Estimating the tempo and mode of gene family evolution from comparative genomic data
Estimating the tempo and mode of gene family evolution from comparative genomic data
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DOI：
10.1101/gr.3567505
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发表时间：
2005-08-01
期刊：
影响因子：
7
通讯作者：
Cristianini, N
中科院分区：
文献类型：
--
作者：
Hahn, MW;De Bie, T;Cristianini, N
全基因组的比较表明，生物间基因家族大小的变化十分普遍。然而，目前还没有基因家族进化的模型能够估计祖先状态，或推断基因家族在哪些谱系中发生了收缩或扩张。此外，基因家族大小的巨大差异通常被归因于自然选择的作用，但这些结论并没有强有力的统计依据。在此，我们使用一个基因家族进化的随机出生和死亡模型，并表明它可以有效地应用于多物种基因组比较。该模型考虑了系统发育树的分支长度以及复制和缺失率，从而为谱系间基因家族大小的差异提供了预期。这个模型既提供了识别基因组进化大规模模式的机会，也提供了对自然选择在基因家族扩张或收缩中所起作用进行更有力推断的能力。我们将我们的方法应用于五个酵母物种的基因组数据，以证明其适用性。
Comparison of whole genomes has revealed that changes in the size of gene families among organisms is quite common. However, there are as yet no models of gene family evolution that make it possible to estimate ancestral states or to infer upon which lineages gene families have contracted or expanded. In addition, large differences in family size have generally been attributed to the effects of natural selection, without a strong statistical basis for these conclusions. Here we use a model of stochastic birth and death for gene family evolution and show that it can be efficiently applied to multispecies genome comparisons. This model takes into account the lengths of branches on phylogenetic trees, as well as duplication and deletion rates, and hence provides expectations for divergence in gene family size among lineages. The model offers both the opportunity to identify large-scale patterns in genome evolution and the ability to make stronger inferences regarding the role of natural selection in gene family expansion or contraction. We apply our method to data from the genomes of five yeast species to show its applicability.