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Monitoring primate populations in natural environments via third-generation genomic technologies (CENTA2-GENE2-JOBL)

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  • Full or part time
    Prof Mark Jobling
    Dr C A May
    Dr Jon Wetton
  • Application Deadline
    No more applications being accepted

Project Description

Based on the most recent data, 63% of the world’s ~600 species and subspecies of primates are currently threatened (Critically Endangered, Endangered, or Vulnerable). A major factor in species decline is genetic erosion within populations, and the consequent decline in fitness [1]. Monitoring of genetic diversity through suitable metrics [2] can detect the drivers of genetic erosion (such as inbreeding, demographic fluctuation, population fragmentation, and hybridisation via introgression) as well as its effects, which include inbreeding / outbreeding depression and maladaptation. Primate species are not only the end users of environments, but shape them, too, affecting the niches in which numerous other species can adapt and flourish.

Recent advances in genomics allow the rapid production of whole-genome reference sequences (through programmes such as the Tree of Life and the Earth BioGenome Projects), and the discovery of genome-wide genetic variants via resequencing. With such variants, particularly SNPs (single-nucleotide polymorphisms) in hand, assays can be designed that enable monitoring (Figure 1). SNP panels are well suited to environmental monitoring because PCR amplicons can be small, allowing the recovery of data from non-invasive field samples in which DNA is degraded. Such panels are also in principle adaptable for MinION third-generation sequencing [3], an affordable technology that can be implemented in the field.

This project will design SNP panels for the monitoring of genetic diversity in a number of primate species, using samples from our CASE partner Twycross Zoo (TZ; 33 species) for validation and demonstration of effectiveness in non-invasive samples. These panels will also allow kinship estimation and individual identification, which has application in zoo management and in forensic analysis in cases of wildlife crime. In the initial stages, work will focus on chimpanzee and bonobo since the genomic resources are relatively rich [4].

Further Reading:

1. Lawler RR (2018) Emerging and enduring issues in primate conservation genetics. Annu. Rev. Anthropol. 47: 395–415.

2. Leroy G, Carroll EL, Bruford MW, DeWoody JA, Strand A, Waits L, Wang J (2018) Next-generation metrics for monitoring genetic erosion within populations of conservation concern. Evol. Appl. 11: 1066-1083.

3. Cornelis S, Gansemans Y, Deleye L, Deforce D, Van Nieuwerburgh F (2017) Forensic SNP Genotyping using Nanopore MinION Sequencing. Sci. Rep. 7: 41759.

4. Prado-Martinez J, Sudmant PH, Kidd JM, Li H, Kelley JL, Lorente-Galdos B, Veeramah KR, Woerner AE, O'Connor TD, Santpere G et al (2013) Great ape genetic diversity and population history. Nature 499: 471-475.

Entry Requirements:

UK Bachelor Degree with at least 2:1 in a relevant subject or overseas equivalent.

Available for UK and EU applicants only.

Applicants must meet requirements for both academic qualifications and residential eligibility: http://www.nerc.ac.uk/skills/postgrad/

How to Apply:

Please follow refer to the How to Apply section at http://www2.le.ac.uk/study/research/funding/centa/how-to-apply-for-a-centa-project and use the Genetics Apply button to submit your PhD application.

Upload your CENTA Studentship Form in the proposal section of the application form.

In the funding section of the application please indicate you wish to be considered for NERC CENTA Studentship.

Under the proposal section please provide the name of the supervisor and project title/project code you want to apply for.

Funding Notes

This project is one of a number of fully funded studentships available to the best UK and EU candidates available as part of the NERC DTP CENTA consortium.

For more details of the CENTA consortium please see the CENTA website: www.centa.org.uk.

Applicants must meet requirements for both academic qualifications and residential eligibility: http://www.nerc.ac.uk/skills/postgrad/

The studentship includes a 3.5 year tuition fee waiver at UK/EU rates

An annual tax free stipend (For 2019/20 this is currently £15,009)

Research Training Support Grant (RTSG) of £8,000.

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