THE IMPACT OF GENE-TREE/SPECIES-TREE DISCORDANCE ON DIVERSIFICATION-RATE ESTIMATION
THE IMPACT OF GENE-TREE/SPECIES-TREE DISCORDANCE ON DIVERSIFICATION-RATE ESTIMATION
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DOI：
10.1111/j.1558-5646.2011.01260.x
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发表时间：
2011-07-01
期刊：
影响因子：
3.3
通讯作者：
Pyron, R. Alexander
中科院分区：
文献类型：
--
作者：
Burbrink, Frank T.;Pyron, R. Alexander
分子生物学经常被用来检验关于物种形成和灭绝的克里思和模式的假设。一个常用的统计量是Pybus和Harvey's gamma，它测量超度量树上有序的节间距离的密度，以推断更早（负gamma）或更晚（正gamma）的多样化爆发。然而，结合理论预测，伽玛可能偏向负值（推断早期爆发的多样化）时，使用基因树，而不是物种树。基因分歧早于物种分歧，在更高的有效种群规模（N-e）中越来越明显，并且在树的顶端比例更大。因此，基因树在许多情况下（特别是在较高的N-e下）会有更高密度的老节点，这是由于末端分支的不成比例的延长。这将在估算时产生一个人为的早期多样化爆发的特征。基因树。我们模拟基因树的物种树下的圣诞节（纯出生）和出生-死亡过程，并证明这些预测的支持。然而，对于自然种群中最现实的θ估计，基因树提供了相对较好的γ估计，尽管年轻节点年龄的不成比例的高估。这与北美栅栏蜥蜴（Sceloporus）的经验数据集相印证。
Molecular phylogenies are often used to test hypotheses about the tempo and mode of speciation and extinction. One commonly used statistic is Pybus and Harvey's gamma, which measures the density of ordered internode distances on an ultrametric tree to infer earlier (negative gamma) or later (positive gamma) bursts of diversification. However, coalescent theory predicts that gamma might be biased toward negative values (inferring early bursts of diversification) when using gene trees rather than species trees. Gene divergences predate species divergences, increasingly so at higher effective population sizes (N-e), and proportionally more so toward the tips of the tree. Thus, gene trees will have a higher density of older nodes inmany cases (particularly at higher N-e), due to the disproportionate lengthening of terminal branches. This will yield an artifactual signature of early bursts of diversification when estimating. from gene trees. We simulate gene trees within species trees under both Yule (pure-birth) and birth-death processes, and demonstrate support for these predictions. However, for most realistic estimates of theta in natural populations, gene trees provide relatively good estimates of gamma, despite the disproportionate overestimation of younger node ages. This is corroborated with an empirical dataset of North American fence lizards (Sceloporus).