Copy numbers of homologous gene families vary greatly among different species, which is caused by the differences in the rates of gene gain and loss. It is well known that gene copy number variation can be responsible for the phenotypic novelties of particular species. In this study, 64 species that represent the main vertebrate groups spanning evolutionary period of about 600 million years were selected and the homology of gene families across these species were established, thereby revealing the evolutionary patterns of gene family size in vertebrates. The results show that among the6857 gene families inferred to be present in the most recent common ancestor of the vertebrates, 6712 had changed their sizes in at least one lineage, and these gene families had contracted in most cases. Gene families in Choloepus hoffmanniand Danio rerio had undergone the greatest contraction and expansion, respectively. Based on the highly dynamic evolution of vertebrate gene family size, we sought to identify any genomic signals that might be related to the evolution of specific vertebrate populations from the perspective of the distinct gene family size changes. We observed a high proportion of gene family amplification occurred, probably due to genome-wide duplication in the recent common ancestral genome of teleosts, which was followed by contraction in the decedents due to the extensive gene fractionation. Furthermore, we found evidence that orphan genes in the bony fish might contribute to the adaptive evolution of fish in aquatic environment. For example, some orphan genes were involved in fin development, tail development and kidney physiology. Overall, our work provides novel insights into the evolution of vertebrate gene family size and provides several lines of evidence for understanding the relationship between the genome evolution and phenotypic diversity in vertebrates.%同源基因家族的拷贝数在不同物种间普遍存在差异,这种差异是由不同的基因得失速率引起.众所周知,基因拷贝数变异是特定物种表型创新的可能原因.本研究选取具有代表性的脊椎动物主要类群并跨约6亿年进化时间的64个物种,鉴定了它们的同源基因家族,揭示了脊椎动物基因家族大小的进化模式.结果表明:在推断的存在于脊椎动物最近共同祖先的6857个基因家族中,有6712个都在至少一个种系中发生了大小的变化,而且基因家族在大多数种系中都是收缩的;其中,霍氏树懒(Choloepus hoffmanni)中有最高的基因家族收缩水平,而在斑马鱼(Danio rerio)中则相反.基于脊椎动物基因家族大小进化的高度动态性,本研究从基因家族大小变化的角度鉴定了一些可能与特定脊椎动物类群进化有关的基因组信号.结果观察到在现存真骨鱼类最近共同祖先基因组中出现了可能因全基因组复制所导致的高比例的基因家族扩增现象,随后在后裔物种中发生基因收缩事件.此外,本研究还发现了硬骨鱼特异性的orphan基因可能对这些鱼类在水生环境中的适应性进化有所贡献的证据,如在有些硬骨鱼中orphan基因与鳍、尾巴、肾脏等发育有关.本研究结果有助于深入了解脊椎动物基因家族大小的进化,同时为理解脊椎动物基因组进化与表型多样性的联系提供了理论证据.
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