Phylogenetic informativeness reconciles ray-finned fish molecular divergence times.
Phylogenetic informativeness reconciles ray-finned fish molecular divergence times.
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DOI：
10.1186/s12862-014-0169-0
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发表时间：
2014-08-08
影响因子：
3.4
通讯作者：
Near TJ
中科院分区：
文献类型：
--
作者：
Dornburg A;Townsend JP;Friedman M;Near TJ
在生命之树的许多分支中，观察到了个体分子年龄估计值之间的不一致，或者分子年龄估计值与化石记录之间的不一致。这种不一致性归因于多种变量，包括校准年龄不确定性、校准位置、核苷酸取代率异质性或指定的分子钟模型。然而，随着时间的推移，单个基因的系统发育信息的变化对系统发育推断的影响很少分析。使用核和线粒体序列数据的射线鳍鱼（Actinoparti）为例，我们扩展了系统发育信息配置文件的效用，以预测核苷酸取代饱和的时间间隔时，在分子年龄估计之间的不一致。我们证明，即使有相同的校准制度和分子钟方法，线粒体的分子年龄估计系统的年龄比从核序列估计。这种不一致对于对应于较新的（即，侏罗纪-最近）分歧。通过删除被认为饱和的数据，我们调和了相互竞争的年龄估计，并强调了基于mtDNA的年龄是由核苷酸饱和度驱动的。DNA序列比对中的同源位点模式可以系统地偏置分子趋异时间估计。我们的研究表明，PI配置文件可以提供一个非任意的数据排除标准，以减轻时间校准的分支长度估计的同质性的影响。分析actinopterygian分子钟表明，详细审查的时间尺度上的序列数据是翔实的是一个基本的，但通常被忽视，在分子分歧时间估计的步骤。
Discordance among individual molecular age estimates, or between molecular age estimates and the fossil record, is observed in many clades across the Tree of Life. This discordance is attributed to a variety of variables including calibration age uncertainty, calibration placement, nucleotide substitution rate heterogeneity, or the specified molecular clock model. However, the impact of changes in phylogenetic informativeness of individual genes over time on phylogenetic inferences is rarely analyzed. Using nuclear and mitochondrial sequence data for ray-finned fishes (Actinopterygii) as an example, we extend the utility of phylogenetic informativeness profiles to predict the time intervals when nucleotide substitution saturation results in discordance among molecular ages estimated. We demonstrate that even with identical calibration regimes and molecular clock methods, mitochondrial based molecular age estimates are systematically older than those estimated from nuclear sequences. This discordance is most severe for highly nested nodes corresponding to more recent (i.e., Jurassic-Recent) divergences. By removing data deemed saturated, we reconcile the competing age estimates and highlight that the older mtDNA based ages were driven by nucleotide saturation. Homoplasious site patterns in a DNA sequence alignment can systematically bias molecular divergence time estimates. Our study demonstrates that PI profiles can provide a non-arbitrary criterion for data exclusion to mitigate the influence of homoplasy on time calibrated branch length estimates. Analyses of actinopterygian molecular clocks demonstrate that scrutiny of the time scale on which sequence data is informative is a fundamental, but generally overlooked, step in molecular divergence time estimation.
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系统基因分析支持海龟作为姊妹鸟类和鳄鱼（Archosauria）的位置。
影响因子：
5.4
作者：
Chiari Y;Cahais V;Galtier N;Delsuc F
通讯作者：
Delsuc F
影响因子：
6.5
作者：
Dornburg, Alex;Beaulieu, Jeremy M.;Near, Thomas J.
通讯作者：
Near, Thomas J.
影响因子：
3.3
作者：
Dornburg, Alex;Sidlauskas, Brian;Alfaro, Michael E.
通讯作者：
Alfaro, Michael E.
DOI：
10.1371/currents.tol.53ba26640df0ccaee75bb165c8c26288
发表时间：
2013-01-01
期刊：
PLOS CURRENTS-TREE OF LIFE
影响因子：
--
作者：
Betancur-R, Ricardo;Broughton, Richard E.;Orti, Guillermo
通讯作者：
Orti, Guillermo
影响因子：
10.7
作者：
Blouin, MS;Yowell, CA;Dame, JB
通讯作者：
Dame, JB