The impact of rate heterogeneity on inference of phylogenetic models of trait evolution.
The impact of rate heterogeneity on inference of phylogenetic models of trait evolution.
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DOI：
10.1111/jeb.12979
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发表时间：
2016-12
影响因子：
2.1
通讯作者：
Thomas GH
中科院分区：
文献类型：
--
作者：
Chira AM;Thomas GH
众所周知，特征进化的速度在不同的系统发育中是不同的；然而，标准的进化模型假定特征变化的过程是相同的。这些简单的方法被广泛应用于小规模的系统发育研究，而速率异质性的模型则不是，因此在多达数百个物种的群体中的流行率和潜在的速率差异的模式仍然不清楚。性状进化在多大程度上准确地模拟了给定的系统发育，也在很大程度上是未知的，因为研究通常缺乏绝对的模型拟合检验。我们通过对(I)10-318个种的88个鸟类分支的体重数据和(Ii)在一系列速率异质性情景下模拟的数据应用速率静态和可变速率方法来研究这些问题。我们的结果表明，在小规模的鸟类分支中存在速率异质性，因此，只应用标准的单过程模型会提示对生成进化过程的不准确推断。具体地说，这些方法低估了比率变异，并系统性地错误地标记了性状进化的时间趋势。相反，可变利率方法具有优越的相对拟合度(它们是最佳模型)和绝对拟合度(它们很好地描述了数据)。我们发现，即使在可变速率模型中，诸如单个内部分支变化、速率降低和早期突发之类的速率变化也很难检测到。我们还使用最近开发的绝对充分性测试来强调仅基于相对匹配的误导性结论(例如，当存在孤立的终端分支速率增加时，一致倾向于受限进化)。这项工作突出了在与绝对模型匹配测试相结合的情况下，对特征进化进行稳健推断的潜力。
Rates of trait evolution are known to vary across phylogenies; however, standard evolutionary models assume a homogeneous process of trait change. These simple methods are widely applied in small‐scale phylogenetic studies, whereas models of rate heterogeneity are not, so the prevalence and patterns of potential rate variation in groups up to hundreds of species remain unclear. The extent to which trait evolution is modelled accurately on a given phylogeny is also largely unknown because studies typically lack absolute model fit tests. We investigated these issues by applying both rate‐static and variable‐rates methods on (i) body mass data for 88 avian clades of 10–318 species, and (ii) data simulated under a range of rate‐heterogeneity scenarios. Our results show that rate heterogeneity is present across small‐scaled avian clades, and consequently applying only standard single‐process models prompts inaccurate inferences about the generating evolutionary process. Specifically, these approaches underestimate rate variation, and systematically mislabel temporal trends in trait evolution. Conversely, variable‐rates approaches have superior relative fit (they are the best model) and absolute fit (they describe the data well). We show that rate changes such as single internal branch variations, rate decreases and early bursts are hard to detect, even by variable‐rates models. We also use recently developed absolute adequacy tests to highlight misleading conclusions based on relative fit alone (e.g. a consistent preference for constrained evolution when isolated terminal branch rate increases are present). This work highlights the potential for robust inferences about trait evolution when fitting flexible models in conjunction with tests for absolute model fit.
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DOI：
10.1126/science.1253451
发表时间：
2014-12-12
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Jarvis ED;Mirarab S;Aberer AJ;Li B;Houde P;Li C;Ho SY;Faircloth BC;Nabholz B;Howard JT;Suh A;Weber CC;da Fonseca RR;Li J;Zhang F;Li H;Zhou L;Narula N;Liu L;Ganapathy G;Boussau B;Bayzid MS;Zavidovych V;Subramanian S;Gabaldón T;Capella-Gutiérrez S;Huerta-Cepas J;Rekepalli B;Munch K;Schierup M;Lindow B;Warren WC;Ray D;Green RE;Bruford MW;Zhan X;Dixon A;Li S;Li N;Huang Y;Derryberry EP;Bertelsen MF;Sheldon FH;Brumfield RT;Mello CV;Lovell PV;Wirthlin M;Schneider MP;Prosdocimi F;Samaniego JA;Vargas Velazquez AM;Alfaro-Núñez A;Campos PF;Petersen B;Sicheritz-Ponten T;Pas A;Bailey T;Scofield P;Bunce M;Lambert DM;Zhou Q;Perelman P;Driskell AC;Shapiro B;Xiong Z;Zeng Y;Liu S;Li Z;Liu B;Wu K;Xiao J;Yinqi X;Zheng Q;Zhang Y;Yang H;Wang J;Smeds L;Rheindt FE;Braun M;Fjeldsa J;Orlando L;Barker FK;Jønsson KA;Johnson W;Koepfli KP;O'Brien S;Haussler D;Ryder OA;Rahbek C;Willerslev E;Graves GR;Glenn TC;McCormack J;Burt D;Ellegren H;Alström P;Edwards SV;Stamatakis A;Mindell DP;Cracraft J;Braun EL;Warnow T;Jun W;Gilbert MT;Zhang G
通讯作者：
Zhang G
影响因子：
2.9
作者：
Butler, MA;King, AA
通讯作者：
King, AA
影响因子：
3.3
作者：
Eastman, Jonathan M.;Alfaro, Michael E.;Harmon, Luke J.
通讯作者：
Harmon, Luke J.
影响因子：
1.9
作者：
Alhajeri, Bader H.;Schenk, John J.;Steppan, Scott J.
通讯作者：
Steppan, Scott J.
影响因子：
3.3
作者：
Martin, Paul R.;Montgomerie, Robert;Lougheed, Stephen C.
通讯作者：
Lougheed, Stephen C.