基因家族进化的模式和过程
The pattern and process of gene family evolution
摘要：
大规模的数据库是可用的，其包含从跨越生命的三个域的数百个完整基因组序列构建的同源基因家族。在这里，我们讨论的方法越来越复杂，旨在从这样的数据集提取基因家族进化的模式和过程的信息。特别是，我们认为模型调用基因出生（复制和转移）和死亡（损失）的过程来解释基因家族的进化。首先，我们回顾了家庭规模演化的出生和死亡模型及其含义，在不同物种和生命的三个领域中观察到的家庭规模分布的普遍特征。随后，我们进行到最近的事态发展，能够更全面地考虑信息的同源基因家族的序列，通过概率和解的个体基因的系统发育历史与系统发育历史的基因组中，他们居住的模型。为了说明所提出的方法和结果，我们使用HOGENOM数据库的数据，证明真核生物、古细菌和细菌基因组中同源基因家族大小的分布表现出非常相似的形状。我们发现，这些分布是最好的基因家族规模的进化模型，其中个别基因的死亡（损失）率大于出生（复制和转移）率，但新的家庭不断提供给基因组的起源过程。最后，我们使用概率调和方法，考虑到额外的信息，从基因遗传，并发现，对于原核生物，大多数的出生事件是转移的结果。
英文摘要：
Large scale databases are available that contain homologous gene families constructed from hundreds of complete genome sequences from across the three domains of Life. Here we discuss approches of increasing complexity aimed at extracting information on the pattern and process of gene family evolution from such datasets. In particular, we consider models that invoke processes of gene birth (duplication and transfer) and death (loss) to explain the evolution of gene families. First, we review birth-and-death models of family size evolution and their implications in light of the universal features of family size distribution observed across different species and the three domains of life. Subsequently, we proceed to recent developments on models capable of more completely considering information in the sequences of homologous gene families through the probabilistic reconciliation of the phylogenetic histories of individual genes with the phylogenetic history of the genomes in which they have resided. To illustrate the methods and results presented, we use data from the HOGENOM database, demonstrating that the distribution of homologous gene family sizes in the genomes of the Eukaryota, Archaea and Bacteria exhibit remarkably similar shapes. We shown that these distributions are best described by models of gene family size evolution where for individual genes the death (loss) rate is larger than the birth (duplication and transfer) rate, but new families are continually supplied to the genome by a process of origination. Finally, we use probabilistic reconciliation methods to take into consideration additional information from gene phylogenies, and find that, for prokaryotes, the majority of birth events are the result of transfer.
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