Gene trees in species trees
Gene trees in species trees
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DOI：
10.1093/sysbio/46.3.523
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发表时间：
1997-09-01
影响因子：
6.5
通讯作者：
Maddison, WP
中科院分区：
文献类型：
--
作者：
Maddison, WP
对基因树及其包含的物种树之间关系的探索导致了对如何从基因树重建物种树以及作为基因历史云的系统发育概念的考虑。当从不同物种中采集基因拷贝时，与这些拷贝相关的基因树可能与物种系统发育不一致。这种不一致可能是由水平转移（包括杂交）、谱系分类以及基因复制和灭绝引起的。谱系排序也可以称为深度合并，即祖先副本未能合并（向后看时间）成一个共同的祖先副本，直到比之前的物种形成事件更深。这些事件取决于多种因素；例如，如果物种树的分支短（以世代为单位）且宽（以种群规模为单位），则更有可能进行深度合并。在历史生物地理学和宿主-寄生虫关系中也发现了类似的过程依赖性。每个不和谐的过程都可以产生不同的简约标准，用于从一组基因树重建物种树：通过水平转移，选择最小化转移事件数量的物种树；通过深度合并，选择树以最大限度地减少必须沿着物种谱系共存的额外基因谱系的数量；通过基因复制，选择最小化复制和/或灭绝事件的树。用于重建物种树的最大似然方法也是可能的，因为合并理论提供了给定物种树（指定分支长度和宽度）时出现特定基因树的概率。在考虑这些问题时，人们不禁重新思考什么是系统发育。也许将某些基因树视为与物种树一致而将其他基因树视为不同意是一种误导。相反，所有基因树都是物种树的一部分，可以将其可视化为模糊统计分布，即基因历史云。或者，系统发育可能（并且一直）被视为遗传上发生的事情的历史，而是可能发生的事情的历史，即杂交概率变化的历史。
Exploration of the relationship between gene trees and their containing species trees leads to consideration of how to reconstruct species trees from gene trees and of the concept of phylogeny as a cloud of gene histories. When gene copies are sampled from various species, the gene tree relating these copies might disagree with the species phylogeny. This discord can arise from horizontal transfer (including hybridization), lineage sorting, and gene duplication and extinction. Lineage sorting could also be called deep coalescence, the failure of ancestral copies to coalesce (looking backwards in time) into a common ancestral copy until deeper than previous speciation events. These events depend on various factors; for instance, deep coalescence is more likely if the branches of the species tree are short (in generations) and wide (in population size). A similar dependence on process is found in historical biogeography and host-parasite relationships. Each of the processes of discord could yield a different parsimony criterion for reconstructing the species tree from a set of gene trees: with horizontal transfer, choose the species tree that minimizes the number of transfer events; with deep coalescence, choose the tree minimizing the number of extra gene lineages that had to coexist along species lineages; with gene duplication, choose the tree minimizing duplication and/or extinction events. Maximum likelihood methods for reconstructing the species tree are also possible because coalescence theory provides the probability that a particular gene tree would occur given a species tree (with branch lengths and widths specified). In considering these issues, one is provoked to reconsider precisely what is phylogeny. Perhaps it is misleading to view some gene trees as agreeing and other gene trees as disagreeing with the species tree; rather, all of the gene trees are part of the species tree, which can be visualized like a fuzzy statistical distribution, a cloud of gene histories. Alternatively phylogeny might be (and has been) viewed not as a history of what happened, genetically, but as a history of what could have happened, i.e., a history of changes in the probabilities of interbreeding.