Mitochondrial sequences show diverse evolutionary histories of African hominoids

Abstract

Phylogenetic trees for the four extant species of African hominoids are presented, based on mtDNA control region-1 sequences from 1,158 unique haplotypes. We include 83 new haplotypes of western chimpanzees and bonobos. Phylogenetic analysis of this enlarged database, which takes intraspecific geographic variability into account, reveals different patterns of evolution among species and great heterogeneity in species-level variation. Several chimpanzee and bonobo clades (and even single social groups) have retained substantially more mitochondrial variation than is seen in the entire human species. Among the 811 human haplotypes, those that branch off early are predominantly but not exclusively African. Neighbor joining trees provide strong evidence that eastern chimpanzee and human clades have experienced reduced effective population sizes, the latter apparently since the Homo sapiens-neanderthalensis split. Application of topiary pruning resolves ambiguities in the phylogenetic tree that are attributable to homoplasies in the data set. The diverse patterns of mtDNA sequence variation seen in today's hominoid taxa probably ref lect historical differences in ecological plasticity, female-biased dispersal, range fragmentation over differing periods of time, and competition among social groups. These results are relevant to the origin of zoonotic diseases, including HIV-1, and call into question some aspects of the current taxonomic treatment and conservation management of gorillas and chimpanzees.In spite of the absence of relevant fossils, studies of genetic variation have settled the question of whether humans are more closely related to gorillas or chimpanzees in favor of the latter (1). However, most such comparative studies have been based on no more than six individuals of each taxon with the exception of humans (2-9). Furthermore, the individual apes used in these comparisons are typically of unknown geographic origin, and there has been a tendency to treat all chimpanzees as a homogeneous group. Advances in DNA sequencing technology and noninvasive genotyping (10-13) now permit a more thorough analysis of the geographic variation within and among mitochondrial DNA (mtDNA) sequences in each of the living African hominoids. The noncoding control region 1 (CR1) was selected for analysis because it is hypervariable and was thought to be relatively free from direct natural selection and therefore was thought to provide a less ambiguous record of mutational change and phylogenetic relationships (9).Here we present a comparison of genetic variation in all nine recognized taxa of African or African-derived hominoid: (i) western lowland gorilla (Gorilla g. gorilla); (ii) eastern moun- (14). We also include three other groups in our analyses: a Neandertal (Homo s. neanderthalensis) and Bornean and Sumatran orangutans (Pongo p. pygmaeus and Pongo p. abelii, respectively). Using common names except when ambiguous, we show that these taxa have very different amounts and patterns of genetic variation, with hum...

Body composition and susceptibility to type 2 diabetes: an evolutionary perspective

“…50,51 The pattern 221 of dispersal has clearly contributed to contemporary human diversity, mediated by the 222 regional geographical routes taken, contrasting selective pressures, and periodic local 223 isolations, all of which have promoted inter-group differences and some genetic 224 diversification. 52,53 Despite this, our species is characterised by remarkably high levels of 225 genetic unity, 54 fundamentally linked with our high levels of phenotypic plasticity. The 226 selective pressures that favoured the capacity to tolerate ecological instability during 227 hominin evolution have made modern humans extremely well adapted to colonising diverse 228 environments.…”

A Novel γ2-Herpesvirus of the Rhadinovirus 2 Lineage in Chimpanzees

“…Four chimpanzee subspecies with nonoverlapping geographic ranges have been proposed on the basis of genetic differences in mitochondrial DNA sequences (Morin et al 1994;Gonder et al 1997;Gagneux et al 1999). We amplified and sequenced a 498-bp fragment of mitochondrial DNA displacement loop (mtDNA D-loop) for the 15 chimpanzees infected by PanRHV1a, PanRHV1b, or PanRHV2.…”

Evolution of Human Parental Behavior and the Human Family

“…In an analysis of variation in the mitochondrial DNA (inherited from mother), Gagneux et al (1999) found considerably less variability in human populations than in populations of other African hominoids. The restricted variability indicates that "something unusual happened in the early history of our species" (Gagneux et al, 1999, p. 5081), including the possibility of repeated bottlenecks and selective populations sweeps -that is, repeated expansions and contractions of early human populations.…”

“…In an analysis of variation in the mitochondrial DNA (inherited from mother), Gagneux et al (1999) found considerably less variability in human populations than in populations of other African hominoids. The restricted variability indicates that "something unusual happened in the early history of our species" (Gagneux et al, 1999, p. 5081), including the possibility of repeated bottlenecks and selective populations sweeps -that is, repeated expansions and contractions of early human populations. This cyclical pattern operating in the context of the changes in hominid social structure (e.g., coalition-based male -male competition) creates a mechanism that could result in hand-over-hand coevolutionary change in traits that support social competition, including brain size, social competencies, length of the developmental period, and intensive parenting.…”