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Phylogenetic comparative methods
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<h2 id="applications">Applications</h2> <p>Phylogenetic comparative approaches can complement other ways of studying adaptation, such as studying natural populations, experimental studies, and mathematical models.<a class="footnote-ref" id="fnref:6" href="#fn:6"><sup>6</sup></a> Interspecific comparisons allow researchers to assess the generality of evolutionary phenomena by considering independent evolutionary events. Such an approach is particularly useful when there is little or no variation within species. And because they can be used to explicitly model evolutionary processes occurring over very long time periods, they can provide insight into macroevolutionary questions, once the exclusive domain of <a href="/facts/Paleontology/60n5yldd">paleontology</a>.<a class="footnote-ref" id="fnref:7" href="#fn:7"><sup>7</sup></a> </p> <p>Phylogenetic comparative methods are commonly applied to such questions as: </p> <ul><li>What is the <a href="/facts/Slope/a2L3k0j5">slope</a> of an <a href="/facts/Allometric/jERkArka">allometric</a> scaling relationship?</li></ul> <p>→ <i>Example: how does <a href="/facts/Brain-to-body_mass_ratio/VXcs2NLh">brain mass vary in relation to body mass</a>?</i> </p> <ul><li>Do different <a href="/facts/Clades/XefyYmWn">clades</a> of organisms differ with respect to some <a href="/facts/Phenotypic/vxWXKGLj">phenotypic</a> trait?</li></ul> <p>→ <i>Example: do <a href="/facts/Canidae/5Fj02eeS">canids</a> have larger hearts than <a href="/facts/Felidae/Fryfw7gm">felids</a>?</i> </p> <ul><li>Do groups of species that share a <a href="/facts/Behavioral/0Y1VqmVX">behavioral</a> or ecological feature (e.g., <a href="/facts/Social_system/crIBHftt">social system</a>, <a href="/facts/Diet_(nutrition)/7qzDHpop">diet</a>) differ in average phenotype?</li></ul> <p>→ <i>Example: do carnivores have larger <a href="/facts/Home_range/X6KwWmIJ">home ranges</a> than herbivores?</i> </p> <ul><li>What was the <a href="/facts/Ancestral/oslX3GRb">ancestral</a> state of a <a href="/facts/Phenotypic_trait/seYSUTul">trait</a>?</li></ul> <p>→ <i>Example: where did <a href="/facts/Endothermy/qs3DIGHx">endothermy</a> evolve in the lineage that led to mammals?</i> </p><p>→ <i>Example: where, when, and why did <a href="/facts/Placenta/7XUoks1b">placentas</a> and <a href="/facts/Viviparity/EEMn4rVx">viviparity</a> evolve?</i> </p> <ul><li>Does a trait exhibit significant phylogenetic signal in a particular group of organisms? Do certain types of traits tend to "follow phylogeny" more than others?</li></ul> <p>→ <i>Example: are behavioral traits <a href="/facts/Phenotypic_plasticity/JXuG0IlF">more labile</a> during evolution?</i> </p> <ul><li>Do species differences in <a href="/facts/Life_history_theory/yy5FjMJs">life history traits</a> trade-off, as in the so-called fast-slow continuum?</li></ul> <p>→ <i>Example: why do small-bodied species have shorter <a href="/facts/Life_expectancy/uPc8bWWW">life spans</a> than their larger relatives?</i> </p> <h2 id="phylogenetically-independent-contrasts">Phylogenetically independent contrasts</h2> <p><a href="/facts/Joseph_Felsenstein/Y1GtDJa4">Felsenstein</a><a class="footnote-ref" id="fnref:8" href="#fn:8"><sup>8</sup></a> proposed the first general statistical method in 1985 for incorporating phylogenetic information, i.e., the first that could use any arbitrary <a href="/facts/Topology/2EqW47cU">topology</a> (branching order) and a specified set of branch lengths. The method is now recognized as an <a href="/facts/Algorithm/fnl5NmRt">algorithm</a> that implements a special case of what are termed phylogenetic <a href="/facts/Generalized_least-squares/NI2GL3RK">generalized least-squares</a> models.<a class="footnote-ref" id="fnref:9" href="#fn:9"><sup>9</sup></a> The <a href="/facts/Logic/8JnpJLtt">logic</a> of the method is to use phylogenetic information (and an assumed <a href="/facts/Brownian_motion/Th0g0wkr">Brownian motion</a> like model of trait evolution) to transform the original tip data (mean values for a set of species) into values that are <a href="/facts/Statistically_independent/NUzQtnUL">statistically independent</a> and <a href="/facts/Identically_distributed/othIRaWt">identically distributed</a>. </p><p>The algorithm involves computing values at <a href="/facts/Internal_node/RcXz9noF">internal nodes</a> as an intermediate step, but they are generally not used for <a href="/facts/Inferences/RBbe95bP">inferences</a> by themselves. An exception occurs for the basal (root) node, which can be interpreted as an estimate of the ancestral value for the entire tree (assuming that no directional evolutionary trends [e.g., <a href="/facts/Cope%2527s_rule/bYRMtxMP">Cope's rule</a>] have occurred) or as a phylogenetically weighted estimate of the mean for the entire set of tip species (terminal taxa). The value at the root is equivalent to that obtained from the "squared-change parsimony" algorithm and is also the maximum likelihood estimate under Brownian motion. The independent contrasts algebra can also be used to compute a <a href="/facts/Standard_error/Iv96AyCD">standard error</a> or <a href="/facts/Confidence_interval/NS8mG5UE">confidence interval</a>. </p> <h2 id="phylogenetic-generalized-least-squares-pgls">Phylogenetic generalized least squares (PGLS)</h2> <p>Probably the most commonly used PCM is phylogenetic generalized least squares (PGLS).<a class="footnote-ref" id="fnref:10" href="#fn:10"><sup>10</sup></a><a class="footnote-ref" id="fnref:11" href="#fn:11"><sup>11</sup></a> This approach is used to test whether there is a relationship between two (or more) variables while accounting for the fact that lineage are not independent. The method is a special case of <a href="/facts/Generalized_least_squares/NI2GL3RK">generalized least squares</a> (GLS) and as such the PGLS estimator is also <a href="/facts/Bias_of_an_estimator/oxIvEgmd">unbiased</a>, <a href="/facts/Consistent_estimator/HAKDWYEM">consistent</a>, <a href="/facts/Efficiency_(statistics)/wTmgEqte">efficient</a>, and <a href="/facts/Asymptotic_distribution/dN7jVHqm">asymptotically normal</a>.<a class="footnote-ref" id="fnref:12" href="#fn:12"><sup>12</sup></a> In many statistical situations where GLS (or, <a href="/facts/Ordinary_least_squares/q7H9k5vM">ordinary least squares</a> [OLS]) is used residual errors <i>ε</i> are assumed to be independent and identically distributed random variables that are assumed to be normal </p> ε ∣ X ∼ N ( 0 , σ 2 I n ) . {\displaystyle \varepsilon \mid X\sim {\mathcal {N}}(0,\sigma ^{2}I_{n}).} <p>whereas in PGLS the errors are assumed to be distributed as </p> ε ∣ X ∼ N ( 0 , V ) . {\displaystyle \varepsilon \mid X\sim {\mathcal {N}}(0,\mathbf {V} ).} <p>where <i>V</i> is a matrix of expected variance and covariance of the residuals given an evolutionary model and a phylogenetic tree. Therefore, it is the structure of residuals and not the variables themselves that show <a href="/facts/Phylogenetic_signal/hW6xx7lc">phylogenetic signal</a>. This has long been a source of confusion in the scientific literature.<a class="footnote-ref" id="fnref:13" href="#fn:13"><sup>13</sup></a> A number of models have been proposed for the structure of <i>V</i> such as <a href="/facts/Brownian_motion/Th0g0wkr">Brownian motion</a><a class="footnote-ref" id="fnref:14" href="#fn:14"><sup>14</sup></a> <a href="/facts/Ornstein%25E2%2580%2593Uhlenbeck_process/oFaDcovm">Ornstein-Uhlenbeck</a>,<a class="footnote-ref" id="fnref:15" href="#fn:15"><sup>15</sup></a> and Pagel's λ model.<a class="footnote-ref" id="fnref:16" href="#fn:16"><sup>16</sup></a> (When a Brownian motion model is used, PGLS is identical to the independent contrasts estimator.<a class="footnote-ref" id="fnref:17" href="#fn:17"><sup>17</sup></a>). In PGLS, the parameters of the evolutionary model are typically co-estimated with the regression parameters. </p><p>PGLS can only be applied to questions where the <a href="/facts/Dependent_variable/dINfzIF2">dependent variable</a> is continuously distributed; however, the phylogenetic tree can also be incorporated into the residual distribution of <a href="/facts/Generalized_linear_models/Sf1htm5W">generalized linear models</a>, making it possible to generalize the approach to a broader set of distributions for the response.<a class="footnote-ref" id="fnref:18" href="#fn:18"><sup>18</sup></a><a class="footnote-ref" id="fnref:19" href="#fn:19"><sup>19</sup></a><a class="footnote-ref" id="fnref:20" href="#fn:20"><sup>20</sup></a> </p> <h2 id="phylogenetically-informed-monte-carlo-computer-simulations">Phylogenetically informed Monte Carlo computer simulations</h2> <p>Martins and Garland<a class="footnote-ref" id="fnref:21" href="#fn:21"><sup>21</sup></a> proposed in 1991 that one way to account for phylogenetic relations when conducting statistical analyses was to use computer simulations to create many data sets that are consistent with the null hypothesis under test (e.g., no correlation between two traits, no difference between two ecologically defined groups of species) but that mimic evolution along the relevant phylogenetic tree. If such data sets (typically 1,000 or more) are analyzed with the same statistical procedure that is used to analyze a real data set, then results for the simulated data sets can be used to create phylogenetically correct (or "PC"<a class="footnote-ref" id="fnref:22" href="#fn:22"><sup>22</sup></a>) null distributions of the test statistic (e.g., a correlation coefficient, t, F). Such simulation approaches can also be combined with such methods as phylogenetically independent contrasts or PGLS (see above). </p> <h2 id="see-also">See also</h2> <ul><li><a href="/facts/Allometry/jERkArka">Allometry</a></li> <li><a href="/facts/Behavioral_ecology/P5Jm5ba7">Behavioral ecology</a></li> <li><a href="/facts/Biodiversity/GruakEzs">Biodiversity</a></li> <li><a href="/facts/Bioinformatics/D5x2L8ee">Bioinformatics</a></li> <li><a href="/facts/Cladistics/JasKVABk">Cladistics</a></li> <li><a href="/facts/Comparative_anatomy/UycBTvDH">Comparative anatomy</a></li> <li><a href="/facts/Comparative_method/VKJAa3zy">Comparative method</a> in linguistics</li> <li><a href="/facts/Comparative_physiology/npmqESvw">Comparative physiology</a></li> <li><a href="/facts/Computational_phylogenetics/MTyNUhHg">Computational phylogenetics</a></li> <li><a href="/facts/Disk-covering_method/zU8p65jg">Disk-covering method</a></li> <li><a href="/facts/Ecophysiology/BX6xkfhg">Ecophysiology</a></li> <li><a href="/facts/Evolutionary_neurobiology/oD2ERUET">Evolutionary neurobiology</a></li> <li><a href="/facts/Evolutionary_physiology/TwkhPN95">Evolutionary physiology</a></li> <li><a href="/facts/Generalized_least_squares/NI2GL3RK">Generalized least squares</a> (GLS)</li> <li><a href="/facts/Generalized_linear_model/Sf1htm5W">Generalized linear model</a></li> <li><a href="/facts/Joe_Felsenstein/Y1GtDJa4">Joe Felsenstein</a></li> <li><a href="/facts/Mark_Pagel/HfcIE81A">Mark Pagel</a></li> <li><a href="/facts/Maximum_likelihood/0Yq2dpQD">Maximum likelihood</a></li> <li><a href="/facts/Maximum_parsimony/sxccmrfR">Maximum parsimony</a></li> <li><a href="/facts/Paul_H._Harvey/7lHqezNL">Paul H. Harvey</a></li> <li><a href="/facts/Phylogenetics/bw4rsovt">Phylogenetics</a></li> <li><a href="/facts/Phylogenetic_reconciliation/w7hDoGz5">Phylogenetic reconciliation</a></li> <li><a href="/facts/Roderic_D.M._Page/X3cBpNNm">Roderic D.M. Page</a></li> <li><a href="/facts/Sexual_selection/AjDd8Tam">Sexual selection</a></li> <li><a href="/facts/Statistics/DNPsKGYU">Statistics</a></li> <li><a href="/facts/Systematics/fagPXIkh">Systematics</a></li> <li><a href="/facts/Theodore_Garland_Jr./7IUxm67p">Theodore Garland Jr.</a></li></ul> <h2 id="further-reading">Further reading</h2> <ul><li>Ackerly, D. D. 1999. Comparative plant ecology and the role of phylogenetic information. Pages 391–413 in M. C. Press, J. D. Scholes, and M. G. Braker, eds. Physiological plant ecology. The 39th symposium of the British Ecological Society held at the University of York 7–9 September 1998. Blackwell Science, Oxford, U.K.</li> <li>Berenbrink, M.; Koldkjær, P.; Kepp, O.; Cossins, A. R. (2005). "Evolution of oxygen secretion in fishes and the emergence of a complex physiological system". <i>Science</i>. 307 (5716): 1752–1757. <a href="/facts/Bibcode_(identifier)/9HtdQSGB">Bibcode</a>:<a href="https://ui.adsabs.harvard.edu/abs/2005Sci...307.1752B">2005Sci...307.1752B</a>. <a href="/facts/Doi_(identifier)/muM9Etpq">doi</a>:<a href="https://doi.org/10.1126%2Fscience.1107793">10.1126/science.1107793</a>. <a href="/facts/PMID_(identifier)/JlHAvMHt">PMID</a> <a href="https://pubmed.ncbi.nlm.nih.gov/15774753">15774753</a>. <a href="/facts/S2CID_(identifier)/ldJsHa2Y">S2CID</a> <a href="https://api.semanticscholar.org/CorpusID:36391252">36391252</a>.</li> <li>Blomberg, S. P.; <a href="/facts/Theodore_Garland_Jr./7IUxm67p">Garland, T. Jr.</a>; Ives, A. R. (2003). <a href="http://biology.ucr.edu/people/faculty/Garland/BlomEA03.pdf">"Testing for phylogenetic signal in comparative data: behavioral traits are more labile"</a> (PDF). <i>Evolution</i>. 57 (4): 717–745. <a href="/facts/Doi_(identifier)/muM9Etpq">doi</a>:<a href="https://doi.org/10.1554%2F0014-3820%282003%29057%5B0717%3Atfpsic%5D2.0.co%3B2">10.1554/0014-3820(2003)057[0717:tfpsic]2.0.co;2</a>. <a href="/facts/PMID_(identifier)/JlHAvMHt">PMID</a> <a href="https://pubmed.ncbi.nlm.nih.gov/12778543">12778543</a>.</li> <li>Brooks, D. R., and D. A. McLennan. 1991. Phylogeny, ecology, and behavior: a research program in comparative biology. Univ. Chicago Press, Chicago. 434 pp.</li> <li>Cheverud, J. M.; Dow, M. M.; Leutenegger, W. (1985). "The quantitative assessment of phylogenetic constraints in comparative analyses: sexual dimorphism in body weight among primates". <i>Evolution</i>. 39 (6): 1335–1351. <a href="/facts/Doi_(identifier)/muM9Etpq">doi</a>:<a href="https://doi.org/10.2307%2F2408790">10.2307/2408790</a>. <a href="/facts/JSTOR_(identifier)/YTeVmaJ7">JSTOR</a> <a href="https://www.jstor.org/stable/2408790">2408790</a>. <a href="/facts/PMID_(identifier)/JlHAvMHt">PMID</a> <a href="https://pubmed.ncbi.nlm.nih.gov/28564267">28564267</a>.</li> <li>Eggleton, P., and R. I. Vane-Wright, eds. 1994. Phylogenetics and ecology. Linnean Society Symposium Series Number 17. Academic Press, London.</li> <li><a href="/facts/Joe_Felsenstein/Y1GtDJa4">Felsenstein, J.</a> 2004. Inferring phylogenies. Sinauer Associates, Sunderland, Mass. xx + 664 pp.</li> <li>Freckleton, R. P.; Harvey, P. H.; Pagel, M. (2002). "Phylogenetic analysis and comparative data: a test and review of evidence". <i>American Naturalist</i>. 160 (6): 712–726. <a href="/facts/Doi_(identifier)/muM9Etpq">doi</a>:<a href="https://doi.org/10.1086%2F343873">10.1086/343873</a>. <a href="/facts/PMID_(identifier)/JlHAvMHt">PMID</a> <a href="https://pubmed.ncbi.nlm.nih.gov/18707460">18707460</a>. <a href="/facts/S2CID_(identifier)/ldJsHa2Y">S2CID</a> <a href="https://api.semanticscholar.org/CorpusID:19796539">19796539</a>.</li> <li><a href="/facts/Theodore_Garland_Jr./7IUxm67p">Garland, T. Jr.</a>; Ives, A. R. (2000). <a href="http://biology.ucr.edu/people/faculty/Garland/GarlIv00.pdf">"Using the past to predict the present: Confidence intervals for regression equations in phylogenetic comparative methods"</a> (PDF). <i>American Naturalist</i>. 155 (3): 346–364. <a href="/facts/Doi_(identifier)/muM9Etpq">doi</a>:<a href="https://doi.org/10.1086%2F303327">10.1086/303327</a>. <a href="/facts/PMID_(identifier)/JlHAvMHt">PMID</a> <a href="https://pubmed.ncbi.nlm.nih.gov/10718731">10718731</a>. <a href="/facts/S2CID_(identifier)/ldJsHa2Y">S2CID</a> <a href="https://api.semanticscholar.org/CorpusID:4384701">4384701</a>.</li> <li>Garland, T. Jr.; Bennett, A. F.; Rezende, E. L. (2005). <a href="http://biology.ucr.edu/people/faculty/Garland/GarlandEA2005_JEBCM.pdf">"Phylogenetic approaches in comparative physiology"</a> (PDF). <i>Journal of Experimental Biology</i>. 208 (16): 3015–3035. <a href="/facts/Doi_(identifier)/muM9Etpq">doi</a>:<a href="https://doi.org/10.1242%2Fjeb.01745">10.1242/jeb.01745</a>. <a href="/facts/PMID_(identifier)/JlHAvMHt">PMID</a> <a href="https://pubmed.ncbi.nlm.nih.gov/16081601">16081601</a>. <a href="/facts/S2CID_(identifier)/ldJsHa2Y">S2CID</a> <a href="https://api.semanticscholar.org/CorpusID:14871059">14871059</a>.</li> <li>Garland, T. Jr.; Harvey, P. H.; Ives, A. R. (1992). <a href="http://biology.ucr.edu/people/faculty/Garland/GarlEA92.pdf">"Procedures for the analysis of comparative data using phylogenetically independent contrasts"</a> (PDF). <i>Systematic Biology</i>. 41 (1): 18–32. <a href="/facts/Doi_(identifier)/muM9Etpq">doi</a>:<a href="https://doi.org/10.2307%2F2992503">10.2307/2992503</a>. <a href="/facts/JSTOR_(identifier)/YTeVmaJ7">JSTOR</a> <a href="https://www.jstor.org/stable/2992503">2992503</a>.</li> <li>Gittleman, J. L.; Kot, M. (1990). "Adaptation: statistics and a null model for estimating phylogenetic effects". <i>Systematic Zoology</i>. 39 (3): 227–241. <a href="/facts/Doi_(identifier)/muM9Etpq">doi</a>:<a href="https://doi.org/10.2307%2F2992183">10.2307/2992183</a>. <a href="/facts/JSTOR_(identifier)/YTeVmaJ7">JSTOR</a> <a href="https://www.jstor.org/stable/2992183">2992183</a>.</li> <li>Hadfield, J. D; Nakagawa, S. (2010). <a href="https://doi.org/10.1111%2Fj.1420-9101.2009.01915.x">"General quantitative genetic methods for comparative biology: phylogenies, taxonomies and multi-trait models for continuous and categorical characters"</a>. <i>Journal of Evolutionary Biology</i>. 23 (3): 494–508. <a href="/facts/Doi_(identifier)/muM9Etpq">doi</a>:<a href="https://doi.org/10.1111%2Fj.1420-9101.2009.01915.x">10.1111/j.1420-9101.2009.01915.x</a>. <a href="/facts/PMID_(identifier)/JlHAvMHt">PMID</a> <a href="https://pubmed.ncbi.nlm.nih.gov/20070460">20070460</a>. <a href="/facts/S2CID_(identifier)/ldJsHa2Y">S2CID</a> <a href="https://api.semanticscholar.org/CorpusID:27706318">27706318</a>.</li> <li>Herrada, E. A.; Tessone, C. J.; Klemm, K.; Eguiluz, V. M.; Hernandez-Garcia, E.; Duarte, C. M. (2008). <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447175">"Universal Scaling in the Branching of the Tree of Life"</a>. <i>PLOS ONE</i>. 3 (7): e2757. <a href="/facts/ArXiv_(identifier)/H6EtgnBe">arXiv</a>:<a href="https://arxiv.org/abs/0807.4042">0807.4042</a>. <a href="/facts/Bibcode_(identifier)/9HtdQSGB">Bibcode</a>:<a href="https://ui.adsabs.harvard.edu/abs/2008PLoSO...3.2757H">2008PLoSO...3.2757H</a>. <a href="/facts/Doi_(identifier)/muM9Etpq">doi</a>:<a href="https://doi.org/10.1371%2Fjournal.pone.0002757">10.1371/journal.pone.0002757</a>. <a href="/facts/PMC_(identifier)/dX1zMt71">PMC</a> <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447175">2447175</a>. <a href="/facts/PMID_(identifier)/JlHAvMHt">PMID</a> <a href="https://pubmed.ncbi.nlm.nih.gov/18648500">18648500</a>. <a href="/facts/Open_access/r7rLYN6C"></a></li> <li>Housworth, E. A.; Martins, E. P.; Lynch, M. (2004). <a href="http://www.indiana.edu/~martinsl/pub/PMM.pdf">"The phylogenetic mixed model"</a> (PDF). <i>American Naturalist</i>. 163 (1): 84–96. <a href="/facts/Doi_(identifier)/muM9Etpq">doi</a>:<a href="https://doi.org/10.1086%2F380570">10.1086/380570</a>. <a href="/facts/PMID_(identifier)/JlHAvMHt">PMID</a> <a href="https://pubmed.ncbi.nlm.nih.gov/14767838">14767838</a>. <a href="/facts/S2CID_(identifier)/ldJsHa2Y">S2CID</a> <a href="https://api.semanticscholar.org/CorpusID:10568814">10568814</a>.</li> <li>Ives, A. R. 2018. Mixed and phylogenetic models: a conceptual introduction to correlated data. leanpub.com, 125 pp., <a href="https://leanpub.com/correlateddata">https://leanpub.com/correlateddata</a></li> <li>Ives, A. R.; Midford, P. E.; Garland, T. Jr. (2007). <a href="https://doi.org/10.1080%2F10635150701313830">"Within-species variation and measurement error in phylogenetic comparative methods"</a>. <i>Systematic Biology</i>. 56 (2): 252–270. <a href="/facts/Doi_(identifier)/muM9Etpq">doi</a>:<a href="https://doi.org/10.1080%2F10635150701313830">10.1080/10635150701313830</a>. <a href="/facts/PMID_(identifier)/JlHAvMHt">PMID</a> <a href="https://pubmed.ncbi.nlm.nih.gov/17464881">17464881</a>.</li> <li>Maddison, D. R. (1994). "Phylogenetic methods for inferring the evolutionary history and process of change in discretely valued characters". <i>Annual Review of Entomology</i>. 39: 267–292. <a href="/facts/Doi_(identifier)/muM9Etpq">doi</a>:<a href="https://doi.org/10.1146%2Fannurev.ento.39.1.267">10.1146/annurev.ento.39.1.267</a>.</li> <li>Maddison, W. P. (1990). 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"Phylogenies and the comparative method: a general approach to incorporating phylogenetic information into the analysis of interspecific data". <i>American Naturalist</i>. 149 (4): 646–667. <a href="/facts/Doi_(identifier)/muM9Etpq">doi</a>:<a href="https://doi.org/10.1086%2F286013">10.1086/286013</a>. <a href="/facts/S2CID_(identifier)/ldJsHa2Y">S2CID</a> <a href="https://api.semanticscholar.org/CorpusID:29362369">29362369</a>. Erratum Am. Nat. 153:448.</li> <li>Nunn, C. L.; Barton, R. A. (2001). <a href="https://doi.org/10.1002%2Fevan.1019">"Comparative methods for studying primate adaptation and allometry"</a>. <i>Evolutionary Anthropology</i>. 10 (3): 81–98. <a href="/facts/Doi_(identifier)/muM9Etpq">doi</a>:<a href="https://doi.org/10.1002%2Fevan.1019">10.1002/evan.1019</a>. <a href="/facts/S2CID_(identifier)/ldJsHa2Y">S2CID</a> <a href="https://api.semanticscholar.org/CorpusID:16959643">16959643</a>.</li> <li>Oakley, T. H.; Gu, Z.; Abouheif, E.; Patel, N. H.; Li, W.-H. 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"Evolutionary relationships between body shape and habitat use in lacertid lizards". <i>Evolutionary Ecology Research</i>. 1: 785–805.</li></ul> <h2 id="external-links">External links</h2> <ul><li><a href="http://idea.ucr.edu/documents/flash/adaptation_and_the_comparative_method_1/story.htm">Adaptation and the comparative method online lecture, with worked example of phylogenetically independent contrasts and mastery quiz</a></li> <li><a href="http://evolution.genetics.washington.edu/phylip/software.html">List of phylogeny programs</a></li> <li><a href="https://web.archive.org/web/20020706093004/http://www.phylodiversity.net/phylocom/">Phylocomm</a>[<i>usurped</i>]</li> <li><a href="http://blog.phytools.org/">Phylogenetic Tools for Comparative Biology</a></li> <li><a href="http://www.bu.edu/phylogeny/">Phylogeny of Sleep website</a></li> <li><a href="http://tolweb.org/tree/">Tree of Life</a></li></ul> <h3>Journals</h3> <ul><li><a href="http://www.journals.uchicago.edu/AN/">American Naturalist</a></li> <li><a href="https://web.archive.org/web/20050630025024/http://beheco.oxfordjournals.org/">Behavioral Ecology</a></li> <li><a href="http://esapubs.org/esapubs/journals/ecology.htm">Ecology</a></li> <li><a href="https://web.archive.org/web/20120905123820/http://www.blackwellpublishing.com/journal.asp?ref=0014-3820&site=1">Evolution</a></li> <li><a href="https://web.archive.org/web/20041206154841/http://evolutionary-ecology.com/">Evolutionary Ecology Research</a></li> <li><a href="https://web.archive.org/web/20120905123910/http://www.blackwellpublishing.com/journal.asp?ref=0269-8463&site=1">Functional Ecology</a></li> <li><a href="https://web.archive.org/web/20081007020934/http://www.blackwellpublishing.com/journal.asp?ref=1010-061X&site=1">Journal of Evolutionary Biology</a></li> <li><a href="https://web.archive.org/web/20070609124819/http://www.pubs.royalsoc.ac.uk/index.cfm?page=1085">Philosophical Transactions of the Royal Society of London B</a></li> <li><a href="http://www.journals.uchicago.edu/PBZ/home.html">Physiological and Biochemical Zoology</a></li> <li><a href="http://systbiol.org/">Systematic Biology</a></li></ul> <h3>Software packages (incomplete list)</h3> <ul><li><a href="http://ape-package.ird.fr/">Analyses of Phylogenetics and Evolution</a></li> <li><a href="http://www.evolution.rdg.ac.uk/BayesTraits.html">BayesTraits</a></li> <li><a href="http://www.bio.ic.ac.uk/evolve/software/caic/">Comparative Analysis by Independent Contrasts</a></li> <li><a href="http://www.indiana.edu/~martinsl/compare/">COMPARE</a></li> <li><a href="http://evolution.genetics.washington.edu/phylip/software.html">Felsenstein's List</a></li> <li><a href="https://web.archive.org/web/20140531065423/http://mesquiteproject.org/mesquite/download/download.html">Mesquite</a> <a href="http://mesquiteproject.org/pdap_mesquite/index.html">PDAP:PDTree for Mesquite</a></li> <li><a href="https://cran.r-project.org/web/packages/mvMORPH/">mvMorph</a></li> <li><a href="https://kingaa.github.io/ouch/">ouch: Ornstein-Uhlenbeck for Comparative Hypotheses</a></li> <li><a href="http://biology.ucr.edu/people/faculty/Garland/PDAP.html">PDAP: Phenotypic Diversity Analysis Programs</a></li> <li><a href="https://web.archive.org/web/20020706093004/http://www.phylodiversity.net/phylocom/">Phylocom</a>[<i>usurped</i>]</li> <li><a href="http://users.ox.ac.uk/~grafen/phylo/index.html">Phylogenetic Regression</a></li> <li><a href="http://biology.ucr.edu/people/faculty/Garland/PHYSIG.html">PHYSIG</a></li></ul> <h3>Laboratories</h3> <ul><li><a href="http://ib.berkeley.edu/labs/ackerly/">Ackerly</a></li> <li><a href="https://web.archive.org/web/20080604125526/http://www.personal.uni-jena.de/~b6biol2/">Bininda-Emonds</a></li> <li><a href="http://www.evolutionarystatistics.org/">Blomberg</a></li> <li><a href="http://www2.hawaii.edu/~mbutler/">Butler</a></li> <li><a href="http://www.biology.washington.edu/index.html?navID=42&parecID=106">Felsenstein</a></li> <li><a href="https://web.archive.org/web/20110606180504/http://www.shef.ac.uk/aps/staff/acadstaff/freckleton.html">Freckleton</a></li> <li><a href="http://biology.ucr.edu/people/faculty/Garland.html">Garland</a></li> <li><a href="http://www.virginia.edu/biology/Fac/Gittleman.html">Gittleman</a></li> <li><a href="http://users.ox.ac.uk/~grafen/">Grafen</a></li> <li><a href="http://www.cees.no/?option=com_staff&person=thomasha">Hansen</a></li> <li><a href="http://www.webpages.uidaho.edu/~lukeh/">Harmon</a></li> <li><a href="https://web.archive.org/web/20110927224434/http://evolve.zoo.ox.ac.uk/people.html?id=harveyp">Harvey</a></li> <li><a href="http://mypage.iu.edu/~ehouswor/">Housworth</a></li> <li><a href="http://www.bio.umass.edu/biology/irschick/irschickcv.html">Irschick</a></li> <li><a href="https://ives.labs.wisc.edu">Ives</a></li> <li><a href="http://www.oeb.harvard.edu/faculty/losos/">Losos</a></li> <li><a href="https://web.archive.org/web/20100102155539/http://www.bio.indiana.edu/facultyresearch/faculty/Martins.html">Martins</a></li> <li><a href="https://www.sfu.ca/~amooers/index.html">Mooers</a></li> <li><a href="http://www2.ku.edu/~eeb/faculty/mort.shtml">Mort</a></li> <li><a href="https://web.archive.org/web/20100916221703/http://www.eva.mpg.de/primat/staff/charles_nunn/">Nunn</a></li> <li><a href="http://www.lifesci.ucsb.edu/eemb/labs/oakley/">Oakley</a></li> <li><a href="https://web.archive.org/web/20180715223255/http://taxonomy.zoology.gla.ac.uk/rod/rod.html">Page</a></li> <li><a href="http://www.evolution.rdg.ac.uk/index.html">Pagel</a></li> <li><a href="http://ape-package.ird.fr/ep/">Paradis</a></li> <li><a href="http://www.bio.ic.ac.uk/research/apurvis/ajpurvis.htm">Purvis</a></li> <li><a href="http://tree.bio.ed.ac.uk/">Rambaut</a></li> <li><a href="http://life.bio.sunysb.edu/ee/rohlf/">Rohlf</a></li> <li><a href="https://web.archive.org/web/20070204124825/http://ginger.ucdavis.edu/">Sanderson</a></li></ul> <h2 id="references">References</h2> <ol> <li id="fn:1"><p>Felsenstein, Joseph (January 1985). 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