Data from: Phylogenomic analyses reveal convergent patterns of adaptive evolution in elephant and human ancestries

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 approximately 6000 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.

特定的脑表达基因集（如有氧能量代谢基因）在人类祖先中经历了适应性演化，且可能在其他大颅哺乳动物的祖先中也发生了适应性演化。
近期，两种非洲兽总目动物（大象、马岛猬）的基因组被加入到不断扩充的公开哺乳动物测序基因组集合中，为验证这一假说提供了契机。大象与人类相似，均拥有较大脑容量与较长寿命；而马岛猬则与之相反，脑容量较小且寿命较短。
因此，本研究旨在探究：大象与人类谱系间的适应性演化系统基因组模式，是否比大象与马岛猬谱系、人类与小鼠谱系间的更为相似；以及有氧能量代谢基因是否在大象和人类的演化模式中呈现出显著富集。
本研究针对上述各谱系共分析了约6000个基因，每个基因在目间比对中均可获得大量编码序列匹配结果。
我们测定了各基因的非同义核苷酸替换率、同义核苷酸替换率以及dN/dS比值。
随后，我们基于dN/dS比值较高的基因的基因本体（Gene Ontology, GO）注释信息，筛选出了富集于特定功能类别且经历适应性演化的基因集。
相较于马岛猬与小鼠谱系，大象与人类谱系的核苷酸替换速率显著更慢，但携带更多适应性演化基因。
鉴于大象的绝对脑容量与脑氧消耗量均为最高，人类次之，适应性演化的有氧能量代谢基因在大象谱系中表现最为显著，人类谱系则次之。