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White LC, Städele V, Ramirez Amaya S, Langergraber K, Vigilant L. Female chimpanzees avoid inbreeding even in the presence of substantial bisexual philopatry. ROYAL SOCIETY OPEN SCIENCE 2024; 11:230967. [PMID: 38234436 PMCID: PMC10791533 DOI: 10.1098/rsos.230967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 12/13/2023] [Indexed: 01/19/2024]
Abstract
Inbreeding (reproduction between relatives) often decreases the fitness of offspring and is thus expected to lead to the evolution of inbreeding avoidance strategies. Chimpanzees (Pan troglodytes) are expected to avoid inbreeding as they are long-lived, invest heavily in offspring and may encounter adult, opposite sex kin frequently, especially in populations where both males and females commonly remain in the group in which they were born (bisexual philopatry). However, it is unclear whether substantial bisexual philopatry has been a feature of chimpanzees' evolutionary history or whether it is a result of recent anthropogenic interference, as the only groups for which it has been documented are significantly impacted by human encroachment and experience notable rates of potentially unsustainable inbreeding. Here we use 14 years of observational data and a large genomic dataset of 256 481 loci sequenced from 459 individuals to document dispersal and inbreeding dynamics in an eastern chimpanzee (P. t. schweinfurthii) community with low levels of anthropogenic disturbance. We document the first case of substantial bisexual philopatry in a relatively undisturbed chimpanzee community and show that, despite an increased inbreeding risk incurred by females who do not disperse before reaching reproductive age, natal females were still able to avoid producing inbred offspring.
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Affiliation(s)
- Lauren C. White
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Arthur Rylah Institute for Environmental Research, Department of Energy, Environment and Climate Action, Melbourne, Australia
| | - Veronika Städele
- Institute of Human Origins, School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA
| | - Sebastian Ramirez Amaya
- Institute of Human Origins, School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA
| | - Kevin Langergraber
- Institute of Human Origins, School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA
| | - Linda Vigilant
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
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2
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Barrett KG, Amaral G, Elphinstone M, McAdie ML, Davis CS, Janes JK, Carnio J, Moehrenschlager A, Gorrell JC. Genetic management on the brink of extinction: sequencing microsatellites does not improve estimates of inbreeding in wild and captive Vancouver Island marmots (Marmota vancouverensis). CONSERV GENET 2022; 23:417-428. [PMID: 35401067 PMCID: PMC8948115 DOI: 10.1007/s10592-022-01429-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 01/04/2022] [Indexed: 11/27/2022]
Abstract
Captive breeding is often a last resort management option in the conservation of endangered species which can in turn lead to increased risk of inbreeding depression and loss of genetic diversity. Thus, recording breeding events via studbook for the purpose of estimating relatedness, and facilitating mating pair selection to minimize inbreeding, is common practice. However, as founder relatedness is often unknown, loss of genetic variation and inbreeding cannot be entirely avoided. Molecular genotyping is slowly being adopted in captive breeding programs, however achieving sufficient resolution can be challenging in small, low diversity, populations. Here, we evaluate the success of the Vancouver Island marmot (Marmota vancouverensis; VIM; among the worlds most endangered mammals) captive breeding program in preventing inbreeding and maintaining genetic diversity. We explored the use of high-throughput amplicon sequencing of microsatellite regions to assay greater genetic variation in both captive and wild populations than traditional length-based fragment analysis. Contrary to other studies, this method did not considerably increase diversity estimates, suggesting: (1) that the technique does not universally improve resolution, and (2) VIM have exceedingly low diversity. Studbook estimates of pairwise relatedness and inbreeding in the current population were weakly, but positively, correlated to molecular estimates. Thus, current studbooks are moderately effective at predicting genetic similarity when founder relatedness is known. Finally, we found that captive and wild populations did not differ in allelic frequencies, and conservation efforts to maintain diversity have been successful with no significant decrease in diversity over the last three generations.
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Affiliation(s)
- Kimberley G. Barrett
- Biology Department, Vancouver Island University, Nanaimo, BC V9R 5S5 Canada
- Present Address: Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2R3 Canada
| | - Geneviève Amaral
- Biology Department, Vancouver Island University, Nanaimo, BC V9R 5S5 Canada
- Present Address: Island Medical Program, University of Victoria, 3800 Finnerty Road, Victoria, BC V8P 5C2 Canada
| | | | | | - Corey S. Davis
- Present Address: Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2R3 Canada
| | - Jasmine K. Janes
- Biology Department, Vancouver Island University, Nanaimo, BC V9R 5S5 Canada
- School of Environmental and Rural Science, University of New England, Armidale, NSW 2351 Australia
| | - John Carnio
- Marmot Recovery Foundation, Nanaimo, BC V9R 6X9 Canada
| | - Axel Moehrenschlager
- Wilder Institute Calgary Zoo, Calgary, AB T2E 7V6 Canada
- IUCN Species Survival Commission, Conservation Translocation Specialist Group, Calgary, AB Canada
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3
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Foster Y, Dutoit L, Grosser S, Dussex N, Foster BJ, Dodds KG, Brauning R, Van Stijn T, Robertson F, McEwan JC, Jacobs JME, Robertson BC. Genomic signatures of inbreeding in a critically endangered parrot, the kākāpō. G3 (BETHESDA, MD.) 2021; 11:jkab307. [PMID: 34542587 PMCID: PMC8527487 DOI: 10.1093/g3journal/jkab307] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 08/23/2021] [Indexed: 02/06/2023]
Abstract
Events of inbreeding are inevitable in critically endangered species. Reduced population sizes and unique life-history traits can increase the severity of inbreeding, leading to declines in fitness and increased risk of extinction. Here, we investigate levels of inbreeding in a critically endangered flightless parrot, the kākāpō (Strigops habroptilus), wherein a highly inbred island population and one individual from the mainland of New Zealand founded the entire extant population. Genotyping-by-sequencing (GBS), and a genotype calling approach using a chromosome-level genome assembly, identified a filtered set of 12,241 single-nucleotide polymorphisms (SNPs) among 161 kākāpō, which together encompass the total genetic potential of the extant population. Multiple molecular-based estimates of inbreeding were compared, including genome-wide estimates of heterozygosity (FH), the diagonal elements of a genomic-relatedness matrix (FGRM), and runs of homozygosity (RoH, FRoH). In addition, we compared levels of inbreeding in chicks from a recent breeding season to examine if inbreeding is associated with offspring survival. The density of SNPs generated with GBS was sufficient to identify chromosomes that were largely homozygous with RoH distributed in similar patterns to other inbred species. Measures of inbreeding were largely correlated and differed significantly between descendants of the two founding populations. However, neither inbreeding nor ancestry was found to be associated with reduced survivorship in chicks, owing to unexpected mortality in chicks exhibiting low levels of inbreeding. Our study highlights important considerations for estimating inbreeding in critically endangered species, such as the impacts of small population sizes and admixture between diverse lineages.
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Affiliation(s)
- Yasmin Foster
- Department of Zoology, University of Otago, Dunedin 9054, New Zealand
| | - Ludovic Dutoit
- Department of Zoology, University of Otago, Dunedin 9054, New Zealand
| | - Stefanie Grosser
- Department of Zoology, University of Otago, Dunedin 9054, New Zealand
| | - Nicolas Dussex
- Centre for Palaeogenetics, SE-106 91 Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-104 05 Stockholm, Sweden
- Department of Zoology, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Brodie J Foster
- Department of Zoology, University of Otago, Dunedin 9054, New Zealand
| | - Ken G Dodds
- AgResearch Invermay Agricultural Centre, Mosgiel 9053, New Zealand
| | - Rudiger Brauning
- AgResearch Invermay Agricultural Centre, Mosgiel 9053, New Zealand
| | - Tracey Van Stijn
- AgResearch Invermay Agricultural Centre, Mosgiel 9053, New Zealand
| | - Fiona Robertson
- Department of Zoology, University of Otago, Dunedin 9054, New Zealand
| | - John C McEwan
- AgResearch Invermay Agricultural Centre, Mosgiel 9053, New Zealand
| | | | - Bruce C Robertson
- Department of Zoology, University of Otago, Dunedin 9054, New Zealand
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4
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Duntsch L, Whibley A, Brekke P, Ewen JG, Santure AW. Genomic data of different resolutions reveal consistent inbreeding estimates but contrasting homozygosity landscapes for the threatened Aotearoa New Zealand hihi. Mol Ecol 2021; 30:6006-6020. [PMID: 34242449 DOI: 10.1111/mec.16068] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 07/01/2021] [Indexed: 12/19/2022]
Abstract
Inbreeding can lead to a loss of heterozygosity in a population and when combined with genetic drift may reduce the adaptive potential of a species. However, there is uncertainty about whether resequencing data can provide accurate and consistent inbreeding estimates. Here, we performed an in-depth inbreeding analysis for hihi (Notiomystis cincta), an endemic and nationally vulnerable passerine bird of Aotearoa New Zealand. We first focused on subsampling variants from a reference genome male, and found that low-density data sets tend to miss runs of homozygosity (ROH) in some places and overestimate ROH length in others, resulting in contrasting homozygosity landscapes. Low-coverage resequencing and 50 K SNP array densities can yield comparable inbreeding results to high-coverage resequencing approaches, but the results for all data sets are highly dependent on the software settings employed. Second, we extended our analysis to 10 hihi where low-coverage whole genome resequencing, RAD-seq and SNP array genotypes are available. We inferred ROH and individual inbreeding to evaluate the relative effects of sequencing depth versus SNP density on estimating inbreeding coefficients and found that high rates of missingness downwardly bias both the number and length of ROH. In summary, when using genomic data to evaluate inbreeding, studies must consider that ROH estimates are heavily dependent on analysis parameters, data set density and individual sequencing depth.
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Affiliation(s)
- Laura Duntsch
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Annabel Whibley
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Patricia Brekke
- Institute of Zoology, Zoological Society of London, London, UK
| | - John G Ewen
- Institute of Zoology, Zoological Society of London, London, UK
| | - Anna W Santure
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
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5
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Hauber ME, Louder MI, Griffith SC. Neurogenomic insights into the behavioral and vocal development of the zebra finch. eLife 2021; 10:61849. [PMID: 34106827 PMCID: PMC8238503 DOI: 10.7554/elife.61849] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 06/08/2021] [Indexed: 02/06/2023] Open
Abstract
The zebra finch (Taeniopygia guttata) is a socially monogamous and colonial opportunistic breeder with pronounced sexual differences in singing and plumage coloration. Its natural history has led to it becoming a model species for research into sex differences in vocal communication, as well as behavioral, neural and genomic studies of imitative auditory learning. As scientists tap into the genetic and behavioral diversity of both wild and captive lineages, the zebra finch will continue to inform research into culture, learning, and social bonding, as well as adaptability to a changing climate.
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Affiliation(s)
- Mark E Hauber
- Department of Evolution, Ecology, and Behavior, School of Integrative Biology, University of Illinois at Urbana-Champaign, Urbana-Champaign, United States
| | - Matthew Im Louder
- International Research Center for Neurointelligence, University of Tokyo, Tokyo, Japan.,Department of Biology, Texas A&M University, College Station, United States
| | - Simon C Griffith
- Department of Biological Sciences, Macquarie University, Sydney, Australia
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6
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Knief U, Forstmeier W, Pei Y, Wolf J, Kempenaers B. A test for meiotic drive in hybrids between Australian and Timor zebra finches. Ecol Evol 2020; 10:13464-13475. [PMID: 33304552 PMCID: PMC7713956 DOI: 10.1002/ece3.6951] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 09/14/2020] [Accepted: 09/28/2020] [Indexed: 12/16/2022] Open
Abstract
Meiotic drivers have been proposed as a potent evolutionary force underlying genetic and phenotypic variation, genome structure, and also speciation. Due to their strong selective advantage, they are expected to rapidly spread through a population despite potentially detrimental effects on organismal fitness. Once fixed, autosomal drivers are cryptic within populations and only become visible in between-population crosses lacking the driver or corresponding suppressor. However, the assumed ubiquity of meiotic drivers has rarely been assessed in crosses between populations or species. Here we test for meiotic drive in hybrid embryos and offspring of Timor and Australian zebra finches-subspecies that have evolved in isolation for about two million years-using 38,541 informative transmissions of 56 markers linked to either centromeres or distal chromosome ends. We did not find evidence for meiotic driver loci on specific chromosomes. However, we observed a weak overall transmission bias toward Timor alleles at centromeres in females (transmission probability of Australian alleles of 47%, nominal p = 6 × 10-5). While this is in line with the centromere drive theory, it goes against the expectation that the subspecies with the larger effective population size (i.e., the Australian zebra finch) should have evolved the more potent meiotic drivers. We thus caution against interpreting our finding as definite evidence for centromeric drive. Yet, weak centromeric meiotic drivers may be more common than generally anticipated and we encourage further studies that are designed to detect also small effect meiotic drivers.
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Affiliation(s)
- Ulrich Knief
- Department of Behavioural Ecology and Evolutionary GeneticsMax Planck Institute for OrnithologySeewiesenGermany
- Division of Evolutionary BiologyFaculty of BiologyLudwig Maximilian University of MunichPlanegg‐MartinsriedGermany
| | - Wolfgang Forstmeier
- Department of Behavioural Ecology and Evolutionary GeneticsMax Planck Institute for OrnithologySeewiesenGermany
| | - Yifan Pei
- Department of Behavioural Ecology and Evolutionary GeneticsMax Planck Institute for OrnithologySeewiesenGermany
| | - Jochen Wolf
- Division of Evolutionary BiologyFaculty of BiologyLudwig Maximilian University of MunichPlanegg‐MartinsriedGermany
| | - Bart Kempenaers
- Department of Behavioural Ecology and Evolutionary GeneticsMax Planck Institute for OrnithologySeewiesenGermany
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7
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Pei 裴一凡 Y, Forstmeier W, Wang 王代平 D, Martin K, Rutkowska J, Kempenaers B. Proximate Causes of Infertility and Embryo Mortality in Captive Zebra Finches. Am Nat 2020; 196:577-596. [PMID: 33064590 DOI: 10.1086/710956] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractSome species show high rates of reproductive failure, which is puzzling because natural selection works against such failure in every generation. Hatching failure is common in both captive and wild zebra finches (Taeniopygia guttata), yet little is known about its proximate causes. Here we analyze data on reproductive performance (the fate of >23,000 eggs) based on up to 14 years of breeding of four captive zebra finch populations. We find that virtually all aspects of reproductive performance are negatively affected by inbreeding (mean r=-0.117); by an early-starting, age-related decline (mean r=-0.132); and by poor early-life nutrition (mean r=-0.058). However, these effects together explain only about 3% of the variance in infertility, offspring mortality, fecundity, and fitness. In contrast, individual repeatability of different fitness components varied between 15% and 50%. As expected, we found relatively low heritability in fitness components (median: 7% of phenotypic variation and 29% of individually repeatable variation). Yet some of the heritable variation in fitness appears to be maintained by antagonistic pleiotropy (negative genetic correlations) between male fitness traits and female and offspring fitness traits. The large amount of unexplained variation suggests a potentially important role of local dominance and epistasis, including the possibility of segregating genetic incompatibilities.
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8
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Santana ML. Quantitative genetic analyses provide parameters for selection and conservation of captive Great-billed Seed-finches (Sporophila maximiliani). PLoS One 2020; 15:e0236647. [PMID: 32730350 PMCID: PMC7392336 DOI: 10.1371/journal.pone.0236647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 07/09/2020] [Indexed: 11/18/2022] Open
Abstract
The Great-billed Seed-finch (Sporophila maximiliani) is an endangered South American bird that has suffered from trafficking and the destruction of its natural habitat. In contrast, there are over 180,000 Great-billed Seed-finches legally raised in captivity in Brazil. The interest as a pet for Great-billed Seed-finches is due to their exceptional ability to sing. In the present research, the unknown genetic structure of the Great-billed Seed-finch captive population was investigated by quantitative analysis of 6,226 pedigree records. Additionally, 7,671 phenotypic records were available to estimate genetic parameters such as heritability and evolvability of a song-related trait of these birds for competitions. The captive Great-billed Seed-Finch population faces many of the problems commonly encountered in domestic animal populations such as a high level of inbreeding (average of 8.26%, 70.47% of birds were inbred), pedigree bottlenecks, unbalanced contribution of breeding animals and structuring (equivalent number of subpopulations of 2.91). Despite this, most genetic diversity remains preserved within aviaries. The high generation interval (5.74 years) found for this population should help to prevent a rapid increase in inbreeding and genetic drift. These results should serve as strong motivation and support for urgent actions to manage the genetic diversity of captive Great-billed Seed-Finches. From the viewpoint of genetic improvement for singing time in tournaments (STT), this trait presents sufficient variability to allow response to artificial selection given the heritability of 18.7% and evolvability of 2,447%. In contrast, inbreeding and high generation interval appear to be the most considerable barriers that may limit the genetic gain for STT. Widespread adoption of techniques such as optimal genetic contribution selection and implementation of routine genetic diversity monitoring via pedigree analysis and molecular tools can be crucial both in terms of breeding and conservation of genetic diversity of captive Great-billed Seed-Finches.
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Affiliation(s)
- Mário L. Santana
- Grupo de Melhoramento Animal de Mato Grosso (GMAT), Instituto de Ciências Agrárias e Tecnológicas, Universidade Federal de Rondonópolis, Rondonópolis, Mato Grosso, Brazil
- * E-mail:
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9
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Galla SJ, Moraga R, Brown L, Cleland S, Hoeppner MP, Maloney RF, Richardson A, Slater L, Santure AW, Steeves TE. A comparison of pedigree, genetic and genomic estimates of relatedness for informing pairing decisions in two critically endangered birds: Implications for conservation breeding programmes worldwide. Evol Appl 2020; 13:991-1008. [PMID: 32431748 PMCID: PMC7232769 DOI: 10.1111/eva.12916] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 12/27/2019] [Accepted: 01/02/2020] [Indexed: 12/18/2022] Open
Abstract
Conservation management strategies for many highly threatened species include conservation breeding to prevent extinction and enhance recovery. Pairing decisions for these conservation breeding programmes can be informed by pedigree data to minimize relatedness between individuals in an effort to avoid inbreeding, maximize diversity and maintain evolutionary potential. However, conservation breeding programmes struggle to use this approach when pedigrees are shallow or incomplete. While genetic data (i.e., microsatellites) can be used to estimate relatedness to inform pairing decisions, emerging evidence indicates this approach may lack precision in genetically depauperate species, and more effective estimates will likely be obtained from genomic data (i.e., thousands of genome-wide single nucleotide polymorphisms, or SNPs). Here, we compare relatedness estimates and subsequent pairing decisions using pedigrees, microsatellites and SNPs from whole-genome resequencing approaches in two critically endangered birds endemic to New Zealand: kakī/black stilt (Himantopus novaezelandiae) and kākāriki karaka/orange-fronted parakeet (Cyanoramphus malherbi). Our findings indicate that SNPs provide more precise estimates of relatedness than microsatellites when assessing empirical parent-offspring and full sibling relationships. Further, our results show that relatedness estimates and subsequent pairing recommendations using PMx are most similar between pedigree- and SNP-based approaches. These combined results indicate that in lieu of robust pedigrees, SNPs are an effective tool for informing pairing decisions, which has important implications for many poorly pedigreed conservation breeding programmes worldwide.
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Affiliation(s)
- Stephanie J. Galla
- School of Biological SciencesUniversity of CanterburyChristchurchNew Zealand
| | - Roger Moraga
- Tea Break Bioinformatics, LtdPalmerston NorthNew Zealand
| | - Liz Brown
- New Zealand Department of ConservationTwizelNew Zealand
| | | | - Marc P. Hoeppner
- Institute for Clinical Molecular BiologyChristian‐Albrechts‐University KielKielGermany
| | | | - Anne Richardson
- The Isaac Conservation and Wildlife TrustChristchurchNew Zealand
| | - Lyndon Slater
- New Zealand Department of ConservationRangioraNew Zealand
| | - Anna W. Santure
- School of Biological SciencesUniversity of AucklandAucklandNew Zealand
| | - Tammy E. Steeves
- School of Biological SciencesUniversity of CanterburyChristchurchNew Zealand
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10
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Nietlisbach P, Muff S, Reid JM, Whitlock MC, Keller LF. Nonequivalent lethal equivalents: Models and inbreeding metrics for unbiased estimation of inbreeding load. Evol Appl 2019; 12:266-279. [PMID: 30697338 PMCID: PMC6346663 DOI: 10.1111/eva.12713] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Revised: 09/06/2018] [Accepted: 09/09/2018] [Indexed: 02/06/2023] Open
Abstract
Inbreeding depression, the deterioration in mean trait value in progeny of related parents, is a fundamental quantity in genetics, evolutionary biology, animal and plant breeding, and conservation biology. The magnitude of inbreeding depression can be quantified by the inbreeding load, typically measured in numbers of lethal equivalents, a population genetic quantity that allows for comparisons between environments, populations or species. However, there is as yet no quantitative assessment of which combinations of statistical models and metrics of inbreeding can yield such estimates. Here, we review statistical models that have been used to estimate inbreeding load and use population genetic simulations to investigate how unbiased estimates can be obtained using genomic and pedigree-based metrics of inbreeding. We use simulated binary viability data (i.e., dead versus alive) as our example, but the concepts apply to any trait that exhibits inbreeding depression. We show that the increasingly popular generalized linear models with logit link do not provide comparable and unbiased population genetic measures of inbreeding load, independent of the metric of inbreeding used. Runs of homozygosity result in unbiased estimates of inbreeding load, whereas inbreeding measured from pedigrees results in slight overestimates. Due to widespread use of models that do not yield unbiased measures of the inbreeding load, some estimates in the literature cannot be compared meaningfully. We surveyed the literature for reliable estimates of the mean inbreeding load from wild vertebrate populations and found an average of 3.5 haploid lethal equivalents for survival to sexual maturity. To obtain comparable estimates, we encourage researchers to use generalized linear models with logarithmic links or maximum-likelihood estimation of the exponential equation, and inbreeding coefficients calculated from runs of homozygosity, provided an assembled reference genome of sufficient quality and enough genetic marker data are available.
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Affiliation(s)
- Pirmin Nietlisbach
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZurichSwitzerland
- Department of ZoologyUniversity of British ColumbiaVancouverBCCanada
| | - Stefanie Muff
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZurichSwitzerland
| | - Jane M. Reid
- School of Biological SciencesUniversity of AberdeenAberdeenUK
| | | | - Lukas F. Keller
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZurichSwitzerland
- Zoological MuseumUniversity of ZurichZurichSwitzerland
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11
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Nietlisbach P, Keller LF, Camenisch G, Guillaume F, Arcese P, Reid JM, Postma E. Pedigree-based inbreeding coefficient explains more variation in fitness than heterozygosity at 160 microsatellites in a wild bird population. Proc Biol Sci 2018; 284:rspb.2016.2763. [PMID: 28250184 DOI: 10.1098/rspb.2016.2763] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 02/06/2017] [Indexed: 01/14/2023] Open
Abstract
Although the pedigree-based inbreeding coefficient F predicts the expected proportion of an individual's genome that is identical-by-descent (IBD), heterozygosity at genetic markers captures Mendelian sampling variation and thereby provides an estimate of realized IBD. Realized IBD should hence explain more variation in fitness than their pedigree-based expectations, but how many markers are required to achieve this in practice remains poorly understood. We use extensive pedigree and life-history data from an island population of song sparrows (Melospiza melodia) to show that the number of genetic markers and pedigree depth affected the explanatory power of heterozygosity and F, respectively, but that heterozygosity measured at 160 microsatellites did not explain more variation in fitness than F This is in contrast with other studies that found heterozygosity based on far fewer markers to explain more variation in fitness than F Thus, the relative performance of marker- and pedigree-based estimates of IBD depends on the quality of the pedigree, the number, variability and location of the markers employed, and the species-specific recombination landscape, and expectations based on detailed and deep pedigrees remain valuable until we can routinely afford genotyping hundreds of phenotyped wild individuals of genetic non-model species for thousands of genetic markers.
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Affiliation(s)
- Pirmin Nietlisbach
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Lukas F Keller
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Glauco Camenisch
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Frédéric Guillaume
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Peter Arcese
- Department of Forest and Conservation Sciences, University of British Columbia, 2424 Main Mall, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Jane M Reid
- Institute of Biological and Environmental Sciences, School of Biological Sciences, University of Aberdeen, Zoology Building, Tillydrone Avenue, Aberdeen AB24 2TZ, UK
| | - Erik Postma
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.,Centre for Ecology and Conservation, College of Life and Environmental Sciences, University of Exeter, Cornwall Campus, Penryn TR10 9EZ, UK
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12
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Engelhardt A, Muniz L, Perwitasari-Farajallah D, Widdig A. Highly Polymorphic Microsatellite Markers for the Assessment of Male Reproductive Skew and Genetic Variation in Critically Endangered Crested Macaques ( Macaca nigra). INT J PRIMATOL 2017; 38:672-691. [PMID: 28845069 PMCID: PMC5550527 DOI: 10.1007/s10764-017-9973-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 05/11/2017] [Indexed: 11/24/2022]
Abstract
Genetic analyses based on noninvasively collected samples have become an important tool for evolutionary biology and conservation. Crested macaques (Macaca nigra), endemic to Sulawesi, Indonesia, are important for our understanding of primate evolution as Sulawesi macaques represent an exceptional example of primate adaptive radiation. Crested macaques are also Critically Endangered. However, to date we know very little about their genetics. The aim of our study was to find and validate microsatellite markers useful for evolutionary, conservation, and other genetic studies on wild crested macaques. Using fecal samples of 176 wild macaques living in the Tangkoko Reserve, Sulawesi, we identified 12 polymorphic microsatellite loci through cross-species polymerase chain reaction amplification with later modification of some of these primers. We tested their suitability by investigating and exploring patterns of paternity, observed heterozygosity, and evidence for inbreeding. We assigned paternity to 63 of 65 infants with high confidence. Among cases with solved paternity, we found no evidence of extragroup paternity and natal breeding. We found a relatively steep male reproductive skew B index of 0.330 ± 0.267; mean ± SD) and mean alpha paternity of 65% per year with large variation across groups and years (29–100%). Finally, we detected an excess in observed heterozygosity and no evidence of inbreeding across our three study groups, with an observed heterozygosity of 0.766 ± 0.059 and expected heterozygosity of 0.708 ± 0.059, and an inbreeding coefficient of −0.082 ± 0.035. Our results indicate that the selected markers are useful for genetic studies on wild crested macaques, and possibly also on other Sulawesi and closely related macaques. They further suggest that the Tangkoko population of crested macaques is still genetically variable despite its small size, isolation, and the species’ reproductive patterns. This gives us hope that other endangered primate species living in small, isolated populations may also retain a healthy gene pool, at least in the short term.
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Affiliation(s)
- Antje Engelhardt
- School of Natural Sciences and Psychology, Liverpool John Moores University, L3 3AF, Liverpool, UK.,Junior Research Group of Primate Sexual Selection, German Primate Center, 37077 Göttingen, Germany.,Courant Research Center Evolution of Social Behavior, Georg August University, 37077 Göttingen, Germany
| | - Laura Muniz
- Junior Research Group of Primate Kin Selection, Department of Primatology, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany.,Research Group of Behavioural Ecology, Institute of Biology, University of Leipzig, 04103 Leipzig, Germany
| | - Dyah Perwitasari-Farajallah
- Primate Research Centre, Bogor Agricultural University, Bogor, Indonesia.,Department of Biology, Faculty of Mathematics and Natural Sciences, Bogor Agricultural University, Bogor, Indonesia
| | - Anja Widdig
- Junior Research Group of Primate Kin Selection, Department of Primatology, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany.,Research Group of Behavioural Ecology, Institute of Biology, University of Leipzig, 04103 Leipzig, Germany.,German Center for Integrative Biodiversity Research, 04103 Leipzig, Germany
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13
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A sex-chromosome inversion causes strong overdominance for sperm traits that affect siring success. Nat Ecol Evol 2017; 1:1177-1184. [PMID: 29046576 DOI: 10.1038/s41559-017-0236-1] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 06/06/2017] [Indexed: 01/23/2023]
Abstract
Male reproductive success depends on the competitive ability of sperm to fertilize the ova, which should lead to strong selection on sperm characteristics. This raises the question of how heritable variation in sperm traits is maintained. Here we show that in zebra finches (Taeniopygia guttata) nearly half of the variance in sperm morphology is explained by an inversion on the Z chromosome with a 40% allele frequency in the wild. The sperm of males that are heterozygous for the inversion had the longest midpieces and the highest velocity. Furthermore, such males achieved the highest fertility and the highest siring success, both within-pair and extra-pair. Males homozygous for the derived allele show detrimental sperm characteristics and the lowest siring success. Our results suggest heterozygote advantage as the mechanism that maintains the inversion polymorphism and hence variance in sperm design and in fitness.
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14
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Forstmeier W, Ihle M, Opatová P, Martin K, Knief U, Albrechtová J, Albrecht T, Kempenaers B. Testing the phenotype-linked fertility hypothesis in the presence and absence of inbreeding. J Evol Biol 2017; 30:968-976. [DOI: 10.1111/jeb.13062] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 03/02/2017] [Indexed: 12/14/2022]
Affiliation(s)
- W. Forstmeier
- Department of Behavioural Ecology and Evolutionary Genetics; Max Planck Institute for Ornithology; Seewiesen Germany
| | - M. Ihle
- Department of Behavioural Ecology and Evolutionary Genetics; Max Planck Institute for Ornithology; Seewiesen Germany
| | - P. Opatová
- Department of Botany and Zoology; Faculty of Science; Masaryk University; Brno Czech Republic
- External Research Facility Studenec; Institute of Vertebrate Biology; Czech Academy of Sciences; Brno Czech Republic
| | - K. Martin
- Department of Behavioural Ecology and Evolutionary Genetics; Max Planck Institute for Ornithology; Seewiesen Germany
| | - U. Knief
- Department of Behavioural Ecology and Evolutionary Genetics; Max Planck Institute for Ornithology; Seewiesen Germany
| | - J. Albrechtová
- External Research Facility Studenec; Institute of Vertebrate Biology; Czech Academy of Sciences; Brno Czech Republic
- Department of Zoology; Faculty of Science; Charles University; Prague Czech Republic
| | - T. Albrecht
- External Research Facility Studenec; Institute of Vertebrate Biology; Czech Academy of Sciences; Brno Czech Republic
- Department of Zoology; Faculty of Science; Charles University; Prague Czech Republic
| | - B. Kempenaers
- Department of Behavioural Ecology and Evolutionary Genetics; Max Planck Institute for Ornithology; Seewiesen Germany
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15
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Wang D, Kempenaers N, Kempenaers B, Forstmeier W. Male zebra finches have limited ability to identify high-fecundity females. Behav Ecol 2017. [DOI: 10.1093/beheco/arx037] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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16
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Flacke GL, Tomkins JL, Black R, Steck B. Demographics of polycystic kidney disease and captive population viability in pygmy hippopotamus (Choeropsis liberiensis). Zoo Biol 2017; 36:136-151. [PMID: 28198143 DOI: 10.1002/zoo.21351] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 12/09/2016] [Accepted: 01/03/2017] [Indexed: 11/12/2022]
Abstract
Polycystic kidney disease (PKD) was previously diagnosed at necropsy in several pygmy hippopotami (Choeropsis liberiensis) from the Smithsonian National Zoo and Zoo Basel, suggesting a threat to the long-term viability of the captive population. We determined the incidence and demographics of PKD in the captive population historically; we tested if the condition is linked to pedigree; we investigated mode of inheritance; we examined effects of PKD on longevity; we conducted survival analysis; and we examined long-term population viability. Thirty-seven percent of 149 necropsied adult pygmy hippos were affected by PKD, and it was more common in females, controlling for the overall female-biased sex-ratio. Prevalence increased significantly with age, but most hippos were beyond their reproductive prime before developing clinical signs; thus fecundity was likely unaffected. PKD was linked to pedigree and may exhibit X-linked dominance, but further research is needed to definitively establish the mode of inheritance. PKD did not affect longevity, overall or within any age class. There was no significant correlation between inbreeding coefficient (F) and PKD, and the prevalence in wild-caught and captive-born animals was similar. Longevity for both captive-born and inbred hippos (F > 0) was significantly shorter than longevity for their wild-caught and non-inbred counterparts. Demographic projections indicated the extant population will likely experience a slow increase over time, provided there are no space constraints. We conclude that although PKD is an important cause of morbidity and mortality in pygmy hippos, the condition is not a primary concern for overall viability of the captive population.
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Affiliation(s)
- Gabriella L Flacke
- School of Animal Biology, University of Western Australia, Crawley, Australia
| | - Joseph L Tomkins
- School of Animal Biology, University of Western Australia, Crawley, Australia.,Center for Evolutionary Biology, School of Animal Biology, University of Western Australia, Crawley, Australia
| | - Robert Black
- School of Animal Biology, University of Western Australia, Crawley, Australia
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17
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Knief U, Schielzeth H, Backström N, Hemmrich‐Stanisak G, Wittig M, Franke A, Griffith SC, Ellegren H, Kempenaers B, Forstmeier W. Association mapping of morphological traits in wild and captive zebra finches: reliable within, but not between populations. Mol Ecol 2017; 26:1285-1305. [DOI: 10.1111/mec.14009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 12/05/2016] [Accepted: 12/21/2016] [Indexed: 01/17/2023]
Affiliation(s)
- Ulrich Knief
- Department of Behavioural Ecology and Evolutionary Genetics Max Planck Institute for Ornithology 82319 Seewiesen Germany
| | - Holger Schielzeth
- Department of Population Ecology Friedrich Schiller University Jena 07743 Jena Germany
| | - Niclas Backström
- Department of Ecology and Genetics Uppsala University 752 36 Uppsala Sweden
| | | | - Michael Wittig
- Institute of Clinical Molecular Biology Christian‐Albrechts‐University 24105 Kiel Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology Christian‐Albrechts‐University 24105 Kiel Germany
| | - Simon C. Griffith
- Department of Biological Sciences Macquarie University Sydney NSW 2109 Australia
- School of Biological, Earth & Environmental Sciences University of New South Wales Sydney NSW 2057 Australia
| | - Hans Ellegren
- Department of Ecology and Genetics Uppsala University 752 36 Uppsala Sweden
| | - Bart Kempenaers
- Department of Behavioural Ecology and Evolutionary Genetics Max Planck Institute for Ornithology 82319 Seewiesen Germany
| | - Wolfgang Forstmeier
- Department of Behavioural Ecology and Evolutionary Genetics Max Planck Institute for Ornithology 82319 Seewiesen Germany
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18
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Widdig A, Muniz L, Minkner M, Barth Y, Bley S, Ruiz-Lambides A, Junge O, Mundry R, Kulik L. Low incidence of inbreeding in a long-lived primate population isolated for 75 years. Behav Ecol Sociobiol 2016; 71:18. [PMID: 28018027 PMCID: PMC5145906 DOI: 10.1007/s00265-016-2236-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 11/09/2016] [Accepted: 11/11/2016] [Indexed: 11/13/2022]
Abstract
ABSTRACT When close relatives mate, offspring are expected to suffer fitness consequences due to inbreeding depression. Inbreeding has previously been quantified in two ways: using a sufficiently large panel of markers or deep and complete pedigrees over several generations. However, the application of both approaches is still limited by the challenge of compiling such data for species with long generation times, such as primates. Here, we assess inbreeding in rhesus macaques living on Cayo Santiago (Puerto Rico), a population genetically isolated since 1938, but descendant of a large set of presumably unrelated founders. Using comprehensive genetic data, we calculated inbreeding coefficients (F) for 2669 individuals with complete three generation pedigrees and 609 individuals with complete four generation pedigrees. We found that 0.79 and 7.39% of individuals had an F > 0 when using data from three and four generation pedigrees, respectively. No evidence of an increase in inbreeding over the study period (up to 23 years) was found. Furthermore, the observed mean relatedness of breeding pairs differed significantly from the distribution of parental relatedness expected as simulated based on previous reproductive data, suggesting that kin generally avoid breeding with each other. Finally, inbreeding was not a predictor of early mortality measured as survival until weaning and sexual maturation, respectively. Our results remain consistent with three estimators of inbreeding (standardized heterozygosity, internal relatedness, and homozygosity by loci) using up to 42 highly polymorphic microsatellites for the same set of individuals. Together, our results demonstrate that close inbreeding may not be prevalent even in populations isolated over long periods when mechanisms of inbreeding avoidance can operate. SIGNIFICANCE STATEMENT When close relatives mate, offspring may suffer from such inbreeding, e.g., via lower survival and/or fertility. Using (i) a large panel of genetic markers and (ii) complete three or four generation pedigrees, respectively, we show that incidences of inbreeding in a long-lived primate population are rare, even after genetic isolation for 75 years. Moreover, our simulations suggest that kin in our population generally avoid breeding with each other. Finally, the few inbred individuals detected in our large sample did not suffer from lower survival. Given that many animal species face dramatic habitat loss combined with critical population declines, our study provides important implications for conservation biology in general and for population management in particular.
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Affiliation(s)
- Anja Widdig
- Junior Research Group of Primate Kin Selection, Department of Primatology, Max-Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
- Research Group of Behavioural Ecology, Institute of Biology, University of Leipzig, Talstraße 33, 04103 Leipzig, Germany
- German Center for Integrative Biodiversity Research (iDiv), Deutscher Platz 5E, 04103 Leipzig, Germany
| | - Laura Muniz
- Junior Research Group of Primate Kin Selection, Department of Primatology, Max-Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
- Research Group of Behavioural Ecology, Institute of Biology, University of Leipzig, Talstraße 33, 04103 Leipzig, Germany
| | - Mirjam Minkner
- Junior Research Group of Primate Kin Selection, Department of Primatology, Max-Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
- Research Group of Behavioural Ecology, Institute of Biology, University of Leipzig, Talstraße 33, 04103 Leipzig, Germany
| | - Yvonne Barth
- Junior Research Group of Primate Kin Selection, Department of Primatology, Max-Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
- Research Group of Behavioural Ecology, Institute of Biology, University of Leipzig, Talstraße 33, 04103 Leipzig, Germany
| | - Stefanie Bley
- Junior Research Group of Primate Kin Selection, Department of Primatology, Max-Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
- Research Group of Behavioural Ecology, Institute of Biology, University of Leipzig, Talstraße 33, 04103 Leipzig, Germany
| | - Angelina Ruiz-Lambides
- Junior Research Group of Primate Kin Selection, Department of Primatology, Max-Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
- Research Group of Behavioural Ecology, Institute of Biology, University of Leipzig, Talstraße 33, 04103 Leipzig, Germany
- Caribbean Primate Research Center, University of Puerto Rico, Medical Sciences Campus, Punta Santiago, PO Box 906, San Juan, PR 00741 USA
| | - Olaf Junge
- Institute of Medical Informatics and Statistics, University Medical Center Schleswig-Holstein, Campus Kiel, Brunswiker Straße 10, 24105 Kiel, Germany
| | - Roger Mundry
- Max-Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Lars Kulik
- Junior Research Group of Primate Kin Selection, Department of Primatology, Max-Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
- Research Group of Behavioural Ecology, Institute of Biology, University of Leipzig, Talstraße 33, 04103 Leipzig, Germany
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19
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Kardos M, Taylor HR, Ellegren H, Luikart G, Allendorf FW. Genomics advances the study of inbreeding depression in the wild. Evol Appl 2016; 9:1205-1218. [PMID: 27877200 PMCID: PMC5108213 DOI: 10.1111/eva.12414] [Citation(s) in RCA: 143] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 08/05/2016] [Indexed: 12/12/2022] Open
Abstract
Inbreeding depression (reduced fitness of individuals with related parents) has long been a major focus of ecology, evolution, and conservation biology. Despite decades of research, we still have a limited understanding of the strength, underlying genetic mechanisms, and demographic consequences of inbreeding depression in the wild. Studying inbreeding depression in natural populations has been hampered by the inability to precisely measure individual inbreeding. Fortunately, the rapidly increasing availability of high-throughput sequencing data means it is now feasible to measure the inbreeding of any individual with high precision. Here, we review how genomic data are advancing our understanding of inbreeding depression in the wild. Recent results show that individual inbreeding and inbreeding depression can be measured more precisely with genomic data than via traditional pedigree analysis. Additionally, the availability of genomic data has made it possible to pinpoint loci with large effects contributing to inbreeding depression in wild populations, although this will continue to be a challenging task in many study systems due to low statistical power. Now that reliably measuring individual inbreeding is no longer a limitation, a major focus of future studies should be to more accurately quantify effects of inbreeding depression on population growth and viability.
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Affiliation(s)
- Marty Kardos
- Department of Evolutionary BiologyEvolutionary Biology CentreUppsala UniversityUppsalaSweden
| | | | - Hans Ellegren
- Department of Evolutionary BiologyEvolutionary Biology CentreUppsala UniversityUppsalaSweden
| | - Gordon Luikart
- Division of Biological SciencesUniversity of MontanaMissoulaMTUSA
- Flathead Lake Biological StationDivision of Biological SciencesUniversity of MontanaPolsonMTUSA
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20
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Meiotic recombination shapes precision of pedigree- and marker-based estimates of inbreeding. Heredity (Edinb) 2016; 118:239-248. [PMID: 27804967 DOI: 10.1038/hdy.2016.95] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 08/29/2016] [Indexed: 01/17/2023] Open
Abstract
The proportion of an individual's genome that is identical by descent (GWIBD) can be estimated from pedigrees (inbreeding coefficient 'Pedigree F') or molecular markers ('Marker F'), but both estimators come with error. Assuming unrelated pedigree founders, Pedigree F is the expected proportion of GWIBD given a specific inbreeding constellation. Meiotic recombination introduces variation around that expectation (Mendelian noise) and related pedigree founders systematically bias Pedigree F downward. Marker F is an estimate of the actual proportion of GWIBD but it suffers from the sampling error of markers plus the error that occurs when a marker is homozygous without reflecting common ancestry (identical by state). We here show via simulation of a zebra finch and a human linkage map that three aspects of meiotic recombination (independent assortment of chromosomes, number of crossovers and their distribution along chromosomes) contribute to variation in GWIBD and thus the precision of Pedigree and Marker F. In zebra finches, where the genome contains large blocks that are rarely broken up by recombination, the Mendelian noise was large (nearly twofold larger s.d. values compared with humans) and Pedigree F thus less precise than in humans, where crossovers are distributed more uniformly along chromosomes. Effects of meiotic recombination on Marker F were reversed, such that the same number of molecular markers yielded more precise estimates of GWIBD in zebra finches than in humans. As a consequence, in species inheriting large blocks that rarely recombine, even small numbers of microsatellite markers will often be more informative about inbreeding and fitness than large pedigrees.
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21
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Galla SJ, Buckley TR, Elshire R, Hale ML, Knapp M, McCallum J, Moraga R, Santure AW, Wilcox P, Steeves TE. Building strong relationships between conservation genetics and primary industry leads to mutually beneficial genomic advances. Mol Ecol 2016; 25:5267-5281. [PMID: 27641156 DOI: 10.1111/mec.13837] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 08/23/2016] [Accepted: 08/24/2016] [Indexed: 02/06/2023]
Abstract
Several reviews in the past decade have heralded the benefits of embracing high-throughput sequencing technologies to inform conservation policy and the management of threatened species, but few have offered practical advice on how to expedite the transition from conservation genetics to conservation genomics. Here, we argue that an effective and efficient way to navigate this transition is to capitalize on emerging synergies between conservation genetics and primary industry (e.g., agriculture, fisheries, forestry and horticulture). Here, we demonstrate how building strong relationships between conservation geneticists and primary industry scientists is leading to mutually-beneficial outcomes for both disciplines. Based on our collective experience as collaborative New Zealand-based scientists, we also provide insight for forging these cross-sector relationships.
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Affiliation(s)
- Stephanie J Galla
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand.
| | - Thomas R Buckley
- Landcare Research, Private Bag 92170, Auckland Mail Centre, Auckland, 1142, New Zealand.,School of Biological Sciences, University of Auckland, Auckland, 1010, New Zealand
| | - Rob Elshire
- The Elshire Group, Ltd., 52 Victoria Avenue, Palmerston North, 4410, New Zealand
| | - Marie L Hale
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
| | - Michael Knapp
- Department of Anatomy, University of Otago, P.O. Box 913, Dunedin, 9054, New Zealand
| | - John McCallum
- Breeding and Genomics, New Zealand Institute for Plant and Food Research, Private Bag 4704, Christchurch, 8140, New Zealand
| | - Roger Moraga
- AgResearch, Ruakura Research Centre, Bisley Road, Private Bag 3115, Hamilton, 3240, New Zealand
| | - Anna W Santure
- School of Biological Sciences, University of Auckland, Auckland, 1010, New Zealand
| | - Phillip Wilcox
- Department of Mathematics and Statistics, University of Otago, P.O. Box 56, 710 Cumberland Street, Dunedin, 9054, New Zealand
| | - Tammy E Steeves
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
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22
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Knief U, Hemmrich-Stanisak G, Wittig M, Franke A, Griffith SC, Kempenaers B, Forstmeier W. Fitness consequences of polymorphic inversions in the zebra finch genome. Genome Biol 2016; 17:199. [PMID: 27687629 PMCID: PMC5043542 DOI: 10.1186/s13059-016-1056-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 09/05/2016] [Indexed: 12/21/2022] Open
Abstract
Background Inversion polymorphisms constitute an evolutionary puzzle: they should increase embryo mortality in heterokaryotypic individuals but still they are widespread in some taxa. Some insect species have evolved mechanisms to reduce the cost of embryo mortality but humans have not. In birds, a detailed analysis is missing although intraspecific inversion polymorphisms are regarded as common. In Australian zebra finches (Taeniopygia guttata), two polymorphic inversions are known cytogenetically and we set out to detect these two and potentially additional inversions using genomic tools and study their effects on embryo mortality and other fitness-related and morphological traits. Results Using whole-genome SNP data, we screened 948 wild zebra finches for polymorphic inversions and describe four large (12–63 Mb) intraspecific inversion polymorphisms with allele frequencies close to 50 %. Using additional data from 5229 birds and 9764 eggs from wild and three captive zebra finch populations, we show that only the largest inversions increase embryo mortality in heterokaryotypic males, with surprisingly small effect sizes. We test for a heterozygote advantage on other fitness components but find no evidence for heterosis for any of the inversions. Yet, we find strong additive effects on several morphological traits. Conclusions The mechanism that has carried the derived inversion haplotypes to such high allele frequencies remains elusive. It appears that selection has effectively minimized the costs associated with inversions in zebra finches. The highly skewed distribution of recombination events towards the chromosome ends in zebra finches and other estrildid species may function to minimize crossovers in the inverted regions. Electronic supplementary material The online version of this article (doi:10.1186/s13059-016-1056-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ulrich Knief
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology, 82319, Seewiesen, Germany. .,Current address: Division of Evolutionary Biology, Faculty of Biology, Ludwig Maximilian University of Munich, 82152, Planegg-Martinsried, Germany.
| | - Georg Hemmrich-Stanisak
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105, Kiel, Germany
| | - Michael Wittig
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105, Kiel, Germany
| | - Simon C Griffith
- Department of Biological Sciences, Macquarie University, Sydney, NSW, 2109, Australia.,School of Biological, Earth & Environmental Sciences, University of New South Wales, Sydney, NSW, 2057, Australia
| | - Bart Kempenaers
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology, 82319, Seewiesen, Germany
| | - Wolfgang Forstmeier
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology, 82319, Seewiesen, Germany
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23
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Attard CRM, Brauer CJ, Van Zoelen JD, Sasaki M, Hammer MP, Morrison L, Harris JO, Möller LM, Beheregaray LB. Multi-generational evaluation of genetic diversity and parentage in captive southern pygmy perch (Nannoperca australis). CONSERV GENET 2016. [DOI: 10.1007/s10592-016-0873-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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24
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Opatová P, Ihle M, Albrechtová J, Tomášek O, Kempenaers B, Forstmeier W, Albrecht T. Inbreeding depression of sperm traits in the zebra finch Taeniopygia guttata. Ecol Evol 2015; 6:295-304. [PMID: 26811793 PMCID: PMC4716522 DOI: 10.1002/ece3.1868] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 11/05/2015] [Accepted: 11/06/2015] [Indexed: 11/08/2022] Open
Abstract
Inbreeding depression, or the reduction in fitness due to mating between close relatives, is a key issue in biology today. Inbreeding negatively affects many fitness‐related traits, including survival and reproductive success. Despite this, very few studies have quantified the effects of inbreeding on vertebrate gamete traits under controlled breeding conditions using a full‐sib mating approach. Here, we provide comprehensive evidence for the negative effect of inbreeding on sperm traits in a bird, the zebra finch Taeniopygia guttata. We compared sperm characteristics of both inbred (pedigree F = 0.25) and outbred (pedigree F = 0) individuals from two captive populations, one domesticated and one recently wild‐derived, raised under standardized conditions. As normal spermatozoa morphology did not differ consistently between inbred and outbred individuals, our study confirms the hypothesis that sperm morphology is not particularly susceptible to inbreeding depression. Inbreeding did, however, lead to significantly lower sperm motility and a substantially higher percentage of abnormal spermatozoa in ejaculate. These results were consistent across both study populations, confirming the generality and reliability of our findings.
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Affiliation(s)
- Pavlína Opatová
- Institute of Vertebrate Biology Academy of Sciences of the Czech Republic v.v.i. Květná 8CZ-603 65 Brno Czech Republic; Department of Botany and Zoology Faculty of Science Masaryk University Kotlářská 267/2CZ-61137 Brno Czech Republic
| | - Malika Ihle
- Department of Behavioural Ecology and Evolutionary Genetics Max Planck Institute for Ornithology Eberhard-Gwinner-Strasse 7 82319 Seewiesen Germany
| | - Jana Albrechtová
- Institute of Vertebrate Biology Academy of Sciences of the Czech Republic v.v.i. Květná 8CZ-603 65 Brno Czech Republic; Charles University in Prague Faculty of Sciences Department of Zoology Viničná 7CZ-12844 Prague Czech Republic
| | - Oldřich Tomášek
- Institute of Vertebrate Biology Academy of Sciences of the Czech Republic v.v.i. Květná 8CZ-603 65 Brno Czech Republic; Charles University in Prague Faculty of Sciences Department of Zoology Viničná 7CZ-12844 Prague Czech Republic
| | - Bart Kempenaers
- Department of Behavioural Ecology and Evolutionary Genetics Max Planck Institute for Ornithology Eberhard-Gwinner-Strasse 7 82319 Seewiesen Germany
| | - Wolfgang Forstmeier
- Department of Behavioural Ecology and Evolutionary Genetics Max Planck Institute for Ornithology Eberhard-Gwinner-Strasse 7 82319 Seewiesen Germany
| | - Tomáš Albrecht
- Institute of Vertebrate Biology Academy of Sciences of the Czech Republic v.v.i. Květná 8CZ-603 65 Brno Czech Republic; Charles University in Prague Faculty of Sciences Department of Zoology Viničná 7CZ-12844 Prague Czech Republic
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Knief U, Schielzeth H, Ellegren H, Kempenaers B, Forstmeier W. A prezygotic transmission distorter acting equally in female and male zebra finchesTaeniopygia guttata. Mol Ecol 2015; 24:3846-59. [DOI: 10.1111/mec.13281] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 06/13/2015] [Accepted: 06/17/2015] [Indexed: 12/25/2022]
Affiliation(s)
- Ulrich Knief
- Department of Behavioural Ecology and Evolutionary Genetics; Max Planck Institute for Ornithology; Eberhard-Gwinner-Str. 82319 Seewiesen Germany
| | - Holger Schielzeth
- Department of Evolutionary Biology; Bielefeld University; Morgenbreede 45 33615 Bielefeld Germany
| | - Hans Ellegren
- Department of Evolutionary Biology; Uppsala University; Norbyvägen 18D 752 36 Uppsala Sweden
| | - Bart Kempenaers
- Department of Behavioural Ecology and Evolutionary Genetics; Max Planck Institute for Ornithology; Eberhard-Gwinner-Str. 82319 Seewiesen Germany
| | - Wolfgang Forstmeier
- Department of Behavioural Ecology and Evolutionary Genetics; Max Planck Institute for Ornithology; Eberhard-Gwinner-Str. 82319 Seewiesen Germany
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26
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Griffith SC. Genetic similarity is broadly associated with genetic polyandry in birds: a comment on Arct et al. Behav Ecol 2015. [DOI: 10.1093/beheco/arv031] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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