Abstract
Landscape genomics promises to provide novel insights into how neutral and adaptive processes shape genome-wide variation within and among populations. However, there has been little emphasis on examining whether individual-based phenotype–genotype relationships derived from approaches such as genome-wide association (GWAS) manifest themselves as a population-level signature of selection in a landscape context. The two may prove irreconcilable as individual-level patterns become diluted by high levels of gene flow and complex phenotypic or environmental heterogeneity. We illustrate this issue with a case study that examines the role of the highly prevalent gastrointestinal nematode Trichostrongylus tenuis in shaping genomic signatures of selection in red grouse (Lagopus lagopus scotica). Individual-level GWAS involving 384 SNPs has previously identified five SNPs that explain variation in T. tenuis burden. Here, we examine whether these same SNPs display population-level relationships between T. tenuis burden and genetic structure across a small-scale landscape of 21 sites with heterogeneous parasite pressure. Moreover, we identify adaptive SNPs showing signatures of directional selection using FST outlier analysis and relate population- and individual-level patterns of multilocus neutral and adaptive genetic structure to T. tenuis burden. The five candidate SNPs for parasite-driven selection were neither associated with T. tenuis burden on a population level, nor under directional selection. Similarly, there was no evidence of parasite-driven selection in SNPs identified as candidates for directional selection. We discuss these results in the context of red grouse ecology and highlight the broader consequences for the utility of landscape genomics approaches for identifying signatures of selection.
Original language | English |
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Pages (from-to) | 324-341 |
Number of pages | 18 |
Journal | Molecular Ecology |
Volume | 25 |
Issue number | 1 |
Early online date | 12 Dec 2015 |
DOIs | |
Publication status | Published - Jan 2016 |
Bibliographical note
AcknowledgementsThis study was funded by a BBSRC studentship (MAW) and NERC grants NE/H00775X/1 and NE/D000602/1 (SBP). The authors are grateful to Mario Röder and Keliya Bai for fieldwork assistance, and all estate owners, factors and keepers for access to field sites, most particularly MJ Taylor and Mike Nisbet (Airlie), Neil Brown (Allargue), RR Gledson and David Scrimgeour (Delnadamph), Andrew Salvesen and John Hay (Dinnet), Stuart Young and Derek Calder (Edinglassie), Kirsty Donald and David Busfield (Glen Dye), Neil Hogbin and Ab Taylor (Glen Muick), Alistair Mitchell (Glenlivet), Simon Blackett, Jim Davidson and Liam Donald (Invercauld), Richard Cooke and Fred Taylor† (Invermark), Shaila Rao and Christopher Murphy (Mar Lodge), and Ralph Peters and Philip Astor (Tillypronie).
S.B.P. and S.M.R. conceived and designed the study. M.A.W. performed field and laboratory work. A.D. and M.C.J. developed SNP markers. M.A.W. analysed the data. M.A.W. and S.B.P. wrote the manuscript.
Keywords
- landscape genomics
- Population genomics
- FST outliers
- natural selection
- parasites
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Role of parasite-driven selection in shaping landscape genomic structure in red grouse (Lagopus lagopus scotica)
Wenzel, M. (Contributor), Douglas, A. (Contributor), James, M. C. (Contributor), Redpath, S. (Contributor) & Piertney, S. (Contributor), Dryad Digital Repository, 12 Nov 2015
DOI: 10.5061/dryad.4t7jk
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Profiles
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Stuart Piertney
- Engineering, National Decommissioning Centre
- Biological Sciences, Aberdeen Centre For Environmental Sustainability - Chair in Molecular Ecology and Evolution
Person: Academic
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Marius Wenzel
Person: Academic