Adaptive genetic variation at three loci in South African vervet monkeys (Chlorocebus pygerythrus) and the role of selection within Primates
- Published
- Accepted
- Subject Areas
- Anthropology, Biodiversity, Biogeography, Genetics
- Keywords
- pathogen diversity, environmental factors, adaptive variation, vervet monkey
- Copyright
- © 2018 Coetzer et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
- Cite this article
- 2018. Adaptive genetic variation at three loci in South African vervet monkeys (Chlorocebus pygerythrus) and the role of selection within Primates. PeerJ Preprints 6:e26577v4 https://doi.org/10.7287/peerj.preprints.26577v4
Abstract
Vervet monkeys (Chlorocebus pygerythrus) are one of the most widely distributed non-human primate species found in South Africa. They occur across all the South African provinces, inhabiting a large variety of habitats. These habitats vary sufficiently that it can be assumed that various factors such as pathogen diversity could influence populations in different ways. In turn, these factors could lead to varied levels of selection at specific fitness linked loci. The Toll-like Receptor (TLR) gene family, which play an integral role in vertebrate innate immunity, is a group of fitness linked loci which has been the focus of much research. In this study, we assessed the level of genetic variation at partial sequences of two TLR loci (TLR4 and 7) and a reproductively linked gene, acrosin (ACR), across the different habitat types within the vervet monkey distribution range. Gene variation and selection estimates were also made among 11 – 21 primate species. Low levels of genetic variation for all three gene regions were observed within vervet monkeys , with only two polymorphic sites identified for TLR4, three sites for TLR7 and one site for ACR . TLR7 variation was positively correlated with high mean annual rainfall, which was linked to increased pathogen abundance. The observed genetic variation at TLR4 might have been influenced by numerous factors including pathogens and climatic conditions. The ACR exonic regions showed no variation in vervet monkeys, which could point to the occurrence of a selective sweep. The TLR4 and TLR7 results for the among primate analyses was mostly in line with previous studies, indicating a higher rate of evolution for TLR4. Within primates, ACR coding regions also showed signs of positive selection, which was congruent with previous reports on mammals. Important additional information to the already existing vervet monkey knowledge base was gained from this study, which can guide future research projects on this highly researched taxon as well as help conservation agencies with future management planning involving possible translocations of this species.
Author Comment
A number of minor corrections, in line with reviewer and editor requests, were made to this version of the manuscript.
Supplemental Information
Supplementary Table S1. Sample list of 81 vervet monkeys sampled from across the vervet monkey distribution range for the current study
Locality information, group ID, no of troops per group, sex, sample ID and DNA amplification success for each gene fragment is provided.
Supplementary Table S2. Sample list of all outgroup taxa used during analyses, with the associated GenBank accession numbers
Supplementary Table S3. The statistical results from the Generalized linear model (GLM) analyses performed on the vervet monkey ACR, TLR4, TLR7 sequences from the current study and D-loop DNA sequences from Turner et al (2016b)
Values of very small magnitude were rounded to four decimal places.
Supplementary Table S4. Site-by-site results for selection obtained from three different selection analyses
Significance values (p-value/Posterior probability) are in bold. Candidate sites identified are highlighted in grey