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Han Y, Tu W, Zhang Y, Huang J, Meng X, Wu Q, Li S, Liu B, Michal JJ, Jiang Z, Tan Y, Zhou X, Wang H. Comprehensive analysis of single-nucleotide variants and alternative polyadenylation between inbred and outbred pigs. Int J Biol Macromol 2024; 278:134416. [PMID: 39098700 DOI: 10.1016/j.ijbiomac.2024.134416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 07/28/2024] [Accepted: 07/30/2024] [Indexed: 08/06/2024]
Abstract
Inbreeding can lead to the accumulation of homozygous single nucleotide polymorphisms (SNPs) in the genome, which can significantly affect gene expression and phenotype. In this study, we examined the impact of homozygous SNPs resulting from inbreeding on alternative polyadenylation (APA) site selection and the underlying genetic mechanisms using inbred Luchuan pigs. Genome resequencing revealed that inbreeding results in a high accumulation of homozygous SNPs within the pig genome. 3' mRNA-seq on leg muscle, submandibular lymph node, and liver tissues was performed to identify differences in APA events between inbred and outbred Luchuan pigs. We revealed different tissue-specific APA usage caused by inbreeding, which were associated with different biological processes. Furthermore, we explored the role of polyadenylation signal (PAS) SNPs in APA regulation under inbreeding and identified key genes such as PUM1, SCARF1, RIPOR2, C1D, and LRRK2 that are involved in biological processes regulation. This study provides resources and sheds light on the impact of genomic homozygosity on APA regulation, offering insights into genetic characteristics and biological processes associated with inbreeding.
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Affiliation(s)
- Yu Han
- Key Laboratory of Livestock and Poultry Resources (Pig) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Institute of Animal Husbandry & Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China; Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Weilong Tu
- Key Laboratory of Livestock and Poultry Resources (Pig) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Institute of Animal Husbandry & Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China; Shanghai Engineering Research Center of Breeding Pig, Shanghai 201106, China
| | - Yingying Zhang
- Key Laboratory of Livestock and Poultry Resources (Pig) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Institute of Animal Husbandry & Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China; Shanghai Engineering Research Center of Breeding Pig, Shanghai 201106, China
| | - Ji Huang
- Key Laboratory of Livestock and Poultry Resources (Pig) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Institute of Animal Husbandry & Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China; Shanghai Engineering Research Center of Breeding Pig, Shanghai 201106, China
| | - Xiangge Meng
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Qingqing Wu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Songyu Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Bang Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Jennifer J Michal
- Department of Animal Sciences, Washington State University, Pullman, WA, USA
| | - Zhihua Jiang
- Department of Animal Sciences, Washington State University, Pullman, WA, USA
| | - Yongsong Tan
- Key Laboratory of Livestock and Poultry Resources (Pig) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Institute of Animal Husbandry & Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China; Shanghai Engineering Research Center of Breeding Pig, Shanghai 201106, China
| | - Xiang Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China.
| | - Hongyang Wang
- Key Laboratory of Livestock and Poultry Resources (Pig) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Institute of Animal Husbandry & Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China; Shanghai Engineering Research Center of Breeding Pig, Shanghai 201106, China.
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2
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DiLeo MF, Nair A, Kardos M, Husby A, Saastamoinen M. Demography and environment modulate the effects of genetic diversity on extinction risk in a butterfly metapopulation. Proc Natl Acad Sci U S A 2024; 121:e2309455121. [PMID: 39116125 PMCID: PMC11331070 DOI: 10.1073/pnas.2309455121] [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: 07/17/2023] [Accepted: 07/04/2024] [Indexed: 08/10/2024] Open
Abstract
Linking genetic diversity to extinction is a common goal in genomic studies. Recently, a debate has arisen regarding the importance of genetic variation in conservation as some studies have failed to find associations between genome-wide genetic diversity and extinction risk. However, only rarely are genetic diversity and fitness measured together in the wild, and typically demographic history and environment are ignored. It is therefore difficult to infer whether a lack of an association is real or obscured by confounding factors. To address these shortcomings, we analyzed genetic data from 7,501 individuals with extinction data from 279 meadows and mortality of 1,742 larval nests in a butterfly metapopulation. We found a strong negative association between genetic diversity and extinction when considering only heterozygosity in models. However, this association disappeared when accounting for ecological covariates, suggesting a confounding between demography and genetics and a more complex role for heterozygosity in extinction risk. Modeling interactions between heterozygosity and demographic variables revealed that associations between extinction and heterozygosity were context-dependent. For example, extinction declined with increasing heterozygosity in large, but not currently small populations, although negative associations between heterozygosity, extinction, and mortality were detected in small populations with a recent history of decline. We conclude that low genetic diversity is an important predictor of extinction, predicting >25% increase in extinction beyond ecological factors in certain contexts. These results highlight that inferences about the importance of genetic diversity for population viability should not rely on genomic data alone but require investments in obtaining demographic and environmental data from natural populations.
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Affiliation(s)
- Michelle F. DiLeo
- Research Centre for Ecological Change, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki00014, Finland
- Wildlife Research and Monitoring Section, Ontario Ministry of Natural Resources, Peterborough, ONK9L 1Z8, Canada
| | - Abhilash Nair
- Research Centre for Ecological Change, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki00014, Finland
| | - Marty Kardos
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA98112
| | - Arild Husby
- Evolutionary Biology, Department of Ecology and Genetics, Uppsala University, Uppsala75236, Sweden
| | - Marjo Saastamoinen
- Research Centre for Ecological Change, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki00014, Finland
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3
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Subalusky AL, Sethi SA, Anderson EP, Jiménez G, Echeverri-Lopez D, García-Restrepo S, Nova-León LJ, Reátiga-Parrish JF, Post DM, Rojas A. Rapid population growth and high management costs have created a narrow window for control of introduced hippos in Colombia. Sci Rep 2023; 13:6193. [PMID: 37062768 PMCID: PMC10106455 DOI: 10.1038/s41598-023-33028-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 04/06/2023] [Indexed: 04/18/2023] Open
Abstract
The introduction of hippos into the wild in Colombia has been marked by their rapid population growth and widespread dispersal on the landscape, high financial costs of management, and conflicting social perspectives on their management and fate. Here we use population projection models to investigate the effectiveness and cost of management options under consideration for controlling introduced hippos. We estimate there are 91 hippos in the middle Magdalena River basin, Colombia, and the hippo population is growing at an estimated rate of 9.6% per year. At this rate, there will be 230 hippos by 2032 and over 1,000 by 2050. Applying the population control methods currently under consideration will cost at least 1-2 million USD to sufficiently decrease hippo population growth to achieve long-term removal, and depending on the management strategy selected, there may still be hippos on the landscape for 50-100 years. Delaying management actions for a single decade will increase minimum costs by a factor of 2.5, and some methods may become infeasible. Our approach illustrates the trade-offs inherent between cost and effort in managing introduced species, as well as the importance of acting quickly, especially when dealing with species with rapid population growth rates and potential for significant ecological and social impacts.
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Affiliation(s)
| | - Suresh A Sethi
- Fisheries, Aquatic Science, and Technology Laboratory, Alaska Pacific University, Anchorage, Alaska, USA
| | - Elizabeth P Anderson
- Department of Earth and Environment and Institute of Environment, Florida International University, 11200 SW 8Th St, Miami, FL, USA
| | - Germán Jiménez
- Departamento de Biología, Pontificia Universidad Javeriana, Carrera 7 No. 43-82, Edificio Jesús Emilio Ramírez, Bogotá, Colombia
| | - David Echeverri-Lopez
- Corporación Autónoma Regional de Las Cuencas de los Ríos Negro Y Nare (CORNARE), Carrera 59 44-48, El Santuario, Antioquia, Colombia
| | - Sebastián García-Restrepo
- Departamento de Ciencias Biológicas, Universidad de los Andes, Carrera 1 No. 18A-10, Bogotá, Colombia
| | - Laura J Nova-León
- Departamento de Biología, Pontificia Universidad Javeriana, Carrera 7 No. 43-82, Edificio Jesús Emilio Ramírez, Bogotá, Colombia
- Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Bogotá D.C., Colombia
| | - Juan F Reátiga-Parrish
- Departamento de Biología, Pontificia Universidad Javeriana, Carrera 7 No. 43-82, Edificio Jesús Emilio Ramírez, Bogotá, Colombia
| | - David M Post
- Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, CT, USA
| | - Ana Rojas
- Department of Earth and Environment and Institute of Environment, Florida International University, 11200 SW 8Th St, Miami, FL, USA
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4
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James C, Pemberton JM, Navarro P, Knott S. The impact of SNP density on quantitative genetic analyses of body size traits in a wild population of Soay sheep. Ecol Evol 2022; 12:e9639. [PMID: 36532132 PMCID: PMC9750819 DOI: 10.1002/ece3.9639] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 11/01/2022] [Accepted: 11/29/2022] [Indexed: 12/23/2022] Open
Abstract
Understanding the genetic architecture underpinning quantitative traits in wild populations is pivotal to understanding the processes behind trait evolution. The 'animal model' is a popular method for estimating quantitative genetic parameters such as heritability and genetic correlation and involves fitting an estimate of relatedness between individuals in the study population. Genotypes at genome-wide markers can be used to estimate relatedness; however, relatedness estimates vary with marker density, potentially affecting results. Increasing density of markers is also expected to increase the power to detect quantitative trait loci (QTL). In order to understand how the density of genetic markers affects the results of quantitative genetic analyses, we estimated heritability and performed genome-wide association studies (GWAS) on five body size traits in an unmanaged population of Soay sheep using two different SNP densities: a dataset of 37,037 genotyped SNPs and an imputed dataset of 417,373 SNPs. Heritability estimates did not differ between the two SNP densities, but the high-density imputed SNP dataset revealed four new SNP-trait associations that were not found with the lower density dataset, as well as confirming all previously-found QTL. We also demonstrated that fitting fixed and random effects in the same step as performing GWAS is a more powerful approach than pre-correcting for covariates in a separate model.
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Affiliation(s)
- Caelinn James
- Institute of Ecology and EvolutionSchool of Biological SciencesThe University of EdinburghEdinburghScotland
| | - Josephine M. Pemberton
- Institute of Ecology and EvolutionSchool of Biological SciencesThe University of EdinburghEdinburghScotland
| | - Pau Navarro
- MRC Human Genetics UnitInstitute of Genetics and CancerThe University of EdinburghEdinburghScotland
| | - Sara Knott
- Institute of Ecology and EvolutionSchool of Biological SciencesThe University of EdinburghEdinburghScotland
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5
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Cockerill CA, Hasselgren M, Dussex N, Dalén L, von Seth J, Angerbjörn A, Wallén JF, Landa A, Eide NE, Flagstad Ø, Ehrich D, Sokolov A, Sokolova N, Norén K. Genomic Consequences of Fragmentation in the Endangered Fennoscandian Arctic Fox ( Vulpes lagopus). Genes (Basel) 2022; 13:2124. [PMID: 36421799 PMCID: PMC9690288 DOI: 10.3390/genes13112124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/06/2022] [Accepted: 10/10/2022] [Indexed: 11/17/2022] Open
Abstract
Accelerating climate change is causing severe habitat fragmentation in the Arctic, threatening the persistence of many cold-adapted species. The Scandinavian arctic fox (Vulpes lagopus) is highly fragmented, with a once continuous, circumpolar distribution, it struggled to recover from a demographic bottleneck in the late 19th century. The future persistence of the entire Scandinavian population is highly dependent on the northernmost Fennoscandian subpopulations (Scandinavia and the Kola Peninsula), to provide a link to the viable Siberian population. By analyzing 43 arctic fox genomes, we quantified genomic variation and inbreeding in these populations. Signatures of genome erosion increased from Siberia to northern Sweden indicating a stepping-stone model of connectivity. In northern Fennoscandia, runs of homozygosity (ROH) were on average ~1.47-fold longer than ROH found in Siberia, stretching almost entire scaffolds. Moreover, consistent with recent inbreeding, northern Fennoscandia harbored more homozygous deleterious mutations, whereas Siberia had more in heterozygous state. This study underlines the value of documenting genome erosion following population fragmentation to identify areas requiring conservation priority. With the increasing fragmentation and isolation of Arctic habitats due to global warming, understanding the genomic and demographic consequences is vital for maintaining evolutionary potential and preventing local extinctions.
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Affiliation(s)
| | - Malin Hasselgren
- Department of Zoology, Stockholm University, 10691 Stockholm, Sweden
| | - Nicolas Dussex
- Department of Zoology, Stockholm University, 10691 Stockholm, Sweden
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 11418 Stockholm, Sweden
| | - Love Dalén
- Department of Zoology, Stockholm University, 10691 Stockholm, Sweden
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 11418 Stockholm, Sweden
| | - Johanna von Seth
- Department of Zoology, Stockholm University, 10691 Stockholm, Sweden
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden
| | - Anders Angerbjörn
- Department of Zoology, Stockholm University, 10691 Stockholm, Sweden
| | - Johan F. Wallén
- Department of Zoology, Stockholm University, 10691 Stockholm, Sweden
| | - Arild Landa
- Norwegian Institute for Nature Research, 7485 Trondheim, Norway
| | - Nina E. Eide
- Norwegian Institute for Nature Research, 7485 Trondheim, Norway
| | | | - Dorothee Ehrich
- Department of Arctic and Marine Biology, UiT Arctic University of Tromsø, 9037 Tromsø, Norway
| | - Aleksandr Sokolov
- Arctic Research Station of Institute of Plant and Animal Ecology, Ural Branch, Russian Academy of Sciences, Zelenaya Gorka Str. 21, 629400 Labytnangi, Russia
| | - Natalya Sokolova
- Arctic Research Station of Institute of Plant and Animal Ecology, Ural Branch, Russian Academy of Sciences, Zelenaya Gorka Str. 21, 629400 Labytnangi, Russia
| | - Karin Norén
- Department of Zoology, Stockholm University, 10691 Stockholm, Sweden
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6
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Rafter P, McHugh N, Pabiou T, Berry D. Inbreeding trends and genetic diversity in purebred sheep populations. Animal 2022; 16:100604. [DOI: 10.1016/j.animal.2022.100604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 07/01/2022] [Accepted: 07/11/2022] [Indexed: 11/30/2022] Open
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7
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Pérez‐Pereira N, López‐Cortegano E, García‐Dorado A, Caballero A. Prediction of fitness under different breeding designs in conservation programs. Anim Conserv 2022. [DOI: 10.1111/acv.12804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- N. Pérez‐Pereira
- Centro de Investigación Mariña Universidade de Vigo, Facultade de Bioloxía Vigo Spain
| | - E. López‐Cortegano
- Centro de Investigación Mariña Universidade de Vigo, Facultade de Bioloxía Vigo Spain
| | - A. García‐Dorado
- Departamento de Genética, Facultad de Ciencias Biológicas Universidad Complutense Madrid Spain
| | - A. Caballero
- Centro de Investigación Mariña Universidade de Vigo, Facultade de Bioloxía Vigo Spain
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8
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Decomposing phenotypic skew and its effects on the predicted response to strong selection. Nat Ecol Evol 2022; 6:774-785. [PMID: 35422480 DOI: 10.1038/s41559-022-01694-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 02/08/2022] [Indexed: 12/29/2022]
Abstract
The major frameworks for predicting evolutionary change assume that a phenotype's underlying genetic and environmental components are normally distributed. However, the predictions of these frameworks may no longer hold if distributions are skewed. Despite this, phenotypic skew has never been decomposed, meaning the fundamental assumptions of quantitative genetics remain untested. Here we demonstrate that the substantial phenotypic skew in the body size of juvenile blue tits (Cyanistes caeruleus) is driven by environmental factors. Although skew had little impact on our predictions of selection response in this case, our results highlight the impact of skew on the estimation of inheritance and selection. Specifically, the nonlinear parent-offspring regressions induced by skew, alongside selective disappearance, can strongly bias estimates of heritability. The ubiquity of skew and strong directional selection on juvenile body size imply that heritability is commonly overestimated, which may in part explain the discrepancy between predicted and observed trait evolution.
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9
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Thompson KA, Peichel CL, Rennison DJ, McGee MD, Albert AYK, Vines TH, Greenwood AK, Wark AR, Brandvain Y, Schumer M, Schluter D. Analysis of ancestry heterozygosity suggests that hybrid incompatibilities in threespine stickleback are environment dependent. PLoS Biol 2022; 20:e3001469. [PMID: 35007278 PMCID: PMC8746713 DOI: 10.1371/journal.pbio.3001469] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 11/04/2021] [Indexed: 12/25/2022] Open
Abstract
Hybrid incompatibilities occur when interactions between opposite ancestry alleles at different loci reduce the fitness of hybrids. Most work on incompatibilities has focused on those that are "intrinsic," meaning they affect viability and sterility in the laboratory. Theory predicts that ecological selection can also underlie hybrid incompatibilities, but tests of this hypothesis using sequence data are scarce. In this article, we compiled genetic data for F2 hybrid crosses between divergent populations of threespine stickleback fish (Gasterosteus aculeatus L.) that were born and raised in either the field (seminatural experimental ponds) or the laboratory (aquaria). Because selection against incompatibilities results in elevated ancestry heterozygosity, we tested the prediction that ancestry heterozygosity will be higher in pond-raised fish compared to those raised in aquaria. We found that ancestry heterozygosity was elevated by approximately 3% in crosses raised in ponds compared to those raised in aquaria. Additional analyses support a phenotypic basis for incompatibility and suggest that environment-specific single-locus heterozygote advantage is not the cause of selection on ancestry heterozygosity. Our study provides evidence that, in stickleback, a coarse-albeit indirect-signal of environment-dependent hybrid incompatibility is reliably detectable and suggests that extrinsic incompatibilities can evolve before intrinsic incompatibilities.
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Affiliation(s)
- Ken A. Thompson
- Department of Zoology & Biodiversity Research Centre, University of British Columbia, Canada
| | - Catherine L. Peichel
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Diana J. Rennison
- Division of Biological Sciences, University of California San Diego, San Diego, California, United States of America
| | - Matthew D. McGee
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | | | - Timothy H. Vines
- DataSeer Research Data Services, Vancouver, British Columbia, Canada
| | | | - Abigail R. Wark
- Harvard Medical School, Cambridge, Massachusetts, United States of America
| | - Yaniv Brandvain
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Molly Schumer
- Department of Biology, Stanford University, Stanford, California, United States of America
- Howard Hughes Medical Institute, Maryland, United States of America
| | - Dolph Schluter
- Department of Zoology & Biodiversity Research Centre, University of British Columbia, Canada
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10
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Pérez-Pereira N, Pouso R, Rus A, Vilas A, López-Cortegano E, García-Dorado A, Quesada H, Caballero A. Long-term exhaustion of the inbreeding load in Drosophila melanogaster. Heredity (Edinb) 2021; 127:373-383. [PMID: 34400819 PMCID: PMC8478893 DOI: 10.1038/s41437-021-00464-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 07/29/2021] [Accepted: 07/29/2021] [Indexed: 02/07/2023] Open
Abstract
Inbreeding depression, the decline in fitness of inbred individuals, is a ubiquitous phenomenon of great relevance in evolutionary biology and in the fields of animal and plant breeding and conservation. Inbreeding depression is due to the expression of recessive deleterious alleles that are concealed in heterozygous state in noninbred individuals, the so-called inbreeding load. Genetic purging reduces inbreeding depression by removing these alleles when expressed in homozygosis due to inbreeding. It is generally thought that fast inbreeding (such as that generated by full-sib mating lines) removes only highly deleterious recessive alleles, while slow inbreeding can also remove mildly deleterious ones. However, a question remains regarding which proportion of the inbreeding load can be removed by purging under slow inbreeding in moderately large populations. We report results of two long-term slow inbreeding Drosophila experiments (125-234 generations), each using a large population and a number of derived lines with effective sizes about 1000 and 50, respectively. The inbreeding load was virtually exhausted after more than one hundred generations in large populations and between a few tens and over one hundred generations in the lines. This result is not expected from genetic drift alone, and is in agreement with the theoretical purging predictions. Computer simulations suggest that these results are consistent with a model of relatively few deleterious mutations of large homozygous effects and partially recessive gene action.
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Affiliation(s)
- Noelia Pérez-Pereira
- grid.6312.60000 0001 2097 6738Centro de Investigación Mariña, Universidade de Vigo, Facultade de Bioloxía, Vigo, Spain
| | - Ramón Pouso
- grid.6312.60000 0001 2097 6738Centro de Investigación Mariña, Universidade de Vigo, Facultade de Bioloxía, Vigo, Spain
| | - Ana Rus
- grid.6312.60000 0001 2097 6738Centro de Investigación Mariña, Universidade de Vigo, Facultade de Bioloxía, Vigo, Spain
| | - Ana Vilas
- grid.6312.60000 0001 2097 6738Centro de Investigación Mariña, Universidade de Vigo, Facultade de Bioloxía, Vigo, Spain
| | - Eugenio López-Cortegano
- grid.6312.60000 0001 2097 6738Centro de Investigación Mariña, Universidade de Vigo, Facultade de Bioloxía, Vigo, Spain ,grid.4305.20000 0004 1936 7988Present Address: Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Aurora García-Dorado
- grid.4795.f0000 0001 2157 7667Facultad de Ciencias Biológicas, Departamento de Genética, Universidad Complutense, Madrid, Spain
| | - Humberto Quesada
- grid.6312.60000 0001 2097 6738Centro de Investigación Mariña, Universidade de Vigo, Facultade de Bioloxía, Vigo, Spain
| | - Armando Caballero
- grid.6312.60000 0001 2097 6738Centro de Investigación Mariña, Universidade de Vigo, Facultade de Bioloxía, Vigo, Spain
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11
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Yengo L, Yang J, Keller MC, Goddard ME, Wray NR, Visscher PM. Genomic partitioning of inbreeding depression in humans. Am J Hum Genet 2021; 108:1488-1501. [PMID: 34214457 DOI: 10.1016/j.ajhg.2021.06.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 06/01/2021] [Indexed: 02/05/2023] Open
Abstract
Across species, offspring of related individuals often exhibit significant reduction in fitness-related traits, known as inbreeding depression (ID), yet the genetic and molecular basis for ID remains elusive. Here, we develop a method to quantify enrichment of ID within specific genomic annotations and apply it to human data. We analyzed the phenomes and genomes of ∼350,000 unrelated participants of the UK Biobank and found, on average of over 11 traits, significant enrichment of ID within genomic regions with high recombination rates (>21-fold; p < 10-5), with conserved function across species (>19-fold; p < 10-4), and within regulatory elements such as DNase I hypersensitive sites (∼5-fold; p = 8.9 × 10-7). We also quantified enrichment of ID within trait-associated regions and found suggestive evidence that genomic regions contributing to additive genetic variance in the population are enriched for ID signal. We find strong correlations between functional enrichment of SNP-based heritability and that of ID (r = 0.8, standard error: 0.1). These findings provide empirical evidence that ID is most likely due to many partially recessive deleterious alleles in low linkage disequilibrium regions of the genome. Our study suggests that functional characterization of ID may further elucidate the genetic architectures and biological mechanisms underlying complex traits and diseases.
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12
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Sole-Navais P, Bacelis J, Helgeland Ø, Modzelewska D, Vaudel M, Flatley C, Andreassen O, Njølstad PR, Muglia LJ, Johansson S, Zhang G, Jacobsson B. Autozygosity mapping and time-to-spontaneous delivery in Norwegian parent-offspring trios. Hum Mol Genet 2020; 29:3845-3858. [PMID: 33291140 PMCID: PMC7861013 DOI: 10.1093/hmg/ddaa255] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 11/21/2020] [Accepted: 11/24/2020] [Indexed: 11/18/2022] Open
Abstract
Parental genetic relatedness may lead to adverse health and fitness outcomes in the offspring. However, the degree to which it affects human delivery timing is unknown. We use genotype data from ≃25 000 parent-offspring trios from the Norwegian Mother, Father and Child Cohort Study to optimize runs of homozygosity (ROH) calling by maximizing the correlation between parental genetic relatedness and offspring ROHs. We then estimate the effect of maternal, paternal and fetal autozygosity and that of autozygosity mapping (common segments and gene burden test) on the timing of spontaneous onset of delivery. The correlation between offspring ROH using a variety of parameters and parental genetic relatedness ranged between −0.2 and 0.6, revealing the importance of the minimum number of genetic variants included in an ROH and the use of genetic distance. The optimized compared to predefined parameters showed a ≃45% higher correlation between parental genetic relatedness and offspring ROH. We found no evidence of an effect of maternal, paternal nor fetal overall autozygosity on spontaneous delivery timing. Yet, through autozygosity mapping, we identified three maternal loci TBC1D1, SIGLECs and EDN1 gene regions reducing the median time-to-spontaneous onset of delivery by ≃2–5% (P-value < 2.3 × 10−6). We also found suggestive evidence of a fetal locus at 3q22.2, near the RYK gene region (P-value = 2.0 × 10−6). Autozygosity mapping may provide new insights on the genetic determinants of delivery timing beyond traditional genome-wide association studies, but particular and rigorous attention should be given to ROH calling parameter selection.
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Affiliation(s)
- Pol Sole-Navais
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg 41685, Sweden
| | - Jonas Bacelis
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg 41685, Sweden
| | - Øyvind Helgeland
- Center for Diabetes Research, Department of Clinical Science, University of Bergen, 5020 Bergen, Norway.,Division of Health Data and Digitalization, Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo 0213, Norway
| | - Dominika Modzelewska
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg 41685, Sweden
| | - Marc Vaudel
- Center for Diabetes Research, Department of Clinical Science, University of Bergen, 5020 Bergen, Norway.,Department of Pediatrics and Adolescents, Haukeland University Hospital, Bergen 5021, Norway
| | - Christopher Flatley
- Division of Health Data and Digitalization, Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo 0213, Norway
| | - Ole Andreassen
- NORMENT, University of Oslo, Oslo 0450, Norway.,Division of Mental Health and Addiction, Oslo University Hospital, Oslo 0450, Norway.,Department of Psychiatry, University of California San Diego, San Diego, CA 92093, USA
| | - Pål R Njølstad
- Center for Diabetes Research, Department of Clinical Science, University of Bergen, 5020 Bergen, Norway.,Department of Pediatrics and Adolescents, Haukeland University Hospital, Bergen 5021, Norway
| | - Louis J Muglia
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA.,Division of Human Genetics, The Center for Prevention of Preterm Birth, Perinatal Institute, March of Dimes Prematurity Research Center Ohio Collaborative, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45267, USA
| | - Stefan Johansson
- Center for Diabetes Research, Department of Clinical Science, University of Bergen, 5020 Bergen, Norway.,Center for Medical Genetics, Haukeland University Hospital, Bergen 5021, Norway
| | - Ge Zhang
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA.,Division of Human Genetics, The Center for Prevention of Preterm Birth, Perinatal Institute, March of Dimes Prematurity Research Center Ohio Collaborative, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45267, USA
| | - Bo Jacobsson
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg 41685, Sweden.,Division of Health Data and Digitalization, Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo 0213, Norway.,Department of Obstetrics and Gynecology, Sahlgrenska University Hospital, Gothenburg 41685, Sweden
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13
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de Jong JF, van Hooft P, Megens HJ, Crooijmans RPMA, de Groot GA, Pemberton JM, Huisman J, Bartoš L, Iacolina L, van Wieren SE, Ydenberg RC, Prins HHT. Fragmentation and Translocation Distort the Genetic Landscape of Ungulates: Red Deer in the Netherlands. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.535715] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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14
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Zilko JP, Harley D, Hansen B, Pavlova A, Sunnucks P. Accounting for cryptic population substructure enhances detection of inbreeding depression with genomic inbreeding coefficients: an example from a critically endangered marsupial. Mol Ecol 2020; 29:2978-2993. [PMID: 32627274 DOI: 10.1111/mec.15540] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 05/16/2020] [Accepted: 06/18/2020] [Indexed: 12/21/2022]
Abstract
Characterizing inbreeding depression in wildlife populations can be critical to their conservation. Coefficients of individual inbreeding can be estimated from genome-wide marker data. The degree to which sensitivity of inbreeding coefficients to population genetic substructure alters estimates of inbreeding depression in wild populations is not well understood. Using generalized linear models, we tested the power of two frequently used inbreeding coefficients that are calculated from genome-wide SNP markers, FH and F^III , to predict four fitness traits estimated over two decades in an isolated population of the critically endangered Leadbeater's possum. FH estimates inbreeding as excess observed homozygotes relative to equilibrium expectations, whereas F^III quantifies allelic similarity between the gametes that formed an individual, and upweights rare homozygotes. We estimated FH and F^III from 1,575 genome-wide SNP loci in individuals with fitness trait data (N = 179-237 per trait), and computed revised coefficients, FH by group and F^IIIby group , adjusted for population genetic substructure by calculating them separately within two different genetic groups of individuals identified in the population. Using FH or F^III in the models, inbreeding depression was detected for survival to sexual maturity, longevity and whether individuals bred during their lifetime. F^IIIby group (but not FH by group ) additionally revealed significant inbreeding depression for lifetime reproductive output (total offspring assigned to each individual). Estimates of numbers of lethal equivalents indicated substantial inbreeding load, but differing between inbreeding estimators. Inbreeding depression, declining population size, and low and declining genetic diversity suggest that genetic rescue may assist in preventing extinction of this unique Leadbeater's possum population.
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Affiliation(s)
- Joseph P Zilko
- School of Biological Sciences, Monash University, Clayton, Vic, Australia
| | - Dan Harley
- Zoos Victoria, Parkville, Vic, Australia
| | - Birgita Hansen
- Centre for eResearch and Digital Innovation, Federation University, Ballarat, Vic, Australia
| | - Alexandra Pavlova
- School of Biological Sciences, Monash University, Clayton, Vic, Australia
| | - Paul Sunnucks
- School of Biological Sciences, Monash University, Clayton, Vic, Australia
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15
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Curik I, Kövér G, Farkas J, Szendrő Z, Romvári R, Sölkner J, Nagy I. Inbreeding depression for kit survival at birth in a rabbit population under long-term selection. Genet Sel Evol 2020; 52:39. [PMID: 32640975 PMCID: PMC7346452 DOI: 10.1186/s12711-020-00557-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Accepted: 06/26/2020] [Indexed: 01/01/2023] Open
Abstract
Background Accumulation of detrimental mutations in small populations leads to inbreeding depression of fitness traits and a higher frequency of genetic defects, thus increasing risk of extinction. Our objective was to quantify the magnitude of inbreeding depression for survival at birth, in a closed rabbit population under long-term selection. Methods We used an information theory-based approach and multi-model inference to estimate inbreeding depression and its purging with respect to the trait ‘kit survival at birth’ over a 25-year period in a closed population of Pannon White rabbits, by analysing 22,718 kindling records. Generalised linear mixed models based on the logit link function were applied, which take polygenic random effects into account. Results Our results indicated that inbreeding depression occurred during the period 1992–1997, based on significant estimates of the z-standardised classical inbreeding coefficient z.FL (CI95% − 0.12 to − 0.03) and of the new inbreeding coefficient of the litter z.FNEWL (CI95% − 0.13 to − 0.04) as well as a 59.2% reduction in contributing founders. Inbreeding depression disappeared during the periods 1997–2007 and 2007–2017. For the period 1992–1997, the best model resulted in a significantly negative standardised estimate of the new inbreeding coefficient of the litter and a significantly positive standardised estimate of Kalinowski’s ancestral inbreeding coefficient of the litter (CI95% 0.01 to 0.17), which indicated purging of detrimental load. Kindling season and parity had effects on survival at birth that differed across the three periods of 1992–1997, 1997–2007 and 2007–2017. Conclusions Our results support the existence of inbreeding depression and its purging with respect to kit survival at birth in this Pannon White rabbit population. However, we were unable to exclude possible confounding from the effects of parity and potentially other environmental factors during the study period, thus our results need to be extended and confirmed in other populations.
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Affiliation(s)
- Ino Curik
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia.
| | - György Kövér
- Institute of Methodology, Faculty of Economic Science, Kaposvár University, Kaposvár, Hungary
| | - János Farkas
- Institute of Methodology, Faculty of Economic Science, Kaposvár University, Kaposvár, Hungary
| | - Zsolt Szendrő
- Institute of Animal Science, Faculty of Agricultural and Environmental Sciences, Kaposvár University, Kaposvár, Hungary
| | - Róbert Romvári
- Institute of Animal Science, Faculty of Agricultural and Environmental Sciences, Kaposvár University, Kaposvár, Hungary
| | - Johann Sölkner
- Division of Livestock Sciences, University of Natural Resources and Applied Life Sciences, Vienna, Austria
| | - Istvan Nagy
- Institute of Animal Science, Faculty of Agricultural and Environmental Sciences, Kaposvár University, Kaposvár, Hungary.
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16
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Consistent scaling of inbreeding depression in space and time in a house sparrow metapopulation. Proc Natl Acad Sci U S A 2020; 117:14584-14592. [PMID: 32513746 DOI: 10.1073/pnas.1909599117] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Inbreeding may increase the extinction risk of small populations. Yet, studies using modern genomic tools to investigate inbreeding depression in nature have been limited to single populations, and little is known about the dynamics of inbreeding depression in subdivided populations over time. Natural populations often experience different environmental conditions and differ in demographic history and genetic composition, characteristics that can affect the severity of inbreeding depression. We utilized extensive long-term data on more than 3,100 individuals from eight islands in an insular house sparrow metapopulation to examine the generality of inbreeding effects. Using genomic estimates of realized inbreeding, we discovered that inbred individuals had lower survival probabilities and produced fewer recruiting offspring than noninbred individuals. Inbreeding depression, measured as the decline in fitness-related traits per unit inbreeding, did not vary appreciably among populations or with time. As a consequence, populations with more resident inbreeding (due to their demographic history) paid a higher total fitness cost, evidenced by a larger variance in fitness explained by inbreeding within these populations. Our results are in contrast to the idea that effects of inbreeding generally depend on ecological factors and genetic differences among populations, and expand the understanding of inbreeding depression in natural subdivided populations.
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17
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18
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Hasselgren M, Norén K. Inbreeding in natural mammal populations: historical perspectives and future challenges. Mamm Rev 2019. [DOI: 10.1111/mam.12169] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Malin Hasselgren
- Department of Zoology Stockholm University 106 91 Stockholm Sweden
| | - Karin Norén
- Department of Zoology Stockholm University 106 91 Stockholm Sweden
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19
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Extreme inbreeding in a European ancestry sample from the contemporary UK population. Nat Commun 2019; 10:3719. [PMID: 31481654 PMCID: PMC6722066 DOI: 10.1038/s41467-019-11724-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Accepted: 07/18/2019] [Indexed: 01/22/2023] Open
Abstract
In most human societies, there are taboos and laws banning mating between first- and second-degree relatives, but actual prevalence and effects on health and fitness are poorly quantified. Here, we leverage a large observational study of ~450,000 participants of European ancestry from the UK Biobank (UKB) to quantify extreme inbreeding (EI) and its consequences. We use genotyped SNPs to detect large runs of homozygosity (ROH) and call EI when >10% of an individual's genome comprise ROHs. We estimate a prevalence of EI of ~0.03%, i.e., ~1/3652. EI cases have phenotypic means between 0.3 and 0.7 standard deviation below the population mean for 7 traits, including stature and cognitive ability, consistent with inbreeding depression estimated from individuals with low levels of inbreeding. Our study provides DNA-based quantification of the prevalence of EI in a European ancestry sample from the UK and measures its effects on health and fitness traits.
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20
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Trask AE, Fenn SR, Bignal EM, McCracken DI, Monaghan P, Reid JM. Evaluating the efficacy of independent versus simultaneous management strategies to address ecological and genetic threats to population viability. J Appl Ecol 2019. [DOI: 10.1111/1365-2664.13464] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Amanda E. Trask
- School of Biological Sciences, Zoology Building University of Aberdeen Aberdeen UK
| | - Sarah R. Fenn
- School of Biological Sciences, Zoology Building University of Aberdeen Aberdeen UK
| | | | - Davy I. McCracken
- Department of Integrated Land Management Scotland's Rural College Auchincruive Ayr UK
| | - Pat Monaghan
- Institute of Biodiversity, Animal Health & Comparative Medicine University of Glasgow Glasgow UK
| | - Jane M. Reid
- School of Biological Sciences, Zoology Building University of Aberdeen Aberdeen UK
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21
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Pineaux M, Blanchard P, Danchin É, Hatch SA, Helfenstein F, Mulard H, White J, Leclaire S, Wagner RH. Behavioural avoidance of sperm ageing depends on genetic similarity of mates in a monogamous seabird. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz079] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Inbreeding, i.e. the mating of genetically related individuals, can lead to reduced fitness and is considered to be a major selective force of mate choice. Although inbreeding avoidance has been found in numerous taxa, individuals may face constraints when pairing, leading to mating with suboptimal partners. In such circumstances, individuals that are able to avoid factors exacerbating detrimental effects of inbreeding should be favoured. Using the socially and genetically monogamous black-legged kittiwake (Rissa tridactyla), we explored whether the detrimental effects of inbreeding are exacerbated by sperm ageing (i.e. the post-meiotic senescence of sperm cells, mainly occurring within the female tracts after copulation), and whether they can be mitigated by behavioural tactics. First, by experimentally manipulating the age of the fertilizing sperm, we found that hatching failure due to sperm ageing increased with higher genetic similarity between mates. We then investigated whether more genetically similar pairs exhibited mating behaviours that prevent fertilization by old sperm. The more genetically similar mates were, the less likely they were to copulate early in the reproductive season and the more females performed post-copulatory sperm ejections. By flexibly adapting their behaviour in response to within-pair genetic similarity, kittiwakes may avoid exacerbation of inbreeding costs due to sperm ageing.
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Affiliation(s)
- Maxime Pineaux
- Laboratoire Évolution & Diversité Biologique (EDB UMR), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS, route de Narbonne, Bat, Toulouse cedex, France
| | - Pierrick Blanchard
- Laboratoire Évolution & Diversité Biologique (EDB UMR), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS, route de Narbonne, Bat, Toulouse cedex, France
| | - Étienne Danchin
- Laboratoire Évolution & Diversité Biologique (EDB UMR), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS, route de Narbonne, Bat, Toulouse cedex, France
| | - Scott A Hatch
- Institute for Seabird Research and Conservation, Mountain Place, Anchorage, AK, USA
| | - Fabrice Helfenstein
- Laboratory of Evolutionary Ecophysiology, Institute of Biology, Faculty of Sciences, University of Neuchâtel, Neuchâtel, Switzerland
| | - Hervé Mulard
- Laboratoire Évolution & Diversité Biologique (EDB UMR), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS, route de Narbonne, Bat, Toulouse cedex, France
| | - Joël White
- Laboratoire Évolution & Diversité Biologique (EDB UMR), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS, route de Narbonne, Bat, Toulouse cedex, France
| | - Sarah Leclaire
- Laboratoire Évolution & Diversité Biologique (EDB UMR), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS, route de Narbonne, Bat, Toulouse cedex, France
| | - Richard H Wagner
- Konrad-Lorenz-Institute of Ethology, Department of Integrative Biology and Evolution, University of Veterinarian Medicine Vienna, Savoyenstr., Vienna, Austria
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22
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Rehling F, Matthies D, Sandner TM. Responses of a legume to inbreeding and the intensity of novel and familiar stresses. Ecol Evol 2019; 9:1255-1267. [PMID: 30805157 PMCID: PMC6374648 DOI: 10.1002/ece3.4831] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 11/14/2018] [Indexed: 01/17/2023] Open
Abstract
It is often assumed that the negative effects of inbreeding on fitness (inbreeding depression, ID) are particularly strong under stressful conditions. However, ID may be relatively mild under types of stress that plant populations have experienced for a long time, because environment-specific deleterious alleles may already have been purged. We examined the performance of open- and self-pollinated progeny of the short-lived calcareous grassland plant Anthyllis vulneraria under three intensities of each of five types of stress. Drought, nutrient deficiency, and defoliation were chosen as stresses typical for the habitat of origin, while shade and waterlogging were expected to be novel, unfamiliar stresses for A. vulneraria. The stresses reduced plant biomass by up to 91%, and the responses of the plants were mostly in line with the functional equilibrium hypothesis. There was significant ID in biomass (δ = 0.17), leaf chlorophyll content, and the number of root nodules of the legume, but the magnitude of ID was independent of the stress treatments. In particular, there was no significant interaction between inbreeding and the intensity of any stress type, and ID was not higher under novel than under familiar stresses. In addition, phenotypic plasticity in biomass allocation, leaf functional traits and in root nodulation of the legume to the various stress treatments was not influenced by inbreeding. Our findings do not support the common hypothesis of stronger ID under stressful environments, not even if the stresses are novel to the plants.
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Affiliation(s)
- Finn Rehling
- Department of Nature Conservation, Faculty of BiologyPhilipps‐University MarburgMarburgGermany
- Department of Ecology, Faculty of BiologyPhilipps‐University MarburgMarburgGermany
| | - Diethart Matthies
- Department of Ecology, Faculty of BiologyPhilipps‐University MarburgMarburgGermany
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23
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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] [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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24
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Moss JB, Gerber GP, Schwirian A, Jackson AC, Welch ME. Evidence for dominant males but not choosy females in an insular rock iguana. Behav Ecol 2018. [DOI: 10.1093/beheco/ary131] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Jeanette B Moss
- Biological Sciences Department, Mississippi State University, Mississippi State, MS, USA
| | - Glenn P Gerber
- Institute for Conservation Research, San Diego Zoo Global, Escondido, CA, USA
| | - Aumbriel Schwirian
- Biological Sciences Department, Mississippi State University, Mississippi State, MS, USA
| | - Anna C Jackson
- Biological Sciences Department, Mississippi State University, Mississippi State, MS, USA
| | - Mark E Welch
- Biological Sciences Department, Mississippi State University, Mississippi State, MS, USA
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25
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Hajduk GK, Cockburn A, Margraf N, Osmond HL, Walling CA, Kruuk LEB. Inbreeding, inbreeding depression, and infidelity in a cooperatively breeding bird. Evolution 2018; 72:1500-1514. [PMID: 29761484 PMCID: PMC6099473 DOI: 10.1111/evo.13496] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 04/06/2018] [Accepted: 04/18/2018] [Indexed: 01/17/2023]
Abstract
Inbreeding depression plays a major role in shaping mating systems: in particular, inbreeding avoidance is often proposed as a mechanism explaining extra-pair reproduction in socially monogamous species. This suggestion relies on assumptions that are rarely comprehensively tested: that inbreeding depression is present, that higher kinship between social partners increases infidelity, and that infidelity reduces the frequency of inbreeding. Here, we test these assumptions using 26 years of data for a cooperatively breeding, socially monogamous bird with high female infidelity, the superb fairy-wren (Malurus cyaneus). Although inbred individuals were rare (∼6% of offspring), we found evidence of inbreeding depression in nestling mass (but not in fledgling survival). Mother-son social pairings resulted in 100% infidelity, but kinship between a social pair did not otherwise predict female infidelity. Nevertheless, extra-pair offspring were less likely to be inbred than within-pair offspring. Finally, the social environment (the number of helpers in a group) did not affect offspring inbreeding coefficients or inbreeding depression levels. In conclusion, despite some agreement with the assumptions that are necessary for inbreeding avoidance to drive infidelity, the apparent scarcity of inbreeding events and the observed levels of inbreeding depression seem insufficient to explain the ubiquitous infidelity in this system, beyond the mother-son mating avoidance.
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Affiliation(s)
- Gabriela K. Hajduk
- Institute of Evolutionary Biology, School of Biological SciencesUniversity of EdinburghEdinburghUnited Kingdom
| | - Andrew Cockburn
- Division of Evolution and Ecology, Research School of BiologyThe Australian National UniversityCanberraACTAustralia
| | - Nicolas Margraf
- Division of Evolution and Ecology, Research School of BiologyThe Australian National UniversityCanberraACTAustralia
- Current Address: Nicolas Margraf, Musée d'histoire naturelle de La Chaux‐de‐FondsAv. Léopold‐Robert 63CH‐2300La Chaux‐de‐FondsSwitzerland
| | - Helen L. Osmond
- Division of Evolution and Ecology, Research School of BiologyThe Australian National UniversityCanberraACTAustralia
| | - Craig A. Walling
- Institute of Evolutionary Biology, School of Biological SciencesUniversity of EdinburghEdinburghUnited Kingdom
| | - Loeske E. B. Kruuk
- Division of Evolution and Ecology, Research School of BiologyThe Australian National UniversityCanberraACTAustralia
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26
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Hayward AD, Pemberton JM, Berenos C, Wilson AJ, Pilkington JG, Kruuk LEB. Evidence for Selection-by-Environment but Not Genotype-by-Environment Interactions for Fitness-Related Traits in a Wild Mammal Population. Genetics 2018; 208:349-364. [PMID: 29127262 PMCID: PMC5753868 DOI: 10.1534/genetics.117.300498] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 11/07/2017] [Indexed: 11/18/2022] Open
Abstract
How do environmental conditions influence selection and genetic variation in wild populations? There is widespread evidence for selection-by-environment interactions (S*E), but we reviewed studies of natural populations estimating the extent of genotype-by-environment interactions (G*E) in response to natural variation in environmental conditions and found that evidence for G*E appears to be rare within single populations in the wild. Studies estimating the simultaneous impact of environmental variation on both selection and genetic variation are especially scarce. Here, we used 24 years of data collected from a wild Soay sheep population to quantify how an important environmental variable, population density, impacts upon (1) selection through annual contribution to fitness and (2) expression of genetic variation, in six morphological and life history traits: body weight, hind leg length, parasite burden, horn length, horn growth, and testicular circumference. Our results supported the existence of S*E: selection was stronger in years of higher population density for all traits apart from horn growth, with directional selection being stronger under more adverse conditions. Quantitative genetic models revealed significant additive genetic variance for body weight, leg length, parasite burden, horn length, and testes size, but not for horn growth or our measure of annual fitness. However, random regression models found variation between individuals in their responses to the environment in only three traits, and did not support the presence of G*E for any trait. Our analyses of St Kilda Soay sheep data thus concurs with our cross-study review that, while natural environmental variation within a population can profoundly alter the strength of selection on phenotypic traits, there is less evidence for its effect on the expression of genetic variance in the wild.
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Affiliation(s)
- Adam D Hayward
- Department of Biological and Environmental Sciences, School of Natural Sciences, University of Stirling, FK9 4LA, UK
| | - Josephine M Pemberton
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, EH9 3FL, UK
| | - Camillo Berenos
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, EH9 3FL, UK
| | - Alastair J Wilson
- Centre for Ecology and Conservation, University of Exeter, Penryn, Cornwall TR10 9FE, UK
| | - Jill G Pilkington
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, EH9 3FL, UK
| | - Loeske E B Kruuk
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, EH9 3FL, UK
- Research School of Biology, The Australian National University, Acton, Australian Capital Territory 2601, Australia
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Luikart G, Kardos M, Hand BK, Rajora OP, Aitken SN, Hohenlohe PA. Population Genomics: Advancing Understanding of Nature. POPULATION GENOMICS 2018. [DOI: 10.1007/13836_2018_60] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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28
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Detection and quantification of inbreeding depression for complex traits from SNP data. Proc Natl Acad Sci U S A 2017; 114:8602-8607. [PMID: 28747529 DOI: 10.1073/pnas.1621096114] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Quantifying the effects of inbreeding is critical to characterizing the genetic architecture of complex traits. This study highlights through theory and simulations the strengths and shortcomings of three SNP-based inbreeding measures commonly used to estimate inbreeding depression (ID). We demonstrate that heterogeneity in linkage disequilibrium (LD) between causal variants and SNPs biases ID estimates, and we develop an approach to correct this bias using LD and minor allele frequency stratified inference (LDMS). We quantified ID in 25 traits measured in [Formula: see text] participants of the UK Biobank, using LDMS, and confirmed previously published ID for 4 traits. We find unique evidence of ID for handgrip strength, waist/hip ratio, and visual and auditory acuity (ID between -2.3 and -5.2 phenotypic SDs for complete inbreeding; [Formula: see text]). Our results illustrate that a careful choice of the measure of inbreeding combined with LDMS stratification improves both detection and quantification of ID using SNP data.
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29
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Gooley R, Hogg CJ, Belov K, Grueber CE. No evidence of inbreeding depression in a Tasmanian devil insurance population despite significant variation in inbreeding. Sci Rep 2017; 7:1830. [PMID: 28500329 PMCID: PMC5431960 DOI: 10.1038/s41598-017-02000-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 04/06/2017] [Indexed: 01/08/2023] Open
Abstract
Inbreeding depression occurs when inbred individuals experience reduced fitness as a result of reduced genome-wide heterozygosity. The Tasmanian devil faces extinction due to a contagious cancer, devil facial tumour disease (DFTD). An insurance metapopulation was established in 2006 to ensure the survival of the species and to be used as a source population for re-wilding and genetic rescue. The emergence of DFTD and the rapid decline of wild devil populations have rendered the species at risk of inbreeding depression. We used 33 microsatellite loci to (1) reconstruct a pedigree for the insurance population and (2) estimate genome-wide heterozygosity for 200 individuals. Using heterozygosity-fitness correlations, we investigated the effect of heterozygosity on six diverse fitness measures (ulna length, asymmetry, weight-at-weaning, testes volume, reproductive success and survival). Despite statistically significant evidence of variation in individual inbreeding in this population, we found no associations between inbreeding and any of our six fitness measurements. We propose that the benign environment in captivity may decrease the intensity of inbreeding depression, relative to the stressful conditions in the wild. Future work will need to measure fitness of released animals to facilitate translation of this data to the broader conservation management of the species in its native range.
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Affiliation(s)
- Rebecca Gooley
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Carolyn J Hogg
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia.,Zoo and Aquarium Association Australasia, Mosman, NSW, 2088, Australia
| | - Katherine Belov
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia.
| | - Catherine E Grueber
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia.,San Diego Zoo Global, PO Box 120551, San Diego, CA, 92112, USA
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30
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Revisiting Adaptive Potential, Population Size, and Conservation. Trends Ecol Evol 2017; 32:506-517. [PMID: 28476215 DOI: 10.1016/j.tree.2017.03.012] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 03/28/2017] [Accepted: 03/31/2017] [Indexed: 11/24/2022]
Abstract
Additive genetic variance (VA) reflects the potential for evolutionary shifts and can be low for some traits or populations. High VA is critical for the conservation of threatened species under selection to facilitate adaptation. Theory predicts tight associations between population size and VA, but data from some experimental models, and managed and natural populations do not always support this prediction. However, VA comparisons often have low statistical power, are undertaken in highly controlled environments distinct from natural habitats, and focus on traits with limited ecological relevance. Moreover, investigations of VA typically fail to consider rare alleles, genetic load, or linkage disequilibrium, resulting in deleterious effects associated with favored alleles in small populations. Large population size remains essential for ensuring adaptation.
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31
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Genetic variation, selection and evolution: special issue in celebration of the 50th anniversary of the population genetics group meeting. Heredity (Edinb) 2016; 118:1. [PMID: 27827388 DOI: 10.1038/hdy.2016.97] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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