Birth-death models and coalescent point processes: The shape and probability of reconstructed phylogenies
Birth-death models and coalescent point processes: The shape and probability of reconstructed phylogenies
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DOI：
10.1016/j.tpb.2013.10.002
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发表时间：
2013-12-01
影响因子：
1.4
通讯作者：
Stadler, Tanja
中科院分区：
文献类型：
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作者：
Lambert, Amaury;Stadler, Tanja
多元化的时间前瞻模型（即，物种形成和灭绝）产生随着时间推移“垂直”生长的系统发育树。从这样的树中修剪灭绝的谱系导致重建树的自然模型（即，现存物种的进化）。或者，重建的树木可以通过聚结点过程（CPP）来建模，其中树木通过顺序添加垂直边缘来“水平”生长。每个新的边缘开始于某个随机的物种形成时间，并在当前时间结束;物种形成时间独立地来自同一分布。CPP导致非常快速的树似然计算和重建树的模拟。它们的拓扑结构总是遵循均匀分布的排序树形状（URT）。我们刻画了哪些时间向前模型导致URT重建树，以及在这些模型中，哪些导致CPP重建树。我们表明，对于任何“不对称”多样化模型，其中物种形成率仅取决于时间，灭绝率仅取决于时间和非遗传性状（例如，年龄），重建的树是CPP，即使现存物种不完全采样。如果利率还取决于物种的数量，重建的树是（只有）URT（但不是CPP）。我们刻画了CPP描述中常见的物种形成时间分布，并详细讨论了不完全物种采样以及三种特殊的模型情况：（1）灭绝率不依赖于性状;（2）灭绝率不依赖于时间;（3）大规模灭绝可能在过去的某些点额外发生。(c)2013 Elsevier Inc. All rights reserved.
Forward-in-time models of diversification (i.e., speciation and extinction) produce phylogenetic trees that grow "vertically" as time goes by. Pruning the extinct lineages out of such trees leads to natural models for reconstructed trees (i.e., phylogenies of extant species). Alternatively, reconstructed trees can be modelled by coalescent point processes (CPPs), where trees grow "horizontally" by the sequential addition of vertical edges. Each new edge starts at some random speciation time and ends at the present time; speciation times are drawn from the same distribution independently. CPPs lead to extremely fast computation of tree likelihoods and simulation of reconstructed trees. Their topology always follows the uniform distribution on ranked tree shapes (URT).We characterize which forward-in-time models lead to URT reconstructed trees and among these, which lead to CPP reconstructed trees. We show that for any "asymmetric" diversification model in which speciation rates only depend on time and extinction rates only depend on time and on a non-heritable trait (e.g., age), the reconstructed tree is CPP, even if extant species are incompletely sampled. If rates additionally depend on the number of species, the reconstructed tree is (only) URT (but not CPP). We characterize the common distribution of speciation times in the CPP description, and discuss incomplete species sampling as well as three special model cases in detail: (1) the extinction rate does not depend on a trait; (2) rates do not depend on time; (3) mass extinctions may happen additionally at certain points in the past. (c) 2013 Elsevier Inc. All rights reserved.