Genomic tracking of UK otter (Lutra lutra) population expansion after anthropogenic declines in the 20th century
This research project is in competition for funding with one or more projects available across the NERC GW4 Doctoral Training Partnership (DTP). Usually the projects which receive the best applicants will be awarded the funding. Find out more information about the DTP and how to apply.
Application deadline: 7 January 2019
Start date: October 2019
DTP research theme: Living World and Changing Planet
At a time of global biodiversity crisis, a detailed understanding of how management actions can facilitate the recovery of endangered populations is critical. This project offers a unique opportunity to study the genomics of a large-scale population recovery from bottleneck to carrying capacity.
The Eurasian otter Lutra lutra experienced dramatic declines in the 1950s-70s, due to persistent bioaccumulative and toxic chemicals. The species is currently used across Europe as an indicator species for clean freshwater environments. UK otters have recently recovered from isolated, bottlenecked fragments to near carrying capacity, allowing us to study this entire demographic process.
The project proposal capitalises on >3000 archival otter samples collected UK-wide over three decades by Cardiff University Otter Project. You will also have access to the newly generated ‘platinum-standard’ otter reference genome, resulting from an ongoing collaboration with the Wellcome Sanger Institute, who will also be involved in this PhD project as a collaborative partner.
Project aims and methods
The goals of this PhD project will be to:
- Utilise the genomic resource of the recently sequenced Eurasian otter genome to develop genome-wide methods to screen for genetic variation in archival samples of UK otters. Genome analysis can include comparative genomics work, if desired.
- To track specific lineages and alleles through space and time throughout the population expansion.
- To shed light on the demographic factors (inbreeding, gene flow, admixture) of this rapidly expanding population.
- To investigate potential signals of local adaptation in otters, e.g. to different food resources or habitat conditions.
The supervisory team looks forward to developing more specific questions and directions together with the PhD student, depending on her or his scientific interests.
We are looking for an enthusiastic and motivated candidate who is keen to develop expertise in bioinformatics and population genomics. A background in evolutionary genetics is desired, and relevant training in statistics and/or programming will be highly beneficial.
If desired, the PhD can contain an element of field work, and some work intersecting with the Cardiff University Otter Project sample archives is anticipated. In addition, ample opportunities will exist to engage with a broader community of ecologists and genomicists in the ‘Organisms and Environment’ group at Cardiff University School of Biosciences, as well as with the various project partners and collaborators.
Case or Collaborative Partner
Wellcome Sanger Institute: access to selected biocomputational resources and state-of-the-art analytical pipelines.
At least two separate visits are foreseen; one focussing on gaining understanding of the otter genome sequencing and assembly, and another visit that is more targetted towards your own generated additional data.
You will gain extensive experience in handling and analysing high-throughout sequencing data, as well as in-depth evolutionary and population genetic analyses.
This training will be provided jointly by the main supervisor (Hailer), co-supervisor Bridle and the Collaborative Partner (Sanger). Bridle will provide expertise in analysis of allele frequencies in a context of local adaptation. supported by a postdoc working on a NERC thematic grant to test the role of evolution in explaining species distributions in time and space. Several visits, plus regular interactions via skype and email with both Bristol and the Collaborative Partner at the Wellcome Sanger Institute are planned.
The project will also provide experience in interpretation of genomic data against a background of ecological knowledge, which is extensive in the case of the Eurasian otter. Co-supervisor Chadwick will supervise the statistical training and modelling, provide access to the Cardiff University Otter Project archives, and provide critical context about otter natural history.
Besides the supervisory team, you will have an Assessor at Cardiff who provides an independent evaluation of their annual progress. Supervision arrangements are overseen by the Director of Postgraduate Research, who also acts as advisor to supervisors.
References and background reading
- Hobbs GI, Chadwick EA, Bruford MW, Slater FM. 2011. Bayesian clustering techniques and progressive partitioning to identify population structuring within a recovering otter population in the UK. J Appl Ecol. 48(5):1206–17.
- Hagen SB, Kopatz A, Aspi J, Kojola I, Eiken HG. 2015. Evidence of rapid change in genetic structure and diversity during range expansion in a recovering large terrestrial carnivore. Proc R Soc B, 282: 20150092
- Bidon T, Janke A, Fain SR, Eiken HG, Hagen SB, Saarma U, Hallström BM, Lecomte N, Hailer F. 2014. Brown and polar bear Y chromosomes reveal extensive male-biased gene flow within brother lineages. Mol Biol Evol, 31:1353–1363
- Bidon T, Schreck N, Hailer F, Nilsson MA, Janke A. 2015. Genome-wide search identifies 1.9 Mb from the Polar Bear Y chromosome for evolutionary analyses. Genome Biol Evol, 7:2010–2022