1
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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] [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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2
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Carbeck K, Arcese P, Lovette I, Pruett C, Winker K, Walsh J. Candidate genes under selection in song sparrows co-vary with climate and body mass in support of Bergmann's Rule. Nat Commun 2023; 14:6974. [PMID: 37935683 PMCID: PMC10630373 DOI: 10.1038/s41467-023-42786-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 10/19/2023] [Indexed: 11/09/2023] Open
Abstract
Ecogeographic rules denote spatial patterns in phenotype and environment that may reflect local adaptation as well as a species' capacity to adapt to change. To identify genes underlying Bergmann's Rule, which posits that spatial correlations of body mass and temperature reflect natural selection and local adaptation in endotherms, we compare 79 genomes from nine song sparrow (Melospiza melodia) subspecies that vary ~300% in body mass (17 - 50 g). Comparing large- and smaller-bodied subspecies revealed 9 candidate genes in three genomic regions associated with body mass. Further comparisons to the five smallest subspecies endemic to California revealed eight SNPs within four of the candidate genes (GARNL3, RALGPS1, ANGPTL2, and COL15A1) associated with body mass and varying as predicted by Bergmann's Rule. Our results support the hypothesis that co-variation in environment, body mass and genotype reflect the influence of natural selection on local adaptation and a capacity for contemporary evolution in this diverse species.
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Affiliation(s)
- Katherine Carbeck
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, T6T 1Z4, Canada.
| | - Peter Arcese
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, T6T 1Z4, Canada
| | - Irby Lovette
- Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, Cornell University, Ithaca, NY, 14850, USA
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14850, USA
| | - Christin Pruett
- Department of Biology, Ouachita Baptist University, Arkadelphia, AR, 71998, USA
| | - Kevin Winker
- University of Alaska Museum, University of Alaska Fairbanks, Fairbanks, AK, 99775, USA
| | - Jennifer Walsh
- Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, Cornell University, Ithaca, NY, 14850, USA
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3
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Carbeck K, Wang T, Reid JM, Arcese P. Adaptation to climate change through seasonal migration revealed by climatic versus demographic niche models. GLOBAL CHANGE BIOLOGY 2022; 28:4260-4275. [PMID: 35366358 DOI: 10.1111/gcb.16185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 03/15/2022] [Indexed: 06/14/2023]
Abstract
Predicting the geographic range of species and their response to climatic variation and change are entwined goals in conservation and evolutionary ecology. Species distribution models (SDMs) are foundational in this effort and used to visualize the geographic range of species as the spatial representation of its realized niche. SDMs are also used to forecast range shifts under climate change, but often in the absence of empirical evidence that climate limits population growth. We explored the influence of climate on demography, seasonal migration, and the extent of the geographic range in song sparrows (Melospiza melodia), a species thought to display marked local adaptation to regional climate. To do so, we developed SDMs to predict the demographic and climate niches of migratory and resident song sparrows across our study area in western North America from California to Alaska, using 48 years of demographic data from a focal population in British Columbia and 1.2 million continental-scale citizen science observations. Spatial agreement of our demographic and climate niche models in the region of our focal population was strong (76%), supporting the hypothesis that demographic performance and the occurrence of seasonal migration varied predictably with climatic conditions. In contrast, agreement at the northern (58%) and southern (40%) extents of our study area was lower, as expected if the factors limiting population growth vary regionally. Our results support the hypothesis that local climate drives spatial variation in the occurrence of seasonal migration in song sparrows by limiting the fitness of year-round residents, and suggest that climate warming has favored range expansions and facilitated an upward shift in elevational range song sparrows that forgo seasonal migration. Our work highlights the potential role of seasonal migration in climate adaptation and limits on the reliability of climate niche models not validated with demographic data.
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Affiliation(s)
- Katherine Carbeck
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Tongli Wang
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jane M Reid
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
- Centre for Biodiversity Dynamics, Institutt for Biologi, NTNU, Trondheim, Norway
| | - 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: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [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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5
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Moiron M, Araya-Ajoy YG, Teplitsky C, Bouwhuis S, Charmantier A. Understanding the Social Dynamics of Breeding Phenology: Indirect Genetic Effects and Assortative Mating in a Long-Distance Migrant. Am Nat 2020; 196:566-576. [PMID: 33064582 DOI: 10.1086/711045] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractPhenological traits, such as the timing of reproduction, are often influenced by social interactions between paired individuals. Such partner effects may occur when pair members affect each other's prebreeding environment. Partner effects can be environmentally and/or genetically determined, and quantifying direct and indirect genetic effects is important for understanding the evolutionary dynamics of phenological traits. Here, using 26 years of data from a pedigreed population of a migratory seabird, the common tern (Sterna hirundo), we investigate male and female effects on female laying date. We find that female laying date harbors both genetic and environmental variation and is additionally influenced by the environmental and, to a lesser extent, genetic component of its mate. We demonstrate this partner effect to be largely explained by male arrival date. Interestingly, analyses of mating patterns with respect to arrival date show mating to be strongly assortative, and using simulations we show that assortative mating leads to overestimation of partner effects. Our study provides evidence for partner effects on breeding phenology in a long-distance migrant while uncovering the potential causal pathways underlying the observed effects and raising awareness for confounding effects resulting from assortative mating or other common environmental effects.
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6
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Evans SR, Postma E, Sheldon BC. It takes two: Heritable male effects on reproductive timing but not clutch size in a wild bird population*. Evolution 2020; 74:2320-2331. [DOI: 10.1111/evo.13980] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 03/19/2020] [Accepted: 04/02/2020] [Indexed: 12/29/2022]
Affiliation(s)
- Simon R. Evans
- Edward Grey Institute, Department of Zoology University of Oxford Oxford OX1 3SZ UK
- Centre for Ecology and Conservation University of Exeter Penryn TR10 9FE UK
| | - Erik Postma
- Centre for Ecology and Conservation University of Exeter Penryn TR10 9FE UK
| | - Ben C. Sheldon
- Edward Grey Institute, Department of Zoology University of Oxford Oxford OX1 3SZ UK
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7
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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] [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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8
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Kasper C, Schreier T, Taborsky B. Heritabilities, social environment effects and genetic correlations of social behaviours in a cooperatively breeding vertebrate. J Evol Biol 2019; 32:955-973. [PMID: 31152617 DOI: 10.1111/jeb.13494] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 04/25/2019] [Accepted: 05/20/2019] [Indexed: 11/28/2022]
Abstract
Social animals interact frequently with conspecifics, and their behaviour is influenced by social context, environmental cues and the behaviours of interaction partners, allowing for adaptive, flexible adjustments to social encounters. This flexibility can be limited by part of the behavioural variation being genetically determined. Furthermore, behaviours can be genetically correlated, potentially constraining independent evolution. Understanding social behaviour thus requires carefully disentangling genetic, environmental, maternal and social sources of variations as well as the correlation structure between behaviours. Here, we assessed heritability, maternal, common environment and social effects of eight social behaviours in Neolamprologus pulcher, a cooperatively breeding cichlid. We bred wild-caught fish in a paternal half-sibling design and scored ability to defend a resource against conspecifics, to integrate into a group and the propensity to help defending the group territory ("helping behaviour"). We assessed genetic, social and phenotypic correlations within clusters of behaviours predicted to be functionally related, namely "competition," "aggression," "aggression-sociability," "integration" and "integration-help." Helping behaviour and two affiliative behaviours were heritable, whereas there was little evidence for a genetic basis in all other traits. Phenotypic social effects explained part of the variation in a sociable and a submissive behaviour, but there were no maternal or common environment effects. Genetic and phenotypic correlation within clusters was mostly positive. A group's social environment influenced covariances of social behaviours. Genetic correlations were similar in magnitude but usually exceeding the phenotypic ones, indicating that conclusions about the evolution of social behaviours in this species could be provisionally drawn from phenotypic data in cases where data for genetic analyses are unobtainable.
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Affiliation(s)
- Claudia Kasper
- Behavioural Ecology, University of Bern, Hinterkappelen, Switzerland
| | - Tanja Schreier
- Behavioural Ecology, University of Bern, Hinterkappelen, Switzerland
| | - Barbara Taborsky
- Behavioural Ecology, University of Bern, Hinterkappelen, Switzerland
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9
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Muff S, Niskanen AK, Saatoglu D, Keller LF, Jensen H. Animal models with group-specific additive genetic variances: extending genetic group models. Genet Sel Evol 2019; 51:7. [PMID: 30819110 PMCID: PMC6394059 DOI: 10.1186/s12711-019-0449-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 02/07/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The animal model is a key tool in quantitative genetics and has been used extensively to estimate fundamental parameters, such as additive genetic variance or heritability. An implicit assumption of animal models is that all founder individuals derive from a single population. This assumption is commonly violated, for instance in crossbred livestock or when a meta-population is split into genetically differentiated subpopulations. Ignoring that base populations are genetically heterogeneous and thus split into different 'genetic groups' may lead to biased parameter estimates, especially for additive genetic variance. To avoid such biases, genetic group animal models, which account for the presence of more than one genetic group, have been proposed. Unfortunately, the method to date is only computationally feasible when the breeding values of the groups are allowed to differ in their means, but not in their variances. RESULTS We present an extension of the animal model that permits estimation of group-specific additive genetic variances. This is achieved by employing group-specific relatedness matrices for the breeding value components to different genetic groups. We derive these matrices by decomposing the full relatedness matrix via the generalized Cholesky decomposition, and by scaling the respective matrix components for each group. We propose a computationally convenient approximation for the matrix component that encodes for the Mendelian sampling variance, and show that this approximation is not critical. In addition, we explain why segregation variances are often negligible when analyzing the complex polygenic traits that are frequently the focus of evolutionary ecologists and animal breeders. Simulations and an example from an insular meta-population of house sparrows in Norway with three distinct genetic groups illustrate that the method is successful in estimating group-specific additive genetic variances, and that segregation variances are indeed negligible in the empirical example. CONCLUSIONS Quantifying differences in additive genetic variance within and among populations is of major biological interest in ecology, evolution, and animal and plant breeding. The proposed method allows to estimate such differences for subpopulations that form a connected set of populations, and may thus also be useful to study temporal or spatial variation of additive genetic variances.
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Affiliation(s)
- Stefanie Muff
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, Zurich, Switzerland. .,Department of Biostatistics, Epidemiology, Biostatistics and Prevention Institute, University of Zurich, Hirschengraben 84, Zurich, Switzerland.
| | - Alina K Niskanen
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Høgskoleringen 5, Trondheim, Norway.,Department of Ecology and Genetics, University of Oulu, P.O. Box 3000, Oulu, Finland
| | - Dilan Saatoglu
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Høgskoleringen 5, Trondheim, Norway
| | - Lukas F Keller
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, Zurich, Switzerland.,Zoological Museum, University of Zurich, Karl-Schmid-Strasse 4, Zurich, Switzerland
| | - Henrik Jensen
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Høgskoleringen 5, Trondheim, Norway
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10
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Hendry AP, Schoen DJ, Wolak ME, Reid JM. The Contemporary Evolution of Fitness. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2018. [DOI: 10.1146/annurev-ecolsys-110617-062358] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The rate of evolution of population mean fitness informs how selection acting in contemporary populations can counteract environmental change and genetic degradation (mutation, gene flow, drift, recombination). This rate influences population increases (e.g., range expansion), population stability (e.g., cryptic eco-evolutionary dynamics), and population recovery (i.e., evolutionary rescue). We review approaches for estimating such rates, especially in wild populations. We then review empirical estimates derived from two approaches: mutation accumulation (MA) and additive genetic variance in fitness (IAw). MA studies inform how selection counters genetic degradation arising from deleterious mutations, typically generating estimates of <1% per generation. IAw studies provide an integrated prediction of proportional change per generation, nearly always generating estimates of <20% and, more typically, <10%. Overall, considerable, but not unlimited, evolutionary potential exists in populations facing detrimental environmental or genetic change. However, further studies with diverse methods and species are required for more robust and general insights.
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Affiliation(s)
- Andrew P. Hendry
- Redpath Museum, McGill University, Montréal, Québec H3A 0C4, Canada
- Department of Biology, McGill University, Montréal, Québec H3A 1B1, Canada
| | - Daniel J. Schoen
- Department of Biology, McGill University, Montréal, Québec H3A 1B1, Canada
| | - Matthew E. Wolak
- Department of Biological Sciences, Auburn University, Auburn, Alabama 36849, USA
- School of Biological Sciences, University of Aberdeen, Aberdeen AB24 2TZ, United Kingdom
| | - Jane M. Reid
- School of Biological Sciences, University of Aberdeen, Aberdeen AB24 2TZ, United Kingdom
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11
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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] [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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12
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Germain RR, Wolak ME, Reid JM. Individual repeatability and heritability of divorce in a wild population. Biol Lett 2018; 14:rsbl.2018.0061. [PMID: 29899127 DOI: 10.1098/rsbl.2018.0061] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Accepted: 05/16/2018] [Indexed: 11/12/2022] Open
Abstract
Understanding micro-evolutionary responses of mating systems to contemporary selection requires estimating sex-specific additive genetic variances and cross-sex genetic covariances in key reproductive strategy traits. One key trait comprises the occurrence of divorce versus mate fidelity across sequential reproductive attempts. If divorce represents an evolving behavioural strategy that responds to selection it must have non-zero individual repeatability and heritability, but quantitative estimates from wild populations are scarce. We used 39 years of individual breeding records and pedigree data from free-living song sparrows (Melospiza melodia) to quantify sex-specific permanent individual and additive genetic variances, and hence estimate repeatability and heritability, in liability for divorce. We estimated moderate repeatability among females, but little repeatability among males. Estimates of additive genetic variance were small in both sexes, and the cross-sex genetic covariance was close to zero. Consequently, the total heritability was small but likely non-zero, indicating low potential for micro-evolutionary response to selection. Rapid micro-evolutionary change of divorce rate, therefore, appears unlikely, even if there were substantial fitness benefits of divorce and resulting selection.
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Affiliation(s)
- Ryan R Germain
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - Matthew E Wolak
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - Jane M Reid
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
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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] [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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Losdat S, Germain RR, Nietlisbach P, Arcese P, Reid JM. No evidence of inbreeding depression in sperm performance traits in wild song sparrows. Ecol Evol 2018; 8:1842-1852. [PMID: 29435258 PMCID: PMC5792576 DOI: 10.1002/ece3.3721] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 09/28/2017] [Accepted: 11/20/2017] [Indexed: 11/14/2022] Open
Abstract
Inbreeding is widely hypothesized to shape mating systems and population persistence, but such effects will depend on which traits show inbreeding depression. Population and evolutionary consequences could be substantial if inbreeding decreases sperm performance and hence decreases male fertilization success and female fertility. However, the magnitude of inbreeding depression in sperm performance traits has rarely been estimated in wild populations experiencing natural variation in inbreeding. Further, the hypothesis that inbreeding could increase within-ejaculate variation in sperm traits and thereby further affect male fertilization success has not been explicitly tested. We used a wild pedigreed song sparrow (Melospiza melodia) population, where frequent extrapair copulations likely create strong postcopulatory competition for fertilization success, to quantify effects of male coefficient of inbreeding (f) on key sperm performance traits. We found no evidence of inbreeding depression in sperm motility, longevity, or velocity, and the within-ejaculate variance in sperm velocity did not increase with male f. Contrary to inferences from highly inbred captive and experimental populations, our results imply that moderate inbreeding will not necessarily constrain sperm performance in wild populations. Consequently, the widely observed individual-level and population-level inbreeding depression in male and female fitness may not stem from reduced sperm performance in inbred males.
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Affiliation(s)
- Sylvain Losdat
- Institute of Biological and Environmental SciencesSchool of Biological SciencesUniversity of AberdeenAberdeenScotland
- Institute of BiologyUniversity of NeuchâtelNeuchâtelSwitzerland
| | - Ryan R. Germain
- Institute of Biological and Environmental SciencesSchool of Biological SciencesUniversity of AberdeenAberdeenScotland
| | - Pirmin Nietlisbach
- Institute of Evolutionary Biology and Environmental StudiesUniversity of ZurichZurichSwitzerland
- Department of ZoologyUniversity of British ColumbiaVancouverBCCanada
| | - Peter Arcese
- Department of Forest and Conservation SciencesUniversity of British ColumbiaVancouverBCCanada
| | - Jane M. Reid
- Institute of Biological and Environmental SciencesSchool of Biological SciencesUniversity of AberdeenAberdeenScotland
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Sztepanacz JL, Blows MW. Accounting for Sampling Error in Genetic Eigenvalues Using Random Matrix Theory. Genetics 2017; 206:1271-1284. [PMID: 28476865 PMCID: PMC5500129 DOI: 10.1534/genetics.116.198606] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Accepted: 04/17/2017] [Indexed: 11/18/2022] Open
Abstract
The distribution of genetic variance in multivariate phenotypes is characterized by the empirical spectral distribution of the eigenvalues of the genetic covariance matrix. Empirical estimates of genetic eigenvalues from random effects linear models are known to be overdispersed by sampling error, where large eigenvalues are biased upward, and small eigenvalues are biased downward. The overdispersion of the leading eigenvalues of sample covariance matrices have been demonstrated to conform to the Tracy-Widom (TW) distribution. Here we show that genetic eigenvalues estimated using restricted maximum likelihood (REML) in a multivariate random effects model with an unconstrained genetic covariance structure will also conform to the TW distribution after empirical scaling and centering. However, where estimation procedures using either REML or MCMC impose boundary constraints, the resulting genetic eigenvalues tend not be TW distributed. We show how using confidence intervals from sampling distributions of genetic eigenvalues without reference to the TW distribution is insufficient protection against mistaking sampling error as genetic variance, particularly when eigenvalues are small. By scaling such sampling distributions to the appropriate TW distribution, the critical value of the TW statistic can be used to determine if the magnitude of a genetic eigenvalue exceeds the sampling error for each eigenvalue in the spectral distribution of a given genetic covariance matrix.
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Affiliation(s)
- Jacqueline L Sztepanacz
- School of Biological Sciences, University of Queensland, St. Lucia, Queensland, Australia 4072
| | - Mark W Blows
- School of Biological Sciences, University of Queensland, St. Lucia, Queensland, Australia 4072
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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] [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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18
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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] [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] [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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