Department of Genetics and Evolution, Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland.
Genome Biol Evol. 2013;5(10):1949-68. doi: 10.1093/gbe/evt142.
Phenotypic traits derive from the selective recruitment of genetic materials over macroevolutionary times, and protein-coding genes constitute an essential component of these materials. We took advantage of the recent production of genomic scale data from sponges and cnidarians, sister groups from eumetazoans and bilaterians, respectively, to date the emergence of human proteins and to infer the timing of acquisition of novel traits through metazoan evolution. Comparing the proteomes of 23 eukaryotes, we find that 33% human proteins have an ortholog in nonmetazoan species. This premetazoan proteome associates with 43% of all annotated human biological processes. Subsequently, four major waves of innovations can be inferred in the last common ancestors of eumetazoans, bilaterians, euteleostomi (bony vertebrates), and hominidae, largely specific to each epoch, whereas early branching deuterostome and chordate phyla show very few innovations. Interestingly, groups of proteins that act together in their modern human functions often originated concomitantly, although the corresponding human phenotypes frequently emerged later. For example, the three cnidarians Acropora, Nematostella, and Hydra express a highly similar protein inventory, and their protein innovations can be affiliated either to traits shared by all eumetazoans (gut differentiation, neurogenesis); or to bilaterian traits present in only some cnidarians (eyes, striated muscle); or to traits not identified yet in this phylum (mesodermal layer, endocrine glands). The variable correspondence between phenotypes predicted from protein enrichments and observed phenotypes suggests that a parallel mechanism repeatedly produce similar phenotypes, thanks to novel regulatory events that independently tie preexisting conserved genetic modules.
表型特征源于宏观进化过程中对遗传物质的选择性招募，而蛋白质编码基因是这些物质的重要组成部分。我们利用最近从海绵动物和刺胞动物（分别为后生动物和两侧对称动物的姐妹群）产生的基因组规模数据，来确定人类蛋白质的出现时间，并推断通过后生动物进化获得新特征的时间。通过比较 23 种真核生物的蛋白质组，我们发现 33%的人类蛋白质在非后生动物物种中有直系同源物。这个后生动物前的蛋白质组与所有注释的人类生物学过程的 43%相关联。随后，可以推断出后生动物、两侧对称动物、真骨鱼（硬骨鱼）和人科动物的最后共同祖先经历了四次主要的创新浪潮，这些创新在很大程度上是每个时期特有的，而早期分支的后口动物和脊索动物门则很少有创新。有趣的是，在其现代人类功能中共同作用的蛋白质组通常同时起源，尽管相应的人类表型经常在后来出现。例如，三种刺胞动物珊瑚、海葵和水螅表达了高度相似的蛋白质库，它们的蛋白质创新可以归属于所有后生动物共有的特征（肠道分化、神经发生）；或者是仅在一些刺胞动物中存在的两侧对称动物特征（眼睛、横纹肌）；或者是尚未在这个门中识别的特征（中胚层、内分泌腺）。从蛋白质丰度预测的表型与观察到的表型之间的可变对应关系表明，一种平行的机制通过独立地将现有的保守遗传模块联系起来的新的调控事件，反复产生类似的表型。
