Gene trees in species trees
Gene trees in species trees
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DOI：
10.2307/2413694
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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的关系的探索导致了如何从基因树重建物种树的考虑，以及作为基因历史云的系统发育的概念。当从不同物种采集基因拷贝时，与这些拷贝相关的基因树可能与物种系统发育不一致。这种不和谐可能是由水平转移(包括杂交)、世系排序以及基因复制和灭绝引起的。世系分选也可以称为深度融合，指的是祖先的复制品在比之前的物种形成事件更深之前未能结合(回顾时间)成为一个共同的祖先复制品。这些事件取决于各种因素；例如，如果物种树的分枝短(以世代计)和宽(以种群规模计)，则更有可能发生深度合并。在历史生物地理学和宿主-寄生虫关系中也发现了对过程的类似依赖。每一种不和谐的过程都可能产生不同的简约标准来从一组基因树中重建物种树：对于水平转移，选择转移事件数量最小的物种树；对于深度结合，选择将必须与物种谱系共存的额外基因谱系数量最小化的树；对于基因复制，选择最小化重复和/或灭绝事件的树。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在给定物种树(指定分支长度和宽度)的情况下特定基因树出现的概率。在考虑这些问题时，人们会被激起重新思考到底什么是进化史。也许认为一些基因树与物种树一致，而另一些基因树与物种树不一致，这可能是误导；相反，所有的基因树都是物种树的一部分，这可以被可视化为模糊的统计分布，即基因历史的云。或者，系统发育学可能(也一直被)视为遗传上已发生的事情的历史，而是可能发生的事情的历史，即杂交繁殖概率的变化史。
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.