A" sort="Bazykin, Georgii A" uniqKey="Bazykin G" first="Georgii A." last="Bazykin">Georgii A. Bazykin</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Dushoff, Jonathan" sort="Dushoff, Jonathan" uniqKey="Dushoff J" first="Jonathan" last="Dushoff">Jonathan Dushoff</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">18321967</idno><idno type="pmc">2346729</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2346729</idno><idno type="RBID">PMC:2346729</idno><idno type="doi">10.1128/JVI.02415-07</idno><date when="2008">2008</date><idno type="wicri:Area/Pmc/Corpus">000359</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000359</idno><idno type="wicri:Area/Pmc/Curation">000359</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000359</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Natural Selection for Nucleotide Usage at Synonymous and Nonsynonymous Sites in Influenza A Virus Genes<xref ref-type="fn" rid="fn1">▿</xref> </title><author><name sortKey="Kryazhimskiy, Sergey" sort="Kryazhimskiy, Sergey" uniqKey="Kryazhimskiy S" first="Sergey" last="Kryazhimskiy">Sergey Kryazhimskiy</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Bazykin, Georgii A" sort="Bazykin, Georgii A" uniqKey="Bazykin G" first="Georgii A." last="Bazykin">Georgii A. Bazykin</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Dushoff, Jonathan" sort="Dushoff, Jonathan" uniqKey="Dushoff J" first="Jonathan" last="Dushoff">Jonathan Dushoff</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author></analytic><series><title level="j">Journal of Virology</title><idno type="ISSN">0022-538X</idno><idno type="eISSN">1098-5514</idno><imprint><date when="2008">2008</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Influenza A virus is one of the best-studied viruses and a model organism for the study of molecular evolution; in particular, much research has focused on detecting natural selection on influenza virus proteins. Here, we study the dynamics of the synonymous and nonsynonymous nucleotide composition of influenza A virus genes. In several genes, the nucleotide frequencies at synonymous positions drift away from the equilibria predicted from the synonymous substitution matrices. We investigate possible reasons for this unexpected behavior by fitting several regression models. Relaxation toward a mutation-selection equilibrium following a host jump fails to explain the dynamics of the synonymous nucleotide composition, even if we allow for slow temporal changes in the substitution matrix. Instead, we find that deep internal branches of the phylogeny show distinct patterns of nucleotide substitution and that these branches strongly influence the dynamics of nucleotide composition, suggesting that the observed trends are at least in part a result of natural selection acting on synonymous sites. Moreover, we find that the dynamics of the nucleotide composition at synonymous and nonsynonymous sites are highly correlated, providing evidence that even nonsynonymous sites can be influenced by selection pressure for nucleotide composition.</p></div></front></TEI><pmc article-type="research-article"><pmc-comment>The publisher of this article does not allow downloading of the full text in XML form.</pmc-comment>
<front><journal-meta><journal-id journal-id-type="nlm-ta">J Virol</journal-id><journal-id journal-id-type="publisher-id">jvi</journal-id><journal-title>Journal of Virology</journal-title><issn pub-type="ppub">0022-538X</issn><issn pub-type="epub">1098-5514</issn><publisher><publisher-name>American Society for Microbiology (ASM)</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">18321967</article-id><article-id pub-id-type="pmc">2346729</article-id><article-id pub-id-type="publisher-id">2415-07</article-id><article-id pub-id-type="doi">10.1128/JVI.02415-07</article-id><article-categories><subj-group subj-group-type="heading"><subject>Genetic Diversity and Evolution</subject></subj-group></article-categories><title-group><article-title>Natural Selection for Nucleotide Usage at Synonymous and Nonsynonymous Sites in Influenza A Virus Genes<xref ref-type="fn" rid="fn1">▿</xref> </article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Kryazhimskiy</surname><given-names>Sergey</given-names></name><xref ref-type="aff" rid="aff1">1</xref><xref ref-type="aff" rid="aff1">2</xref><xref ref-type="corresp" rid="cor1">*</xref></contrib><contrib contrib-type="author"><name><surname>Bazykin</surname><given-names>Georgii A.</given-names></name><xref ref-type="aff" rid="aff1">3</xref><xref ref-type="aff" rid="aff1">4</xref></contrib><contrib contrib-type="author"><name><surname>Dushoff</surname><given-names>Jonathan</given-names></name><xref ref-type="aff" rid="aff1">3</xref><xref ref-type="aff" rid="aff1">5</xref></contrib></contrib-group><aff id="aff1">Program in Applied and Computational Mathematics, Princeton University, Princeton, New Jersey,<label>1</label> Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania,<label>2</label> Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey,<label>3</label> Institute for Information Transmission Problems, Russian Academy of Sciences (Kharkevich Institute), Moscow, Russia,<label>4</label> Department of Biology, McMaster University, Hamilton, Ontario, Canada<label>5</label></aff><author-notes><fn id="cor1"><label>*</label><p>Corresponding author. Mailing address: 204K Carolyn Lynch Laboratory, University of Pennsylvania, 434 S. University Ave., Philadelphia, PA 19104. Phone: (215) 746-2188. Fax: (215) 898-8780. E-mail: <email>skr@sas.upenn.edu</email></p></fn></author-notes><pub-date pub-type="ppub"><month>5</month><year>2008</year></pub-date><pub-date pub-type="epub"><day>5</day><month>3</month><year>2008</year></pub-date><volume>82</volume><issue>10</issue><fpage>4938</fpage><lpage>4945</lpage><history><date date-type="received"><day>8</day><month>11</month><year>2007</year></date><date date-type="accepted"><day>26</day><month>2</month><year>2008</year></date></history><permissions><copyright-statement>Copyright © 2008, American Society for Microbiology</copyright-statement></permissions><self-uri xlink:title="pdf" xlink:href="zjv01008004938.pdf"></self-uri><abstract><p>Influenza A virus is one of the best-studied viruses and a model organism for the study of molecular evolution; in particular, much research has focused on detecting natural selection on influenza virus proteins. Here, we study the dynamics of the synonymous and nonsynonymous nucleotide composition of influenza A virus genes. In several genes, the nucleotide frequencies at synonymous positions drift away from the equilibria predicted from the synonymous substitution matrices. We investigate possible reasons for this unexpected behavior by fitting several regression models. Relaxation toward a mutation-selection equilibrium following a host jump fails to explain the dynamics of the synonymous nucleotide composition, even if we allow for slow temporal changes in the substitution matrix. Instead, we find that deep internal branches of the phylogeny show distinct patterns of nucleotide substitution and that these branches strongly influence the dynamics of nucleotide composition, suggesting that the observed trends are at least in part a result of natural selection acting on synonymous sites. Moreover, we find that the dynamics of the nucleotide composition at synonymous and nonsynonymous sites are highly correlated, providing evidence that even nonsynonymous sites can be influenced by selection pressure for nucleotide composition.</p></abstract></article-meta></front><floats-wrap><fig position="float" id="f1"><label>FIG. 1.</label><caption><p>Absolute values of the linear regression coefficients between the nucleotide composition at FFD sites and the year of isolation of the sequence.</p></caption><graphic xlink:href="zjv0100805780001"></graphic></fig><fig position="float" id="f2"><label>FIG. 2.</label><caption><p>Selected cases of frequencies of nucleotides at FFD sites diverging away from the predicted equilibria. Best-fit lines (solid) are displayed for visual convenience only. Dashed lines indicate the equilibrium nucleotide frequencies as inferred from the full phylogenetic trees. Gray areas around these lines represent the 95% confidence intervals for the corresponding equilibria. Dash-dotted lines indicate the equilibrium nucleotide frequencies as inferred only from the trunk branches of the corresponding trees.</p></caption><graphic xlink:href="zjv0100805780002"></graphic></fig><table-wrap position="float" id="t1"><label>TABLE 1.</label><caption><p>Dynamics of nucleotide frequencies at FFD sites<xref ref-type="table-fn" rid="t1fn1"><italic>a</italic></xref></p></caption><table frame="hsides" rules="groups"><thead><tr><th colspan="1" rowspan="1" align="center" valign="bottom">Gene</th><th colspan="1" rowspan="1" align="center" valign="bottom">Base</th><th colspan="1" rowspan="1" align="center" valign="bottom">RC (10<sup>−4</sup>)</th><th colspan="1" rowspan="1" align="center" valign="bottom">DE (10<sup>−2</sup>)</th><th colspan="1" rowspan="1" align="center" valign="bottom">δ<sub>trunk</sub> (10<sup>−2</sup>)</th><th colspan="1" rowspan="1" align="center" valign="bottom">δ<sub>time</sub> (10<sup>−2</sup>)</th></tr></thead><tbody><tr><td colspan="1" rowspan="4" align="left" valign="top">PB2</td><td colspan="1" rowspan="1" align="center" valign="top"><bold>A</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>2.1**</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>0.9</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>10.8</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>9.5</bold></td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top"><bold>C</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>1.5**</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>0.0</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>24.2*</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>14.8**</bold></td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top">G</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−6.9**</td><td colspan="1" rowspan="1" align="char" char="." valign="top">0.2</td><td colspan="1" rowspan="1" align="char" char="." valign="top">2.1</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−19.1**</td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top">T</td><td colspan="1" rowspan="1" align="char" char="." valign="top">3.3**</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−1.1</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−15.6</td><td colspan="1" rowspan="1" align="char" char="." valign="top">24.4**</td></tr><tr><td colspan="1" rowspan="4" align="left" valign="top">PB1(1)</td><td colspan="1" rowspan="1" align="center" valign="top"><bold>A</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>3.5**</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>1.3</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>54.8</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>26.0</bold></td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top">C</td><td colspan="1" rowspan="1" align="char" char="." valign="top">3.0<bold>**</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−2.1</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−6.8</td><td colspan="1" rowspan="1" align="char" char="." valign="top">4.3</td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top">G</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−1.2**</td><td colspan="1" rowspan="1" align="char" char="." valign="top">3.3</td><td colspan="1" rowspan="1" align="char" char="." valign="top">42.7</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−27.5*</td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top"><bold>T</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>1.6</bold>**</td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>0.0</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>19.4</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>3.4</bold></td></tr><tr><td colspan="1" rowspan="4" align="left" valign="top">PB1(3)</td><td colspan="1" rowspan="1" align="center" valign="top">A</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−1.4<bold>**</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">0.9</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−5.3</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−0.9</td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top">C</td><td colspan="1" rowspan="1" align="char" char="." valign="top">3.4<bold>**</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−0.2</td><td colspan="1" rowspan="1" align="char" char="." valign="top">2.9</td><td colspan="1" rowspan="1" align="char" char="." valign="top">4.4</td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top"><bold>G</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>1.5</bold>**</td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>0.5</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>14.5</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>0.2</bold></td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top"><bold>T</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>3.5</bold>**</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>1.2</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>12.1</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>3.7</bold></td></tr><tr><td colspan="1" rowspan="4" align="left" valign="top">PA</td><td colspan="1" rowspan="1" align="center" valign="top">A</td><td colspan="1" rowspan="1" align="char" char="." valign="top">1.2<bold>**</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−3.0</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−0.5</td><td colspan="1" rowspan="1" align="char" char="." valign="top">8.1</td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top"><bold>C</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>3.2**</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>5.9</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>25.8*</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>5.0</bold></td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top"><bold>G</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>0.4</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>2.2</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>4.4</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>12.0*</bold></td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top"><bold>T</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>4.0</bold>**</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>0.7</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>20.9*</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>1.2</bold></td></tr><tr><td colspan="1" rowspan="4" align="left" valign="top">HA(1)</td><td colspan="1" rowspan="1" align="center" valign="top"><bold>A</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>3.6**</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>1.4</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>14.6</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>13.5</bold></td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top">C</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−2.5<bold>**</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">4.5</td><td colspan="1" rowspan="1" align="char" char="." valign="top">12.2*</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−28.2**</td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top"><bold>G</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>7.2</bold>**</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>2.5</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>21.6*</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>13.5*</bold></td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top">T</td><td colspan="1" rowspan="1" align="char" char="." valign="top">6.1**</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−3.4</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−5.2</td><td colspan="1" rowspan="1" align="char" char="." valign="top">28.2**</td></tr><tr><td colspan="1" rowspan="4" align="left" valign="top">HA(3)</td><td colspan="1" rowspan="1" align="center" valign="top"><bold>A</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>19.1**</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>0.5</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>3.9</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>2.1</bold></td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top">C</td><td colspan="1" rowspan="1" align="char" char="." valign="top">2.2<bold>**</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−5.4</td><td colspan="1" rowspan="1" align="char" char="." valign="top">2.3</td><td colspan="1" rowspan="1" align="char" char="." valign="top">0.4</td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top">G</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−24.1**</td><td colspan="1" rowspan="1" align="char" char="." valign="top">5.5</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−4.6</td><td colspan="1" rowspan="1" align="char" char="." valign="top">1.1</td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top"><bold>T</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>2.8</bold>**</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>0.5</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>1.6</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>0.6</bold></td></tr><tr><td colspan="1" rowspan="4" align="left" valign="top">NP</td><td colspan="1" rowspan="1" align="center" valign="top">A</td><td colspan="1" rowspan="1" align="char" char="." valign="top">0.0</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−4.4</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−22.8*</td><td colspan="1" rowspan="1" align="char" char="." valign="top">13.1**</td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top"><bold>C</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>0.3**</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>0.8</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>25.5**</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>4.5</bold></td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top"><bold>G</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>0.4</bold>**</td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>5.6</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>64.0**</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>7.9*</bold></td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top"><bold>T</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>0.1</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>0.5</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>15.6*</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>0.7</bold></td></tr><tr><td colspan="1" rowspan="4" align="left" valign="top">NA(1)</td><td colspan="1" rowspan="1" align="center" valign="top"><bold>A</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>8.9**</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>2.8</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>61.5**</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>14.3</bold></td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top"><bold>C</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>2.0**</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>1.9</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>37.8*</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>3.8</bold></td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top"><bold>G</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>5.4</bold>**</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>4.6</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>49.1*</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>11.7</bold></td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top">T</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−1.5**</td><td colspan="1" rowspan="1" align="char" char="." valign="top">3.7</td><td colspan="1" rowspan="1" align="char" char="." valign="top">25.3</td><td colspan="1" rowspan="1" align="char" char="." valign="top">1.2</td></tr><tr><td colspan="1" rowspan="4" align="left" valign="top">NA(2)</td><td colspan="1" rowspan="1" align="center" valign="top">A</td><td colspan="1" rowspan="1" align="char" char="." valign="top">0.2<bold>**</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−10.2</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−8.7</td><td colspan="1" rowspan="1" align="char" char="." valign="top">3.0</td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top"><bold>C</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>0.2**</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>5.2</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>15.6**</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>1.7</bold></td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top">G</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−0.3**</td><td colspan="1" rowspan="1" align="char" char="." valign="top">0.3</td><td colspan="1" rowspan="1" align="char" char="." valign="top">3.3</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−2.5</td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top">T</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−0.1**</td><td colspan="1" rowspan="1" align="char" char="." valign="top">4.8</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−10.2</td><td colspan="1" rowspan="1" align="char" char="." valign="top">1.3</td></tr><tr><td colspan="1" rowspan="4" align="left" valign="top">M1</td><td colspan="1" rowspan="1" align="center" valign="top">A</td><td colspan="1" rowspan="1" align="char" char="." valign="top">0.9<bold>**</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−0.6</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−0.2</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−2.4</td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top">C</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−2.2<bold>**</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">2.1</td><td colspan="1" rowspan="1" align="char" char="." valign="top">0.5</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−0.2</td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top"><bold>G</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>0.2</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>1.7</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>0.2</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>3.0</bold></td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top"><bold>T</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>1.1</bold>**</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>3.1</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>0.5</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>0.4</bold></td></tr><tr><td colspan="1" rowspan="4" align="left" valign="top">M2</td><td colspan="1" rowspan="1" align="center" valign="top">A</td><td colspan="1" rowspan="1" align="char" char="." valign="top">2.6<bold>**</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−0.7</td><td colspan="1" rowspan="1" align="char" char="." valign="top">1.0</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−1.9*</td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top">C</td><td colspan="1" rowspan="1" align="char" char="." valign="top">10.3<bold>**</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−10.0</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−3.3</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−0.4</td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top"><bold>G</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>0.1</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>3.8</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>4.2</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>1.5</bold></td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top">T</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−12.8**</td><td colspan="1" rowspan="1" align="char" char="." valign="top">14.5</td><td colspan="1" rowspan="1" align="char" char="." valign="top">6.4<bold>*</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">0.8</td></tr><tr><td colspan="1" rowspan="4" align="left" valign="top">NS1</td><td colspan="1" rowspan="1" align="center" valign="top"><bold>A</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>0.2</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>3.0</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>15.1**</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>4.0</bold></td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top">C</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−0.1</td><td colspan="1" rowspan="1" align="char" char="." valign="top">3.0</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−3.9</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−2.9</td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top"><bold>G</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>0.2</bold>*</td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>0.6</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>6.3</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>0.5</bold></td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top"><bold>T</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>0.3</bold>**</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>6.6</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>5.0</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>7.3**</bold></td></tr><tr><td colspan="1" rowspan="4" align="left" valign="top">NEP</td><td colspan="1" rowspan="1" align="center" valign="top">A</td><td colspan="1" rowspan="1" align="char" char="." valign="top">4.6<bold>**</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">-8.2</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−6.1*</td><td colspan="1" rowspan="1" align="char" char="." valign="top">0.0</td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top"><bold>C</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>8.0**</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>1.4</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>0.5</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>1.4</bold></td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top"><bold>G</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>7.4</bold>**</td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>18.0</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>5.9*</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>1.4</bold></td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top"><bold>T</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>4.1</bold>**</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>8.4</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>0.6</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>2.9**</bold></td></tr></tbody></table><table-wrap-foot><fn id="t1fn1"><label>a</label><p>RC, values of the linear regression coefficient between the nucleotide frequency and the time of isolation; DE, the difference between the average observed and the equilibrium nucleotide frequencies; δ<sub>trunk</sub>, the trunk statistic; δ<sub>time</sub>, the time statistic. Gene types are given in parentheses. Bold type indicates cases of divergence from the equilibrium. *, δ<sub>trunk</sub> or δ<sub>time</sub> statistical values significant at the 5% level; **, δ<sub>trunk</sub> or δ<sub>time</sub> statistical values significant at the 1% level (two-tailed test). A positive (negative) RC value implies that the frequency of the considered nucleotide is increasing (decreasing) with time. A positive (negative) DE value implies that the mean nucleotide frequency is above (below) the predicted equilibrium. If the product of RC and DE is positive (negative), the frequency of the considered nucleotide is diverging from (converging to) its equilibrium value. A positive (negative) δ<sub>trunk</sub> value shows how many additional residues of a particular nucleotide are gained (lost) on a typical trunk branch as compared to the rest of the tree. A positive (negative) δ<sub>time</sub> value shows how many additional residues of a particular nucleotide are gained (lost) on a typical branch in the second half of the tree as compared to the first half of the tree.</p></fn></table-wrap-foot></table-wrap><table-wrap position="float" id="t2"><label>TABLE 2.</label><caption><p>Standard partial regression and correlation coefficients for the four linear models<xref ref-type="table-fn" rid="t2fn1"><italic>a</italic></xref></p></caption><table frame="hsides" rules="groups"><thead><tr><th colspan="1" rowspan="1" align="center" valign="bottom">Model</th><th colspan="1" rowspan="1" align="center" valign="bottom">α<sub><italic>i</italic></sub></th><th colspan="1" rowspan="1" align="center" valign="bottom">β<sub><italic>i</italic></sub></th><th colspan="1" rowspan="1" align="center" valign="bottom">γ<sub><italic>i</italic></sub></th><th colspan="1" rowspan="1" align="center" valign="bottom"><italic>R</italic><sub><italic>i</italic></sub><sup>2</sup></th></tr></thead><tbody><tr><td colspan="1" rowspan="1" align="center" valign="top">1</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−0.16</td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top">0.02</td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top">2</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−0.12</td><td colspan="1" rowspan="1" align="char" char="." valign="top">0.20</td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top">0.07 (<italic>P</italic> = 0.12)</td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top">3</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−0.28</td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="char" char="." valign="top">0.34</td><td colspan="1" rowspan="1" align="left" valign="top">0.12 (<italic>P</italic> < 0.05)</td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top">4</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−0.26</td><td colspan="1" rowspan="1" align="char" char="." valign="top">0.27</td><td colspan="1" rowspan="1" align="char" char="." valign="top">0.39</td><td colspan="1" rowspan="1" align="left" valign="top">0.19 (<italic>P</italic><sub>time</sub> < 0.01, <italic>P</italic><sub>trunk</sub> < 0.05)</td></tr></tbody></table><table-wrap-foot><fn id="t2fn1"><label>a</label><p>Standard partial regression and correlation coefficients (described in Materials and Methods) for predicting dynamics of the nucleotide composition at FFD sites. <italic>P</italic> values for Models 2 and 3 are for comparison with model 1. <italic>P</italic> values for Model 4 are for comparison with Models 2 (<italic>P</italic><sub>trunk</sub>) and 3 (<italic>P</italic><sub>time</sub>).</p></fn></table-wrap-foot></table-wrap><table-wrap position="float" id="t3"><label>TABLE 3.</label><caption><p>Dynamics of nucleotide frequencies at SCP sites<xref ref-type="table-fn" rid="t3fn1"><italic>a</italic></xref></p></caption><table frame="hsides" rules="groups"><thead><tr><th colspan="1" rowspan="1" align="center" valign="bottom">Gene</th><th colspan="1" rowspan="1" align="center" valign="bottom">Base</th><th colspan="1" rowspan="1" align="center" valign="bottom">RC (10<sup>−5</sup>)</th><th colspan="1" rowspan="1" align="center" valign="bottom">DE (10<sup>−2</sup>)</th><th colspan="1" rowspan="1" align="center" valign="bottom">δ<sub>trunk</sub> (10<sup>−2</sup>)</th><th colspan="1" rowspan="1" align="center" valign="bottom">δ<sub>time</sub> (10<sup>−2</sup>)</th></tr></thead><tbody><tr><td colspan="1" rowspan="4" align="left" valign="bottom">PB2</td><td colspan="1" rowspan="1" align="center" valign="top">A</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−5.8<bold>**</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">4.4</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−8.9</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−2.0</td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top">C</td><td colspan="1" rowspan="1" align="char" char="." valign="top">0.0</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−1.4</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−2.8</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−1.6</td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top"><bold>G</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>4.7</bold>**</td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>10.2</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>14.6*</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>2.7</bold></td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top">T</td><td colspan="1" rowspan="1" align="char" char="." valign="top">1.1**</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−13.3</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−2.9</td><td colspan="1" rowspan="1" align="char" char="." valign="top">0.9</td></tr><tr><td colspan="1" rowspan="4" align="left" valign="bottom">PB1(1)</td><td colspan="1" rowspan="1" align="center" valign="top"><bold>A</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>5.7**</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>13.5</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>24.9</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>8.7</bold></td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top"><bold>C</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>0.1</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>6.0</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>2.7</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>13.6</bold></td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top">G</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−5.7**</td><td colspan="1" rowspan="1" align="char" char="." valign="top">7.5</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−11.7</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−6.5</td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top">T</td><td colspan="1" rowspan="1" align="char" char="." valign="top">0.0</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−14.9</td><td colspan="1" rowspan="1" align="char" char="." valign="top">2.7</td><td colspan="1" rowspan="1" align="char" char="." valign="top">8.4</td></tr><tr><td colspan="1" rowspan="4" align="left" valign="bottom">PB1(3)</td><td colspan="1" rowspan="1" align="center" valign="top"><bold>A</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>4.4**</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>9.3</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>7.9*</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>9.6**</bold></td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top">C</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−1.5<bold>**</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">1.6</td><td colspan="1" rowspan="1" align="char" char="." valign="top">0.4</td><td colspan="1" rowspan="1" align="char" char="." valign="top">2.7*</td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top"><bold>G</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>4.4</bold>**</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>3.0</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>7.6</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>9.3**</bold></td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top">T</td><td colspan="1" rowspan="1" align="char" char="." valign="top">1.4**</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−7.9</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−0.8</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−2.4*</td></tr><tr><td colspan="1" rowspan="4" align="left" valign="bottom">PA</td><td colspan="1" rowspan="1" align="center" valign="top"><bold>A</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>11.4**</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>15.4</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>21.8**</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>3.6</bold></td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top"><bold>C</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>1.9**</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>4.1</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>3.5</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>7.2**</bold></td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top">G</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−8.7**</td><td colspan="1" rowspan="1" align="char" char="." valign="top">0.8</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−18.1**</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−3.0</td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top"><bold>T</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>0.8</bold>**</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>12.1</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>0.2</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>6.5**</bold></td></tr><tr><td colspan="1" rowspan="4" align="left" valign="bottom">HA(1)</td><td colspan="1" rowspan="1" align="center" valign="top">A</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−22.7<bold>**</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">11.3</td><td colspan="1" rowspan="1" align="char" char="." valign="top">28.3*</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−61.0**</td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top">C</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−17.1<bold>**</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">8.0</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−15.0*</td><td colspan="1" rowspan="1" align="char" char="." valign="top">23.4**</td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top"><bold>G</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>16.4</bold>**</td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>1.2</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>11.0</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>26.2**</bold></td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top">T</td><td colspan="1" rowspan="1" align="char" char="." valign="top">23.4**</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−20.5</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−2.3</td><td colspan="1" rowspan="1" align="char" char="." valign="top">11.5*</td></tr><tr><td colspan="1" rowspan="4" align="left" valign="bottom">HA(3)</td><td colspan="1" rowspan="1" align="center" valign="top"><bold>A</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>55.5**</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>2.2</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>8.5</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>1.6</bold></td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top">C</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−4.9<bold>**</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">2.1</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−1.1</td><td colspan="1" rowspan="1" align="char" char="." valign="top">0.9</td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top">G</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−27.8**</td><td colspan="1" rowspan="1" align="char" char="." valign="top">6.0</td><td colspan="1" rowspan="1" align="char" char="." valign="top">5.5</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−5.1*</td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top"><bold>T</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>22.8</bold>**</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>10.3</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>12.9**</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>5.8**</bold></td></tr><tr><td colspan="1" rowspan="4" align="left" valign="bottom">NP</td><td colspan="1" rowspan="1" align="center" valign="top">A</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−1.0</td><td colspan="1" rowspan="1" align="char" char="." valign="top">2.5</td><td colspan="1" rowspan="1" align="char" char="." valign="top">31.2**</td><td colspan="1" rowspan="1" align="char" char="." valign="top">0.3</td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top"><bold>C</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>0.3</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>5.6</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>4.9</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>4.5**</bold></td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top">G</td><td colspan="1" rowspan="1" align="char" char="." valign="top">4.5**</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−7.3</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−26.7**</td><td colspan="1" rowspan="1" align="char" char="." valign="top">4.1*</td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top"><bold>T</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>3.9</bold>**</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>0.7</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>9.4**</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>0.0</bold></td></tr><tr><td colspan="1" rowspan="4" align="left" valign="bottom">NA(1)</td><td colspan="1" rowspan="1" align="center" valign="top">A</td><td colspan="1" rowspan="1" align="char" char="." valign="top">16.3<bold>**</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−1.6</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−2.4</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−8.4</td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top">C</td><td colspan="1" rowspan="1" align="char" char="." valign="top">14.2<bold>**</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−9.5</td><td colspan="1" rowspan="1" align="char" char="." valign="top">16.1</td><td colspan="1" rowspan="1" align="char" char="." valign="top">3.4</td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top">G</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−27.7**</td><td colspan="1" rowspan="1" align="char" char="." valign="top">3.8</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−12.5</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−3.2</td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top">T</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−2.8**</td><td colspan="1" rowspan="1" align="char" char="." valign="top">7.3</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−1.2</td><td colspan="1" rowspan="1" align="char" char="." valign="top">8.2</td></tr><tr><td colspan="1" rowspan="4" align="left" valign="bottom">NA(2)</td><td colspan="1" rowspan="1" align="center" valign="top">A</td><td colspan="1" rowspan="1" align="char" char="." valign="top">0.8<bold>**</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−4.0</td><td colspan="1" rowspan="1" align="char" char="." valign="top">5.5</td><td colspan="1" rowspan="1" align="char" char="." valign="top">2.0</td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top">C</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−0.1</td><td colspan="1" rowspan="1" align="char" char="." valign="top">0.6</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−5.3</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−3.6</td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top"><bold>G</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>1.7</bold>**</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>3.8</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>16.1**</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>1.1</bold></td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top"><bold>T</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>1.0</bold>**</td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>7.3</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>15.9**</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>0.5</bold></td></tr><tr><td colspan="1" rowspan="4" align="left" valign="bottom">M1</td><td colspan="1" rowspan="1" align="center" valign="top"><bold>A</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>7.7**</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>6.4</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>0.4</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>0.8</bold></td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top"><bold>C</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>3.0**</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>0.8</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>4.0</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>1.5</bold></td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top">G</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−7.4**</td><td colspan="1" rowspan="1" align="char" char="." valign="top">3.7</td><td colspan="1" rowspan="1" align="char" char="." valign="top">3.3</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−3.4</td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top"><bold>T</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>3.3</bold>**</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>10.9</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−<bold>6.9</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top"><bold>4.1**</bold></td></tr><tr><td colspan="1" rowspan="4" align="left" valign="bottom">M2</td><td colspan="1" rowspan="1" align="center" valign="top">A</td><td colspan="1" rowspan="1" align="char" char="." valign="top">8.7<bold>**</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">9.7</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−0.4</td><td colspan="1" rowspan="1" align="char" char="." valign="top">0.8</td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top">C</td><td colspan="1" rowspan="1" align="char" char="." valign="top">6.7<bold>**</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−10.7</td><td colspan="1" rowspan="1" align="char" char="." valign="top">4.0</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−1.5</td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top">G</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−13.3**</td><td colspan="1" rowspan="1" align="char" char="." valign="top">4.5</td><td colspan="1" rowspan="1" align="char" char="." valign="top">3.3</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−3.4</td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top">T</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−2.1</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−3.5</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−6.9</td><td colspan="1" rowspan="1" align="char" char="." valign="top">4.1**</td></tr><tr><td colspan="1" rowspan="4" align="left" valign="bottom">NS1</td><td colspan="1" rowspan="1" align="center" valign="top">A</td><td colspan="1" rowspan="1" align="char" char="." valign="top">28.0<bold>**</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−0.6</td><td colspan="1" rowspan="1" align="char" char="." valign="top">7.0</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−1.4</td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top">C</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−18.6<bold>**</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−3.9</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−5.9</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−1.3</td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top">G</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−19.3**</td><td colspan="1" rowspan="1" align="char" char="." valign="top">1.3</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−3.7</td><td colspan="1" rowspan="1" align="char" char="." valign="top">3.2</td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top">T</td><td colspan="1" rowspan="1" align="char" char="." valign="top">9.9**</td><td colspan="1" rowspan="1" align="char" char="." valign="top">3.2</td><td colspan="1" rowspan="1" align="char" char="." valign="top">2.7</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−0.4</td></tr><tr><td colspan="1" rowspan="4" align="left" valign="bottom">NEP</td><td colspan="1" rowspan="1" align="center" valign="top">A</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−18.6<bold>**</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">4.2</td><td colspan="1" rowspan="1" align="char" char="." valign="top">7.0</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−1.4</td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top">C</td><td colspan="1" rowspan="1" align="char" char="." valign="top">22.3<bold>**</bold></td><td colspan="1" rowspan="1" align="char" char="." valign="top">−8.9</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−5.9</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−1.3</td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top">G</td><td colspan="1" rowspan="1" align="char" char="." valign="top">18.7**</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−2.6</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−3.7</td><td colspan="1" rowspan="1" align="char" char="." valign="top">3.2</td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top">T</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−22.5**</td><td colspan="1" rowspan="1" align="char" char="." valign="top">7.3</td><td colspan="1" rowspan="1" align="char" char="." valign="top">2.7</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−0.4</td></tr></tbody></table><table-wrap-foot><fn id="t3fn1"><label>a</label><p>The notations are the same as those used in Table <xref ref-type="table" rid="t1">1</xref> (see footnote <italic>a</italic> of Table <xref ref-type="table" rid="t1">1</xref>).</p></fn></table-wrap-foot></table-wrap><table-wrap position="float" id="t4"><label>TABLE 4.</label><caption><p>Standard partial regression and correlation coefficients for the four linear models<xref ref-type="table-fn" rid="t4fn1"><italic>a</italic></xref></p></caption><table frame="hsides" rules="groups"><thead><tr><th colspan="1" rowspan="1" align="center" valign="bottom">Model</th><th colspan="1" rowspan="1" align="center" valign="bottom">α<sub><italic>i</italic></sub></th><th colspan="1" rowspan="1" align="center" valign="bottom">β<sub><italic>i</italic></sub></th><th colspan="1" rowspan="1" align="center" valign="bottom">γ<sub><italic>i</italic></sub></th><th colspan="1" rowspan="1" align="center" valign="bottom"><italic>R</italic><sub><italic>i</italic></sub><sup>2</sup></th></tr></thead><tbody><tr><td colspan="1" rowspan="1" align="center" valign="top">1</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−0.19</td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top">0.04</td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top">2</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−0.15</td><td colspan="1" rowspan="1" align="char" char="." valign="top">0.15</td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="left" valign="top">0.06 (<italic>P</italic> = 0.13)</td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top">3</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−0.28</td><td colspan="1" rowspan="1" align="center" valign="top"></td><td colspan="1" rowspan="1" align="char" char="." valign="top">0.25</td><td colspan="1" rowspan="1" align="left" valign="top">0.09 (<italic>P</italic> = 0.06)</td></tr><tr><td colspan="1" rowspan="1" align="center" valign="top">4</td><td colspan="1" rowspan="1" align="char" char="." valign="top">−0.25</td><td colspan="1" rowspan="1" align="char" char="." valign="top">0.28</td><td colspan="1" rowspan="1" align="char" char="." valign="top">0.36</td><td colspan="1" rowspan="1" align="left" valign="top">0.15 (<italic>P</italic><sub>time</sub> < 0.05, <italic>P</italic><sub>trunk</sub> < 0.05)</td></tr></tbody></table><table-wrap-foot><fn id="t4fn1"><label>a</label><p>Standard partial regression and correlation coefficients for the four linear models described in Materials and Methods for predicting dynamics of the nucleotide composition at SCP sites. Notations are the same as those for Table <xref ref-type="table" rid="t2">2</xref> (see footnote <italic>a</italic> of Table <xref ref-type="table" rid="t2">2</xref>).</p></fn></table-wrap-foot></table-wrap></floats-wrap></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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HfdIndexSelect -h $EXPLOR_AREA/Data/Pmc/Curation/RBID.i -Sk "pubmed:18321967" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Pmc/Curation/biblio.hfd \
| NlmPubMed2Wicri -a H2N2V1
| This area was generated with Dilib version V0.6.33. |  |