and 6 Mya), with 52 AEM genes (cellular component GO:0005739; mitochondrion) in the most enriched cluster of genes showing the signatures of positive selection, that is, faster rate of nonsynonymous substitutions (dN) than synonymous (dS) (Goodman et al., 2009). In the human terminal lineage (from 6 Mya to present), there were also many positively selected AEM genes but not significantly more than expected for any category of genes in the human genome. However, when these analyses were confined to only those positively selected genes that also show brain expression levels equivalent to or greater than the median of all modern human brain-expressed genes (Su et al., 2004), the most enriched clusters in the ape stem and human terminal lineages consisted of 20 and 23 AEM genes, respectively. Of these brain-expressed AEM genes, 14 and 10 in the ape stem and human terminal lineage, respectively, were involved in oxidative phosphorylation (Kyoto Encyclopedia of Genes and Genomes pathway map00190; oxidative phosphorylation). For more detailed information about these data and the methods used to infer enrichment for Gene Ontology terms and Kyoto Encyclopedia of Genes and Genomes pathways, refer to Goodman et al. (2009).
If the evolutionary origins of enlarged hominid brains depended on adaptively evolved AEM genes, then other large-brained mammals should also have in their ancestry AEM genes as principal targets of positive selection. An opportunity to test this hypothesis was provided by the addition of two afrotherian genomes to the growing set of publically available sequenced genomes. These two afrotherian genomes are from a large-brained mammal, the African savanna elephant (Loxodonta africana) and a small-brained mammal, the lesser hedgehog tenrec (Echinops telfairi). The clade Afrotheria, within which are elephants and tenrecs, is anciently separated from the clade Euarchontoglires, within which are humans and mice (Fig. 3.3A). Although elephants and tenrecs are phylogenetically closer to each other than to humans or mice, elephants resemble modern humans by having such features as large brains, empathetic social bonds, high intelligence, and prolonged development and long life spans [Fig. 3.3B; as discussed in Goodman et al. (2009)]. In contrast, tenrecs, as insectivore-grade mammals, have small, poorly encephalized brains and short life spans. 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, with adaptively evolved AEM genes being especially well represented in the elephant and human patterns (Fig. 3.3C) (Goodman et al., 2009). In correlation with brain oxygen consumption and brain mass being largest in elephants and next largest in humans, positively selected AEM genes were most evident in the elephant lineage (indeed more overrepresented than any other gene category), next most evident in the human lineage, and not evident (i.e., not overrepresented)