Mitochondrial sequence diversity within a subspecies of savanna monkeys (Cercopithecus aethiops) is similar to that between subspecies

Localized population divergence of vervet monkeys (Chlorocebus spp.) in South Africa: Evidence from mtDNA

OBJECTIVE

Vervet monkeys are common in most tree-rich areas of South Africa, but their absence from grassland and semi-desert areas of the country suggest potentially restricted and mosaic local population patterns that may have relevance to local phenotype patterns and selection. A portion of the mitochondrial DNA control region was sequenced to study patterns of genetic differentiation.

METHODS

DNA was extracted, and mitochondrial DNA sequences were obtained from 101 vervet monkeys at 15 localities, which represent both an extensive (widely across the distribution range) and intensive (more than one troop at most of the localities) sampling strategy. Analyses utilized Arlequin 3.1, MEGA 6, BEAST v1.5.2, and Network V3.6.1.

RESULTS

The dataset contained 26 distinct haplotypes, with six populations fixed for single haplotypes. Pairwise P-distance among population pairs showed significant differentiation among most population pairs, but with nonsignificant differences among populations within some regions. Populations were grouped into three broad clusters in a maximum likelihood phylogenetic tree and a haplotype network. These clusters correspond to i) north-western, northern, and north-eastern parts of the distribution range as well as the northern coastal belt; ii) central areas of the country; and iii) southern part of the Indian Ocean coastal belt and adjacent inland areas.

CONCLUSIONS

Apparent patterns of genetic structure correspond to current and past distribution of suitable habitat, geographic barriers to gene flow, geographic distance, and female philopatry. However, further work on nuclear markers and other genomic data are necessary to confirm these results.

Mitochondrial diversity and distribution of African green monkeys (chlorocebus gray, 1870)

African green monkeys (Chlorocebus) represent a widely distributed and morphologically diverse primate genus in sub-Saharan Africa. Little attention has been paid to their genetic diversity and phylogeny. Based on morphological data, six species are currently recognized, but their taxonomy remains disputed. Here, we aim to characterize the mitochondrial (mt) DNA diversity, biogeography and phylogeny of African green monkeys. We analyzed the complete mitochondrial cytochrome b gene of 126 samples using feces from wild individuals and material from zoo and museum specimens with clear geographical provenance, including several type specimens. We found evidence for nine major mtDNA clades that reflect geographic distributions rather than taxa, implying that the mtDNA diversity of African green monkeys does not conform to existing taxonomic classifications. Phylogenetic relationships among clades could not be resolved suggesting a rapid early divergence of lineages. Several discordances between mtDNA and phenotype indicate that hybridization may have occurred in contact zones among species, including the threatened Bale monkey (Chlorocebus djamdjamensis). Our results provide both valuable data on African green monkeys' genetic diversity and evolution and a basis for further molecular studies on this genus.

Phylogenomics of African guenons

The karyotypes of 28 specimens belonging to 26 species of Cercopithecinae have been compared with each other and with human karyotype by chromosome banding and, for some of them, by Zoo-FISH (human painting probes) techniques. The study includes the first description of the karyotypes of four species and a synonym of Cercopithecus nictitans. The chromosomal homologies obtained provide us with new data on a large number of rearrangements. This allows us to code chromosomal characters to draw Cercopithecini phylogenetic trees, which are compared to phylogenetic data based on DNA sequences. Our findings show that some of the superspecies proposed by Kingdon (1997 The Kingdon Field Guide to African Mammals, Academic Press.) and Groves (2001 Primates Taxonomy, Smithsonian Institution Press) do not form homogeneous groups and that the genus Cercopithecus is paraphyletic, in agreement with previous molecular analyses. The evolution of Cercopithecini karyotypes is mainly due to non-centromeric chromosome fissions and centromeric shifts or inversions. Non-Robertsonian translocations occurred in C. hamlyni and C. neglectus. The position of chromosomal rearrangements in the phylogenetic tree leads us to propose that the Cercopithecini evolution proceeded by either repeated fission events facilitated by peculiar genomic structures or successive reticulate phases, in which heterozygous populations for few rearranged chromosomes were present, allowing the spreading of chromosomal forms in various combinations, before the speciation process.

A challenge to the ancient origin of SIVagm based on African green monkey mitochondrial genomes

While the circumstances surrounding the origin and spread of HIV are becoming clearer, the particulars of the origin of simian immunodeficiency virus (SIV) are still unknown. Specifically, the age of SIV, whether it is an ancient or recent infection, has not been resolved. Although many instances of cross-species transmission of SIV have been documented, the similarity between the African green monkey (AGM) and SIVagm phylogenies has long been held as suggestive of ancient codivergence between SIVs and their primate hosts. Here, we present well-resolved phylogenies based on full-length AGM mitochondrial genomes and seven previously published SIVagm genomes; these allowed us to perform the first rigorous phylogenetic test to our knowledge of the hypothesis that SIVagm codiverged with the AGMs. Using the Shimodaira-Hasegawa test, we show that the AGM mitochondrial genomes and SIVagm did not evolve along the same topology. Furthermore, we demonstrate that the SIVagm topology can be explained by a pattern of west-to-east transmission of the virus across existing AGM geographic ranges. Using a relaxed molecular clock, we also provide a date for the most recent common ancestor of the AGMs at approximately 3 million years ago. This study substantially weakens the theory of ancient SIV infection followed by codivergence with its primate hosts.