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Adaptive genetic variation at three loci in South African vervet monkeys (Chlorocebus pygerythrus) and the role of selection within Primates

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154 days ago
Adaptive genetic variation at three loci in South African vervet monkeys (Chlorocebus pygerythrus) and the role of selection within Primates https://t.co/Es6Ttdxa1i
205 days ago
Adaptive genetic variation at three loci in South African vervet monkeys (Chlorocebus pygerythrus) and the role of selection within Primates https://t.co/xyVUAOWjBp
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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.

DOI: 10.7287/peerj.preprints.26577v4/supp-1

Supplementary Table S2. Sample list of all outgroup taxa used during analyses, with the associated GenBank accession numbers

DOI: 10.7287/peerj.preprints.26577v4/supp-2

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.

DOI: 10.7287/peerj.preprints.26577v4/supp-3

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

DOI: 10.7287/peerj.preprints.26577v4/supp-4

Additional Information

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Willem G Coetzer conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

Trudy R Turner contributed reagents/materials/analysis tools, approved the final draft.

Christopher A Schmitt approved the final draft, significant contribution to sample and data collection.

J Paul Grobler conceived and designed the experiments, contributed reagents/materials/analysis tools, authored or reviewed drafts of the paper, approved the final draft.

Animal Ethics

The following information was supplied relating to ethical approvals (i.e., approving body and any reference numbers):

Sampling and research ethical clearance was obtained for the original paper (Turner et al. 2016) from the Institutional Care and Use Committee of the University of Wisconsin-Milwaukee, United States of America (Ref no. 07-08 #32) and the Inter-Faculty Animal Ethics Committee of the University of the Free State, South Africa (Ref no. UFS-AED13/2010). All samples from this study were sourced from the Turner et al. (2016) study and no new additional samples were included.

DNA Deposition

The following information was supplied regarding the deposition of DNA sequences:

All sequences generated are accessible via GenBank, accession numbers MG014710 - MG014719.

Data Deposition

The following information was supplied regarding data availability:

Supplementary data. Haplotype DNA sequences for vervet ACR, TLR4 and TLR7 generated during the current study.

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.

Funding

The study was funded by the University of the Free State Postdoctoral Fellowship Grant. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


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