Fine-scale phylogenetic discordance across the house mouse genome.
Fine-scale phylogenetic discordance across the house mouse genome.
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DOI：
10.1371/journal.pgen.1000729
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发表时间：
2009-11
期刊：
影响因子：
4.5
通讯作者：
Payseur BA
中科院分区：
文献类型：
--
作者：
White MA;Ané C;Dewey CN;Larget BR;Payseur BA
群体遗传理论在研究新近分化的物种时，预测了不同基因组区域真实系统发育的不一致性。尽管有这样的期望，但在年轻物种群体中，全基因组的不一致性很少被统计量化。家鼠亚种组为检查系统发育不一致提供了一个模型系统。家鼠亚种是最近衍生出来的，这表明即使有一个简单的树状种群历史，由于不完整的谱系分类，基因树可能与种群历史不一致。家鼠的亚种在自然界中也会杂交，这增加了最近的基因渗入可能导致额外的系统发育不一致的可能性。单位点方法揭示了对相互冲突的拓扑结构的支持，导致亚种树通常被总结为一个多元结构。为了在基因组尺度上分析系统发育历史，我们应用了最近开发的一种方法，贝叶斯一致性分析，对家鼠三个密切相关的亚种：小家鼠（Mus musculus musus）、M. M. castaneus和M. M. domesticus的密集SNP数据进行了分析。我们在整个基因组中记录了系统发育历史的实质性变化。尽管这三种可能的拓扑结构都得到了大量基因座的有力支持，但有统计证据表明，m.m. musculus和m.m. castaneus在初级系统发育史上是姐妹亚种。这些结果强调了在其他最近分化的群体中使用贝叶斯一致性分析等方法测量系统发育不一致性的重要性，这些方法是为此目的而设计的。如果分类群是最近派生的，那么单个基因的系统发育历史可能与物种历史有很大的不同，这使得仅从少数基因推断物种历史在这些情况下特别困难。现在，基因组规模的数据集允许从大量基因中重建系统发育历史。尽管这种规模的数据集正变得越来越普遍，但很少有研究在整个基因组中描述系统发育历史的变化。我们使用一种结合基因树中系统发育不确定性的方法，总结了家鼠基因组中系统发育历史的细微变化，家鼠是最近衍生的一组亚种。我们在14,081个位点中记录了系统发育史上的实质性变化，并描述了面对这种变化的原始历史。这些结果支持使用基因组规模的数据集和方法，以适应系统发育不一致，试图重建密切相关群体的历史。
Population genetic theory predicts discordance in the true phylogeny of different genomic regions when studying recently diverged species. Despite this expectation, genome-wide discordance in young species groups has rarely been statistically quantified. The house mouse subspecies group provides a model system for examining phylogenetic discordance. House mouse subspecies are recently derived, suggesting that even if there has been a simple tree-like population history, gene trees could disagree with the population history due to incomplete lineage sorting. Subspecies of house mice also hybridize in nature, raising the possibility that recent introgression might lead to additional phylogenetic discordance. Single-locus approaches have revealed support for conflicting topologies, resulting in a subspecies tree often summarized as a polytomy. To analyze phylogenetic histories on a genomic scale, we applied a recently developed method, Bayesian concordance analysis, to dense SNP data from three closely related subspecies of house mice: Mus musculus musculus, M. m. castaneus, and M. m. domesticus. We documented substantial variation in phylogenetic history across the genome. Although each of the three possible topologies was strongly supported by a large number of loci, there was statistical evidence for a primary phylogenetic history in which M. m. musculus and M. m. castaneus are sister subspecies. These results underscore the importance of measuring phylogenetic discordance in other recently diverged groups using methods such as Bayesian concordance analysis, which are designed for this purpose. The phylogenetic history of individual genes can differ strongly from the species history if taxa are recently derived, making inferences of a species history from only a handful of genes especially difficult in these cases. Genome-scale data sets now allow phylogenetic histories to be reconstructed from a large number of genes. Although data sets of this size are becoming more common, few studies have characterized variation in phylogenetic history across whole genomes. We summarize fine scale variation in phylogenetic history across the genome of house mice, a recently derived group of subspecies, using a method that combines phylogenetic uncertainty among gene trees. We document substantial variation in phylogenetic history among 14,081 loci and describe a primary history in the face of this variation. These results support the use of genome-scale datasets and methods that accommodate phylogenetic discordance in attempts to reconstruct the history of closely related groups.
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影响因子：
10.7
作者：
Adkins, RM;Gelke, EL;Honeycutt, RL
通讯作者：
Honeycutt, RL
影响因子：
10.7
作者：
Burgess, Ralph;Yang, Ziheng
通讯作者：
Yang, Ziheng
影响因子：
9.8
作者：
Chen, FC;Li, WH
通讯作者：
Li, WH
DOI：
10.1111/j.1095-8312.2005.00446.x
发表时间：
2005-03-01
影响因子：
1.9
作者：
Dod, B;Smadja, C;Boursot, P
通讯作者：
Boursot, P
影响因子：
4.5
作者：
Degnan JH;Rosenberg NA
通讯作者：
Rosenberg NA