Department of Computer Science, Rice University, Houston, Texas, United States of America.
PLoS One. 2012;7(9):e44491. doi: 10.1371/journal.pone.0044491. Epub 2012 Sep 11.
Gene duplication has long been acknowledged by biologists as a major evolutionary force shaping genomic architectures and characteristics across the Tree of Life. Major research has been conducting on elucidating the fate of duplicated genes in a variety of organisms, as well as factors that affect a gene's duplicability--that is, the tendency of certain genes to retain more duplicates than others. In particular, two studies have looked at the correlation between gene duplicability and its degree in a protein-protein interaction network in yeast, mouse, and human, and another has looked at the correlation between gene duplicability and its complexity (length, number of domains, etc.) in yeast. In this paper, we extend these studies to six species, and two trends emerge. There is an increase in the duplicability-connectivity correlation that agrees with the increase in the genome size as well as the phylogenetic relationship of the species. Further, the duplicability-complexity correlation seems to be constant across the species. We argue that the observed correlations can be explained by neutral evolutionary forces acting on the genomic regions containing the genes. For the duplicability-connectivity correlation, we show through simulations that an increasing trend can be obtained by adjusting parameters to approximate genomic characteristics of the respective species. Our results call for more research into factors, adaptive and non-adaptive alike, that determine a gene's duplicability.
基因复制长期以来一直被生物学家认为是塑造基因组结构和特征的主要进化力量，贯穿生命之树。人们一直在研究阐明各种生物体中复制基因的命运，以及影响基因可复制性的因素——即某些基因比其他基因更倾向于保留更多的复制品。特别是有两项研究探讨了基因复制性与其在酵母、小鼠和人类蛋白质-蛋白质相互作用网络中的程度之间的相关性，另一项研究探讨了基因复制性与其在酵母中的复杂性（长度、结构域数量等）之间的相关性。在本文中，我们将这些研究扩展到了六个物种，出现了两种趋势。随着基因组大小以及物种的系统发育关系的增加，可复制性-连接性相关性增加。此外，可复制性-复杂性相关性似乎在物种间保持不变。我们认为，观察到的相关性可以用作用于包含基因的基因组区域的中性进化力量来解释。对于可复制性-连接性相关性，我们通过模拟表明，可以通过调整参数来近似各自物种的基因组特征来获得增加的趋势。我们的研究结果呼吁对决定基因可复制性的因素（包括适应性和非适应性因素）进行更多的研究。
