Widespread discordance of gene trees with species tree in Drosophila: evidence for incomplete lineage sorting.
Widespread discordance of gene trees with species tree in Drosophila: evidence for incomplete lineage sorting.
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DOI：
10.1371/journal.pgen.0020173
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发表时间：
2006-10-27
期刊：
影响因子：
4.5
通讯作者：
Eisen MB
中科院分区：
文献类型：
--
作者：
Pollard DA;Iyer VN;Moses AM;Eisen MB
现已完全测序的果蝇物种和 D. yakuba 物种与黑腹果蝇物种复合体的系统发育关系一直是一个有争议的话题。过去曾报道过该物种的所有三种可能的分组，但最近的多基因研究表明 D.ectera 和 D.yakuba 是姐妹物种。利用这些物种以及槐亚属中其他四个已完全测序的物种的整个基因组，我们开始研究直立果蝇和黑腹果蝇在黑腹果蝇物种组中的位置，并了解过去不一致的原因。尽管我们发现将直立石竹和雅库巴石竹分类在一起的系统发育得到了最好的支持，但我们也发现核苷酸和氨基酸取代、插入和缺失以及基因树方面存在广泛的不一致。推断跨越两个关键物种形成事件的时间足够短，因此在合并模型下，不一致可能是谱系排序不完整的结果。与谱系排序假说一致，支持同一棵树的替代在空间上聚集。发现对不同树的支持与重组有关，使得相邻基因最常在低重组区域支持同一棵树，并且支持同一棵树的替代在与连锁不平衡大致相同的规模上最富集，也与谱系排序一致。发现这种不一致具有统计显着性，并且对于模型和物种选择而言是稳健的。没有发现系统性偏差。我们得出的结论是，黑腹果蝇物种复合体中的系统发育不一致是（至少部分）不完整的谱系排序的结果。不完整的谱系排序可能会导致许多比较基因组学数据集中的系统发育不一致。推断正确物种树的方法、基因组中每个碱基的历史以及控制和/或利用这些信息的比较方法将是比较基因组学领域的宝贵进步。为了充分利用来自不同生物体的不断增长的基因组序列，有必要了解生物体之间的进化关系（系统发育）。不幸的是，从单个基因推断出的系统发育经常发生冲突，要么反映了糟糕的推论，要么反映了基因历史中的真实变异。在这项研究中，作者研究了果蝇物种亚群内的关系，该亚群是一个拥有三个完全测序物种的果蝇群体，其中系统发育一直是争议的根源。尽管大量数据支持黑腹果蝇作为姐妹物种直立果蝇和雅库巴果蝇的外类群的系统发育，但它们的大部分基因支持其他系统发育。这组作者认为，对这些观察结果最合理的解释是，在导致这些物种产生的两次快速物种形成事件期间，祖先种群的多态性得以维持。在物种形成之后，多态性在每个物种中被随机固定，在某些情况下，非姐妹物种固定了相同的祖先多态性，而姐妹物种则没有。在这些情况下，基因被正确推断为具有冲突的系统发育。作者指出，快速的物种形成事件通常会导致这种冲突，这需要在进化分析中加以考虑。
The phylogenetic relationship of the now fully sequenced species Drosophila erecta and D. yakuba with respect to the D. melanogaster species complex has been a subject of controversy. All three possible groupings of the species have been reported in the past, though recent multi-gene studies suggest that D. erecta and D. yakuba are sister species. Using the whole genomes of each of these species as well as the four other fully sequenced species in the subgenus Sophophora, we set out to investigate the placement of D. erecta and D. yakuba in the D. melanogaster species group and to understand the cause of the past incongruence. Though we find that the phylogeny grouping D. erecta and D. yakuba together is the best supported, we also find widespread incongruence in nucleotide and amino acid substitutions, insertions and deletions, and gene trees. The time inferred to span the two key speciation events is short enough that under the coalescent model, the incongruence could be the result of incomplete lineage sorting. Consistent with the lineage-sorting hypothesis, substitutions supporting the same tree were spatially clustered. Support for the different trees was found to be linked to recombination such that adjacent genes support the same tree most often in regions of low recombination and substitutions supporting the same tree are most enriched roughly on the same scale as linkage disequilibrium, also consistent with lineage sorting. The incongruence was found to be statistically significant and robust to model and species choice. No systematic biases were found. We conclude that phylogenetic incongruence in the D. melanogaster species complex is the result, at least in part, of incomplete lineage sorting. Incomplete lineage sorting will likely cause phylogenetic incongruence in many comparative genomics datasets. Methods to infer the correct species tree, the history of every base in the genome, and comparative methods that control for and/or utilize this information will be valuable advancements for the field of comparative genomics. To take full advantage of the growing number of genome sequences from different organisms, it is necessary to understand the evolutionary relationships (phylogeny) between organisms. Unfortunately, phylogenies inferred from individual genes often conflict, reflecting either poor inferences or real variation in the history of genes. In this study, the authors examine relationships within the Drosophila melanogaster species subgroup, a group of flies with three fully sequenced species in which phylogeny has been a source of controversy. Although the bulk of the data support a phylogeny with Drosophila melanogaster as an outgroup to sister species Drosophila erecta and Drosophila yakuba, large portions of their genes support alternative phylogenies. According to the authors, the most plausible explanation for these observations is that polymorphisms in the ancestral population were maintained during the two rapid speciation events that led to these species. Subsequent to speciation, polymorphisms were randomly fixed in each species, and in some cases non-sister species fixed the same ancestral polymorphisms, while sister species did not. In these cases the genes are correctly inferred to have conflicting phylogenies. The authors note that rapid speciation events will often lead to such conflict, which needs to be accounted for in evolutionary analyses.
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影响因子：
7
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