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Hewett AM, Johnston SE, Morris A, Morris S, Pemberton JM. Genetic architecture of inbreeding depression may explain its persistence in a population of wild red deer. Mol Ecol 2024; 33:e17335. [PMID: 38549143 DOI: 10.1111/mec.17335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 03/01/2024] [Accepted: 03/20/2024] [Indexed: 04/23/2024]
Abstract
Inbreeding depression is of major concern in declining populations, but relatively little is known about its genetic architecture in wild populations, such as the degree to which it is composed of large or small effect loci and their distribution throughout the genome. Here, we combine fitness and genomic data from a wild population of red deer to investigate the genomic distribution of inbreeding effects. Based on the runs of homozygosity (ROH)-based inbreeding coefficient, FROH, we use chromosome-specific inbreeding coefficients (FROHChr) to explore whether the effect of inbreeding varies between chromosomes. Under the assumption that within an individual the probability of being identical-by-descent is equal across all chromosomes, we used a multi-membership model to estimate the deviation of FROHChr from the average inbreeding effect. This novel approach ensures effect sizes are not overestimated whilst maximising the power of our available dataset of >3000 individuals genotyped on >35,000 autosomal SNPs. We find that most chromosomes confer a minor reduction in fitness-related traits, which when these effects are summed, results in the observed inbreeding depression in birth weight, survival and lifetime breeding success. However, no chromosomes had a significant detrimental effect compared to the overall effect of inbreeding, indicating no major effect loci. We conclude that in this population, inbreeding depression is likely the result of multiple mildly or moderately deleterious mutations spread across all chromosomes, which are difficult to detect with statistical confidence. Such mutations will be inefficiently purged, which may explain the persistence of inbreeding depression in this population.
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Affiliation(s)
- Anna M Hewett
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
- Department of Ecology and Evolution, University of Lausanne (UNIL), Lausanne, Switzerland
| | - Susan E Johnston
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Alison Morris
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Sean Morris
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Josephine M Pemberton
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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2
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Ravindran S, Underwood SL, Dorrens J, Seeker LA, Watt K, Wilbourn RV, Sparks AM, Sinclair R, Chen Z, Pilkington JG, McNeilly TN, Harrington L, Pemberton JM, Nussey DH, Froy H. No correlative evidence of costs of infection or immunity on leucocyte telomere length in a wild population of Soay sheep. Proc Biol Sci 2024; 291:20232946. [PMID: 38565156 PMCID: PMC10987235 DOI: 10.1098/rspb.2023.2946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 03/04/2024] [Indexed: 04/04/2024] Open
Abstract
Telomere length (TL) is a biomarker hypothesized to capture evolutionarily and ecologically important physiological costs of reproduction, infection and immunity. Few studies have estimated the relationships among infection status, immunity, TL and fitness in natural systems. The hypothesis that short telomeres predict reduced survival because they reflect costly consequences of infection and immune investment remains largely untested. Using longitudinal data from a free-living Soay sheep population, we tested whether leucocyte TL was predicted by infection with nematode parasites and antibody levels against those parasites. Helminth parasite burdens were positively associated with leucocyte TL in both lambs and adults, which is not consistent with TL reflecting infection costs. We found no association between TL and helminth-specific IgG levels in either young or old individuals which suggests TL does not reflect costs of an activated immune response or immunosenescence. Furthermore, we found no support for TL acting as a mediator of trade-offs between infection, immunity and subsequent survival in the wild. Our results suggest that while variation in TL could reflect short-term variation in resource investment or environmental conditions, it does not capture costs of infection and immunity, nor does it behave like a marker of an individual's helminth-specific antibody immune response.
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Affiliation(s)
- Sanjana Ravindran
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Sarah L. Underwood
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Jennifer Dorrens
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Luise A. Seeker
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Kathryn Watt
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Rachael V. Wilbourn
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Alexandra M. Sparks
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
- School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Rona Sinclair
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Zhulin Chen
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Jill G. Pilkington
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Tom N. McNeilly
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik EH26 0PZ, UK
| | - Lea Harrington
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Canada H3C 3J7
| | - Josephine M. Pemberton
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Daniel H. Nussey
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Hannah Froy
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
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3
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James C, Pemberton JM, Navarro P, Knott S. Investigating pedigree- and SNP-associated components of heritability in a wild population of Soay sheep. Heredity (Edinb) 2024; 132:202-210. [PMID: 38341521 PMCID: PMC10997785 DOI: 10.1038/s41437-024-00673-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 01/19/2024] [Accepted: 01/24/2024] [Indexed: 02/12/2024] Open
Abstract
Estimates of narrow sense heritability derived from genomic data that contain related individuals may be biased due to the within-family effects such as dominance, epistasis and common environmental factors. However, for many wild populations, removal of related individuals from the data would result in small sample sizes. In 2013, Zaitlen et al. proposed a method to estimate heritability in populations that include close relatives by simultaneously fitting an identity-by-state (IBS) genomic relatedness matrix (GRM) and an identity-by-descent (IBD) GRM. The IBD GRM is identical to the IBS GRM, except relatedness estimates below a specified threshold are set to 0. We applied this method to a sample of 8557 wild Soay sheep from St. Kilda, with genotypic information for 419,281 single nucleotide polymorphisms. We aimed to see how this method would partition heritability into population-level (IBS) and family-associated (IBD) variance for a range of genetic architectures, and so we focused on a mixture of polygenic and monogenic traits. We also implemented a variant of the model in which the IBD GRM was replaced by a GRM constructed from SNPs with low minor allele frequency to examine whether any additive genetic variance is captured by rare alleles. Whilst the inclusion of the IBD GRM did not significantly improve the fit of the model for the monogenic traits, it improved the fit for some of the polygenic traits, suggesting that dominance, epistasis and/or common environment not already captured by the non-genetic random effects fitted in our models may influence these traits.
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Affiliation(s)
- Caelinn James
- Institute of Ecology and Evolution, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK.
- Scotland's Rural College (SRUC), The Roslin Institute Building, Easter Bush, Midlothian, UK.
| | - Josephine M Pemberton
- Institute of Ecology and Evolution, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
| | - Pau Navarro
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, UK
- MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
| | - Sara Knott
- Institute of Ecology and Evolution, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
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Stoffel MA, Johnston SE, Pilkington JG, Pemberton JM. Purifying and balancing selection on embryonic semi-lethal haplotypes in a wild mammal. Evol Lett 2024; 8:222-230. [PMID: 38525027 PMCID: PMC10959477 DOI: 10.1093/evlett/qrad053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 09/25/2023] [Accepted: 10/12/2023] [Indexed: 03/26/2024] Open
Abstract
Embryonic lethal mutations are arguably the earliest and most severe manifestation of inbreeding depression, but their impact on wild populations is not well understood. Here, we combined genomic, fitness, and life-history data from 5,925 wild Soay sheep sampled over nearly three decades to explore the impact of embryonic lethal mutations and their evolutionary dynamics. We searched for haplotypes that in their homozygous state are unusually rare in the offspring of known carrier parents and found three putatively semi-lethal haplotypes with 27%-46% fewer homozygous offspring than expected. Two of these haplotypes are decreasing in frequency, and gene-dropping simulations through the pedigree suggest that this is partially due to purifying selection. In contrast, the frequency of the third semi-lethal haplotype remains relatively stable over time. We show that the haplotype could be maintained by balancing selection because it is also associated with increased postnatal survival and body weight and because its cumulative frequency change is lower than in most drift-only simulations. Our study highlights embryonic mutations as a largely neglected contributor to inbreeding depression and provides a rare example of how harmful genetic variation can be maintained through balancing selection in a wild mammal population.
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Affiliation(s)
- Martin A Stoffel
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Susan E Johnston
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Jill G Pilkington
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Josephine M Pemberton
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
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5
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Wiersma E, Pakeman RJ, Bal X, Pilkington JG, Pemberton JM, Nussey DH, Sweeny AR. Age-specific impacts of vegetation functional traits on gastrointestinal nematode parasite burdens in a large herbivore. J Anim Ecol 2023; 92:1869-1880. [PMID: 37403651 PMCID: PMC10952545 DOI: 10.1111/1365-2656.13978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 06/06/2023] [Indexed: 07/06/2023]
Abstract
Gastrointestinal nematode (GIN) parasites play an important role in the ecological dynamics of many animal populations. Recent studies suggest that fine-scale spatial variation in GIN infection dynamics is important in wildlife systems, but the environmental drivers underlying this variation remain poorly understood. We used data from over two decades of GIN parasite egg counts, host space use, and spatial vegetation data from a long-term study of Soay sheep on St Kilda to test how spatial autocorrelation and vegetation in an individual's home range predict parasite burden across three age groups. We developed a novel approach to quantify the plant functional traits present in a home range to describe the quality of vegetation present. Effects of vegetation and space varied between age classes. In immature lambs, strongyle parasite faecal egg counts (FEC) were spatially structured, being highest in the north and south of our study area. Independent of host body weight and spatial autocorrelation, plant functional traits predicted parasite egg counts. Higher egg counts were associated with more digestible and preferred plant functional traits, suggesting the association could be driven by host density and habitat preference. In contrast, we found no evidence that parasite FEC were related to plant functional traits in the host home range in yearlings or adult sheep. Adult FEC were spatially structured, with highest burdens in the north-east of our study area, while yearling FEC showed no evidence of spatial structuring. Parasite burdens in immature individuals appear more readily influenced by fine-scale spatial variation in the environment, highlighting the importance of such heterogeneity for our understanding of wildlife epidemiology and health. Our findings support the importance of fine-scale environmental variation for wildlife disease ecology and provides new evidence that such effects may vary across demographic groups within a population.
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Affiliation(s)
- Ellis Wiersma
- Institute of Ecology & Evolution, School of Biological ScienceUniversity of EdinburghEdinburghUK
| | | | - Xavier Bal
- Institute of Ecology & Evolution, School of Biological ScienceUniversity of EdinburghEdinburghUK
| | - Jill G. Pilkington
- Institute of Ecology & Evolution, School of Biological ScienceUniversity of EdinburghEdinburghUK
| | - Josephine M. Pemberton
- Institute of Ecology & Evolution, School of Biological ScienceUniversity of EdinburghEdinburghUK
| | - Daniel H. Nussey
- Institute of Ecology & Evolution, School of Biological ScienceUniversity of EdinburghEdinburghUK
| | - Amy R. Sweeny
- Institute of Ecology & Evolution, School of Biological ScienceUniversity of EdinburghEdinburghUK
- School of BiosciencesUniversity of SheffieldSheffieldUK
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6
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McKenna-Ell C, Ravindran S, Pilkington JG, Pemberton JM, Nussey DH, Froy H. Trait-dependent associations between early- and late-life reproduction in a wild mammal. Biol Lett 2023; 19:20230050. [PMID: 37433328 DOI: 10.1098/rsbl.2023.0050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 06/23/2023] [Indexed: 07/13/2023] Open
Abstract
Early- versus late-life trade-offs are a central prediction of life-history theory that are expected to shape the evolution of ageing. While ageing is widely observed in wild vertebrates, evidence that early-late trade-offs influence ageing rates remains limited. Vertebrate reproduction is a complex, multi-stage process, yet few studies have examined how different aspects of early-life reproductive allocation shape late-life performance and ageing. Here, we use longitudinal data from a 36-year study of wild Soay sheep to show that early-life reproduction predicts late-life reproductive performance in a trait-dependent manner. Females that started breeding earlier showed more rapid declines in annual breeding probability with age, consistent with a trade-off. However, age-related declines in offspring first-year survival and birth weight were not associated with early-life reproduction. Selective disappearance was evident in all three late-life reproductive measures, with longer-lived females having higher average performance. Our results provide mixed support for early-late reproductive trade-offs and show that the way early-life reproduction shapes late-life performance and ageing can differ among reproductive traits.
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Affiliation(s)
- Chris McKenna-Ell
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Sanjana Ravindran
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Jill G Pilkington
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Josephine M Pemberton
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Daniel H Nussey
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Hannah Froy
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
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7
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Chapman EG, Pilkington JG, Pemberton JM. Correlates of early reproduction and apparent fitness consequences in male Soay sheep. Ecol Evol 2023; 13:e10058. [PMID: 37168987 PMCID: PMC10164647 DOI: 10.1002/ece3.10058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 04/05/2023] [Accepted: 04/17/2023] [Indexed: 05/13/2023] Open
Abstract
Life history trade-offs are ubiquitous across species and place constraints on the timing of life history events, including the optimal age at first reproduction. However, studies on lifetime breeding success of male mammals are rare due to sex-biased dispersal and the requirement for genetic paternity inferences. We studied the correlates and apparent fitness consequences of early life reproduction among males in a free-living population of Soay sheep (Ovis aries) on St Kilda, Scotland. We investigated the factors associated with early breeding success and the apparent consequences of early success for survival and future reproduction. We used genetic paternity inferences, population data, and individual morphology measurements collected over 30 years. We found that individuals born in years with low-density population size had the highest early life breeding success and singletons were more likely to be successful than twins. Individuals that bred successfully at 7 months were more likely to survive their first winter. For individuals that survived their first winter, early breeding success was not associated with later breeding success. As individual heterogeneity affects breeding success, we believe that variation in individual quality masks the costs of early reproduction in this population. Our findings provide no evidence for selection for delayed age at reproduction in male Soay sheep.
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Affiliation(s)
- Elisabeth G. Chapman
- School of Biological Sciences, Institute of Ecology and EvolutionUniversity of EdinburghEdinburghUK
| | - Jill G. Pilkington
- School of Biological Sciences, Institute of Ecology and EvolutionUniversity of EdinburghEdinburghUK
| | - Josephine M. Pemberton
- School of Biological Sciences, Institute of Ecology and EvolutionUniversity of EdinburghEdinburghUK
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Gauzere J, Pemberton JM, Slate J, Morris A, Morris S, Walling CA, Johnston SE. A polygenic basis for birth weight in a wild population of red deer (Cervus elaphus). G3 (Bethesda) 2023; 13:jkad018. [PMID: 36652410 PMCID: PMC10085764 DOI: 10.1093/g3journal/jkad018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 01/09/2023] [Accepted: 01/13/2023] [Indexed: 01/19/2023]
Abstract
The genetic architecture of traits under selection has important consequences for the response to selection and potentially for population viability. Early QTL mapping studies in wild populations have reported loci with large effect on trait variation. However, these results are contradicted by more recent genome-wide association analyses, which strongly support the idea that most quantitative traits have a polygenic basis. This study aims to re-evaluate the genetic architecture of a key morphological trait, birth weight, in a wild population of red deer (Cervus elaphus), using genomic approaches. A previous study using 93 microsatellite and allozyme markers and linkage mapping on a kindred of 364 deer detected a pronounced QTL on chromosome 21 explaining 29% of the variance in birth weight, suggesting that this trait is partly controlled by genes with large effects. Here, we used data for more than 2,300 calves genotyped at >39,000 SNP markers and two approaches to characterise the genetic architecture of birth weight. First, we performed a genome-wide association (GWA) analysis, using a genomic relatedness matrix to account for population structure. We found no SNPs significantly associated with birth weight. Second, we used genomic prediction to estimate the proportion of variance explained by each SNP and chromosome. This analysis confirmed that most genetic variance in birth weight was explained by loci with very small effect sizes. Third, we found that the proportion of variance explained by each chromosome was slightly positively correlated with its size. These three findings highlight a highly polygenic architecture for birth weight, which contradicts the previous QTL study. These results are probably explained by the differences in how associations are modelled between QTL mapping and GWA. Our study suggests that models of polygenic adaptation are the most appropriate to study the evolutionary trajectory of this trait.
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Affiliation(s)
- Julie Gauzere
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
- AGAP, Université Montpellier, CIRAD, INRAE, Institut Agro, 34090 Montpellier, France
| | | | - Jon Slate
- School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Alison Morris
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Sean Morris
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Craig A Walling
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Susan E Johnston
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
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Hewett AM, Stoffel MA, Peters L, Johnston SE, Pemberton JM. Selection, recombination and population history effects on runs of homozygosity (ROH) in wild red deer (Cervus elaphus). Heredity (Edinb) 2023; 130:242-250. [PMID: 36801920 PMCID: PMC10076382 DOI: 10.1038/s41437-023-00602-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 02/07/2023] [Accepted: 02/07/2023] [Indexed: 02/19/2023] Open
Abstract
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.
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Affiliation(s)
- Anna M Hewett
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FL, UK.
| | - Martin A Stoffel
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - Lucy Peters
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FL, UK.,GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Castanet-Tolosan, France
| | - Susan E Johnston
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - Josephine M Pemberton
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FL, UK
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10
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James C, Pemberton JM, Navarro P, Knott S. The impact of SNP density on quantitative genetic analyses of body size traits in a wild population of Soay sheep. Ecol Evol 2022; 12:e9639. [PMID: 36532132 PMCID: PMC9750819 DOI: 10.1002/ece3.9639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 11/01/2022] [Accepted: 11/29/2022] [Indexed: 12/23/2022] Open
Abstract
Understanding the genetic architecture underpinning quantitative traits in wild populations is pivotal to understanding the processes behind trait evolution. The 'animal model' is a popular method for estimating quantitative genetic parameters such as heritability and genetic correlation and involves fitting an estimate of relatedness between individuals in the study population. Genotypes at genome-wide markers can be used to estimate relatedness; however, relatedness estimates vary with marker density, potentially affecting results. Increasing density of markers is also expected to increase the power to detect quantitative trait loci (QTL). In order to understand how the density of genetic markers affects the results of quantitative genetic analyses, we estimated heritability and performed genome-wide association studies (GWAS) on five body size traits in an unmanaged population of Soay sheep using two different SNP densities: a dataset of 37,037 genotyped SNPs and an imputed dataset of 417,373 SNPs. Heritability estimates did not differ between the two SNP densities, but the high-density imputed SNP dataset revealed four new SNP-trait associations that were not found with the lower density dataset, as well as confirming all previously-found QTL. We also demonstrated that fitting fixed and random effects in the same step as performing GWAS is a more powerful approach than pre-correcting for covariates in a separate model.
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Affiliation(s)
- Caelinn James
- Institute of Ecology and EvolutionSchool of Biological SciencesThe University of EdinburghEdinburghScotland
| | - Josephine M. Pemberton
- Institute of Ecology and EvolutionSchool of Biological SciencesThe University of EdinburghEdinburghScotland
| | - Pau Navarro
- MRC Human Genetics UnitInstitute of Genetics and CancerThe University of EdinburghEdinburghScotland
| | - Sara Knott
- Institute of Ecology and EvolutionSchool of Biological SciencesThe University of EdinburghEdinburghScotland
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11
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Ashraf B, Hunter DC, Bérénos C, Ellis PA, Johnston SE, Pilkington JG, Pemberton JM, Slate J. Genomic prediction in the wild: A case study in Soay sheep. Mol Ecol 2022; 31:6541-6555. [PMID: 34719074 DOI: 10.1111/mec.16262] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 10/13/2021] [Accepted: 10/25/2021] [Indexed: 01/13/2023]
Abstract
Genomic prediction, the technique whereby an individual's genetic component of their phenotype is estimated from its genome, has revolutionised animal and plant breeding and medical genetics. However, despite being first introduced nearly two decades ago, it has hardly been adopted by the evolutionary genetics community studying wild organisms. Here, genomic prediction is performed on eight traits in a wild population of Soay sheep. The population has been the focus of a >30 year evolutionary ecology study and there is already considerable understanding of the genetic architecture of the focal Mendelian and quantitative traits. We show that the accuracy of genomic prediction is high for all traits, but especially those with loci of large effect segregating. Five different methods are compared, and the two methods that can accommodate zero-effect and large-effect loci in the same model tend to perform best. If the accuracy of genomic prediction is similar in other wild populations, then there is a real opportunity for pedigree-free molecular quantitative genetics research to be enabled in many more wild populations; currently the literature is dominated by studies that have required decades of field data collection to generate sufficiently deep pedigrees. Finally, some of the potential applications of genomic prediction in wild populations are discussed.
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Affiliation(s)
- Bilal Ashraf
- School of Biosciences, University of Sheffield, Sheffield, UK.,Department of Anthropology, Durham University, Durham, UK
| | - Darren C Hunter
- School of Biosciences, University of Sheffield, Sheffield, UK.,School of Biology, University of St Andrews, St Andrews, UK
| | - Camillo Bérénos
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Philip A Ellis
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Susan E Johnston
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Jill G Pilkington
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | | | - Jon Slate
- School of Biosciences, University of Sheffield, Sheffield, UK
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12
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Ravindran S, Froy H, Underwood SL, Dorrens J, Seeker LA, Watt K, Wilbourn RV, Pilkington JG, Harrington L, Pemberton JM, Nussey DH. The association between female reproductive performance and leukocyte telomere length in wild Soay sheep. Mol Ecol 2022; 31:6184-6196. [PMID: 34514660 DOI: 10.1111/mec.16175] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 08/03/2021] [Indexed: 01/31/2023]
Abstract
Telomere length (TL), typically measured across a sample of blood cells, has emerged as an exciting potential marker of physiological state and of the costs of investment in growth and reproduction within evolutionary ecology. While there is mounting evidence from studies of wild vertebrates that short TL predicts raised subsequent mortality risk, the relationship between reproductive investment and TL is less clear cut, and previous studies report both negative and positive associations. In this study, we examined the relationship between TL and different aspects of maternal reproductive performance in a free-living population of Soay sheep. We find evidence for shorter TL in females that bred, and thus paid any costs of gestation, compared to females that did not breed. However, we found no evidence for any association between TL and litter size. Furthermore, females that invested in gestation and lactation actually had longer TL than females who only invested in gestation because their offspring died shortly after birth. We used multivariate models to decompose these associations into among- and within-individual effects, and discovered that within-individual effects were driving both the negative association between TL and gestation, and the positive association between TL and lactation. This suggests that telomere dynamics may reflect recent physiologically costly investment or variation in physiological condition, depending on the aspect of reproduction being investigated. Our results highlight the physiological complexity of vertebrate reproduction, and the need to better understand how and why different aspects of physiological variation underpinning life histories impact blood cell TL.
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Affiliation(s)
- Sanjana Ravindran
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Hannah Froy
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.,Centre for Biodiversity Dynamics, Institute for Biology, Norwegian University for Science and Technology (NTNU), Trondheim, Norway
| | - Sarah L Underwood
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Jennifer Dorrens
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Luise A Seeker
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Kathryn Watt
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Rachael V Wilbourn
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Jill G Pilkington
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Lea Harrington
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Canada
| | - Josephine M Pemberton
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Daniel H Nussey
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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13
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Pemberton JM, Kruuk LE, Clutton-Brock T. The Unusual Value of Long-Term Studies of Individuals: The Example of the Isle of Rum Red Deer Project. Annu Rev Ecol Evol Syst 2022. [DOI: 10.1146/annurev-ecolsys-012722-024041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Long-term studies of individuals enable incisive investigations of questions across ecology and evolution. Here, we illustrate this claim by reference to our long-term study of red deer on the Isle of Rum, Scotland. This project has established many of the characteristics of social organization, selection, and population ecology typical of large, polygynous, seasonally breeding mammals, with wider implications for our understanding of sexual selection and the evolution of sex differences, as well as for their population dynamics and population management. As molecular genetic techniques have developed, the project has pivoted to investigate evolutionary genetic questions, also breaking new ground in this field. With ongoing advances in genomics and statistical approaches and the development of increasingly sophisticated ways to assay new phenotypic traits, the questions that long-term studies such as the red deer study can answer become both broader and ever more sophisticated. They also offer powerful means of understanding the effects of ongoing climate change on wild populations.
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Affiliation(s)
- Josephine M. Pemberton
- Institute of Ecology and Evolution, School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom
| | - Loeske E.B. Kruuk
- Institute of Ecology and Evolution, School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom
| | - Tim Clutton-Brock
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
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14
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Gauzere J, Pemberton JM, Kruuk LEB, Morris A, Morris S, Walling CA. Maternal effects do not resolve the paradox of stasis in birth weight in a wild red deer populaton. Evolution 2022; 76:2605-2617. [PMID: 36111977 PMCID: PMC9828841 DOI: 10.1111/evo.14622] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 08/14/2022] [Indexed: 01/22/2023]
Abstract
In natural populations, quantitative traits seldom show short-term evolution at the rate predicted by evolutionary models. Resolving this "paradox of stasis" is a key goal in evolutionary biology, as it directly challenges our capacity to predict evolutionary change. One particularly promising hypothesis to explain the lack of evolutionary responses in a key offspring trait, body weight, is that positive selection on juveniles is counterbalanced by selection against maternal investment in offspring growth, given that reproduction is costly for the mothers. Here, we used data from one of the longest individual-based studies of a wild mammal population to test this hypothesis. We first showed that despite positive directional selection on birth weight, and heritable variation for this trait, no genetic change has been observed for birth weight over the past 47 years in the study population. Contrarily to our expectation, we found no evidence of selection against maternal investment in birth weight-if anything, selection favors mothers that produce large calves. Accordingly, we show that genetic change in birth weight over the study period is actually lower than that predicted from models including selection on maternal performance; ultimately our analysis here only deepens rather than resolves the paradox of stasis.
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Affiliation(s)
- Julie Gauzere
- Institute of Evolutionary Biology, School of Biological SciencesUniversity of EdinburghEdinburghEH9 3FLUK
| | - Josephine M. Pemberton
- Institute of Evolutionary Biology, School of Biological SciencesUniversity of EdinburghEdinburghEH9 3FLUK
| | - Loeske E. B. Kruuk
- Institute of Evolutionary Biology, School of Biological SciencesUniversity of EdinburghEdinburghEH9 3FLUK,Research School of BiologyThe Australian National UniversityCanberraACT 0200Australia
| | - Alison Morris
- Institute of Evolutionary Biology, School of Biological SciencesUniversity of EdinburghEdinburghEH9 3FLUK
| | - Sean Morris
- Institute of Evolutionary Biology, School of Biological SciencesUniversity of EdinburghEdinburghEH9 3FLUK
| | - Craig A. Walling
- Institute of Evolutionary Biology, School of Biological SciencesUniversity of EdinburghEdinburghEH9 3FLUK
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15
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Acerini CI, Morris S, Morris A, Kenyon F, McBean D, Pemberton JM, Albery GF. Helminth parasites are associated with reduced survival probability in young red deer. Parasitology 2022; 149:1702-1708. [PMID: 36052566 PMCID: PMC11010593 DOI: 10.1017/s0031182022001111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 07/06/2022] [Accepted: 07/28/2022] [Indexed: 12/14/2022]
Abstract
Helminths are common parasites of wild ungulates that can have substantial costs for growth, mortality and reproduction. Whilst these costs are relatively well documented for mature animals, knowledge of helminths' impacts on juveniles is more limited. Identifying these effects is important because young individuals are often heavily infected, and juvenile mortality is a key process regulating wild populations. Here, we investigated associations between helminth infection and overwinter survival in juvenile wild red deer (Cervus elaphus) on the Isle of Rum, Scotland. We collected fecal samples non-invasively from known individuals and used them to count propagules of 3 helminth taxa (strongyle nematodes, Fasciola hepatica and Elaphostrongylus cervi). Using generalized linear models, we investigated associations between parasite counts and overwinter survival for calves and yearlings. Strongyles were associated with reduced survival in both age classes, and F. hepatica was associated with reduced survival in yearlings, whilst E. cervi infection showed no association with survival in either age class. This study provides observational evidence for fitness costs of helminth infection in juveniles of a wild mammal, and suggests that these parasites could play a role in regulating population dynamics.
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Affiliation(s)
- Claudia I. Acerini
- School of Biological Sciences, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Sean Morris
- School of Biological Sciences, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Alison Morris
- School of Biological Sciences, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Fiona Kenyon
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Midlothian EH26 0PZ, UK
| | - David McBean
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Midlothian EH26 0PZ, UK
| | - Josephine M. Pemberton
- School of Biological Sciences, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Gregory F. Albery
- Wissenschaftskolleg zu Berlin, Berlin 14193, Germany
- Department of Biology, Georgetown University, Washington, DC 20007, USA
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16
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Regan CE, Pemberton JM, Pilkington JG, Smiseth P. Having a better home range does not reduce the cost of reproduction in Soay sheep. J Evol Biol 2022; 35:1352-1362. [PMID: 36063153 PMCID: PMC9826142 DOI: 10.1111/jeb.14083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 06/13/2022] [Accepted: 07/19/2022] [Indexed: 01/11/2023]
Abstract
A cost of reproduction may not be observable in the presence of environmental or individual heterogeneity because they affect the resources available to individuals. Individual space use is critical in determining both the resources available to individuals and the exposure to factors that mediate the value of these resources (e.g. competition and parasitism). Despite this, there has, to our knowledge, been little research to understand how between-individual differences in resource acquisition, caused by variation in space use, interact with environmental variation occurring at the population scale to influence estimates of the cost of reproduction in natural populations. We used long-term data from the St. Kilda Soay sheep population to understand how differences in age, relative home range quality, and average adult body mass, interacted with annual variation in population density and winter North Atlantic Oscillation index to influence over-winter survival and reproduction in the subsequent year, for females that had invested into reproduction to varying degrees. Our results suggest that Soay sheep females experience costs both in terms of future survival and future reproduction. However, we found little evidence that estimated costs of reproduction vary depending on relative home range quality. There are several possible causes for the lack of a relationship between relative home range quality and our estimate of the costs experienced by females. These include the potential for a correlation between relative home range quality and reproductive allocation to mask a relationship between home range quality and reproductive costs, as well as the potential for the benefit of higher quality home ranges being offset by higher densities. Nevertheless, our results raise questions regarding the presence or context-dependence of relationships between resource access and the estimated cost of reproduction.
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Affiliation(s)
- Charlotte E. Regan
- Institute for Evolutionary Biology, University of EdinburghEdinburghUK,Department of ZoologyEdward Grey Institute, University of OxfordOxfordUK
| | | | | | - Per T. Smiseth
- Institute for Evolutionary Biology, University of EdinburghEdinburghUK
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17
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Sparks AM, Johnston SE, Handel I, Pilkington JG, Berry J, Pemberton JM, Nussey DH, Mellanby RJ. Vitamin D status is heritable and under environment-dependent selection in the wild. Mol Ecol 2022; 31:4607-4621. [PMID: 34888965 PMCID: PMC9545857 DOI: 10.1111/mec.16318] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 11/12/2021] [Accepted: 11/24/2021] [Indexed: 11/30/2022]
Abstract
Vitamin D has a well-established role in skeletal health and is increasingly linked to chronic disease and mortality in humans and companion animals. Despite the clear significance of vitamin D for health and obvious implications for fitness under natural conditions, no longitudinal study has tested whether the circulating concentration of vitamin D is under natural selection in the wild. Here, we show that concentrations of dietary-derived vitamin D2 and endogenously produced vitamin D3 metabolites are heritable and largely polygenic in a wild population of Soay sheep (Ovis aries). Vitamin D2 status was positively associated with female adult survival, and vitamin D3 status predicted female fecundity in particular, good environment years when sheep density and competition for resources was low. Our study provides evidence that vitamin D status has the potential to respond to selection, and also provides new insights into how vitamin D metabolism is associated with fitness in the wild.
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Affiliation(s)
- Alexandra M. Sparks
- Institute of Evolutionary BiologySchool of Biological SciencesUniversity of EdinburghEdinburghUK
- Faculty of Biological SciencesSchool of BiologyUniversity of LeedsLeedsUK
| | - Susan E. Johnston
- Institute of Evolutionary BiologySchool of Biological SciencesUniversity of EdinburghEdinburghUK
| | - Ian Handel
- Royal (Dick) School of Veterinary Studies and The Roslin InstituteThe University of EdinburghHospital for Small AnimalsRoslinUK
| | - Jill G. Pilkington
- Institute of Evolutionary BiologySchool of Biological SciencesUniversity of EdinburghEdinburghUK
| | - Jacqueline Berry
- Specialist Assay Laboratory (Vitamin D)Clinical BiochemistryManchester Royal InfirmaryManchesterUK
| | - Josephine M. Pemberton
- Institute of Evolutionary BiologySchool of Biological SciencesUniversity of EdinburghEdinburghUK
| | - Daniel H. Nussey
- Institute of Evolutionary BiologySchool of Biological SciencesUniversity of EdinburghEdinburghUK
| | - Richard J. Mellanby
- Royal (Dick) School of Veterinary Studies and The Roslin InstituteThe University of EdinburghHospital for Small AnimalsRoslinUK
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18
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Albery GF, Clutton-Brock TH, Morris A, Morris S, Pemberton JM, Nussey DH, Firth JA. Ageing red deer alter their spatial behaviour and become less social. Nat Ecol Evol 2022; 6:1231-1238. [PMID: 35864228 PMCID: PMC10859100 DOI: 10.1038/s41559-022-01817-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 05/27/2022] [Indexed: 01/19/2023]
Abstract
Social relationships are important to many aspects of animals' lives, and an individual's connections may change over the course of their lifespan. Currently, it is unclear whether social connectedness declines within individuals as they age, and what the underlying mechanisms might be, so the role of age in structuring animal social systems remains unresolved, particularly in non-primates. Here we describe senescent declines in social connectedness using 46 years of data in a wild, individually monitored population of a long-lived mammal (European red deer, Cervus elaphus). Applying a series of spatial and social network analyses, we demonstrate that these declines occur because of within-individual changes in social behaviour, with correlated changes in spatial behaviour (smaller home ranges and movements to lower-density, lower-quality areas). These findings demonstrate that within-individual socio-spatial behavioural changes can lead older animals in fission-fusion societies to become less socially connected, shedding light on the ecological and evolutionary processes structuring wild animal populations.
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Affiliation(s)
- Gregory F Albery
- Department of Biology, Georgetown University, Washington DC, USA.
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.
- Wissenschaftskolleg zu Berlin, Berlin, Germany.
| | | | - Alison Morris
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Sean Morris
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | | | - Daniel H Nussey
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Josh A Firth
- Department of Zoology, University of Oxford, Oxford, UK
- Merton College, University of Oxford, Oxford, UK
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19
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Hill EW, Stoffel MA, McGivney BA, MacHugh DE, Pemberton JM. Inbreeding depression and the probability of racing in the Thoroughbred horse. Proc Biol Sci 2022; 289:20220487. [PMID: 35765835 PMCID: PMC9240673 DOI: 10.1098/rspb.2022.0487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Small effective population sizes and active inbreeding can lead to inbreeding depression due to deleterious recessive mutations exposed in the homozygous state. The Thoroughbred racehorse has low levels of population genetic diversity, but the effects of genomic inbreeding in the population are unknown. Here, we quantified inbreeding based on runs of homozygosity (ROH) using 297 K SNP genotypes from 6128 horses born in Europe and Australia, of which 13.2% were unraced. We show that a 10% increase in inbreeding (FROH) is associated with a 7% lower probability of ever racing. Moreover, a ROH-based genome-wide association study identified a haplotype on ECA14 which, in its homozygous state, is linked to a 32.1% lower predicted probability of ever racing, independent of FROH. The haplotype overlaps a candidate gene, EFNA5, that is highly expressed in cartilage tissue, which when damaged is one of the most common causes of catastrophic musculoskeletal injury in racehorses. Genomics-informed breeding aiming to reduce inbreeding depression and avoid damaging haplotype carrier matings will improve population health and racehorse welfare.
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Affiliation(s)
- Emmeline W. Hill
- Plusvital Ltd, The Highline, Dún Laoghaire Industrial Estate, Pottery Road, Dún Laoghaire, Co. Dublin, Ireland,UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin D04 V1W8, Ireland
| | - Martin A. Stoffel
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Beatrice A. McGivney
- Plusvital Ltd, The Highline, Dún Laoghaire Industrial Estate, Pottery Road, Dún Laoghaire, Co. Dublin, Ireland
| | - David E. MacHugh
- UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin D04 V1W8, Ireland,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin D04 V1W8, Ireland
| | - Josephine M. Pemberton
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
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20
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Bonnet T, Morrissey MB, de Villemereuil P, Alberts SC, Arcese P, Bailey LD, Boutin S, Brekke P, Brent LJN, Camenisch G, Charmantier A, Clutton-Brock TH, Cockburn A, Coltman DW, Courtiol A, Davidian E, Evans SR, Ewen JG, Festa-Bianchet M, de Franceschi C, Gustafsson L, Höner OP, Houslay TM, Keller LF, Manser M, McAdam AG, McLean E, Nietlisbach P, Osmond HL, Pemberton JM, Postma E, Reid JM, Rutschmann A, Santure AW, Sheldon BC, Slate J, Teplitsky C, Visser ME, Wachter B, Kruuk LEB. Genetic variance in fitness indicates rapid contemporary adaptive evolution in wild animals. Science 2022; 376:1012-1016. [PMID: 35617403 DOI: 10.1126/science.abk0853] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The rate of adaptive evolution, the contribution of selection to genetic changes that increase mean fitness, is determined by the additive genetic variance in individual relative fitness. To date, there are few robust estimates of this parameter for natural populations, and it is therefore unclear whether adaptive evolution can play a meaningful role in short-term population dynamics. We developed and applied quantitative genetic methods to long-term datasets from 19 wild bird and mammal populations and found that, while estimates vary between populations, additive genetic variance in relative fitness is often substantial and, on average, twice that of previous estimates. We show that these rates of contemporary adaptive evolution can affect population dynamics and hence that natural selection has the potential to partly mitigate effects of current environmental change.
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Affiliation(s)
- Timothée Bonnet
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | | | - Pierre de Villemereuil
- Institut de Systématique, Évolution, Biodiversité (ISYEB), École Pratique des Hautes Études, PSL, MNHN, CNRS, SU, UA, Paris, France.,School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Susan C Alberts
- Departments of Biology and Evolutionary Anthropology, Duke University, Durham, NC, USA
| | - Peter Arcese
- Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Liam D Bailey
- Departments of Evolutionary Ecology and Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Stan Boutin
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Patricia Brekke
- Institute of Zoology, Zoological Society of London, Regents Park, London, UK
| | - Lauren J N Brent
- Centre for Research in Animal Behaviour, University of Exeter, Penryn, UK
| | - Glauco Camenisch
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Anne Charmantier
- Centre d'Écologie Fonctionnelle et Évolutive, Université de Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Tim H Clutton-Brock
- Department of Zoology, University of Cambridge, Cambridge, UK.,Mammal Research Institute, University of Pretoria, Pretoria, South Africa
| | - Andrew Cockburn
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - David W Coltman
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Alexandre Courtiol
- Departments of Evolutionary Ecology and Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Eve Davidian
- Departments of Evolutionary Ecology and Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Simon R Evans
- Edward Grey Institute, Department of Zoology, University of Oxford, Oxford, UK.,Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden.,Centre for Ecology and Conservation, University of Exeter, Penryn, UK
| | - John G Ewen
- Institute of Zoology, Zoological Society of London, Regents Park, London, UK
| | | | - Christophe de Franceschi
- Centre d'Écologie Fonctionnelle et Évolutive, Université de Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Lars Gustafsson
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Oliver P Höner
- Departments of Evolutionary Ecology and Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Thomas M Houslay
- Department of Zoology, University of Cambridge, Cambridge, UK.,Centre for Ecology and Conservation, University of Exeter, Penryn, UK
| | - Lukas F Keller
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.,Zoological Museum, University of Zurich,, Zurich, Switzerland
| | - Marta Manser
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.,Mammal Research Institute, University of Pretoria, Pretoria, South Africa
| | - Andrew G McAdam
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Emily McLean
- Biology Department, Oxford College, Emory University, Oxford, GA, USA
| | - Pirmin Nietlisbach
- School of Biological Sciences, Illinois State University, Normal, IL, USA
| | - Helen L Osmond
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | | | - Erik Postma
- Centre for Ecology and Conservation, University of Exeter, Penryn, UK
| | - Jane M Reid
- Centre for Biodiversity Dynamics, Norwegian University of Science and Technology (NTNU), Trondheim, Norway.,School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - Alexis Rutschmann
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Anna W Santure
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Ben C Sheldon
- Edward Grey Institute, Department of Zoology, University of Oxford, Oxford, UK
| | - Jon Slate
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield, UK
| | - Céline Teplitsky
- Centre d'Écologie Fonctionnelle et Évolutive, Université de Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Marcel E Visser
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - Bettina Wachter
- Departments of Evolutionary Ecology and Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Loeske E B Kruuk
- Research School of Biology, Australian National University, Canberra, ACT, Australia.,Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
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21
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Corripio-Miyar Y, Hayward A, Lemon H, Sweeny AR, Bal X, Kenyon F, Pilkington JG, Pemberton JM, Nussey DH, McNeilly TN. Functionally distinct T-helper cell phenotypes predict resistance to different types of parasites in a wild mammal. Sci Rep 2022; 12:3197. [PMID: 35210503 PMCID: PMC8873199 DOI: 10.1038/s41598-022-07149-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 02/04/2022] [Indexed: 12/31/2022] Open
Abstract
The adaptive immune system is critical to an effective response to infection in vertebrates, with T-helper (Th) cells pivotal in orchestrating these responses. In natural populations where co-infections are the norm, different Th responses are likely to play an important role in maintaining host health and fitness, a relationship which remains poorly understood in wild animals. In this study, we characterised variation in functionally distinct Th responses in a wild population of Soay sheep by enumerating cells expressing Th-subset specific transcription factors and quantifying Th-associated cytokines. We tested the prediction that raised Th1 and Th2 responses should predict reduced apicomplexan and helminth parasite burdens, respectively. All measures of Th-associated cytokine production increased with age, while Th17- and regulatory Th-associated cytokine production increased more rapidly with age in males than females. Independent of age, sex, and each other, IL-4 and Gata3 negatively predicted gastro-intestinal nematode faecal egg count, while IFN-γ negatively predicted coccidian faecal oocyst count. Our results provide important support from outside the laboratory that Th1 and Th2 responses predict resistance to different kinds of parasites, and illustrate how harnessing specific reagents and tools from laboratory immunology will illuminate our understanding of host-parasite interactions in the wild.
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Affiliation(s)
- Yolanda Corripio-Miyar
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Midlothian, EH26 0PZ, UK.
| | - Adam Hayward
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Midlothian, EH26 0PZ, UK
| | - Hannah Lemon
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - Amy R Sweeny
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - Xavier Bal
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - Fiona Kenyon
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Midlothian, EH26 0PZ, UK
| | - Jill G Pilkington
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - Josephine M Pemberton
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - Daniel H Nussey
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - Tom N McNeilly
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Midlothian, EH26 0PZ, UK
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22
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Huang W, Dicks KL, Hadfield JD, Johnston SE, Ballingall KT, Pemberton JM. Contemporary selection on MHC genes in a free-living ruminant population. Ecol Lett 2022; 25:828-838. [PMID: 35050541 PMCID: PMC9306867 DOI: 10.1111/ele.13957] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 10/21/2021] [Accepted: 12/08/2021] [Indexed: 11/27/2022]
Abstract
Genes within the major histocompatibility complex (MHC) are the most variable identified in vertebrates. Pathogen-mediated selection is believed to be the main force maintaining MHC diversity. However, relatively few studies have demonstrated contemporary selection on MHC genes. Here, we examine associations between MHC variation and several fitness measurements including total fitness and five fitness components, in 3400 wild Soay sheep (Ovis aries) monitored between 1989 and 2012. In terms of total fitness, measured as lifetime breeding success of all individuals born, we found haplotypes named C and D were associated with decreased and increased male total fitness respectively. In terms of fitness components, juvenile survival was associated with haplotype divergence while individual haplotypes (C, D and F) were associated with adult fitness components. Consistent with the increased male total fitness, the rarest haplotype D has increased in frequency throughout the study period more than expected under neutral expectations. Our results demonstrate contemporary natural selection is acting on MHC class II genes in Soay sheep and the mode of selection on specific fitness components can be different mode from selection on total fitness.
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Affiliation(s)
- Wei Huang
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Kara L Dicks
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.,Royal Zoological Society of Scotland, Edinburgh, UK
| | - Jarrod D Hadfield
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Susan E Johnston
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | | - Josephine M Pemberton
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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23
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Peters L, Huisman J, Kruuk LEB, Pemberton JM, Johnston SE. Genomic analysis reveals a polygenic architecture of antler morphology in wild red deer (Cervus elaphus). Mol Ecol 2021; 31:1281-1298. [PMID: 34878674 DOI: 10.1111/mec.16314] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 11/26/2021] [Accepted: 12/01/2021] [Indexed: 11/28/2022]
Abstract
Sexually selected traits show large variation and rapid evolution across the animal kingdom, yet genetic variation often persists within populations despite apparent directional selection. A key step in solving this long-standing paradox is to determine the genetic architecture of sexually selected traits to understand evolutionary drivers and constraints at the genomic level. Antlers are a form of sexual weaponry in male red deer (Cervus elaphus). On the island of Rum, Scotland, males with larger antlers have increased breeding success, yet there has been no evidence of any response to selection at the genetic level. To try and understand the mechanisms underlying this observation, we investigate the genetic architecture of ten antler traits and their principal components using genomic data from >38,000 SNPs. We estimate the heritabilities and genetic correlations of the antler traits using a genomic relatedness approach. We then use genome-wide association and haplotype-based regional heritability to identify regions of the genome underlying antler morphology, and an empirical Bayes approach to estimate the underlying distributions of allele effect sizes. We show that antler morphology is highly repeatable over an individual's lifetime, heritable and has a polygenic architecture and that almost all antler traits are positively genetically correlated with some loci identified as having pleiotropic effects. Our findings suggest that a large mutational target and genetic covariances among antler traits, in part maintained by pleiotropy, are likely to contribute to the maintenance of genetic variation in antler morphology in this population.
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Affiliation(s)
- Lucy Peters
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Jisca Huisman
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Loeske E B Kruuk
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.,Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Josephine M Pemberton
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Susan E Johnston
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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24
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Huang W, Dicks KL, Ballingall KT, Johnston SE, Sparks AM, Watt K, Pilkington JG, Pemberton JM. Associations between MHC class II variation and phenotypic traits in a free-living sheep population. Mol Ecol 2021; 31:902-915. [PMID: 34748666 DOI: 10.1111/mec.16265] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 10/22/2021] [Accepted: 11/03/2021] [Indexed: 01/03/2023]
Abstract
Pathogen-mediated selection (PMS) is thought to maintain the high level of allelic diversity observed in the major histocompatibility complex (MHC) class II genes. A comprehensive way to demonstrate contemporary selection is to examine associations between MHC variation and individual fitness. As individual fitness is hard to measure, many studies examine associations between MHC variation and phenotypic traits, including direct or indirect measures of adaptive immunity thought to contribute to fitness. Here, we tested associations between MHC class II variation and five phenotypic traits measured in free-living sheep captured in August: weight, strongyle faecal egg count, and plasma IgA, IgE and IgG immunoglobulin titres against the gastrointestinal nematode parasite Teladorsagia circumcincta. We found no association between MHC class II variation and weight or strongyle faecal egg count. We did, however, find associations between MHC class II variation and immunoglobulin levels which varied with isotype, age and sex. Our results suggest associations between MHC and phenotypic traits are more likely to be found for traits more closely associated with pathogen defence than integrative traits such as bodyweight and highlight the association between MHC variation and antibodies in wild populations.
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Affiliation(s)
- Wei Huang
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Kara L Dicks
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | | - Susan E Johnston
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Alexandra M Sparks
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.,School of Biology, University of Leeds, Leeds, UK
| | - Kathryn Watt
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Jill G Pilkington
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Josephine M Pemberton
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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25
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McFarlane SE, Pemberton JM. Admixture mapping reveals loci for carcass mass in red deer x sika hybrids in Kintyre, Scotland. G3 (Bethesda) 2021; 11:jkab274. [PMID: 34568926 PMCID: PMC8473967 DOI: 10.1093/g3journal/jkab274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 07/16/2021] [Indexed: 12/21/2022]
Abstract
We deployed admixture mapping on a sample of 386 deer from a hybrid swarm between native red deer (Cervus elaphus) and introduced Japanese sika (Cervus nippon) sampled in Kintyre, Scotland to search for quantitative trait loci (QTLs) underpinning phenotypic differences between the species. These two species are highly diverged genetically [Fst between pure species, based on 50K single nucleotide polymorphism (SNPs) = 0.532] and phenotypically: pure red have on average twice the carcass mass of pure sika in our sample (38.7 kg vs 19.1 kg). After controlling for sex, age, and population genetic structure, we found 10 autosomal genomic locations with QTL for carcass mass. Effect sizes ranged from 0.191 to 1.839 kg and as expected, in all cases the allele derived from sika conferred lower carcass mass. The sika population was fixed for all small carcass mass alleles, whereas the red deer population was typically polymorphic. GO term analysis of genes lying in the QTL regions are associated with oxygen transport. Although body mass is a likely target of selection, none of the SNPs marking QTL are introgressing faster or slower than expected in either direction.
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Affiliation(s)
- S Eryn McFarlane
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
- Department of Biology, Lund University, 22100 Lund, Sweden
| | - Josephine M Pemberton
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
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26
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Dicks KL, Pemberton JM, Ballingall KT, Johnston SE. MHC class IIa haplotypes derived by high-throughput SNP screening in an isolated sheep population. G3 (Bethesda) 2021; 11:6298591. [PMID: 34568908 PMCID: PMC8496268 DOI: 10.1093/g3journal/jkab200] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 05/12/2021] [Indexed: 12/01/2022]
Abstract
Investigating the current evolutionary processes acting on a highly polymorphic gene region, such as the major histocompatibility complex (MHC), requires extensive population data for both genotypes and phenotypes. The MHC consists of several tightly linked loci with both allelic and gene content variation, making it challenging to genotype. Eight class IIa haplotypes have previously been identified in the Soay sheep (Ovis aries) of St. Kilda using Sanger sequencing and cloning, but no single locus is representative of all haplotypes. Here, we exploit the closed nature of the island population of Soay sheep and its limited haplotypic variation to identify a panel of SNPs that enable imputation of MHC haplotypes. We compared MHC class IIa haplotypes determined by Sanger sequence-based genotyping of 135 individuals to their SNP profiles generated using the Ovine Infinium HD BeadChip. A panel of 11 SNPs could reliably determine MHC diplotypes, and two additional SNPs within the DQA1 gene enabled detection of a recombinant haplotype affecting only the SNPs downstream of the expressed genes. The panel of 13 SNPs was genotyped in 5951 Soay sheep, of which 5349 passed quality control. Using the Soay sheep pedigree, we were able to trace the origin and inheritance of the recombinant SNP haplotype. This SNP-based method has enabled the rapid generation of locus-specific MHC genotypes for large numbers of Soay sheep. This volume of high-quality genotypes in a well-characterized population of free-living sheep will be valuable for investigating the mechanisms maintaining diversity at the MHC.
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Affiliation(s)
- Kara L Dicks
- School of Biological Sciences, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Josephine M Pemberton
- School of Biological Sciences, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Keith T Ballingall
- Moredun Research Institute, Pentlands Science Park, Edinburgh EH26 0PZ, UK
| | - Susan E Johnston
- School of Biological Sciences, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
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27
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Paquet M, Knape J, Arlt D, Forslund P, Pärt T, Flagstad Ø, Jones CG, Nicoll MAC, Norris K, Pemberton JM, Sand H, Svensson L, Tatayah V, Wabakken P, Wikenros C, Åkesson M, Low M. Integrated population models poorly estimate the demographic contribution of immigration. Methods Ecol Evol 2021. [DOI: 10.1111/2041-210x.13667] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Matthieu Paquet
- Department of Ecology Swedish University of Agricultural Sciences Uppsala Sweden
| | - Jonas Knape
- Department of Ecology Swedish University of Agricultural Sciences Uppsala Sweden
| | - Debora Arlt
- Department of Ecology Swedish University of Agricultural Sciences Uppsala Sweden
- SLU Swedish Species Information Centre Swedish University of Agricultural Sciences Uppsala Sweden
| | - Pär Forslund
- Department of Ecology Swedish University of Agricultural Sciences Uppsala Sweden
| | - Tomas Pärt
- Department of Ecology Swedish University of Agricultural Sciences Uppsala Sweden
| | | | - Carl G. Jones
- Mauritian Wildlife Foundation Vacoas Mauritius
- Durrell Wildlife Conservation Trust Trinity UK
| | | | | | - Josephine M. Pemberton
- Institute of Evolutionary Biology School of Biological Sciences University of Edinburgh Edinburgh UK
| | - Håkan Sand
- Department of Ecology Swedish University of Agricultural Sciences Uppsala Sweden
| | - Linn Svensson
- Department of Ecology Swedish University of Agricultural Sciences Uppsala Sweden
| | | | - Petter Wabakken
- Faculty of Applied Ecology and Agricultural Sciences Inland Norway University of Applied Sciences Hamar Norway
| | - Camilla Wikenros
- Department of Ecology Swedish University of Agricultural Sciences Uppsala Sweden
| | - Mikael Åkesson
- Department of Ecology Swedish University of Agricultural Sciences Uppsala Sweden
| | - Matthew Low
- Department of Ecology Swedish University of Agricultural Sciences Uppsala Sweden
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28
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Gauzere J, Walling CA, Pick JL, Watt K, Jack P, Morris A, Morris S, Pemberton JM. The role of maternally transferred antibodies in maternal performance in red deer. Ecol Lett 2021; 24:2065-2076. [PMID: 34245475 DOI: 10.1111/ele.13834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/25/2021] [Accepted: 06/04/2021] [Indexed: 11/28/2022]
Abstract
Maternal effects are ubiquitous. Yet, the pathways through which maternal effects occur in wild mammals remain largely unknown. We hypothesise that maternal immune transfer is a key mechanism by which mothers can affect their offspring fitness, and that individual variation in maternally derived antibodies mainly depends on a mother's characteristics and the environmental conditions she experiences. To test this, we assayed six colostrum-derived antibodies in the plasma of 1447 neonates in a wild red deer population. Neonatal antibody levels were mainly affected by maternal genes, environmental variation and costs of prior reproductive investment. We found consistent heterogeneity in maternal performance across traits, with mothers producing the heaviest calves also having calves with more antibodies. Unexpectedly, antibody levels were not associated with calf survival. We provide a unique example of how evolutionary theory on maternal effects can be used to gain insight into the causes of maternal effects in wild populations.
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Affiliation(s)
- Julie Gauzere
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - Craig A Walling
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - Joel L Pick
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - Kathryn Watt
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - Penny Jack
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - Alison Morris
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - Sean Morris
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - Josephine M Pemberton
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FL, UK
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29
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Stoffel MA, Johnston SE, Pilkington JG, Pemberton JM. Mutation load decreases with haplotype age in wild Soay sheep. Evol Lett 2021; 5:187-195. [PMID: 34136268 PMCID: PMC8190445 DOI: 10.1002/evl3.229] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 04/06/2021] [Accepted: 04/13/2021] [Indexed: 01/01/2023] Open
Abstract
Runs of homozygosity (ROH) are pervasive in diploid genomes and expose the effects of deleterious recessive mutations, but how exactly these regions contribute to variation in fitness remains unclear. Here, we combined empirical analyses and simulations to explore the deleterious effects of ROH with varying genetic map lengths in wild Soay sheep. Using a long-term dataset of 4879 individuals genotyped at 417K SNPs, we found that inbreeding depression increases with ROH length. A 1% genomic increase in long ROH (>12.5 cM) reduced the odds of first-year survival by 12.4% compared to only 7.7% for medium ROH (1.56-12.5 cM), whereas short ROH (<1.56 cM) had no effect on survival. We show by forward genetic simulations that this is predicted: compared to shorter ROH, long ROH will have higher densities of deleterious alleles, with larger average effects on fitness and lower population frequencies. Taken together, our results are consistent with the idea that the mutation load decreases in older haplotypes underlying shorter ROH, where purifying selection has had more time to purge deleterious mutations. Finally, our study demonstrates that strong inbreeding depression can persist despite ongoing purging in a historically small population.
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Affiliation(s)
- Martin A. Stoffel
- School of Biological Sciences, Institute of Evolutionary BiologyUniversity of EdinburghEdinburghEH9 3FLUnited Kingdom
| | - Susan E. Johnston
- School of Biological Sciences, Institute of Evolutionary BiologyUniversity of EdinburghEdinburghEH9 3FLUnited Kingdom
| | - Jill G. Pilkington
- School of Biological Sciences, Institute of Evolutionary BiologyUniversity of EdinburghEdinburghEH9 3FLUnited Kingdom
| | - Josephine M. Pemberton
- School of Biological Sciences, Institute of Evolutionary BiologyUniversity of EdinburghEdinburghEH9 3FLUnited Kingdom
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30
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Stoffel MA, Johnston SE, Pilkington JG, Pemberton JM. Genetic architecture and lifetime dynamics of inbreeding depression in a wild mammal. Nat Commun 2021; 12:2972. [PMID: 34016997 PMCID: PMC8138023 DOI: 10.1038/s41467-021-23222-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 03/29/2021] [Indexed: 02/03/2023] Open
Abstract
Inbreeding depression is ubiquitous, but we still know little about its genetic architecture and precise effects in wild populations. Here, we combine long-term life-history data with 417 K imputed SNP genotypes for 5952 wild Soay sheep to explore inbreeding depression on a key fitness component, annual survival. Inbreeding manifests in long runs of homozygosity (ROH), which make up nearly half of the genome in the most inbred individuals. The ROH landscape varies widely across the genome, with islands where up to 87% and deserts where only 4% of individuals have ROH. The fitness consequences of inbreeding are severe; a 10% increase in individual inbreeding FROH is associated with a 60% reduction in the odds of survival in lambs, though inbreeding depression decreases with age. Finally, a genome-wide association scan on ROH shows that many loci with small effects and five loci with larger effects contribute to inbreeding depression in survival.
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Affiliation(s)
- M A Stoffel
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.
| | - S E Johnston
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - J G Pilkington
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - J M Pemberton
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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31
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Huang W, Pilkington JG, Pemberton JM. Patterns of MHC-dependent sexual selection in a free-living population of sheep. Mol Ecol 2021; 30:6733-6742. [PMID: 33960549 DOI: 10.1111/mec.15938] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 02/18/2021] [Accepted: 04/23/2021] [Indexed: 12/12/2022]
Abstract
The MHC is one of the most polymorphic gene clusters in vertebrates and play an essential role in adaptive immunity. Apart from pathogen-mediated selection, sexual selection can also contribute to the maintenance of MHC diversity. MHC-dependent sexual selection could occur via several mechanisms but at present there is no consensus as to which of these mechanisms are involved and their importance. Previous studies have often suffered from limited genetic and behavioural data and small sample size, and were rarely able to examine all the mechanisms together, determine whether signatures of MHC-based non-random mating are independent of genomic effects or differentiate whether MHC-dependent sexual selection takes place at the pre- or post-copulatory stage. In this study, we use Monte Carlo simulation to investigate evidence for non-random MHC-dependent mating patterns by all three mechanisms in a free-living population of Soay sheep. Using 1710 sheep diplotyped at the MHC class IIa region and genome-wide SNPs, together with field observations of consorts, we found sexual selection against a particular haplotype in males at the pre-copulatory stage and sexual selection against female MHC heterozygosity during the rut. We also found MHC-dependent disassortative mating at the post-copulatory stage, along with strong evidence of inbreeding avoidance at both stages. However, results from generalized linear mixed models suggest that the pattern of MHC-dependent disassortative mating could be a by-product of inbreeding avoidance. Our results therefore suggest that while multiple apparent mechanisms of non-random mating with respect to the MHC may occur, some of them have alternative explanations.
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Affiliation(s)
- Wei Huang
- Institute of Evolutionary Biology,School of Biological Science, University of Edinburgh, Edinburgh, UK
| | - Jill G Pilkington
- Institute of Evolutionary Biology,School of Biological Science, University of Edinburgh, Edinburgh, UK
| | - Josephine M Pemberton
- Institute of Evolutionary Biology,School of Biological Science, University of Edinburgh, Edinburgh, UK
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32
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McFarlane SE, Senn HV, Smith SL, Pemberton JM. Locus-specific introgression in young hybrid swarms: Drift may dominate selection. Mol Ecol 2021; 30:2104-2115. [PMID: 33638185 DOI: 10.1111/mec.15862] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 02/01/2021] [Accepted: 02/17/2021] [Indexed: 12/17/2022]
Abstract
Closely related species that have previously inhabited geographically separated ranges are hybridizing at an increasing rate due to human disruptions. These human-mediated hybrid zones can be used to study reproductive isolation between species at secondary contact, including examining locus-specific rates of introgression. Introgression is expected to be heterogenous across the genome, reflecting variation in selection. Those loci that introgress especially slowly are good candidates for being involved in reproductive isolation, while those loci that introgress quickly may be involved in adaptive introgression. In the context of conservation, policy makers are especially concerned about introduced alleles moving quickly into the background of a native or endemic species, as these alleles could replace the native alleles in the population, leading to extinction via hybridization. We applied genomic cline analyses to 44,997 SNPs to identify loci introgressing more or less when compared to the genome wide expectation in a human-mediated hybridizing population of red deer and sika in Kintyre Scotland. We found 11.4% of SNPs had cline centres that were significantly different from the genome wide expectation, and 17.6% of all SNPs had excess rates of introgression. Based on simulations, we believe that many of these markers have diverged from the genome-wide average due to drift, rather than because of selection, and we suggest that these simulations can be useful as a null distribution for future studies of genomic clines. Future work on red deer and sika could determine the policy implications of allelic-replacement due to drift rather than selection, and could use replicate, geographically distinct hybrid zones to narrow down those loci that are responding to selection.
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Affiliation(s)
- S Eryn McFarlane
- School of Biological Sciences, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.,Department of Biology, Lund University, Lund, Sweden
| | - Helen V Senn
- School of Biological Sciences, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.,WildGenes Laboratory, Royal Zoological Society of Scotland, Edinburgh, UK
| | - Stephanie L Smith
- School of Biological Sciences, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.,The Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Edinburgh, UK
| | - Josephine M Pemberton
- School of Biological Sciences, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
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33
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Albery GF, Morris A, Morris S, Pemberton JM, Clutton-Brock TH, Nussey DH, Firth JA. Multiple spatial behaviours govern social network positions in a wild ungulate. Ecol Lett 2021; 24:676-686. [PMID: 33583128 DOI: 10.1111/ele.13684] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 12/22/2020] [Accepted: 12/23/2020] [Indexed: 01/19/2023]
Abstract
The structure of wild animal social systems depends on a complex combination of intrinsic and extrinsic drivers. Population structuring and spatial behaviour are key determinants of individuals' observed social behaviour, but quantifying these spatial components alongside multiple other drivers remains difficult due to data scarcity and analytical complexity. We used a 43-year dataset detailing a wild red deer population to investigate how individuals' spatial behaviours drive social network positioning, while simultaneously assessing other potential contributing factors. Using Integrated Nested Laplace Approximation (INLA) multi-matrix animal models, we demonstrate that social network positions are shaped by two-dimensional landscape locations, pairwise space sharing, individual range size, and spatial and temporal variation in population density, alongside smaller but detectable impacts of a selection of individual-level phenotypic traits. These results indicate strong, multifaceted spatiotemporal structuring in this society, emphasising the importance of considering multiple spatial components when investigating the causes and consequences of sociality.
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Affiliation(s)
- Gregory F Albery
- Department of Biology, Georgetown University, Washington, DC, USA.,Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Alison Morris
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Sean Morris
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | | | - Tim H Clutton-Brock
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.,Department of Zoology, University of Cambridge, Cambridge, UK
| | - Daniel H Nussey
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Josh A Firth
- Department of Zoology, University of Oxford, Oxford, UK.,Merton College, University of Oxford, Oxford, UK
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34
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Albery GF, Morris A, Morris S, Kenyon F, Nussey DH, Pemberton JM. Fitness Costs of Parasites Explain Multiple Life-History Trade-Offs in a Wild Mammal. Am Nat 2021; 197:324-335. [PMID: 33625970 DOI: 10.1086/712633] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractReproduction in wild animals can divert limited resources away from immune defense, resulting in increased parasite burdens. A long-standing prediction of life-history theory states that these parasites can harm the reproductive individual, reducing its subsequent survival and fecundity, producing reproduction-fitness trade-offs. Here, we examined associations among reproductive allocation, immunity, parasitism, and subsequent survival and fecundity in a wild population of individually identified red deer (Cervus elaphus). Using path analysis, we investigated whether costs of lactation in terms of downstream survival and fecundity were mediated by changes in strongyle nematode count and mucosal antibody levels. Lactating females exhibited increased parasite counts, which were in turn associated with substantially decreased fitness in the following year in terms of overwinter survival, fecundity, subsequent calf weight, and parturition date. This study offers observational evidence for parasite regulation of multiple life-history trade-offs, supporting the role of parasites as an important mediating factor in wild mammal populations.
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35
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de Villemereuil P, Charmantier A, Arlt D, Bize P, Brekke P, Brouwer L, Cockburn A, Côté SD, Dobson FS, Evans SR, Festa-Bianchet M, Gamelon M, Hamel S, Hegelbach J, Jerstad K, Kempenaers B, Kruuk LEB, Kumpula J, Kvalnes T, McAdam AG, McFarlane SE, Morrissey MB, Pärt T, Pemberton JM, Qvarnström A, Røstad OW, Schroeder J, Senar JC, Sheldon BC, van de Pol M, Visser ME, Wheelwright NT, Tufto J, Chevin LM. Fluctuating optimum and temporally variable selection on breeding date in birds and mammals. Proc Natl Acad Sci U S A 2020; 117:31969-31978. [PMID: 33257553 PMCID: PMC7116484 DOI: 10.1073/pnas.2009003117] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 09/24/2020] [Indexed: 01/01/2023] Open
Abstract
Temporal variation in natural selection is predicted to strongly impact the evolution and demography of natural populations, with consequences for the rate of adaptation, evolution of plasticity, and extinction risk. Most of the theory underlying these predictions assumes a moving optimum phenotype, with predictions expressed in terms of the temporal variance and autocorrelation of this optimum. However, empirical studies seldom estimate patterns of fluctuations of an optimum phenotype, precluding further progress in connecting theory with observations. To bridge this gap, we assess the evidence for temporal variation in selection on breeding date by modeling a fitness function with a fluctuating optimum, across 39 populations of 21 wild animals, one of the largest compilations of long-term datasets with individual measurements of trait and fitness components. We find compelling evidence for fluctuations in the fitness function, causing temporal variation in the magnitude, but not the direction of selection. However, fluctuations of the optimum phenotype need not directly translate into variation in selection gradients, because their impact can be buffered by partial tracking of the optimum by the mean phenotype. Analyzing individuals that reproduce in consecutive years, we find that plastic changes track movements of the optimum phenotype across years, especially in bird species, reducing temporal variation in directional selection. This suggests that phenological plasticity has evolved to cope with fluctuations in the optimum, despite their currently modest contribution to variation in selection.
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Affiliation(s)
- Pierre de Villemereuil
- Centre d'Écologie Fonctionnelle et Évolutive, CNRS, Université de Montpellier, Université Paul Valéry Montpellier 3, École Pratique des Hautes Études | Paris Science et Lettres, Institut de Recherche pour le Développement, 34000 Montpellier, France;
- Institut de Systématique, Évolution, Biodiversité, École Pratique des Hautes Études | Paris Sciences et Lettres, Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, Université des Antilles, 75005 Paris, France
| | - Anne Charmantier
- Centre d'Écologie Fonctionnelle et Évolutive, CNRS, Université de Montpellier, Université Paul Valéry Montpellier 3, École Pratique des Hautes Études | Paris Science et Lettres, Institut de Recherche pour le Développement, 34000 Montpellier, France
| | - Debora Arlt
- Department of Ecology, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden
| | - Pierre Bize
- School of Biological Sciences, University of Aberdeen, AB24 2TZ Aberdeen, United Kingdom
| | - Patricia Brekke
- Institute of Zoology, Zoological Society of London, NW1 4RY London, United Kingdom
| | - Lyanne Brouwer
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT 2600 Australia
- Department of Animal Ecology, Netherlands Institute of Ecology, 6700 AB Wageningen, The Netherlands
- Department of Animal Ecology and Physiology, Institute for Water and Wetland Research, Radboud University, 6500 GL Nijmegen, The Netherlands
| | - Andrew Cockburn
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT 2600 Australia
| | - Steeve D Côté
- Département de Biologie and Centre d'Études Nordiques, Université Laval, Québec, G1V 0A6 QC, Canada
| | - F Stephen Dobson
- Department of Biological Sciences, Auburn University, Auburn, AL 36849
| | - Simon R Evans
- Edward Grey Institute, Department of Zoology, University of Oxford, Oxford OX1 3PS, United Kingdom
- Centre for Ecology and Conservation, University of Exeter, Penryn TR10 9FE, United Kingdom
| | - Marco Festa-Bianchet
- Département de biologie, Université de Sherbrooke, J1K 2R1 Sherbrooke, Québec, Canada
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT 2600 Australia
| | - Marlène Gamelon
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Sandra Hamel
- Département de Biologie, Université Laval, Québec, G1V 0A6 QC, Canada
| | - Johann Hegelbach
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, CH-8057 Zurich, Switzerland
| | | | - Bart Kempenaers
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology, 82319 Seewiesen, Germany
| | - Loeske E B Kruuk
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT 2600 Australia
| | - Jouko Kumpula
- Terrestrial Population Dynamics, Natural Resources Institute Finland, FIN-999870, Inari, Finland
| | - Thomas Kvalnes
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Andrew G McAdam
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309
| | - S Eryn McFarlane
- Department of Ecology and Genetics, Uppsala University, 75236 Uppsala, Sweden
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
| | - Michael B Morrissey
- School of Biology, University of St. Andrews, St. Andrews, Fife KY16 9TH, United Kingdom
| | - Tomas Pärt
- Department of Ecology, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden
| | - Josephine M Pemberton
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
| | - Anna Qvarnström
- Department of Ecology and Genetics, Uppsala University, 75236 Uppsala, Sweden
| | - Ole Wiggo Røstad
- Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, 1432 Ås, Norway
| | - Julia Schroeder
- Department of Life Sciences, Imperial College London, SL5 7PY Ascot, Berks,
| | - Juan Carlos Senar
- Behavioural and Evolutionary Ecology Research Unit, Museu de Ciències Naturals de Barcelona, E-08003 Barcelona, Spain
| | - Ben C Sheldon
- Edward Grey Institute, Department of Zoology, University of Oxford, Oxford OX1 3PS, United Kingdom
| | - Martijn van de Pol
- Department of Animal Ecology, Netherlands Institute of Ecology, 6700 AB Wageningen, The Netherlands
| | - Marcel E Visser
- Department of Animal Ecology, Netherlands Institute of Ecology, 6700 AB Wageningen, The Netherlands
| | | | - Jarle Tufto
- Centre for Biodiversity Dynamics, Department of Mathematics, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
| | - Luis-Miguel Chevin
- Centre d'Écologie Fonctionnelle et Évolutive, CNRS, Université de Montpellier, Université Paul Valéry Montpellier 3, École Pratique des Hautes Études | Paris Science et Lettres, Institut de Recherche pour le Développement, 34000 Montpellier, France;
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36
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Sparks AM, Hayward AD, Watt K, Pilkington JG, Pemberton JM, Johnston SE, McNeilly TN, Nussey DH. Maternally derived anti-helminth antibodies predict offspring survival in a wild mammal. Proc Biol Sci 2020; 287:20201931. [PMID: 33234082 PMCID: PMC7739501 DOI: 10.1098/rspb.2020.1931] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The transfer of antibodies from mother to offspring provides crucial protection against infection to offspring during early life in humans and domestic and laboratory animals. However, few studies have tested the consequences of variation in maternal antibody transfer for offspring fitness in the wild. Further, separating the immunoprotective effects of antibodies from their association with nutritional resources provided by mothers is difficult. Here, we measured plasma levels of total and parasite-specific antibodies in neonatal (less than 10 days old) wild Soay sheep over 25 years to quantify variation in maternal antibody transfer and test its association with offspring survival. Maternal antibody transfer was predicted by maternal age and previous antibody responses, and was consistent within mothers across years. Neonatal total IgG antibody levels were positively related to early growth, suggesting they reflected nutritional transfer. Neonatal parasite-specific IgG levels positively predicted first-year survival, independent of lamb weight, total IgG levels and subsequent lamb parasite-specific antibody levels. This relationship was partly mediated via an indirect negative association with parasite burden. We show that among-female variation in maternal antibody transfer can have long-term effects on offspring growth, parasite burden and fitness in the wild, and is likely to impact naturally occurring host–parasite dynamics.
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Affiliation(s)
- Alexandra M Sparks
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK.,Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK.,Faculty of Biological Sciences, School of Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Adam D Hayward
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Midlothian EH26 0PZ, UK
| | - Kathryn Watt
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Jill G Pilkington
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Josephine M Pemberton
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Susan E Johnston
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Tom N McNeilly
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Midlothian EH26 0PZ, UK
| | - Daniel H Nussey
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK.,Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
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37
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Marden E, Abbott RJ, Austerlitz F, Ortiz-Barrientos D, Baucom RS, Bongaerts P, Bonin A, Bonneaud C, Browne L, Alex Buerkle C, Caicedo AL, Coltman DW, Cruzan MB, Davison A, DeWoody JA, Dumbrell AJ, Emerson BC, Fountain-Jones NM, Gillespie R, Giraud T, Hansen MM, Hodgins KA, Heuertz M, Hirase S, Hooper R, Hohenlohe P, Kane NC, Kelley JL, Kinziger AP, McKenzie VJ, Moreau CS, Nazareno AG, Pelletier TA, Pemberton JM, Qu Y, Renaut S, Riginos C, Rodríguez-Ezpeleta N, Rogers SM, Russell JA, Schoville SD, Shi S, Smith M, Sork VL, Stone GN, Taberlet P, Videvall E, Waits L, Warschefsky E, Wayne RK, Whibley A, Willoughby J, Yoder JB, Zinger L, Sibbett B, Narum S, Rieseberg LH. Sharing and reporting benefits from biodiversity research. Mol Ecol 2020; 30:1103-1107. [PMID: 33159357 DOI: 10.1111/mec.15702] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 10/19/2020] [Indexed: 11/28/2022]
Affiliation(s)
- Emily Marden
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | | | - Frédéric Austerlitz
- UMR 7206 Eco-Anthropologie, CNRS/MNHN/Université de Paris, Musée de l'Homme, Paris, France
| | | | - Regina S Baucom
- Ecology and Evolutionary Biology Department, University of Michigan, Ann Arbor, MI, USA
| | - Pim Bongaerts
- California Academy of Sciences, San Francisco, CA, USA
| | - Aurélie Bonin
- Laboratoire d'Ecologie Alpine, CNRS, Université Grenoble Alpes, Grenoble, France
| | - Camille Bonneaud
- Biosciences, College of Life and Environmental Science, University of Exeter, Cornwall, UK
| | - Luke Browne
- School of the Environment, Yale University, New Haven, CT, USA
| | - C Alex Buerkle
- Department of Botany, University of Wyoming, Laramie, WY, USA
| | - Ana L Caicedo
- Biology Department, University of Massachusetts, Amherst, MA, USA
| | - David W Coltman
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | | | - Angus Davison
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - J Andrew DeWoody
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN, USA
| | | | - Brent C Emerson
- Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC), La Laguna, Spain
| | | | - Rosemary Gillespie
- Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA
| | - Tatiana Giraud
- Ecologie Systematique Evolution, CNRS, Université Paris-Saclay, Orsay, France
| | | | - Kathryn A Hodgins
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
| | | | - Shotaro Hirase
- Fisheries Laboratory, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Shizuoka, Japan
| | - Rebecca Hooper
- Centre for Ecology and Conservation, University of Exeter, Penryn, UK
| | - Paul Hohenlohe
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, USA
| | - Nolan C Kane
- Department of Ecology and Evolutionary Biology, The University of Colorado, Boulder, CO, USA
| | - Joanna L Kelley
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Andrew P Kinziger
- Department of Fisheries Biology, Humboldt State University, Arcata, CA, USA
| | - Valerie J McKenzie
- Department of Ecology and Evolutionary Biology, The University of Colorado, Boulder, CO, USA
| | - Corrie S Moreau
- Departments of Entomology and Ecology & Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Alison G Nazareno
- Department of Genetics, Ecology and Evolution, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | | | - Josephine M Pemberton
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Yanhua Qu
- Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | | | - Cynthia Riginos
- School of Biological Sciences, University of Queensland, Saint Lucia, QLD, Australia
| | | | - Sean M Rogers
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Jacob A Russell
- Department of Biology, Drexel University, Philadelphia, PA, USA
| | - Sean D Schoville
- Department of Entomology, University of Wisconsin, Madison, WI, USA
| | - Suhua Shi
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Megan Smith
- Department of Biology and Department of Computer Science, Indiana University, Bloomington, IN, USA
| | - Victoria L Sork
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
| | - Graham N Stone
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Pierre Taberlet
- Laboratoire d'Ecologie Alpine, CNRS, Université Grenoble Alpes, Grenoble, France
| | - Elin Videvall
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, Washington, DC, USA
| | - Lisette Waits
- Department of Fish and Wildlife Sciences, University of Idaho, Moscow, ID, USA
| | - Emily Warschefsky
- Department of Ecology and Evolutionary Biology, The University of Colorado, Boulder, CO, USA.,William L. Brown Center, Missouri Botanical Garden, St. Louis, MO, USA
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
| | - Annabel Whibley
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Janna Willoughby
- School of Forestry and Wildlife Sciences, Auburn University, Auburn, AL, USA
| | - Jeremy B Yoder
- Department of Biology, California State University, Northridge, CA, USA
| | - Lucie Zinger
- Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Benjamin Sibbett
- John Wiley & Sons, Atrium Southern Gate, Chichester, West Sussex, UK
| | - Shawn Narum
- Hagerman Genetics Laboratory, Columbia River Inter-Tribal Fish Commission, Hagerman, ID, USA
| | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
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38
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de Jong JF, van Hooft P, Megens HJ, Crooijmans RPMA, de Groot GA, Pemberton JM, Huisman J, Bartoš L, Iacolina L, van Wieren SE, Ydenberg RC, Prins HHT. Fragmentation and Translocation Distort the Genetic Landscape of Ungulates: Red Deer in the Netherlands. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.535715] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Hunter DC, Pemberton JM, Pilkington JG, Morrissey MB. Pedigree-Based Estimation of Reproductive Value. J Hered 2020; 110:433-444. [PMID: 31259373 DOI: 10.1093/jhered/esz033] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 05/10/2019] [Indexed: 01/07/2023] Open
Abstract
How successful an individual or cohort is, in terms of their genetic contribution to the future population, is encapsulated in the concept of reproductive value, and is crucial for understanding selection and evolution. Long-term studies of pedigreed populations offer the opportunity to estimate reproductive values directly. However, the degree to which genetic contributions, as defined by a pedigree, may converge on their long-run values within the time frames of available data sets, such that they may be interpreted as estimates of reproductive value, is unclear. We develop a system for pedigree-based calculation of the expected genetic representation that both individuals and cohorts make to the population in the years following their birth. We apply this system to inference of individual and cohort reproductive values in Soay sheep (Ovis aries) from St Kilda, Outer Hebrides. We observe that these genetic contributions appear to become relatively stable within modest time frames. As such, it may be reasonable to consider pedigree-based calculations of genetic contributions to future generations as estimates of reproductive value. This approach and the knowledge that the estimates can stabilize within decades should offer new opportunities to analyze data from pedigreed wild populations, which will be of value to many fields within evolutionary biology and demography.
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Affiliation(s)
- Darren C Hunter
- Dyers Brae House, School of Biology, University of St Andrews, St Andrews, UK
| | - Josephine M Pemberton
- Dyers Brae House, School of Biology, University of St Andrews, St Andrews, UK.,Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Jill G Pilkington
- Dyers Brae House, School of Biology, University of St Andrews, St Andrews, UK
| | - Michael B Morrissey
- Dyers Brae House, School of Biology, University of St Andrews, St Andrews, UK
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40
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Gauzere J, Pemberton JM, Morris S, Morris A, Kruuk LEB, Walling CA. The genetic architecture of maternal effects across ontogeny in the red deer. Evolution 2020; 74:1378-1391. [DOI: 10.1111/evo.14000] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 04/24/2020] [Accepted: 05/04/2020] [Indexed: 12/22/2022]
Affiliation(s)
- Julie Gauzere
- Institute of Evolutionary Biology, School of Biological Sciences University of Edinburgh Edinburgh EH9 3FL United Kingdom
| | - Josephine M. Pemberton
- Institute of Evolutionary Biology, School of Biological Sciences University of Edinburgh Edinburgh EH9 3FL United Kingdom
| | - Sean Morris
- Institute of Evolutionary Biology, School of Biological Sciences University of Edinburgh Edinburgh EH9 3FL United Kingdom
| | - Alison Morris
- Institute of Evolutionary Biology, School of Biological Sciences University of Edinburgh Edinburgh EH9 3FL United Kingdom
| | - Loeske E. B. Kruuk
- Research School of Biology The Australian National University ACT 0200 Canberra Australia
| | - Craig A. Walling
- Institute of Evolutionary Biology, School of Biological Sciences University of Edinburgh Edinburgh EH9 3FL United Kingdom
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41
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Froy H, Sparks AM, Watt K, Sinclair R, Bach F, Pilkington JG, Pemberton JM, McNeilly TN, Nussey DH. Senescence in immunity against helminth parasites predicts adult mortality in a wild mammal. Science 2020; 365:1296-1298. [PMID: 31604239 DOI: 10.1126/science.aaw5822] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 07/30/2019] [Indexed: 12/14/2022]
Abstract
Our understanding of the deterioration in immune function in old age-immunosenescence-derives principally from studies of modern human populations and laboratory animals. The generality and significance of this process for systems experiencing complex, natural infections and environmental challenges are unknown. Here, we show that late-life declines in an important immune marker of resistance to helminth parasites in wild Soay sheep predict overwinter mortality. We found senescence in circulating antibody levels against a highly prevalent nematode worm, which was associated with reduced adult survival probability, independent of changes in body weight. These findings establish a role for immunosenescence in the ecology and evolution of natural populations.
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Affiliation(s)
- H Froy
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK. .,Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
| | - A M Sparks
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.,School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - K Watt
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - R Sinclair
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - F Bach
- Institute of Immunology and Infection Research, University of Edinburgh, Edinburgh, UK
| | - J G Pilkington
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - J M Pemberton
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - T N McNeilly
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, UK
| | - D H Nussey
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
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42
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Albery GF, Becker DJ, Kenyon F, Nussey DH, Pemberton JM. The Fine-Scale Landscape of Immunity and Parasitism in a Wild Ungulate Population. Integr Comp Biol 2020; 59:1165-1175. [PMID: 30942858 DOI: 10.1093/icb/icz016] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Spatial heterogeneity in susceptibility and exposure to parasites is a common source of confounding variation in disease ecology studies. However, it is not known whether spatial autocorrelation acts on immunity at small scales, within wild animal populations, and whether this predicts spatial patterns in infection. Here we used a well-mixed wild population of individually recognized red deer (Cervus elaphus) inhabiting a heterogeneous landscape to investigate fine-scale spatial patterns of immunity and parasitism. We noninvasively collected 842 fecal samples from 141 females with known ranging behavior over 2 years. We quantified total and helminth-specific mucosal antibodies and counted propagules of three gastrointestinal helminth taxa. These data were analyzed with linear mixed models using the Integrated Nested Laplace Approximation, using a Stochastic Partial Differentiation Equation approach to control for and quantify spatial autocorrelation. We also investigated whether spatial patterns of immunity and parasitism changed seasonally. We discovered substantial spatial heterogeneity in general and helminth-specific antibody levels and parasitism with two helminth taxa, all of which exhibited contrasting seasonal variation in their spatial patterns. Notably, Fasciola hepatica intensity appeared to be strongly influenced by the presence of wet grazing areas, and antibody hotspots did not correlate with distributions of any parasites. Our results suggest that spatial heterogeneity may be an important factor affecting immunity and parasitism in a wide range of study systems. We discuss these findings with regards to the design of sampling regimes and public health interventions, and suggest that disease ecology studies investigate spatial heterogeneity more regularly to enhance their results, even when examining small geographic areas.
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Affiliation(s)
- Gregory F Albery
- Institute of Evolutionary Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - Daniel J Becker
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Fiona Kenyon
- Pentlands Science Park, Moredun Research Institute, Bush Loan, Midlothian EH26 0PZ, UK
| | - Daniel H Nussey
- Institute of Evolutionary Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - Josephine M Pemberton
- Institute of Evolutionary Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, EH9 3FL, UK
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43
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McFarlane SE, Hunter DC, Senn HV, Smith SL, Holland R, Huisman J, Pemberton JM. Increased genetic marker density reveals high levels of admixture between red deer and introduced Japanese sika in Kintyre, Scotland. Evol Appl 2020; 13:432-441. [PMID: 31993087 PMCID: PMC6976951 DOI: 10.1111/eva.12880] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 09/01/2019] [Accepted: 10/10/2019] [Indexed: 12/14/2022] Open
Abstract
Hybridization is a natural process at species range boundaries, but increasing numbers of species are hybridizing due to direct or indirect human activities. In such cases of anthropogenic hybridization, subsequent introgression can threaten the survival of native species. To date, many such systems have been studied with too few genetic markers to assess the level of threat resulting from advanced backcrossing. Here, we use 44,999 single nucleotide polymorphisms (SNPs) and the ADMIXTURE program to study two areas of Scotland where a panel of 22 diagnostic microsatellites previously identified introgression between native red deer (Cervus elaphus) and introduced Japanese sika (Cervus nippon). In Kintyre, we reclassify 26% of deer from the pure species categories to the hybrid category whereas in the NW Highlands we only reclassify 2%. As expected, the reclassified individuals are mostly advanced backcrosses. We also investigate the ability of marker panels selected on different posterior allele frequency criteria to find hybrids assigned by the full marker set and show that in our data, ancestry informative markers (i.e. those that are highly differentiated between the species, but not fixed) are better than diagnostic markers (those markers that are fixed between the species) because they are more evenly distributed in the genome. Diagnostic loci are concentrated on the X chromosome to the detriment of autosomal coverage.
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Affiliation(s)
- S. Eryn McFarlane
- Institute of Evolutionary BiologySchool of Biological ScienceUniversity of EdinburghEdinburghUK
- Department of BiologyLund UniversityLundSweden
| | - Darren C. Hunter
- Institute of Evolutionary BiologySchool of Biological ScienceUniversity of EdinburghEdinburghUK
- Department of Animal and Plant SciencesUniversity of SheffieldSheffieldUK
| | - Helen V. Senn
- Institute of Evolutionary BiologySchool of Biological ScienceUniversity of EdinburghEdinburghUK
- WildGenes LaboratoryRoyal Zoological Society of ScotlandEdinburghUK
| | - Stephanie L. Smith
- Institute of Evolutionary BiologySchool of Biological ScienceUniversity of EdinburghEdinburghUK
- The Royal (Dick) School of Veterinary StudiesUniversity of EdinburghEaster Bush CampusMidlothian, EdinburghUK
| | - Rebecca Holland
- Institute of Evolutionary BiologySchool of Biological ScienceUniversity of EdinburghEdinburghUK
| | - Jisca Huisman
- Institute of Evolutionary BiologySchool of Biological ScienceUniversity of EdinburghEdinburghUK
| | - Josephine M. Pemberton
- Institute of Evolutionary BiologySchool of Biological ScienceUniversity of EdinburghEdinburghUK
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44
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Albery GF, Watt KA, Keith R, Morris S, Morris A, Kenyon F, Nussey DH, Pemberton JM. Reproduction has different costs for immunity and parasitism in a wild mammal. Funct Ecol 2019. [DOI: 10.1111/1365-2435.13475] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Gregory F. Albery
- Institute of Evolutionary Biology School of Biological Sciences University of Edinburgh Edinburgh UK
| | - Kathryn A. Watt
- Institute of Evolutionary Biology School of Biological Sciences University of Edinburgh Edinburgh UK
| | - Rosie Keith
- Institute of Evolutionary Biology School of Biological Sciences University of Edinburgh Edinburgh UK
| | - Sean Morris
- Institute of Evolutionary Biology School of Biological Sciences University of Edinburgh Edinburgh UK
| | - Alison Morris
- Institute of Evolutionary Biology School of Biological Sciences University of Edinburgh Edinburgh UK
| | - Fiona Kenyon
- Moredun Research Institute Pentlands Science Park Midlothian UK
| | - Daniel H. Nussey
- Institute of Evolutionary Biology School of Biological Sciences University of Edinburgh Edinburgh UK
| | - Josephine M. Pemberton
- Institute of Evolutionary Biology School of Biological Sciences University of Edinburgh Edinburgh UK
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45
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Sparks AM, Watt K, Sinclair R, Pilkington JG, Pemberton JM, McNeilly TN, Nussey DH, Johnston SE. The genetic architecture of helminth-specific immune responses in a wild population of Soay sheep (Ovis aries). PLoS Genet 2019; 15:e1008461. [PMID: 31697674 PMCID: PMC6863570 DOI: 10.1371/journal.pgen.1008461] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 11/19/2019] [Accepted: 10/04/2019] [Indexed: 12/22/2022] Open
Abstract
Much of our knowledge of the drivers of immune variation, and how these responses vary over time, comes from humans, domesticated livestock or laboratory organisms. While the genetic basis of variation in immune responses have been investigated in these systems, there is a poor understanding of how genetic variation influences immunity in natural, untreated populations living in complex environments. Here, we examine the genetic architecture of variation in immune traits in the Soay sheep of St Kilda, an unmanaged population of sheep infected with strongyle gastrointestinal nematodes. We assayed IgA, IgE and IgG antibodies against the prevalent nematode Teladorsagia circumcincta in the blood plasma of > 3,000 sheep collected over 26 years. Antibody levels were significantly heritable (h2 = 0.21 to 0.57) and highly stable over an individual’s lifespan. IgA levels were strongly associated with a region on chromosome 24 explaining 21.1% and 24.5% of heritable variation in lambs and adults, respectively. This region was adjacent to two candidate loci, Class II Major Histocompatibility Complex Transactivator (CIITA) and C-Type Lectin Domain Containing 16A (CLEC16A). Lamb IgA levels were also associated with the immunoglobulin heavy constant loci (IGH) complex, and adult IgE levels and lamb IgA and IgG levels were associated with the major histocompatibility complex (MHC). This study provides evidence of high heritability of a complex immunological trait under natural conditions and provides the first evidence from a genome-wide study that large effect genes located outside the MHC region exist for immune traits in the wild. Understanding how immune responses vary in natural populations can give an insight into how infection affects the ability of hosts and parasites to survive and reproduce, and how this drives evolutionary and ecological dynamics. Yet, very little is known about how immune responses vary over an individual’s lifetime and how genes contribute to this variation under natural conditions. Our study investigates the genetic architecture of variation in three antibody types, IgA, IgE and IgG in a wild population of Soay sheep on the St Kilda archipelago in North-West Scotland. Using data collected over 26 years, we show that antibody levels have a heritable basis in lambs and adults and are stable over an individual’s lifetime. We also identify several genomic regions with large effects on immune responses. Our study offers the first insights into the genetic control of immunity in a wild population, which is essential to understand how immune profiles vary in challenging natural conditions and how natural selection maintains genetic variation in complex immune traits.
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Affiliation(s)
- Alexandra M. Sparks
- Institutes of Evolutionary Biology and Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
- Faculty of Biological Sciences, School of Biology, University of Leeds, Leeds, United Kingdom
- * E-mail:
| | - Kathryn Watt
- Institutes of Evolutionary Biology and Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Rona Sinclair
- Institutes of Evolutionary Biology and Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Jill G. Pilkington
- Institutes of Evolutionary Biology and Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Josephine M. Pemberton
- Institutes of Evolutionary Biology and Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Tom N. McNeilly
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Midlothian, United Kingdom
| | - Daniel H. Nussey
- Institutes of Evolutionary Biology and Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Susan E. Johnston
- Institutes of Evolutionary Biology and Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
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46
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Bonnet T, Morrissey MB, Morris A, Morris S, Clutton-Brock TH, Pemberton JM, Kruuk LEB. The role of selection and evolution in changing parturition date in a red deer population. PLoS Biol 2019; 17:e3000493. [PMID: 31689300 PMCID: PMC6830748 DOI: 10.1371/journal.pbio.3000493] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 10/02/2019] [Indexed: 11/17/2022] Open
Abstract
Changing environmental conditions cause changes in the distributions of phenotypic traits in natural populations. However, determining the mechanisms responsible for these changes—and, in particular, the relative contributions of phenotypic plasticity versus evolutionary responses—is difficult. To our knowledge, no study has yet reported evidence that evolutionary change underlies the most widely reported phenotypic response to climate change: the advancement of breeding times. In a wild population of red deer, average parturition date has advanced by nearly 2 weeks in 4 decades. Here, we quantify the contribution of plastic, demographic, and genetic components to this change. In particular, we quantify the role of direct phenotypic plasticity in response to increasing temperatures and the role of changes in the population structure. Importantly, we show that adaptive evolution likely played a role in the shift towards earlier parturition dates. The observed rate of evolution was consistent with a response to selection and was less likely to be due to genetic drift. Our study provides a rare example of observed rates of genetic change being consistent with theoretical predictions, although the consistency would not have been detected with a solely phenotypic analysis. It also provides, to our knowledge, the first evidence of both evolution and phenotypic plasticity contributing to advances in phenology in a changing climate. Adaptive genetic evolution and phenotypic plasticity both contribute to a two-week advancement of birth dates earlier in spring in a deer population subject to temperature warming over four decades.
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Affiliation(s)
- Timothée Bonnet
- Research School of Biology, The Australian National University, Canberra, Australia
| | | | - Alison Morris
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Sean Morris
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | | | - Josephine M Pemberton
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Loeske E B Kruuk
- Research School of Biology, The Australian National University, Canberra, Australia
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47
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Hindle BJ, Pilkington JG, Pemberton JM, Childs DZ. Cumulative weather effects can impact across the whole life cycle. Glob Chang Biol 2019; 25:3282-3293. [PMID: 31237387 PMCID: PMC6771737 DOI: 10.1111/gcb.14742] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 06/06/2019] [Accepted: 06/13/2019] [Indexed: 05/14/2023]
Abstract
Predicting how species will be affected by future climatic change requires the underlying environmental drivers to be identified. As vital rates vary over the lifecycle, structured population models derived from statistical environment-demography relationships are often used to inform such predictions. Environmental drivers are typically identified independently for different vital rates and demographic classes. However, these rates often exhibit positive temporal covariance, suggesting that vital rates respond to common environmental drivers. Additionally, models often only incorporate average weather conditions during a single, a priori chosen time window (e.g. monthly means). Mismatches between these windows and the period when the vital rates are sensitive to variation in climate decrease the predictive performance of such approaches. We used a demographic structural equation model (SEM) to demonstrate that a single axis of environmental variation drives the majority of the (co)variation in survival, reproduction, and twinning across six age-sex classes in a Soay sheep population. This axis provides a simple target for the complex task of identifying the drivers of vital rate variation. We used functional linear models (FLMs) to determine the critical windows of three local climatic drivers, allowing the magnitude and direction of the climate effects to differ over time. Previously unidentified lagged climatic effects were detected in this well-studied population. The FLMs had a better predictive performance than selecting a critical window a priori, but not than a large-scale climate index. Positive covariance amongst vital rates and temporal variation in the effects of environmental drivers are common, suggesting our SEM-FLM approach is a widely applicable tool for exploring the joint responses of vital rates to environmental change.
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Affiliation(s)
- Bethan J. Hindle
- Department of Animal and Plant SciencesUniversity of SheffieldSheffieldUK
- Department of Applied SciencesUniversity of the West of EnglandBristolUK
| | - Jill G. Pilkington
- School of Biological Sciences, Institute of Evolutionary BiologyUniversity of EdinburghEdinburghUK
| | - Josephine M. Pemberton
- School of Biological Sciences, Institute of Evolutionary BiologyUniversity of EdinburghEdinburghUK
| | - Dylan Z. Childs
- Department of Animal and Plant SciencesUniversity of SheffieldSheffieldUK
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48
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Abstract
In nature, selection varies across time in most environments, but we lack an understanding of how specific ecological changes drive this variation. Ecological factors can alter phenotypic selection coefficients through changes in trait distributions or individual mean fitness, even when the trait-absolute fitness relationship remains constant. We apply and extend a regression-based approach in a population of Soay sheep (Ovis aries) and suggest metrics of environment-selection relationships that can be compared across studies. We then introduce a novel method that constructs an environmentally structured fitness function. This allows calculation of full (as in existing approaches) and partial (acting separately through the absolute fitness function slope, mean fitness, and phenotype distribution) sensitivities of selection to an ecological variable. Both approaches show positive overall effects of density on viability selection of lamb mass. However, the second approach demonstrates that this relationship is largely driven by effects of density on mean fitness, rather than on the trait-fitness relationship slope. If such mechanisms of environmental dependence of selection are common, this could have important implications regarding the frequency of fluctuating selection, and how previous selection inferences relate to longer term evolutionary dynamics.
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Affiliation(s)
- Darren C Hunter
- School of Biology, University of St Andrews, St Andrews, Fife KY16 9TH, United Kingdom
| | - Josephine M Pemberton
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
| | - Jill G Pilkington
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
| | - Michael B Morrissey
- School of Biology, University of St Andrews, St Andrews, Fife KY16 9TH, United Kingdom
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49
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Froy H, Martin J, Stopher KV, Morris A, Morris S, Clutton-Brock TH, Pemberton JM, Kruuk LEB. Consistent within-individual plasticity is sufficient to explain temperature responses in red deer reproductive traits. J Evol Biol 2019; 32:1194-1206. [PMID: 31420999 DOI: 10.1111/jeb.13521] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 06/20/2019] [Accepted: 08/13/2019] [Indexed: 11/28/2022]
Abstract
Warming global temperatures are affecting a range of aspects of wild populations, but the exact mechanisms driving associations between temperature and phenotypic traits may be difficult to identify. Here, we use a 36-year data set on a wild population of red deer to investigate the causes of associations between temperature and two important components of female reproduction: timing of breeding and offspring size. By separating within- versus between-individual associations with temperature for each trait, we show that within-individual phenotypic plasticity (changes within a female's lifetime) was entirely sufficient to generate the observed population-level association with temperature at key times of year. However, despite apparently adequate statistical power, we found no evidence of any variation between females in their responses (i.e. no "IxE" interactions). Our results suggest that female deer show plasticity in reproductive traits in response to temperatures in the year leading up to calving and that this response is consistent across individuals, implying no potential for either selection or heritability of plasticity. We estimate that the plastic response to rising temperatures explained 24% of the observed advance in mean calving date over the study period. We highlight the need for comparable analyses of other systems to determine the contribution of within-individual plasticity to population-level responses to climate change.
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Affiliation(s)
- Hannah Froy
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Julien Martin
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - Katie V Stopher
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Alison Morris
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Sean Morris
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | | | | | - Loeske E B Kruuk
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.,Research School of Biology, Australian National University, Canberra, ACT, Australia
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50
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Robinson AL, Williamson H, Güere ME, Tharaldsen H, Baker K, Smith SL, Pérez-Espona S, Krojerová-Prokešová J, Pemberton JM, Goldmann W, Houston F. Variation in the prion protein gene (PRNP) sequence of wild deer in Great Britain and mainland Europe. Vet Res 2019; 50:59. [PMID: 31366372 PMCID: PMC6668158 DOI: 10.1186/s13567-019-0675-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 07/05/2019] [Indexed: 01/01/2023] Open
Abstract
Susceptibility to prion diseases is largely determined by the sequence of the prion protein gene (PRNP), which encodes the prion protein (PrP). The recent emergence of chronic wasting disease (CWD) in Europe has highlighted the need to investigate PRNP gene diversity in European deer species, to better predict their susceptibility to CWD. Here we report a large genetic survey of six British deer species, including red (Cervus elaphus), sika (Cervus nippon), roe (Capreolus capreolus), fallow (Dama dama), muntjac (Muntiacus reevesii), and Chinese water deer (Hydropotes inermis), which establishes PRNP haplotype and genotype frequencies. Two smaller data sets from red deer in Norway and the Czech Republic are also included for comparison. Overall red deer show the most PRNP variation, with non-synonymous/coding polymorphisms at codons 98, 168, 226 and 247, which vary markedly in frequency between different regions. Polymorphisms P168S and I247L were only found in Scottish and Czech populations, respectively. T98A was found in all populations except Norway and the south of England. Significant regional differences in genotype frequencies were observed within both British and European red deer populations. Other deer species showed less variation, particularly roe and fallow deer, in which identical PRNP gene sequences were found in all individuals analysed. Based on comparison with PRNP sequences of North American cervids affected by CWD and limited experimental challenge data, these results suggest that a high proportion of wild deer in Great Britain may be susceptible to CWD.
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Affiliation(s)
- Amy L Robinson
- Division of Infection and Immunity, The Roslin Institute and The Royal Dick School of Veterinary Studies, University of Edinburgh, Midlothian, EH259RG, UK.
| | - Helen Williamson
- Division of Infection and Immunity, The Roslin Institute and The Royal Dick School of Veterinary Studies, University of Edinburgh, Midlothian, EH259RG, UK
| | - Mariella E Güere
- Norwegian University of Life Sciences, Faculty of Veterinary Medicine, Oslo, Norway
| | - Helene Tharaldsen
- Norwegian University of Life Sciences, Faculty of Veterinary Medicine, Oslo, Norway
| | - Karis Baker
- Department of Biosciences, Durham University, South Road, Durham, DH1 3LE, UK
| | - Stephanie L Smith
- The Royal Dick School of Veterinary Studies, University of Edinburgh, Midlothian, EH259RG, UK
| | - Sílvia Pérez-Espona
- Division of Infection and Immunity, The Roslin Institute and The Royal Dick School of Veterinary Studies, University of Edinburgh, Midlothian, EH259RG, UK.,The Royal Dick School of Veterinary Studies, University of Edinburgh, Midlothian, EH259RG, UK
| | - Jarmila Krojerová-Prokešová
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Květná 8, 603 65, Brno, Czech Republic.,Department of Zoology, Fisheries, Hydrobiology and Apiculture, Faculty of AgriSciences, Mendel University in Brno, Zemědělská 1, 613 00, Brno, Czech Republic
| | - Josephine M Pemberton
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Wilfred Goldmann
- Division of Infection and Immunity, The Roslin Institute and The Royal Dick School of Veterinary Studies, University of Edinburgh, Midlothian, EH259RG, UK
| | - Fiona Houston
- Division of Infection and Immunity, The Roslin Institute and The Royal Dick School of Veterinary Studies, University of Edinburgh, Midlothian, EH259RG, UK
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