TY - JOUR
T1 - Selection, recombination and population history effects on runs of homozygosity (ROH) in wild red deer (Cervus elaphus)
AU - Hewett, Anna M.
AU - Stoffel, Martin A.
AU - Peters, Lucy
AU - Johnston, Susan E.
AU - Pemberton, Josephine M.
N1 - Funding Information:
We thank NatureScot for permission to work on the Isle of Rum. We thank the many field workers that have helped to collect samples, particularly Alison and Sean Morris. The long-term project and this research were funded by the UK Natural Environment Research Council, and most of the SNP genotyping was supported by a European Research Council Advanced Grant to J. M. Pemberton. A. Hewett is supported by an E4 NERC DTP studentship (NE/S007407/1). M. Stoffel is funded by The Leverhulme Trust (RPG-2019-072). S.E. Johnston is supported by a Royal Society University Research Fellowship (UF150448). The Argyll sample genotypes were contributed by Eryn McFarlane. Genotyping was conducted at the Wellcome Trust Clinical Research Facility Genetics Core. We are grateful to the Darwin Tree of Life project for the physical map positions used. We thank Ino Curik and two anonymous reviewers for their helpful comments on this manuscript.
Publisher Copyright:
© 2023, The Author(s).
PY - 2023/4
Y1 - 2023/4
N2 - The distribution of runs of homozygosity (ROH) may be shaped by a number of interacting processes such as selection, recombination and population history, but little is known about the importance of these mechanisms in shaping ROH in wild populations. We combined an empirical dataset of >3000 red deer genotyped at >35,000 genome-wide autosomal SNPs and evolutionary simulations to investigate the influence of each of these factors on ROH. We assessed ROH in a focal and comparison population to investigate the effect of population history. We investigated the role of recombination using both a physical map and a genetic linkage map to search for ROH. We found differences in ROH distribution between both populations and map types indicating that population history and local recombination rate have an effect on ROH. Finally, we ran forward genetic simulations with varying population histories, recombination rates and levels of selection, allowing us to further interpret our empirical data. These simulations showed that population history has a greater effect on ROH distribution than either recombination or selection. We further show that selection can cause genomic regions where ROH is common, only when the effective population size (Ne) is large or selection is particularly strong. In populations having undergone a population bottleneck, genetic drift can outweigh the effect of selection. Overall, we conclude that in this population, genetic drift resulting from a historical population bottleneck is most likely to have resulted in the observed ROH distribution, with selection possibly playing a minor role.
AB - The distribution of runs of homozygosity (ROH) may be shaped by a number of interacting processes such as selection, recombination and population history, but little is known about the importance of these mechanisms in shaping ROH in wild populations. We combined an empirical dataset of >3000 red deer genotyped at >35,000 genome-wide autosomal SNPs and evolutionary simulations to investigate the influence of each of these factors on ROH. We assessed ROH in a focal and comparison population to investigate the effect of population history. We investigated the role of recombination using both a physical map and a genetic linkage map to search for ROH. We found differences in ROH distribution between both populations and map types indicating that population history and local recombination rate have an effect on ROH. Finally, we ran forward genetic simulations with varying population histories, recombination rates and levels of selection, allowing us to further interpret our empirical data. These simulations showed that population history has a greater effect on ROH distribution than either recombination or selection. We further show that selection can cause genomic regions where ROH is common, only when the effective population size (Ne) is large or selection is particularly strong. In populations having undergone a population bottleneck, genetic drift can outweigh the effect of selection. Overall, we conclude that in this population, genetic drift resulting from a historical population bottleneck is most likely to have resulted in the observed ROH distribution, with selection possibly playing a minor role.
U2 - 10.1038/s41437-023-00602-z
DO - 10.1038/s41437-023-00602-z
M3 - Article
C2 - 36801920
AN - SCOPUS:85148225932
SN - 0018-067X
VL - 130
SP - 242
EP - 250
JO - Heredity
JF - Heredity
ER -