Unified modeling of gene duplication, loss, and coalescence using a locus tree
Unified modeling of gene duplication, loss, and coalescence using a locus tree
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DOI：
10.1101/gr.123901.111
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发表时间：
2012-04-01
期刊：
影响因子：
7
通讯作者：
Kellis, Manolis
中科院分区：
文献类型：
--
作者：
Rasmussen, Matthew D.;Kellis, Manolis
基因系统学为进化塑造基因组、种群和表型的方式提供了丰富的信息来源。除了替换，基因复制和丢失(以及水平转移)等进化事件在基因进化中起着重要作用，为了重建和研究这些事件，已经建立了许多系统发育模型。然而，这些模型通常作出一个简化的假设，即不完全世系排序(ILS)等与种群相关的影响可以忽略不计。虽然这一假设在某些情况下可能是合理的，但随着基因组测序的增加导致了更密集的系统发育，这一假设变得越来越有问题，其中ILS等影响更加突出。为了应对这一挑战，我们提出了一个新的概率模型DLCoal，该模型定义了群体环境中的基因复制和丢失，从而可以直接解决合并和ILS。有趣的是，这个模型意味着，除了通常的基因树和物种树之外，还有第三棵树，即轨迹树，它可能会有很多应用。使用这个模型，我们开发了第一个通用的协调方法，它可以在ILS存在的情况下准确地推断基因的复制和丢失，并且我们展示了它对包括苍蝇、真菌和灵长类动物在内的各种分支的直系物、同源基因、复制和丢失的改进的推断。此外，我们的模拟表明，基因复制增加了ILS的频率，进一步说明了联合模型的重要性。展望未来，我们相信，这个统一的模型可以为系统发育学和种群遗传学中的问题提供见解。
Gene phylogenies provide a rich source of information about the way evolution shapes genomes, populations, and phenotypes. In addition to substitutions, evolutionary events such as gene duplication and loss (as well as horizontal transfer) play a major role in gene evolution, and many phylogenetic models have been developed in order to reconstruct and study these events. However, these models typically make the simplifying assumption that population-related effects such as incomplete lineage sorting (ILS) are negligible. While this assumption may have been reasonable in some settings, it has become increasingly problematic as increased genome sequencing has led to denser phylogenies, where effects such as ILS are more prominent. To address this challenge, we present a new probabilistic model, DLCoal, that defines gene duplication and loss in a population setting, such that coalescence and ILS can be directly addressed. Interestingly, this model implies that in addition to the usual gene tree and species tree, there exists a third tree, the locus tree, which will likely have many applications. Using this model, we develop the first general reconciliation method that accurately infers gene duplications and losses in the presence of ILS, and we show its improved inference of orthologs, paralogs, duplications, and losses for a variety of clades, including flies, fungi, and primates. Also, our simulations show that gene duplications increase the frequency of ILS, further illustrating the importance of a joint model. Going forward, we believe that this unified model can offer insights to questions in both phylogenetics and population genetics.