Phylogenomic analyses reveal convergent patterns of adaptive evolution in elephant and human ancestries
Phylogenomic analyses reveal convergent patterns of adaptive evolution in elephant and human ancestries
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DOI：
10.1073/pnas.0911239106
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发表时间：
2009-12-08
影响因子：
11.1
通讯作者：
Wildman, Derek E.
中科院分区：
文献类型：
--
作者：
Goodman, Morris;Sterner, Kirstin N.;Wildman, Derek E.
特定的大脑表达基因组，例如有氧能量代谢基因，在人类祖先中适应性进化，并且可能在其他大脑哺乳动物的祖先中适应性进化。最近，两种非洲兽类动物（大象和马岛马蹄鲨）的基因组添加到了不断扩大的公开测序哺乳动物基因组中，这为检验这一假设提供了机会。大象与人类相似，拥有较大的大脑和较长的寿命。相比之下，马岛群岛的大脑较小，寿命较短。因此，我们研究了大象和人类之间的适应性进化的系统发育模式是否比大象和马岛群岛的谱系或人类和小鼠谱系之间更相似，以及有氧能量代谢基因是否在大象和人类的模式中得到了特别好的体现。我们的分析涵盖了每个谱系中大约 6,000 个基因，每个基因在序号间比较中产生广泛的编码序列匹配。确定每个基因的非同义和同义核苷酸取代率以及dN/dS比率。然后，根据具有较高 dN/dS 比率的基因的基因本体信息，我们确定了属于特定功能类别且适应性进化的更普遍的基因组。大象和人类谱系显示出比马岛蝠和小鼠谱系慢得多的核苷酸替换率，但基因的适应性更强。与绝对大脑大小和大脑耗氧量在大象中最大、在人类中次之最大相关，适应性进化的有氧能量代谢基因在大象谱系中最明显，在人类谱系中第二明显。
Specific sets of brain-expressed genes, such as aerobic energy metabolism genes, evolved adaptively in the ancestry of humans and may have evolved adaptively in the ancestry of other large-brained mammals. The recent addition of genomes from two afrotherians (elephant and tenrec) to the expanding set of publically available sequenced mammalian genomes provided an opportunity to test this hypothesis. Elephants resemble humans by having large brains and long life spans; tenrecs, in contrast, have small brains and short life spans. Thus, we investigated whether the phylogenomic patterns of adaptive evolution are more similar between elephant and human than between either elephant and tenrec lineages or human and mouse lineages, and whether aerobic energy metabolism genes are especially well represented in the elephant and human patterns. Our analyses encompassed approximate to 6,000 genes in each of these lineages with each gene yielding extensive coding sequence matches in interordinal comparisons. Each gene's nonsynonymous and synonymous nucleotide substitution rates and dN/dS ratios were determined. Then, from gene ontology information on genes with the higher dN/dS ratios, we identified the more prevalent sets of genes that belong to specific functional categories and that evolved adaptively. Elephant and human lineages showed much slower nucleotide substitution rates than tenrec and mouse lineages but more adaptively evolved genes. In correlation with absolute brain size and brain oxygen consumption being largest in elephants and next largest in humans, adaptively evolved aerobic energy metabolism genes were most evident in the elephant lineage and next most evident in the human lineage.