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Dickel L, Arcese P, Keller LF, Nietlisbach P, Goedert D, Jensen H, Reid JM. Multigenerational Fitness Effects of Natural Immigration Indicate Strong Heterosis and Epistatic Breakdown in a Wild Bird Population. Am Nat 2024; 203:411-431. [PMID: 38358807 DOI: 10.1086/728669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 02/17/2024]
Abstract
AbstractThe fitness of immigrants and their descendants produced within recipient populations fundamentally underpins the genetic and population dynamic consequences of immigration. Immigrants can in principle induce contrasting genetic effects on fitness across generations, reflecting multifaceted additive, dominance, and epistatic effects. Yet full multigenerational and sex-specific fitness effects of regular immigration have not been quantified within naturally structured systems, precluding inference on underlying genetic architectures and population outcomes. We used four decades of song sparrow (Melospiza melodia) life history and pedigree data to quantify fitness of natural immigrants, natives, and their F1, F2, and backcross descendants and test for evidence of nonadditive genetic effects. Values of key fitness components (including adult lifetime reproductive success and zygote survival) of F1 offspring of immigrant-native matings substantially exceeded their parent mean, indicating strong heterosis. Meanwhile, F2 offspring of F1-F1 matings had notably low values, indicating surprisingly strong epistatic breakdown. Furthermore, magnitudes of effects varied among fitness components and differed between female and male descendants. These results demonstrate that strong nonadditive genetic effects on fitness can arise within weakly structured and fragmented populations experiencing frequent natural immigration. Such effects will substantially affect the net degree of effective gene flow and resulting local genetic introgression and adaptation.
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2
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Reid JM, Dickel L, Keller LF, Nietlisbach P, Arcese P. Multi-generation genetic contributions of immigrants reveal cryptic elevated and sex-biased effective gene flow within a natural meta-population. Ecol Lett 2024; 27:e14377. [PMID: 38361472 DOI: 10.1111/ele.14377] [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: 09/12/2023] [Revised: 01/11/2024] [Accepted: 01/11/2024] [Indexed: 02/17/2024]
Abstract
Impacts of immigration on micro-evolution and population dynamics fundamentally depend on net rates and forms of resulting gene flow into recipient populations. Yet, the degrees to which observed rates and sex ratios of physical immigration translate into multi-generational genetic legacies have not been explicitly quantified in natural meta-populations, precluding inference on how movements translate into effective gene flow and eco-evolutionary outcomes. Our analyses of three decades of complete song sparrow (Melospiza melodia) pedigree data show that multi-generational genetic contributions from regular natural immigrants substantially exceeded those from contemporary natives, consistent with heterosis-enhanced introgression. However, while contributions from female immigrants exceeded those from female natives by up to three-fold, male immigrants' lineages typically went locally extinct soon after arriving. Both the overall magnitude, and the degree of female bias, of effective gene flow therefore greatly exceeded those which would be inferred from observed physical arrivals, altering multiple eco-evolutionary implications of immigration.
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Affiliation(s)
- Jane M Reid
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - Lisa Dickel
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Lukas F Keller
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- Natural History Museum, University of Zurich, Zurich, Switzerland
| | - Pirmin Nietlisbach
- School of Biological Sciences, Illinois State University, Normal, Illinois, USA
| | - Peter Arcese
- Department of Forest & Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
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3
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Nelson-Flower MJ, Grieves LA, Reid JM, Germain RR, Lazic S, Taylor SS, MacDougall-Shackleton EA, Arcese P. Immune genotypes, immune responses, and survival in a wild bird population. Mol Ecol 2023. [PMID: 36919652 DOI: 10.1111/mec.16923] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 02/18/2023] [Accepted: 03/02/2023] [Indexed: 03/16/2023]
Abstract
Individuals vary in their immune genotype, inbreeding coefficient f, immune responses, survival to adulthood, and adult longevity. However, whether immune genes predict survival or longevity, whether such relationships are mediated through immune responses, and how f affects immune genotype remain unclear. We use a wild song sparrow (Melospiza melodia) population in which survival to adulthood, adult longevity, and f were measured precisely, and in which immune responses have previously been assessed. We investigate four toll-like receptor (TLR) and the major histocompatibility complex (MHC) class IIB exon 2 genes. We test whether immune genes predict fitness (survival to adulthood or adult longevity); whether immune genes predict immune response; whether immune response predicts fitness and whether fitness, immune responses, or immune genotypes are correlated with f. We find that survival to adulthood is not associated with immune gene variation, but adult longevity is decreased by high MHC allele diversity (especially in birds that were relatively outbred), and by the presence of a specific MHC supertype. Immune responses were affected by specific immune genotypes. Survival to adulthood and adult longevity were not predicted by immune response, implying caution in the use of immune response as a predictor for fitness. We also found no relationship between f and immune genotype. This finding indicates that immune gene associations with longevity and immune response are not artefacts of f, and suggests that pathogen-mediated selection at functional loci can slow the loss of genetic variation arising from genetic drift and small population size.
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Affiliation(s)
- Martha J Nelson-Flower
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Biology, Langara College, Vancouver, British Columbia, Canada
| | - Leanne A Grieves
- Department of Biology, University of Western Ontario, London, Ontario, Canada
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
| | - Jane M Reid
- Centre for Biodiversity Dynamics, Institut for Biologi, NTNU, Trondheim, Norway
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - Ryan R Germain
- Center for Macroecology, Evolution and Climate, GLOBE Institute, University of Copenhagen, Kobenhavn, Denmark
| | - Savo Lazic
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Sabrina S Taylor
- School of Renewable Natural Resources, Louisiana State University and AgCenter, Baton Rouge, Louisiana, USA
| | | | - Peter Arcese
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
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4
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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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Miller JM, Campbell EO, Rotella JJ, Macdonald KR, Gelatt TS, Davis CS. Evaluation of novel genomic markers for pedigree construction in an isolated population of Weddell Seals (Leptonychotes weddellii) at White Island, Antarctica. CONSERV GENET RESOUR. [DOI: 10.1007/s12686-021-01237-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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6
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Dickel L, Arcese P, Nietlisbach P, Keller LF, Jensen H, Reid JM. Are immigrants outbred and unrelated? Testing standard assumptions in a wild metapopulation. Mol Ecol 2021; 30:5674-5686. [PMID: 34516687 DOI: 10.1111/mec.16173] [Citation(s) in RCA: 3] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 08/19/2021] [Accepted: 08/23/2021] [Indexed: 11/30/2022]
Abstract
Immigration into small recipient populations is expected to alleviate inbreeding and increase genetic variation, and hence facilitate population persistence through genetic and/or evolutionary rescue. Such expectations depend on three standard assumptions: that immigrants are outbred, unrelated to existing natives at arrival, and unrelated to each other. These assumptions are rarely explicitly verified, including in key field systems in evolutionary ecology. Yet, they could be violated due to non-random or repeated immigration from adjacent small populations. We combined molecular genetic marker data for 150-160 microsatellite loci with comprehensive pedigree data to test the three assumptions for a song sparrow (Melospiza melodia) population that is a model system for quantifying effects of inbreeding and immigration in the wild. Immigrants were less homozygous than existing natives on average, with mean homozygosity that closely resembled outbred natives. Immigrants can therefore be considered outbred on the focal population scale. Comparisons of homozygosity of real or hypothetical offspring of immigrant-native, native-native and immigrant-immigrant pairings implied that immigrants were typically unrelated to existing natives and to each other. Indeed, immigrants' offspring would be even less homozygous than outbred individuals on the focal population scale. The three standard assumptions of population genetic and evolutionary theory were consequently largely validated. Yet, our analyses revealed some deviations that should be accounted for in future analyses of heterosis and inbreeding depression, implying that the three assumptions should be verified in other systems to probe patterns of non-random or repeated dispersal and facilitate precise and unbiased estimation of key evolutionary parameters.
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Affiliation(s)
- Lisa Dickel
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
| | - Peter Arcese
- Department of Forest & Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Pirmin Nietlisbach
- School of Biological Sciences, Illinois State University, Normal, Illinois, USA
| | - Lukas F Keller
- Department of Evolutionary Biology & Environmental Studies, University of Zurich, Zurich, Switzerland.,Zoological Museum, University of Zurich, Zurich, Switzerland
| | - Henrik Jensen
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
| | - Jane M Reid
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway.,School of Biological Sciences, University of Aberdeen, Aberdeen, UK
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7
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Sumreddee P, Hay EH, Toghiani S, Roberts A, Aggrey SE, Rekaya R. Grid search approach to discriminate between old and recent inbreeding using phenotypic, pedigree and genomic information. BMC Genomics 2021; 22:538. [PMID: 34256689 PMCID: PMC8278650 DOI: 10.1186/s12864-021-07872-z] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 07/05/2021] [Indexed: 12/02/2022] Open
Abstract
Background Although inbreeding caused by the mating of animals related through a recent common ancestor is expected to have more harmful effects on phenotypes than ancient inbreeding (old inbreeding), estimating these effects requires a clear definition of recent (new) and ancient (old) inbreeding. Several methods have been proposed to classify inbreeding using pedigree and genomic data. Unfortunately, these methods are largely based on heuristic criteria such as the number of generations from a common ancestor or length of runs of homozygosity (ROH) segments. To mitigate these deficiencies, this study aimed to develop a method to classify pedigree and genomic inbreeding into recent and ancient classes based on a grid search algorithm driven by the assumption that new inbreeding tends to have a more pronounced detrimental effect on traits. The proposed method was tested using a cattle population characterized by a deep pedigree. Results Effects of recent and ancient inbreeding were assessed on four growth traits (birth, weaning and yearling weights and average daily gain). Thresholds to classify inbreeding into recent and ancient classes were trait-specific and varied across traits and sources of information. Using pedigree information, inbreeding generated in the last 10 to 11 generations was considered as recent. When genomic information (ROH) was used, thresholds ranged between four to seven generations, indicating, in part, the ability of ROH segments to characterize the harmful effects of inbreeding in shorter periods of time. Nevertheless, using the proposed classification method, the discrimination between new and old inbreeding was less robust when ROH segments were used compared to pedigree. Using several model comparison criteria, the proposed approach was generally better than existing methods. Recent inbreeding appeared to be more harmful across the growth traits analyzed. However, both new and old inbreeding were found to be associated with decreased yearling weight and average daily gain. Conclusions The proposed method provided a more objective quantitative approach for the classification of inbreeding. The proposed method detected a clear divergence in the effects of old and recent inbreeding using pedigree data and it was superior to existing methods for all analyzed traits. Using ROH data, the discrimination between old and recent inbreeding was less clear and the proposed method was superior to existing approaches for two out of the four analyzed traits. Deleterious effects of recent inbreeding were detected sooner (fewer generations) using genomic information than pedigree. Difference in the results using genomic and pedigree information could be due to the dissimilarity in the number of generations to a common ancestor. Additionally, the uncertainty associated with the identification of ROH segments and associated inbreeding could have an effect on the results. Potential biases in the estimation of inbreeding effects may occur when new and old inbreeding are discriminated based on arbitrary thresholds. To minimize the impact of inbreeding, mating designs should take the different inbreeding origins into consideration. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07872-z.
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Affiliation(s)
- Pattarapol Sumreddee
- Department of Animal and Dairy Science, The University of Georgia, Athens, GA, 30602, USA
| | - El Hamidi Hay
- USDA Agricultural Research Service, Fort Keogh Livestock and Range Research Laboratory, Miles City, MT, 59301, USA.
| | - Sajjad Toghiani
- USDA Agricultural Research Service, Beltsville Agricultural Research Center, Beltsville, MD, 20705, USA
| | - Andrew Roberts
- USDA Agricultural Research Service, Fort Keogh Livestock and Range Research Laboratory, Miles City, MT, 59301, USA
| | - Samuel E Aggrey
- Department of Poultry Science, The University of Georgia, Athens, GA, 30602, USA.,Institute of Bioinformatics, The University of Georgia, Athens, GA, 30602, USA
| | - Romdhane Rekaya
- Department of Animal and Dairy Science, The University of Georgia, Athens, GA, 30602, USA.,Institute of Bioinformatics, The University of Georgia, Athens, GA, 30602, USA.,Department of Statistics, The University of Georgia, Athens, GA, 30602, USA
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8
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Sin SYW, Hoover BA, Nevitt GA, Edwards SV. Demographic History, Not Mating System, Explains Signatures of Inbreeding and Inbreeding Depression in a Large Outbred Population. Am Nat 2021; 197:658-676. [PMID: 33989142 DOI: 10.1086/714079] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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
AbstractInbreeding depression is often found in small, inbred populations, but whether it can be detected in and have evolutionary consequences for large, wide-ranging populations is poorly known. Here, we investigate the possibility of inbreeding in a large population to determine whether mild levels of inbreeding can still have genetic and phenotypic consequences and how genomically widespread these effects can be. We apply genome-wide methods to investigate whether individual and parental heterozygosity is related to morphological, growth, or life-history traits in a pelagic seabird, Leach's storm-petrel (Oceanodroma leucorhoa). Examining 560 individuals as part of a multiyear study, we found a substantial effect of maternal heterozygosity on chick traits: chicks from less heterozygous (relatively inbred) mothers were significantly smaller than chicks from more heterozygous (noninbred) mothers. We show that these heterozygosity-fitness correlations were due to general genome-wide effects and demonstrate a correlation between heterozygosity and inbreeding, suggesting inbreeding depression. We used population genetic models to further show that the variance in inbreeding was probably due to past demographic events rather than the current mating system and ongoing mate choice. Our findings demonstrate that inbreeding depression can be observed in large populations and illustrate how the integration of genomic techniques and fieldwork can elucidate its underlying causes.
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9
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Reid JM, Arcese P, Nietlisbach P, Wolak ME, Muff S, Dickel L, Keller LF. Immigration counter-acts local micro-evolution of a major fitness component: Migration-selection balance in free-living song sparrows. Evol Lett 2021; 5:48-60. [PMID: 33552535 PMCID: PMC7857281 DOI: 10.1002/evl3.214] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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: 08/24/2020] [Revised: 11/28/2020] [Accepted: 12/18/2020] [Indexed: 01/11/2023] Open
Abstract
Ongoing adaptive evolution, and resulting “evolutionary rescue” of declining populations, requires additive genetic variation in fitness. Such variation can be increased by gene flow resulting from immigration, potentially facilitating evolution. But, gene flow could in fact constrain rather than facilitate local adaptive evolution if immigrants have low additive genetic values for local fitness. Local migration‐selection balance and micro‐evolutionary stasis could then result. However, key quantitative genetic effects of natural immigration, comprising the degrees to which gene flow increases the total local additive genetic variance yet counteracts local adaptive evolutionary change, have not been explicitly quantified in wild populations. Key implications of gene flow for population and evolutionary dynamics consequently remain unclear. Our quantitative genetic analyses of long‐term data from free‐living song sparrows (Melospiza melodia) show that mean breeding value for local juvenile survival to adulthood, a major component of fitness, increased across cohorts more than expected solely due to drift. Such micro‐evolutionary change should be expected given nonzero additive genetic variance and consistent directional selection. However, this evolutionary increase was counteracted by negative additive genetic effects of recent immigrants, which increased total additive genetic variance but prevented a net directional evolutionary increase in total additive genetic value. These analyses imply an approximate quantitative genetic migration‐selection balance in a major fitness component, and hence demonstrate a key mechanism by which substantial additive genetic variation can be maintained yet decoupled from local adaptive evolutionary change.
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Affiliation(s)
- Jane M Reid
- Centre for Biodiversity Dynamics NTNU Trondheim Norway.,School of Biological Sciences University of Aberdeen Aberdeen UK
| | - Peter Arcese
- Forest & Conservation Sciences University of British Columbia Vancouver British Columbia Canada
| | - Pirmin Nietlisbach
- School of Biological Sciences Illinois State University Normal Illinois USA
| | - Matthew E Wolak
- Department of Biological Sciences Auburn University Auburn Alaska USA
| | - Stefanie Muff
- Centre for Biodiversity Dynamics NTNU Trondheim Norway.,Department of Mathematical Sciences NTNU Trondheim Norway
| | - Lisa Dickel
- Centre for Biodiversity Dynamics NTNU Trondheim Norway
| | - Lukas F Keller
- Department of Evolutionary Biology & Environmental Studies University of Zurich Zurich Switzerland.,Zoological Museum University of Zurich Zurich Switzerland
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10
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Reid JM, Arcese P. Recent immigrants alter the quantitative genetic architecture of paternity in song sparrows. Evol Lett 2020; 4:124-136. [PMID: 32313688 PMCID: PMC7156105 DOI: 10.1002/evl3.162] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 09/25/2019] [Revised: 12/11/2019] [Accepted: 01/19/2020] [Indexed: 12/13/2022] Open
Abstract
Quantifying additive genetic variances and cross‐sex covariances in reproductive traits, and identifying processes that shape and maintain such (co)variances, is central to understanding the evolutionary dynamics of reproductive systems. Gene flow resulting from among‐population dispersal could substantially alter additive genetic variances and covariances in key traits in recipient populations, thereby altering forms of sexual conflict, indirect selection, and evolutionary responses. However, the degree to which genes imported by immigrants do in fact affect quantitative genetic architectures of key reproductive traits and outcomes is rarely explicitly quantified. We applied structured quantitative genetic analyses to multiyear pedigree, pairing, and paternity data from free‐living song sparrows (Melospiza melodia) to quantify the differences in mean breeding values for major sex‐specific reproductive traits, specifically female extra‐pair reproduction and male paternity loss, between recent immigrants and the previously existing population. We thereby quantify effects of natural immigration on the means, variances, and cross‐sex covariance in total additive genetic values for extra‐pair paternity arising within the complex socially monogamous but genetically polygynandrous reproductive system. Recent immigrants had lower mean breeding values for male paternity loss, and somewhat lower values for female extra‐pair reproduction, than the local recipient population, and would therefore increase the emerging degree of reproductive fidelity of social pairings. Furthermore, immigration increased the variances in total additive genetic values for these traits, but decreased the magnitudes of the negative cross‐sex genetic covariation and correlation below those evident in the existing population. Immigration thereby increased the total additive genetic variance but could decrease the magnitude of indirect selection acting on sex‐specific contributions to paternity outcomes. These results demonstrate that dispersal and resulting immigration and gene flow can substantially affect quantitative genetic architectures of complex local reproductive systems, implying that comprehensive theoretical and empirical efforts to understand mating system dynamics will need to incorporate spatial population processes.
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Affiliation(s)
- Jane M Reid
- Centre for Biodiversity Dynamics NTNU Trondheim Norway.,School of Biological Sciences University of Aberdeen Aberdeen United Kingdom
| | - Peter Arcese
- Forest & Conservation Sciences University of British Columbia Vancouver British Columbia Canada
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11
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Waters CD, Hard JJ, Fast DE, Knudsen CM, Bosch WJ, Naish KA. Genomic and phenotypic effects of inbreeding across two different hatchery management regimes in Chinook salmon. Mol Ecol 2020; 29:658-672. [PMID: 31957935 DOI: 10.1111/mec.15356] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 07/22/2019] [Revised: 12/09/2019] [Accepted: 01/13/2020] [Indexed: 01/14/2023]
Abstract
Genomic approaches permit direct estimation of inbreeding and its effect on fitness. We used genomic-based estimates of inbreeding to investigate their relationship with eight adult traits in a captive-reared Pacific salmonid that is released into the wild. Estimates were also used to determine whether alternative broodstock management approaches reduced risks of inbreeding. Specifically, 1,100 unlinked restriction-site associated (RAD) loci were used to compare pairwise relatedness, derived from a relationship matrix, and individual inbreeding, estimated by comparing observed and expected homozygosity, across four generations in two hatchery lines of Chinook salmon that were derived from the same source. The lines are managed as "integrated" with the founding wild stock, with ongoing gene flow, and as "segregated" with no gene flow. While relatedness and inbreeding increased in the first generation of both lines, possibly due to population subdivision caused by hatchery initiation, the integrated line had significantly lower levels in some subsequent generations (relatedness: F2 -F4 ; inbreeding F2 ). Generally, inbreeding was similar between the lines despite large differences in effective numbers of breeders. Inbreeding did not affect fecundity, reproductive effort, return timing, fork length, weight, condition factor, and daily growth coefficient. However, it delayed spawn timing by 1.75 days per one standard deviation increase in F (~0.16). The results indicate that integrated management may reduce inbreeding but also suggest that it is relatively low in a small, segregated hatchery population that maximized number of breeders. Our findings demonstrate the utility of genomics to monitor inbreeding under alternative management strategies in captive breeding programs.
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Affiliation(s)
- Charles D Waters
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, USA
| | - Jeffrey J Hard
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA, USA
| | | | | | | | - Kerry A Naish
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, USA
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12
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Nelson-Flower MJ, Germain RR, MacDougall-Shackleton EA, Taylor SS, Arcese P. Purifying Selection in the Toll-Like Receptors of Song Sparrows Melospiza melodia. J Hered 2019; 109:501-509. [PMID: 29893971 DOI: 10.1093/jhered/esy027] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 06/08/2018] [Indexed: 01/22/2023] Open
Abstract
Variation in immune gene sequences is known to influence resistance to infectious diseases and parasites, and hence survival and mate choice, across animal taxa. Toll-like receptors (TLRs) comprise one essential gene family in the vertebrate innate immune system and recognize evolutionarily conserved structures from all major microorganism classes. However, the causes and consequences of TLR variation in passerine birds remain largely unexplored. We examined 7 TLR genes in song sparrows (Melospiza melodia), a species that is studied across North America. We then examined sequences from 4 unduplicated TLRs (TLR1LB, TLR3, TLR4, and TLR15) from birds in 2 parts of the species' range (N = 27, N = 6), tested for evidence of selection, and conducted pilot analyses of the role of TLR heterozygosity in survival. We identified 45 SNPs: 19 caused changes in amino acid sequences and 2 of these were likely deleterious. We found no evidence of codon-level episodic positive selection but detected purifying selection at codons in all TLRs. Contrary to expectations we found no strong correlation between heterozygosity at TLRs and inbreeding coefficient f (estimate ± standard error [SE] = -0.68 ± 0.37, Radj2 = 0.08, F1,25 = 3.38, P = 0.08). In addition, pilot analyses revealed no relationship between TLR heterozygosity and survival (β ± SE: 0.09 ± 2.00, P = 0.96), possibly due to small sample size. Further analyses of genetic diversity in TLRs are likely to advance understanding of the effects of innate immune gene diversity on the fitness and persistence of wild populations.
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Affiliation(s)
- Martha J Nelson-Flower
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada
| | | | | | - Sabrina S Taylor
- The School of Renewable Natural Resources, Louisiana State University and AgCenter, Baton Rouge, LA
| | - Peter Arcese
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada
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13
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Ponzi E, Keller LF, Muff S. The simulation extrapolation technique meets ecology and evolution: A general and intuitive method to account for measurement error. Methods Ecol Evol 2019. [DOI: 10.1111/2041-210x.13255] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Erica Ponzi
- Department of Evolutionary Biology and Environmental Studies University of Zurich Zurich Switzerland
- Department of Biostatistics, Epidemiology, Biostatistics and Prevention Institute University of Zurich Zurich Switzerland
| | - Lukas F. Keller
- Department of Evolutionary Biology and Environmental Studies University of Zurich Zurich Switzerland
- Zoological Museum University of Zurich Zurich Switzerland
| | - Stefanie Muff
- Department of Evolutionary Biology and Environmental Studies University of Zurich Zurich Switzerland
- Department of Biostatistics, Epidemiology, Biostatistics and Prevention Institute University of Zurich Zurich Switzerland
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14
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Reid JM, Nietlisbach P, Wolak ME, Keller LF, Arcese P. Individuals' expected genetic contributions to future generations, reproductive value, and short-term metrics of fitness in free-living song sparrows ( Melospiza melodia). Evol Lett 2019; 3:271-285. [PMID: 31171983 PMCID: PMC6546383 DOI: 10.1002/evl3.118] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [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: 02/07/2019] [Accepted: 04/01/2019] [Indexed: 11/08/2022] Open
Abstract
Appropriately defining and enumerating "fitness" is fundamental to explaining and predicting evolutionary dynamics. Yet, general theoretical concepts of fitness are often hard to translate into quantities that can be measured in wild populations experiencing complex environmental, demographic, genetic, and selective variation. Although the "fittest" entities might be widely understood to be those that ultimately leave most descendants at some future time, such long-term legacies can rarely be measured, impeding evaluation of the degree to which tractable short-term metrics of individual fitness could potentially serve as useful direct proxies. One opportunity for conceptual and empirical convergence stems from the principle of individual reproductive value (V i), here defined as the number of copies of each of an individual's alleles that is expected to be present in future generations given the individual's realized pedigree of descendants. As V i tightly predicts an individual's longer term genetic contribution, quantifying V i provides a tractable route to quantifying what, to date, has been an abstract theoretical fitness concept. We used complete pedigree data from free-living song sparrows (Melospiza melodia) to demonstrate that individuals' expected genetic contributions stabilize within an observed 20-year (i.e. approximately eight generation) time period, allowing estimation of individual V i. Considerable among-individual variation in V i was evident in both sexes. Standard metrics of individual lifetime fitness, comprising lifespan, lifetime reproductive success, and projected growth rate, typically explained less than half the variation. We thereby elucidate the degree to which fitness metrics observed on individuals concur with measures of longer term genetic contributions and consider the degree to which analyses of pedigree structure could provide useful complementary insights into evolutionary outcomes.
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Affiliation(s)
- Jane M. Reid
- School of Biological SciencesUniversity of AberdeenAberdeenUnited Kingdom
| | - Pirmin Nietlisbach
- Department of ZoologyUniversity of British ColumbiaVancouverBritish ColumbiaCanada
| | - Matthew E. Wolak
- Department of Biological SciencesAuburn UniversityAuburnAlabama36849
| | - Lukas F. Keller
- Department of Evolutionary Biology & Environmental StudiesUniversity of ZurichZurichSwitzerland
| | - Peter Arcese
- Forest & Conservation SciencesUniversity of British ColumbiaVancouverBritish ColumbiaCanada
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15
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Nietlisbach P, Muff S, Reid JM, Whitlock MC, Keller LF. Nonequivalent lethal equivalents: Models and inbreeding metrics for unbiased estimation of inbreeding load. Evol Appl 2019; 12:266-279. [PMID: 30697338 PMCID: PMC6346663 DOI: 10.1111/eva.12713] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [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: 02/04/2018] [Revised: 09/06/2018] [Accepted: 09/09/2018] [Indexed: 02/06/2023] Open
Abstract
Inbreeding depression, the deterioration in mean trait value in progeny of related parents, is a fundamental quantity in genetics, evolutionary biology, animal and plant breeding, and conservation biology. The magnitude of inbreeding depression can be quantified by the inbreeding load, typically measured in numbers of lethal equivalents, a population genetic quantity that allows for comparisons between environments, populations or species. However, there is as yet no quantitative assessment of which combinations of statistical models and metrics of inbreeding can yield such estimates. Here, we review statistical models that have been used to estimate inbreeding load and use population genetic simulations to investigate how unbiased estimates can be obtained using genomic and pedigree-based metrics of inbreeding. We use simulated binary viability data (i.e., dead versus alive) as our example, but the concepts apply to any trait that exhibits inbreeding depression. We show that the increasingly popular generalized linear models with logit link do not provide comparable and unbiased population genetic measures of inbreeding load, independent of the metric of inbreeding used. Runs of homozygosity result in unbiased estimates of inbreeding load, whereas inbreeding measured from pedigrees results in slight overestimates. Due to widespread use of models that do not yield unbiased measures of the inbreeding load, some estimates in the literature cannot be compared meaningfully. We surveyed the literature for reliable estimates of the mean inbreeding load from wild vertebrate populations and found an average of 3.5 haploid lethal equivalents for survival to sexual maturity. To obtain comparable estimates, we encourage researchers to use generalized linear models with logarithmic links or maximum-likelihood estimation of the exponential equation, and inbreeding coefficients calculated from runs of homozygosity, provided an assembled reference genome of sufficient quality and enough genetic marker data are available.
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Affiliation(s)
- Pirmin Nietlisbach
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZurichSwitzerland
- Department of ZoologyUniversity of British ColumbiaVancouverBCCanada
| | - Stefanie Muff
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZurichSwitzerland
| | - Jane M. Reid
- School of Biological SciencesUniversity of AberdeenAberdeenUK
| | | | - Lukas F. Keller
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZurichSwitzerland
- Zoological MuseumUniversity of ZurichZurichSwitzerland
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16
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Troianou E, Huisman J, Pemberton JM, Walling CA. Estimating selection on the act of inbreeding in a population with strong inbreeding depression. J Evol Biol 2018; 31:1815-1827. [PMID: 30230082 PMCID: PMC6334283 DOI: 10.1111/jeb.13376] [Citation(s) in RCA: 3] [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: 05/17/2018] [Revised: 08/05/2018] [Accepted: 09/13/2018] [Indexed: 12/15/2022]
Abstract
Inbreeding depression is widely regarded as a driving force in the evolution of dispersal, mate choice and sperm selection. However, due to likely costs of inbreeding avoidance, which are poorly understood, it is unclear to what extent selection to avoid inbreeding is expected in nature. Moreover, there are currently very few empirical estimates of the strength of selection against the act of inbreeding (mating with a relative), as opposed to the fitness costs of being inbred. Here, we use data from the individual-based study of red deer on the Scottish island of Rum, a strongly polygynous system which harbours a large inbreeding load, to estimate selection against the act of inbreeding for each sex. We use pedigree and genomic estimates of relatedness between individuals and measure fitness using both lifetime breeding success (number of calves born) and lifetime reproductive success (number of calves surviving to independence), with the latter incorporating inbreeding depression in calf survival. We find for both sexes that the repeatability of the act of inbreeding was low (< 0.1), suggesting little among-individual variation for this trait on which selection can act. Using the genomic measures, there was significant selection against the act of inbreeding in males, but not in females, and there was considerable uncertainty in the estimate in both sexes. We discuss possible explanations for these patterns and their implications for understanding the evolution of inbreeding avoidance in natural populations.
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Affiliation(s)
- Eva Troianou
- Institute of Evolutionary BiologySchool of Biological SciencesUniversity of EdinburghEdinburghUK
| | - Jisca Huisman
- Institute of Evolutionary BiologySchool of Biological SciencesUniversity of EdinburghEdinburghUK
| | - Josephine M. Pemberton
- Institute of Evolutionary BiologySchool of Biological SciencesUniversity of EdinburghEdinburghUK
| | - Craig A. Walling
- Institute of Evolutionary BiologySchool of Biological SciencesUniversity of EdinburghEdinburghUK
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17
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Wolak ME, Arcese P, Keller LF, Nietlisbach P, Reid JM. Sex‐specific additive genetic variances and correlations for fitness in a song sparrow (
Melospiza melodia
) population subject to natural immigration and inbreeding. Evolution 2018; 72:2057-2075. [DOI: 10.1111/evo.13575] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 07/23/2018] [Indexed: 12/15/2022]
Affiliation(s)
- Matthew E. Wolak
- School of Biological SciencesUniversity of Aberdeen Aberdeen Scotland
- Department of Biological SciencesAuburn University Auburn Alabama 36849
| | - Peter Arcese
- Department of Forest and Conservation SciencesUniversity of British Columbia Vancouver British Columbia Canada
| | - Lukas F. Keller
- Department of Evolutionary Biology and Environmental StudiesUniversity of Zurich Winterthurerstrasse 190 CH‐8057 Zurich Switzerland
- Zoological MuseumUniversity of Zurich Karl‐Schmid‐Strasse 4 CH‐8006 Zurich Switzerland
| | - Pirmin Nietlisbach
- Department of Evolutionary Biology and Environmental StudiesUniversity of Zurich Winterthurerstrasse 190 CH‐8057 Zurich Switzerland
- Department of ZoologyUniversity of British Columbia Vancouver British Columbia Canada
| | - Jane M. Reid
- School of Biological SciencesUniversity of Aberdeen Aberdeen Scotland
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18
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Wells DA, Cant MA, Nichols HJ, Hoffman JI. A high-quality pedigree and genetic markers both reveal inbreeding depression for quality but not survival in a cooperative mammal. Mol Ecol 2018; 27:2271-2288. [PMID: 29603504 DOI: 10.1111/mec.14570] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [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: 07/19/2017] [Revised: 03/05/2018] [Accepted: 03/12/2018] [Indexed: 01/07/2023]
Abstract
Inbreeding depression, the reduced fitness of offspring of closely related parents, is commonplace in both captive and wild populations and has important consequences for conservation and mating system evolution. However, because of the difficulty of collecting pedigree and life-history data from wild populations, relatively few studies have been able to compare inbreeding depression for traits at different points in the life cycle. Moreover, pedigrees give the expected proportion of the genome that is identical by descent (IBDg ) whereas in theory with enough molecular markers realized IBDg can be quantified directly. We therefore investigated inbreeding depression for multiple life-history traits in a wild population of banded mongooses using pedigree-based inbreeding coefficients (fped ) and standardized multilocus heterozygosity (sMLH) measured at 35-43 microsatellites. Within an information theoretic framework, we evaluated support for either fped or sMLH as inbreeding terms and used sequential regression to determine whether the residuals of sMLH on fped explain fitness variation above and beyond fped . We found no evidence of inbreeding depression for survival, either before or after nutritional independence. By contrast, inbreeding was negatively associated with two quality-related traits, yearling body mass and annual male reproductive success. Yearling body mass was associated with fped but not sMLH, while male annual reproductive success was best explained by both fped and residual sMLH. Thus, our study not only uncovers variation in the extent to which different traits show inbreeding depression, but also reveals trait-specific differences in the ability of pedigrees and molecular markers to explain fitness variation and suggests that for certain traits, genetic markers may capture variation in realized IBDg above and beyond the pedigree expectation.
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Affiliation(s)
- David A Wells
- Department of Animal Behaviour, University of Bielefeld, Bielefeld, Germany.,School of Natural Science and Psychology, Liverpool John Moores University, Liverpool, UK
| | - Michael A Cant
- College of Life and Environmental Sciences, University of Exeter, Penryn, UK
| | - Hazel J Nichols
- School of Natural Science and Psychology, Liverpool John Moores University, Liverpool, UK
| | - Joseph I Hoffman
- Department of Animal Behaviour, University of Bielefeld, Bielefeld, Germany
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19
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Germain RR, Arcese P, Reid JM. The Consequences of Polyandry for Sibship Structures, Distributions of Relationships and Relatedness, and Potential for Inbreeding in a Wild Population. Am Nat 2018; 191:638-657. [PMID: 29693437 DOI: 10.1086/696855] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [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
The evolutionary benefits of simultaneous polyandry (female multiple mating within a single reproductive event) remain elusive. One potential benefit could arise if polyandry alters sibship structures and consequent relationships and relatedness among females' descendants, thereby intrinsically reducing future inbreeding risk (the indirect inbreeding avoidance hypothesis). However such effects have not been quantified in naturally complex mating systems that also encompass iteroparity, overlapping generations, sequential polyandry, and polygyny. We used long-term social and genetic pedigree data from song sparrows (Melospiza melodia) to quantify cross-generational consequences of simultaneous polyandry for offspring sibship structures and distributions of relationships and relatedness among possible mates. Simultaneous polyandry decreased full sibships and increased half-sibships, on average, but such effects varied among females and were smaller than would occur in the absence of sequential polyandry or polygyny. Further, while simultaneous polyandry decreased the overall frequencies of possible matings among adult full sibs, it increased the frequencies of possible matings among adult half-sibs and more distant relatives. These results imply that the intrinsic consequences of simultaneous polyandry for inbreeding risk could cause weak indirect selection on polyandry, but the magnitude and direction of such effects will depend on complex interactions with other mating system components and the form of inbreeding depression.
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20
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Nietlisbach P, Keller LF, Camenisch G, Guillaume F, Arcese P, Reid JM, Postma E. Pedigree-based inbreeding coefficient explains more variation in fitness than heterozygosity at 160 microsatellites in a wild bird population. Proc Biol Sci 2018; 284:rspb.2016.2763. [PMID: 28250184 DOI: 10.1098/rspb.2016.2763] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [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: 12/13/2016] [Accepted: 02/06/2017] [Indexed: 01/14/2023] Open
Abstract
Although the pedigree-based inbreeding coefficient F predicts the expected proportion of an individual's genome that is identical-by-descent (IBD), heterozygosity at genetic markers captures Mendelian sampling variation and thereby provides an estimate of realized IBD. Realized IBD should hence explain more variation in fitness than their pedigree-based expectations, but how many markers are required to achieve this in practice remains poorly understood. We use extensive pedigree and life-history data from an island population of song sparrows (Melospiza melodia) to show that the number of genetic markers and pedigree depth affected the explanatory power of heterozygosity and F, respectively, but that heterozygosity measured at 160 microsatellites did not explain more variation in fitness than F This is in contrast with other studies that found heterozygosity based on far fewer markers to explain more variation in fitness than F Thus, the relative performance of marker- and pedigree-based estimates of IBD depends on the quality of the pedigree, the number, variability and location of the markers employed, and the species-specific recombination landscape, and expectations based on detailed and deep pedigrees remain valuable until we can routinely afford genotyping hundreds of phenotyped wild individuals of genetic non-model species for thousands of genetic markers.
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Affiliation(s)
- Pirmin Nietlisbach
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Lukas F Keller
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Glauco Camenisch
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Frédéric Guillaume
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Peter Arcese
- Department of Forest and Conservation Sciences, University of British Columbia, 2424 Main Mall, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Jane M Reid
- Institute of Biological and Environmental Sciences, School of Biological Sciences, University of Aberdeen, Zoology Building, Tillydrone Avenue, Aberdeen AB24 2TZ, UK
| | - Erik Postma
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.,Centre for Ecology and Conservation, College of Life and Environmental Sciences, University of Exeter, Cornwall Campus, Penryn TR10 9EZ, UK
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21
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Wolak ME, Reid JM. Accounting for genetic differences among unknown parents in microevolutionary studies: how to include genetic groups in quantitative genetic animal models. J Anim Ecol 2017; 86:7-20. [PMID: 27731502 PMCID: PMC5217070 DOI: 10.1111/1365-2656.12597] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 09/23/2016] [Indexed: 11/30/2022]
Abstract
Quantifying and predicting microevolutionary responses to environmental change requires unbiased estimation of quantitative genetic parameters in wild populations. 'Animal models', which utilize pedigree data to separate genetic and environmental effects on phenotypes, provide powerful means to estimate key parameters and have revolutionized quantitative genetic analyses of wild populations. However, pedigrees collected in wild populations commonly contain many individuals with unknown parents. When unknown parents are non-randomly associated with genetic values for focal traits, animal model parameter estimates can be severely biased. Yet, such bias has not previously been highlighted and statistical methods designed to minimize such biases have not been implemented in evolutionary ecology. We first illustrate how the occurrence of non-random unknown parents in population pedigrees can substantially bias animal model predictions of breeding values and estimates of additive genetic variance, and create spurious temporal trends in predicted breeding values in the absence of local selection. We then introduce 'genetic group' methods, which were developed in agricultural science, and explain how these methods can minimize bias in quantitative genetic parameter estimates stemming from genetic heterogeneity among individuals with unknown parents. We summarize the conceptual foundations of genetic group animal models and provide extensive, step-by-step tutorials that demonstrate how to fit such models in a variety of software programs. Furthermore, we provide new functions in r that extend current software capabilities and provide a standardized approach across software programs to implement genetic group methods. Beyond simply alleviating bias, genetic group animal models can directly estimate new parameters pertaining to key biological processes. We discuss one such example, where genetic group methods potentially allow the microevolutionary consequences of local selection to be distinguished from effects of immigration and resulting gene flow. We highlight some remaining limitations of genetic group models and discuss opportunities for further development and application in evolutionary ecology. We suggest that genetic group methods should no longer be overlooked by evolutionary ecologists, but should become standard components of the toolkit for animal model analyses of wild population data sets.
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Affiliation(s)
- Matthew E. Wolak
- Institute of Biological and Environmental SciencesSchool of Biological SciencesUniversity of Aberdeen, Zoology Building, Tillydrone AvenueAberdeen AB24 2TZUK
| | - Jane M. Reid
- Institute of Biological and Environmental SciencesSchool of Biological SciencesUniversity of Aberdeen, Zoology Building, Tillydrone AvenueAberdeen AB24 2TZUK
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22
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Pemberton JM, Ellis PE, Pilkington JG, Bérénos C. Inbreeding depression by environment interactions in a free-living mammal population. Heredity (Edinb) 2017; 118:64-77. [PMID: 27876804 DOI: 10.1038/hdy.2016.100] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 08/06/2016] [Accepted: 08/12/2016] [Indexed: 12/12/2022] Open
Abstract
Experimental studies often find that inbreeding depression is more severe in harsh environments, but the few studies of in situ wild populations available to date rarely find strong support for this effect. We investigated evidence for inbreeding depression by environment interactions in nine traits in the individually monitored Soay sheep population of St Kilda, using genomic inbreeding coefficients based on 37 037 single-nucleotide polymorphism loci, and population density as an axis of environmental variation. All traits showed variation with population density and all traits showed some evidence for depression because of either an individual's own inbreeding or maternal inbreeding. However, only six traits showed evidence for an interaction in the expected direction, and only two interactions were statistically significant. We identify three possible reasons why wild population studies may generally fail to find strong support for interactions between inbreeding depression and environmental variation compared with experimental studies. First, for species with biparental inbreeding only, the amount of observed inbreeding in natural populations is generally low compared with that used in experimental studies. Second, it is possible that experimental studies sometimes actually impose higher levels of stress than organisms experience in the wild. Third, some purging of the deleterious recessive alleles that underpin interaction effects may occur in the wild.
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23
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Germain RR, Wolak ME, Arcese P, Losdat S, Reid JM. Direct and indirect genetic and fine-scale location effects on breeding date in song sparrows. J Anim Ecol 2016; 85:1613-1624. [PMID: 27448623 DOI: 10.1111/1365-2656.12575] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [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: 04/21/2016] [Accepted: 07/14/2016] [Indexed: 11/30/2022]
Abstract
Quantifying direct and indirect genetic effects of interacting females and males on variation in jointly expressed life-history traits is central to predicting microevolutionary dynamics. However, accurately estimating sex-specific additive genetic variances in such traits remains difficult in wild populations, especially if related individuals inhabit similar fine-scale environments. Breeding date is a key life-history trait that responds to environmental phenology and mediates individual and population responses to environmental change. However, no studies have estimated female (direct) and male (indirect) additive genetic and inbreeding effects on breeding date, and estimated the cross-sex genetic correlation, while simultaneously accounting for fine-scale environmental effects of breeding locations, impeding prediction of microevolutionary dynamics. We fitted animal models to 38 years of song sparrow (Melospiza melodia) phenology and pedigree data to estimate sex-specific additive genetic variances in breeding date, and the cross-sex genetic correlation, thereby estimating the total additive genetic variance while simultaneously estimating sex-specific inbreeding depression. We further fitted three forms of spatial animal model to explicitly estimate variance in breeding date attributable to breeding location, overlap among breeding locations and spatial autocorrelation. We thereby quantified fine-scale location variances in breeding date and quantified the degree to which estimating such variances affected the estimated additive genetic variances. The non-spatial animal model estimated nonzero female and male additive genetic variances in breeding date (sex-specific heritabilities: 0·07 and 0·02, respectively) and a strong, positive cross-sex genetic correlation (0·99), creating substantial total additive genetic variance (0·18). Breeding date varied with female, but not male inbreeding coefficient, revealing direct, but not indirect, inbreeding depression. All three spatial animal models estimated small location variance in breeding date, but because relatedness and breeding location were virtually uncorrelated, modelling location variance did not alter the estimated additive genetic variances. Our results show that sex-specific additive genetic effects on breeding date can be strongly positively correlated, which would affect any predicted rates of microevolutionary change in response to sexually antagonistic or congruent selection. Further, we show that inbreeding effects on breeding date can also be sex specific and that genetic effects can exceed phenotypic variation stemming from fine-scale location-based variation within a wild population.
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Affiliation(s)
- Ryan R Germain
- Department of Forest and Conservation Sciences, University of British Columbia, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada. .,Institute of Biological and Environmental Sciences, School of Biological Sciences, Zoology Building, University of Aberdeen, Tillydrone Avenue, Aberdeen, AB24 2TZ, UK.
| | - Matthew E Wolak
- Institute of Biological and Environmental Sciences, School of Biological Sciences, Zoology Building, University of Aberdeen, Tillydrone Avenue, Aberdeen, AB24 2TZ, UK
| | - Peter Arcese
- Department of Forest and Conservation Sciences, University of British Columbia, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Sylvain Losdat
- Institute of Biological and Environmental Sciences, School of Biological Sciences, Zoology Building, University of Aberdeen, Tillydrone Avenue, Aberdeen, AB24 2TZ, UK
| | - Jane M Reid
- Institute of Biological and Environmental Sciences, School of Biological Sciences, Zoology Building, University of Aberdeen, Tillydrone Avenue, Aberdeen, AB24 2TZ, UK
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Reid JM, Bocedi G, Nietlisbach P, Duthie AB, Wolak ME, Gow EA, Arcese P. Variation in parent-offspring kinship in socially monogamous systems with extra-pair reproduction and inbreeding. Evolution 2016; 70:1512-29. [PMID: 27174154 PMCID: PMC4949684 DOI: 10.1111/evo.12953] [Citation(s) in RCA: 12] [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] [Received: 11/30/2015] [Revised: 04/19/2016] [Accepted: 05/04/2016] [Indexed: 01/18/2023]
Abstract
Female extra‐pair reproduction in socially monogamous systems is predicted to cause cuckolded socially‐paired males to conditionally reduce paternal care, causing selection against extra‐pair reproduction and underlying polyandry. However, existing models and empirical studies have not explicitly considered that cuckolded males might be related to their socially‐paired female and/or to her extra‐pair mate, and therefore be related to extra‐pair offspring that they did not sire but could rear. Selection against paternal care, and hence against extra‐pair reproduction, might then be weakened. We derive metrics that quantify allele‐sharing between within‐pair and extra‐pair offspring and their mother and her socially‐paired male in terms of coefficients of kinship and inbreeding. We use song sparrow (Melospiza melodia) paternity and pedigree data to quantify these metrics, and thereby quantify the joint effects of extra‐pair reproduction and inbreeding on a brood's total allelic value to its socially‐paired parents. Cuckolded male song sparrows were almost always detectably related to extra‐pair offspring they reared. Consequently, although brood allelic value decreased substantially following female extra‐pair reproduction, this decrease was reduced by within‐pair and extra‐pair reproduction among relatives. Such complex variation in kinship within nuclear families should be incorporated into models considering coevolutionary dynamics of extra‐pair reproduction, parental care, and inbreeding.
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Affiliation(s)
- Jane M Reid
- Institute of Biological and Environmental Sciences, School of Biological Sciences, Zoology Building, University of Aberdeen, Tillydrone Avenue, Aberdeen, AB24 2TZ, Scotland.
| | - Greta Bocedi
- Institute of Biological and Environmental Sciences, School of Biological Sciences, Zoology Building, University of Aberdeen, Tillydrone Avenue, Aberdeen, AB24 2TZ, Scotland
| | - Pirmin Nietlisbach
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - A Bradley Duthie
- Institute of Biological and Environmental Sciences, School of Biological Sciences, Zoology Building, University of Aberdeen, Tillydrone Avenue, Aberdeen, AB24 2TZ, Scotland
| | - Matthew E Wolak
- Institute of Biological and Environmental Sciences, School of Biological Sciences, Zoology Building, University of Aberdeen, Tillydrone Avenue, Aberdeen, AB24 2TZ, Scotland
| | - Elizabeth A Gow
- Department of Forest and Conservation Sciences, 2424 Main Mall, University of British Columbia, Vancouver BC, Canada, V6T 1Z4
| | - Peter Arcese
- Department of Forest and Conservation Sciences, 2424 Main Mall, University of British Columbia, Vancouver BC, Canada, V6T 1Z4
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Wolak ME, Reid JM. Is Pairing with a Relative Heritable? Estimating Female and Male Genetic Contributions to the Degree of Biparental Inbreeding in Song Sparrows (Melospiza melodia). Am Nat 2016; 187:736-52. [DOI: 10.1086/686198] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Trask AE, Bignal EM, McCracken DI, Monaghan P, Piertney SB, Reid JM. Evidence of the phenotypic expression of a lethal recessive allele under inbreeding in a wild population of conservation concern. J Anim Ecol 2016; 85:879-91. [PMID: 26996516 DOI: 10.1111/1365-2656.12503] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [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: 11/12/2015] [Accepted: 01/15/2016] [Indexed: 11/27/2022]
Abstract
Deleterious recessive alleles that are masked in outbred populations are predicted to be expressed in small, inbred populations, reducing both individual fitness and population viability. However, there are few definitive examples of phenotypic expression of lethal recessive alleles under inbreeding conditions in wild populations. Studies that demonstrate the action of such alleles, and infer their distribution and dynamics, are required to understand their potential impact on population viability and inform management responses. The Scottish population of red-billed choughs (Pyrrhocorax pyrrhocorax), which currently totals <60 breeding pairs and is of major conservation concern, has recently been affected by lethal blindness in nestlings. We used family data to show that the pattern of occurrence of blindness within and across affected families that produced blind nestlings was exactly 0·25, matching that expected given a single-locus autosomal lethal recessive allele. Furthermore, the observed distribution of blind nestlings within affected families did not differ from that expected given Mendelian inheritance of such an allele. Relatedness estimates showed that individuals from affected families were not more closely related to each other than they were to individuals from unaffected families that did not produce blind nestlings. Blind individuals tended to be less heterozygous than non-blind individuals, as expected if blindness was caused by the expression of a recessive allele under inbreeding. However, there was no difference in the variance in heterozygosity estimates, suggesting that some blind individuals were relatively outbred. These results suggest carriers of the blindness allele may be widely distributed across contemporary families rather than restricted to a single family lineage, implying that the allele has persisted across multiple generations. Blindness occurred at low frequency (affecting 1·6% of observed nestlings since 1981). However, affected families had larger initial brood sizes than unaffected families. Such high fecundity of carriers of a lethal recessive allele might reflect overdominance, potentially reducing purging and increasing allele persistence probability. We thereby demonstrate the phenotypic expression of a lethal recessive allele in a wild population of conservation concern, and provide a general framework for inferring allele distribution and persistence and informing management responses.
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Affiliation(s)
- Amanda E Trask
- Institute of Biological & Environmental Sciences, School of Biological Sciences, University of Aberdeen, Zoology Building, Tillydrone Avenue, Aberdeen, AB24 2TZ, UK
| | - Eric M Bignal
- Scottish Chough Study Group, Kindrochaid, Bridgend, Isle of Islay, Argyll, PA44 7PT, UK
| | - Davy I McCracken
- Future Farming Systems, Scotland's Rural College, Auchincruive, Ayr, KA6 5HW, UK
| | - Pat Monaghan
- College of Medical, Veterinary & Life Sciences, University of Glasgow, Graham Kerr Building, Glasgow, G12 8QQ, UK
| | - Stuart B Piertney
- Institute of Biological & Environmental Sciences, School of Biological Sciences, University of Aberdeen, Zoology Building, Tillydrone Avenue, Aberdeen, AB24 2TZ, UK
| | - Jane M Reid
- Institute of Biological & Environmental Sciences, School of Biological Sciences, University of Aberdeen, Zoology Building, Tillydrone Avenue, Aberdeen, AB24 2TZ, UK
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Huisman J, Kruuk LE, Ellis PA, Clutton-Brock T, Pemberton JM. Inbreeding depression across the lifespan in a wild mammal population. Proc Natl Acad Sci U S A 2016; 113:3585-90. [PMID: 26979959 DOI: 10.1073/pnas.1518046113] [Citation(s) in RCA: 172] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Inbreeding depression is of major concern for the conservation of threatened species, and inbreeding avoidance is thought to be a key driver in the evolution of mating systems. However, the estimation of individual inbreeding coefficients in natural populations has been challenging, and, consequently, the full effect of inbreeding on fitness remains unclear. Genomic inbreeding coefficients may resolve the long-standing paucity of data on inbreeding depression in adult traits and total fitness. Here we investigate inbreeding depression in a range of life history traits and fitness in a wild population of red deer (Cervus elaphus) in Scotland using individual inbreeding coefficients derived from dense Single-Nucleotide Polymorphism (SNP) data (Fgrm). We find associations between[Formula: see text]and annual breeding success in both sexes, and between maternal inbreeding coefficient and offspring survival. We also confirm previous findings of inbreeding depression in birth weight and juvenile survival. In contrast, inbreeding coefficients calculated from a deep and comparatively complete pedigree detected inbreeding depression in juvenile survival, but not in any adult fitness component. The total effect of inbreeding on lifetime breeding success (LBS) was substantial in both sexes: for Fgrm = 0.125, a value resulting from a half-sib mating, LBS declined by 72% for females and 95% for males. Our results demonstrate that SNP-based estimates of inbreeding provide a powerful tool for evaluating inbreeding depression in natural populations, and suggest that, to date, the prevalence of inbreeding depression in adult traits may have been underestimated.
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Hammerly SC, Cerda DA, Bailey H, Johnson JA. A pedigree gone bad: increased offspring survival after using DNA‐based relatedness to minimize inbreeding in a captive population. Anim Conserv 2015. [DOI: 10.1111/acv.12247] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- S. C. Hammerly
- Department of Biological Sciences Institute of Applied Sciences University of North Texas Denton TX USA
| | - D. A. Cerda
- Department of Biological Sciences Institute of Applied Sciences University of North Texas Denton TX USA
| | | | - J. A. Johnson
- Department of Biological Sciences Institute of Applied Sciences University of North Texas Denton TX USA
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Reid JM, Arcese P, Bocedi G, Duthie AB, Wolak ME, Keller LF. Resolving the conundrum of inbreeding depression but no inbreeding avoidance: Estimating sex-specific selection on inbreeding by song sparrows (Melospiza melodia). Evolution 2015; 69:2846-61. [PMID: 26420476 PMCID: PMC5057356 DOI: 10.1111/evo.12780] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [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: 06/10/2015] [Revised: 09/04/2015] [Accepted: 09/16/2015] [Indexed: 11/29/2022]
Abstract
Inbreeding avoidance among interacting females and males is not always observed despite inbreeding depression in offspring fitness, creating an apparent "inbreeding paradox." This paradox could be resolved if selection against inbreeding was in fact weak, despite inbreeding depression. However, the net magnitude and direction of selection on the degree to which females and males inbreed by pairing with relatives has not been explicitly estimated. We used long-term pedigree data to estimate phenotypic selection gradients on the degree of inbreeding that female and male song sparrows (Melospiza melodia) expressed by forming socially persistent breeding pairs with relatives. Fitness was measured as the total numbers of offspring and grand offspring contributed to the population, and as corresponding expected numbers of identical-by-descent allele copies, thereby accounting for variation in offspring survival, reproduction, and relatedness associated with variation in parental inbreeding. Estimated selection gradients on the degree to which individuals paired with relatives were weakly positive in females, but negative in males that formed at least one socially persistent pairing. However, males that paired had higher mean fitness than males that remained socially unpaired. These analyses suggest that net selection against inbreeding may be weak in both sexes despite strong inbreeding depression, thereby resolving the "inbreeding paradox."
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Affiliation(s)
- Jane M Reid
- Institute of Biological and Environmental Sciences, School of Biological Sciences, Zoology Building, University of Aberdeen, Tillydrone Avenue, Aberdeen AB24 2TZ, Scotland.
| | - Peter Arcese
- Department of Forest and Conservation Sciences, University of British Columbia, 2424 Main Mall, Vancouver, BC, Canada, V6T 1Z4
| | - Greta Bocedi
- Institute of Biological and Environmental Sciences, School of Biological Sciences, Zoology Building, University of Aberdeen, Tillydrone Avenue, Aberdeen AB24 2TZ, Scotland
| | - A Bradley Duthie
- Institute of Biological and Environmental Sciences, School of Biological Sciences, Zoology Building, University of Aberdeen, Tillydrone Avenue, Aberdeen AB24 2TZ, Scotland
| | - Matthew E Wolak
- Institute of Biological and Environmental Sciences, School of Biological Sciences, Zoology Building, University of Aberdeen, Tillydrone Avenue, Aberdeen AB24 2TZ, Scotland
| | - Lukas F Keller
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
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Affiliation(s)
- Ryan R. Germain
- Department of Forest & Conservation Sciences University of British Columbia 2424 Main MallVancouver British Columbia V6T 1Z4 Canada
| | - Richard Schuster
- Department of Forest & Conservation Sciences University of British Columbia 2424 Main MallVancouver British Columbia V6T 1Z4 Canada
| | - Kira E. Delmore
- Department of Zoology University of British Columbia 6270 University Boulevard Vancouver British Columbia V6T 1Z4Canada
| | - Peter Arcese
- Department of Forest & Conservation Sciences University of British Columbia 2424 Main MallVancouver British Columbia V6T 1Z4 Canada
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Firth JA, Hadfield JD, Santure AW, Slate J, Sheldon BC. The influence of nonrandom extra-pair paternity on heritability estimates derived from wild pedigrees. Evolution 2015; 69:1336-44. [PMID: 25800997 PMCID: PMC4950017 DOI: 10.1111/evo.12649] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [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: 12/05/2014] [Accepted: 03/16/2015] [Indexed: 01/06/2023]
Abstract
Quantitative genetic analysis is often fundamental for understanding evolutionary processes in wild populations. Avian populations provide a model system due to the relative ease of inferring relatedness among individuals through observation. However, extra-pair paternity (EPP) creates erroneous links within the social pedigree. Previous work has suggested this causes minor underestimation of heritability if paternal misassignment is random and hence not influenced by the trait being studied. Nevertheless, much literature suggests numerous traits are associated with EPP and the accuracy of heritability estimates for such traits remains unexplored. We show analytically how nonrandom pedigree errors can influence heritability estimates. Then, combining empirical data from a large great tit (Parus major) pedigree with simulations, we assess how heritability estimates derived from social pedigrees change depending on the mode of the relationship between EPP and the focal trait. We show that the magnitude of the underestimation is typically small (<15%). Hence, our analyses suggest that quantitative genetic inference from pedigrees derived from observations of social relationships is relatively robust; our approach also provides a widely applicable method for assessing the consequences of nonrandom EPP.
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Affiliation(s)
- Josh A Firth
- Department of Zoology, Edward Grey Institute, University of Oxford, Oxford, United Kingdom.
| | - Jarrod D Hadfield
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Anna W Santure
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Jon Slate
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Ben C Sheldon
- Department of Zoology, Edward Grey Institute, University of Oxford, Oxford, United Kingdom
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Nietlisbach P, Camenisch G, Bucher T, Slate J, Keller LF, Postma E. A microsatellite-based linkage map for song sparrows (Melospiza melodia). Mol Ecol Resour 2015; 15:1486-96. [PMID: 25865627 DOI: 10.1111/1755-0998.12414] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [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: 09/19/2014] [Revised: 04/01/2015] [Accepted: 04/03/2015] [Indexed: 01/15/2023]
Abstract
Although linkage maps are important tools in evolutionary biology, their availability for wild populations is limited. The population of song sparrows (Melospiza melodia) on Mandarte Island, Canada, is among the more intensively studied wild animal populations. Its long-term pedigree data, together with extensive genetic sampling, have allowed the study of a range of questions in evolutionary biology and ecology. However, the availability of genetic markers has been limited. We here describe 191 new microsatellite loci, including 160 high-quality polymorphic autosomal, 7 Z-linked and 1 W-linked markers. We used these markers to construct a linkage map for song sparrows with a total sex-averaged map length of 1731 cM and covering 35 linkage groups, and hence, these markers cover most of the 38-40 chromosomes. Female and male map lengths did not differ significantly. We then bioinformatically mapped these loci to the zebra finch (Taeniopygia guttata) genome and found that linkage groups were conserved between song sparrows and zebra finches. Compared to the zebra finch, marker order within small linkage groups was well conserved, whereas the larger linkage groups showed some intrachromosomal rearrangements. Finally, we show that as expected, recombination frequency between linked loci explained the majority of variation in gametic phase disequilibrium. Yet, there was substantial overlap in gametic phase disequilibrium between pairs of linked and unlinked loci. Given that the microsatellites described here lie on 35 of the 38-40 chromosomes, these markers will be useful for studies in this species, as well as for comparative genomics studies with other species.
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Affiliation(s)
- Pirmin Nietlisbach
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Glauco Camenisch
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Thomas Bucher
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Jon Slate
- Department of Animal & Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Lukas F Keller
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Erik Postma
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
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Taylor HR, Kardos MD, Ramstad KM, Allendorf FW. Valid estimates of individual inbreeding coefficients from marker-based pedigrees are not feasible in wild populations with low allelic diversity. CONSERV GENET 2015; 16:901-13. [DOI: 10.1007/s10592-015-0709-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Reid JM, Duthie AB, Wolak ME, Arcese P. Demographic mechanisms of inbreeding adjustment through extra-pair reproduction. J Anim Ecol 2015; 84:1029-40. [PMID: 25645743 PMCID: PMC4670719 DOI: 10.1111/1365-2656.12340] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [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: 09/22/2014] [Accepted: 01/15/2015] [Indexed: 11/29/2022]
Abstract
One hypothesis explaining extra-pair reproduction is that socially monogamous females mate with extra-pair males to adjust the coefficient of inbreeding (f) of extra-pair offspring (EPO) relative to that of within-pair offspring (WPO) they would produce with their socially paired male. Such adjustment of offspring f requires non-random extra-pair reproduction with respect to relatedness, which is in turn often assumed to require some mechanism of explicit pre-copulatory or post-copulatory kin discrimination.
We propose three demographic processes that could potentially cause mean f to differ between individual females’ EPO and WPO given random extra-pair reproduction with available males without necessarily requiring explicit kin discrimination. Specifically, such a difference could arise if social pairings formed non-randomly with respect to relatedness or persisted non-randomly with respect to relatedness, or if the distribution of relatedness between females and their sets of potential mates changed during the period through which social pairings persisted.
We used comprehensive pedigree and pairing data from free-living song sparrows (Melospiza melodia) to quantify these three processes and hence investigate how individual females could adjust mean offspring f through instantaneously random extra-pair reproduction.
Female song sparrows tended to form social pairings with unrelated or distantly related males slightly less frequently than expected given random pairing within the defined set of available males. Furthermore, social pairings between more closely related mates tended to be more likely to persist across years than social pairings between less closely related mates. However, these effects were small and the mean relatedness between females and their sets of potential extra-pair males did not change substantially across the years through which social pairings persisted.
Our framework and analyses illustrate how demographic and social structuring within populations might allow females to adjust mean f of offspring through random extra-pair reproduction without necessarily requiring explicit kin discrimination, implying that adjustment of offspring f might be an inevitable consequence of extra-pair reproduction. New theoretical and empirical studies are required to explore the general magnitude of such effects and quantify the degree to which they could facilitate or constrain long-term evolution of extra-pair reproduction.
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Affiliation(s)
- Jane M Reid
- Institute of Biological and Environmental Sciences, School of Biological Sciences, University of Aberdeen, Zoology Building, Tillydrone Avenue, Aberdeen, AB24 2TZ, Scotland
| | - A Bradley Duthie
- Institute of Biological and Environmental Sciences, School of Biological Sciences, University of Aberdeen, Zoology Building, Tillydrone Avenue, Aberdeen, AB24 2TZ, Scotland
| | - Matthew E Wolak
- Institute of Biological and Environmental Sciences, School of Biological Sciences, University of Aberdeen, Zoology Building, Tillydrone Avenue, Aberdeen, AB24 2TZ, Scotland
| | - Peter Arcese
- Department of Forest and Conservation Sciences, University of British Columbia, 2424 Main Mall, Vancouver, BC, Canada, V6T 1Z4
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Reid JM, Arcese P, Keller LF, Germain RR, Duthie AB, Losdat S, Wolak ME, Nietlisbach P. Quantifying inbreeding avoidance through extra-pair reproduction. Evolution 2014; 69:59-74. [PMID: 25346331 PMCID: PMC4312944 DOI: 10.1111/evo.12557] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [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: 05/27/2014] [Accepted: 10/11/2014] [Indexed: 01/13/2023]
Abstract
Extra-pair reproduction is widely hypothesized to allow females to avoid inbreeding with related socially paired males. Consequently, numerous field studies have tested the key predictions that extra-pair offspring are less inbred than females’ alternative within-pair offspring, and that the probability of extra-pair reproduction increases with a female's relatedness to her socially paired male. However, such studies rarely measure inbreeding or relatedness sufficiently precisely to detect subtle effects, or consider biases stemming from failure to observe inbred offspring that die during early development. Analyses of multigenerational song sparrow (Melospiza melodia) pedigree data showed that most females had opportunity to increase or decrease the coefficient of inbreeding of their offspring through extra-pair reproduction with neighboring males. In practice, observed extra-pair offspring had lower inbreeding coefficients than females’ within-pair offspring on average, while the probability of extra-pair reproduction increased substantially with the coefficient of kinship between a female and her socially paired male. However, simulations showed that such effects could simply reflect bias stemming from inbreeding depression in early offspring survival. The null hypothesis that extra-pair reproduction is random with respect to kinship therefore cannot be definitively rejected in song sparrows, and existing general evidence that females avoid inbreeding through extra-pair reproduction requires reevaluation given such biases.
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Affiliation(s)
- Jane M Reid
- School of Biological Sciences, Institute of Biological and Environmental Sciences, Zoology Building, University of Aberdeen, Tillydrone Avenue, Aberdeen, AB24 2TZ, Scotland.
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Reid JM, Arcese P, Losdat S. Genetic covariance between components of male reproductive success: within-pair vs. extra-pair paternity in song sparrows. J Evol Biol 2014; 27:2046-56. [PMID: 25186454 PMCID: PMC4283045 DOI: 10.1111/jeb.12445] [Citation(s) in RCA: 13] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2014] [Revised: 06/09/2014] [Accepted: 06/14/2014] [Indexed: 11/28/2022]
Abstract
The evolutionary trajectories of reproductive systems, including both male and female multiple mating and hence polygyny and polyandry, are expected to depend on the additive genetic variances and covariances in and among components of male reproductive success achieved through different reproductive tactics. However, genetic covariances among key components of male reproductive success have not been estimated in wild populations. We used comprehensive paternity data from socially monogamous but genetically polygynandrous song sparrows (Melospiza melodia) to estimate additive genetic variance and covariance in the total number of offspring a male sired per year outside his social pairings (i.e. his total extra-pair reproductive success achieved through multiple mating) and his liability to sire offspring produced by his socially paired female (i.e. his success in defending within-pair paternity). Both components of male fitness showed nonzero additive genetic variance, and the estimated genetic covariance was positive, implying that males with high additive genetic value for extra-pair reproduction also have high additive genetic propensity to sire their socially paired female's offspring. There was consequently no evidence of a genetic or phenotypic trade-off between male within-pair paternity success and extra-pair reproductive success. Such positive genetic covariance might be expected to facilitate ongoing evolution of polygyny and could also shape the ongoing evolution of polyandry through indirect selection.
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Affiliation(s)
- J M Reid
- Institute of Biological and Environmental Sciences, School of Biological Sciences, University of Aberdeen, Aberdeen, Scotland
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37
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Reid JM, Arcese P, Keller LF, Losdat S. Female and male genetic effects on offspring paternity: additive genetic (co)variances in female extra-pair reproduction and male paternity success in song sparrows (Melospiza melodia). Evolution 2014; 68:2357-70. [PMID: 24724612 PMCID: PMC4285967 DOI: 10.1111/evo.12424] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [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: 10/16/2013] [Accepted: 04/02/2014] [Indexed: 12/19/2022]
Abstract
Ongoing evolution of polyandry, and consequent extra-pair reproduction in socially monogamous systems, is hypothesized to be facilitated by indirect selection stemming from cross-sex genetic covariances with components of male fitness. Specifically, polyandry is hypothesized to create positive genetic covariance with male paternity success due to inevitable assortative reproduction, driving ongoing coevolution. However, it remains unclear whether such covariances could or do emerge within complex polyandrous systems. First, we illustrate that genetic covariances between female extra-pair reproduction and male within-pair paternity success might be constrained in socially monogamous systems where female and male additive genetic effects can have opposing impacts on the paternity of jointly reared offspring. Second, we demonstrate nonzero additive genetic variance in female liability for extra-pair reproduction and male liability for within-pair paternity success, modeled as direct and associative genetic effects on offspring paternity, respectively, in free-living song sparrows (Melospiza melodia). The posterior mean additive genetic covariance between these liabilities was slightly positive, but the credible interval was wide and overlapped zero. Therefore, although substantial total additive genetic variance exists, the hypothesis that ongoing evolution of female extra-pair reproduction is facilitated by genetic covariance with male within-pair paternity success cannot yet be definitively supported or rejected either conceptually or empirically.
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Affiliation(s)
- Jane M Reid
- Institute of Biological and Environmental Sciences, School of Biological Sciences, Zoology Building, University of Aberdeen, Tillydrone Avenue, Aberdeen, AB24 2TZ, Scotland.
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