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Wong W, Wang L, Schaffner SS, Li X, Cheeseman I, Anderson TJC, Vaughan A, Ferdig M, Volkman SK, Hartl DL, Wirth DF. MalKinID: A Likelihood-Based Model for Identifying Malaria Parasite Genealogical Relationships Using Identity-by-Descent. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.12.603328. [PMID: 39071294 PMCID: PMC11275886 DOI: 10.1101/2024.07.12.603328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Pathogen genomics is a powerful tool for tracking infectious disease transmission. In malaria, identity-by-descent (IBD) is used to assess the genetic relatedness between parasites and has been used to study transmission and importation. In theory, IBD can be used to distinguish genealogical relationships to reconstruct transmission history or identify parasites for genotype-to-phenotype quantitative-trait-locus experiments. MalKinID (Malaria Kinship Identifier) is a new likelihood-based classification model designed to identify genealogical relationships among malaria parasites based on genome-wide IBD proportions and IBD segment distributions. MalKinID was calibrated to the genomic data from three laboratory-based genetic crosses (yielding 440 parent-child and 9060 full-sibling comparisons). MalKinID identified lab generated F1 progeny with >80% sensitivity and showed that 0.39 (95% CI 0.28, 0.49) of the second-generation progeny of a NF54 and NHP4026 cross were F1s and 0.56 (0.45, 0.67) were backcrosses of an F1 with the parental NF54 strain. In simulated outcrossed importations, MalKinID accurately reconstructs genealogy history with high precision and sensitivity, with F1-scores exceeding 0.84. However, when importation involves inbreeding, such as during serial co-transmission, the precision and sensitivity of MalKinID declined, with F1-scores of 0.76 (0.56, 0.92) and 0.23 (0.0, 0.4) for PC and FS and <0.05 for second-degree and third-degree relatives. Genealogical inference is most powered 1) when outcrossing is the norm or 2) when multi-sample comparisons based on a predefined pedigree are used. MalKinID lays the foundations for using IBD to track parasite transmission history and for separating progeny for quantitative-trait-locus experiments.
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Affiliation(s)
- Wesley Wong
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Lea Wang
- Harvard College, Harvard University, Cambridge, MA, USA
| | - Stephen S Schaffner
- Infectious Disease and Microbiome Program, The Broad Institute, Cambridge, MA, USA
| | - Xue Li
- Program in Disease Intervention and Prevention, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Ian Cheeseman
- Program in Host Pathogen Interactions, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Timothy J C Anderson
- Program in Disease Intervention and Prevention, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Ashley Vaughan
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, United States
- Department of Pediatrics, University of Washington, Seattle, WA, United States
| | - Michael Ferdig
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Sarah K Volkman
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- School of Nursing, Simmons University, Boston MA USA
| | - Daniel L Hartl
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge MA USA
| | - Dyann F Wirth
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
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2
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vonHoldt BM, DeCandia AL, Cassidy KA, Stahler EE, Sinsheimer JS, Smith DW, Stahler DR. Patterns of reproduction and autozygosity distinguish the breeding from nonbreeding gray wolves of Yellowstone National Park. J Hered 2024; 115:327-338. [PMID: 37793153 PMCID: PMC11235126 DOI: 10.1093/jhered/esad062] [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: 03/25/2023] [Revised: 09/25/2023] [Accepted: 10/03/2023] [Indexed: 10/06/2023] Open
Abstract
For species of management concern, accurate estimates of inbreeding and associated consequences on reproduction are crucial for predicting their future viability. However, few studies have partitioned this aspect of genetic viability with respect to reproduction in a group-living social mammal. We investigated the contributions of foundation stock lineages, putative fitness consequences of inbreeding, and genetic diversity of the breeding versus nonreproductive segment of the Yellowstone National Park gray wolf population. Our dataset spans 25 years and seven generations since reintroduction, encompassing 152 nuclear families and 329 litters. We found more than 87% of the pedigree foundation genomes persisted and report influxes of allelic diversity from two translocated wolves from a divergent source in Montana. As expected for group-living species, mean kinship significantly increased over time but with minimal loss of observed heterozygosity. Strikingly, the reproductive portion of the population carried a significantly lower genome-wide inbreeding coefficients, autozygosity, and more rapid decay for linkage disequilibrium relative to the nonbreeding population. Breeding wolves had significantly longer lifespans and lower inbreeding coefficients than nonbreeding wolves. Our model revealed that the number of litters was negatively significantly associated with heterozygosity (R = -0.11). Our findings highlight genetic contributions to fitness, and the importance of the reproductively active individuals in a population to counteract loss of genetic variation in a wild, free-ranging social carnivore. It is crucial for managers to mitigate factors that significantly reduce effective population size and genetic connectivity, which supports the dispersion of genetic variation that aids in rapid evolutionary responses to environmental challenges.
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Affiliation(s)
- Bridgett M vonHoldt
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, United States
| | - Alexandra L DeCandia
- Department of Biology, Georgetown University, Washington, DC, United States
- Center for Conservation Genomics, Smithsonian’s National Zoo and Conservation Biology Institute, Washington, DC, United States
| | - Kira A Cassidy
- Yellowstone Center for Resources, Yellowstone National Park, WY, United States
| | - Erin E Stahler
- Yellowstone Center for Resources, Yellowstone National Park, WY, United States
| | - Janet S Sinsheimer
- Department of Biostatistics, Fielding School of Public Health, UCLA, Los Angeles, CA, United States
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, United States
- Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA, United States
| | - Douglas W Smith
- Yellowstone Center for Resources, Yellowstone National Park, WY, United States
| | - Daniel R Stahler
- Yellowstone Center for Resources, Yellowstone National Park, WY, United States
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3
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Sagot M, Rose N, Chaverri G. Group vocal composition and decision-making during roost finding in Spix's disk-winged bats. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230187. [PMID: 38768206 DOI: 10.1098/rstb.2023.0187] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 03/18/2024] [Indexed: 05/22/2024] Open
Abstract
Theoretical work suggests that having many informed individuals within social groups can promote efficient resource location. However, it may also give rise to group fragmentation if members fail to reach consensus on their direction of movement. In this study, we investigate whether the number of informed individuals, exemplified by bats emitting calls from different roosts, influences group cohesion in Spix's disk-winged bats (Thyroptera tricolor). Additionally, we explore the role of signal reliability, quantified through signalling rates, in group consensus on where to roost. These bats use contact calls to announce the location of a roost site and recruit conspecifics. The groups they form exhibit high levels of cohesion and consist of both vocal and non-vocal bats, with vocal behaviour being consistent over time. Our findings revealed that an increase in the number of roosts broadcasting calls is strongly associated with the likelihood of groups fragmenting among multiple roosts. Additionally, we found that a majority of group members enter the roost with higher calling rates. This phenomenon can mitigate the risk of group fragmentation, as bats emitting more calls may contribute to greater group consensus on roosting locations, thereby reducing the likelihood of individuals separating and enhancing overall group cohesion. Our results highlight the potential costs of having too many information producers for group coordination, despite their established role in finding critical resources. This article is part of the theme issue 'The power of sound: unravelling how acoustic communication shapes group dynamics'.
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Affiliation(s)
- Maria Sagot
- Department of Biological Sciences, State University of New York at Oswego , Oswego, NY 13126, USA
| | - Nicole Rose
- Department of Biological Sciences, State University of New York at Oswego , Oswego, NY 13126, USA
| | - Gloriana Chaverri
- Sede del Sur, Universidad de Costa Rica , Golfito 60701, Costa Rica
- Smithsonian Tropical Research Institute , Ancón, Panamá 0843-03092, Panama
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4
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Chaverri G, Sagot M, Stynoski JL, Araya-Salas M, Araya-Ajoy Y, Nagy M, Knörnschild M, Chaves-Ramírez S, Rose N, Sánchez-Chavarría M, Jiménez-Torres Y, Ulloa-Sanabria D, Solís-Hernández H, Carter GG. Calling to the collective: contact calling rates within groups of disc-winged bats do not vary by kinship or association. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230195. [PMID: 38768198 DOI: 10.1098/rstb.2023.0195] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 02/23/2024] [Indexed: 05/22/2024] Open
Abstract
Many group-living animals coordinate social behaviours using contact calls, which can be produced for all group members or targeted at specific individuals. In the disc-winged bat, Thyroptera tricolor, group members use 'inquiry' and 'response' calls to coordinate daily movements into new roosts (furled leaves). Rates of both calls show consistent among-individual variation, but causes of within-individual variation remain unknown. Here, we tested whether disc-winged bats produce more contact calls towards group members with higher kinship or association. In 446 experimental trials, we recorded 139 random within-group pairs of one flying bat (producing inquiry calls for roost searching) and one roosting bat (producing response calls for roost advertising). Using generalized linear mixed-effect models (GLMM), we assessed how response and inquiry calling rates varied by sender, receiver, genetic kinship and co-roosting association rate. Calling rates varied consistently across senders but not by receiver. Response calling was influenced by inquiry calling rates, but neither calling rate was higher when the interacting pair had higher kinship or association. Rather than dyadic calling rates indicating within-group relationships, our findings are consistent with the hypothesis that bats produce contact calls to maintain contact with any or all individuals within a group while collectively searching for a new roost site. This article is part of the theme issue 'The power of sound: unravelling how acoustic communication shapes group dynamics'.
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Affiliation(s)
- Gloriana Chaverri
- Sede del Sur, Universidad de Costa Rica , 60701, Costa Rica
- Smithsonian Tropical Research Institute , 0843-03092, Panama
| | - Maria Sagot
- Department of Biological Sciences, State University of New York at Oswego , Oswego, NY 13126, USA
| | - Jennifer L Stynoski
- Instituto Clodomiro Picado, Universidad de Costa Rica , Coronado, San José 11103, Costa Rica
| | - Marcelo Araya-Salas
- Centro de Investigación en Neurociencias, Universidad de Costa Rica , San Pedro, San José 11501-2060, Costa Rica
- Escuela de Biología, Universidad de Costa Rica , , San José 11501-2060, Costa Rica
| | - Yimen Araya-Ajoy
- Department of Biology, Centre for Biodiversity Dynamics (CBD), Norwegian University of Science and Technology (NTNU) , , N-7491, Norway
| | - Martina Nagy
- Museum für Naturkunde, Leibniz-Institute for Evolution and Biodiversity Science , Berlin 10115, Germany
| | - Mirjam Knörnschild
- Museum für Naturkunde, Leibniz-Institute for Evolution and Biodiversity Science , Berlin 10115, Germany
| | - Silvia Chaves-Ramírez
- Programa de Posgrado en Biología, Universidad de Costa Rica , , San José 11501-2060, Costa Rica
| | - Nicole Rose
- Department of Biological Sciences, State University of New York at Oswego , Oswego, NY 13126, USA
| | - Mariela Sánchez-Chavarría
- Programa de Posgrado en Gestión Integrada de Áreas Costeras Tropicales, Universidad de Costa Rica , , San José 11501-2060, Costa Rica
| | | | | | | | - Gerald G Carter
- Smithsonian Tropical Research Institute , 0843-03092, Panama
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University , Columbus, OH 43210, USA
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Mobley KB, Barton HJ, Ellmén M, Ruokolainen A, Guttorm O, Pieski H, Orell P, Erkinaro J, Primmer CR. Sex-specific overdominance at the maturation vgll3 gene for reproductive fitness in wild Atlantic salmon. Mol Ecol 2024; 33:e17435. [PMID: 38877757 DOI: 10.1111/mec.17435] [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: 12/05/2023] [Revised: 04/11/2024] [Accepted: 05/15/2024] [Indexed: 06/16/2024]
Abstract
Linking reproductive fitness with adaptive traits at the genomic level can shed light on the mechanisms that produce and maintain sex-specific selection. Here, we construct a multigenerational pedigree to investigate sex-specific selection on a maturation gene, vgll3, in a wild Atlantic salmon population. The vgll3 locus is responsible for ~40% of the variation in maturation (sea age at first reproduction). Genetic parentage analysis was conducted on 18,265 juveniles (parr) and 685 adults collected at the same spawning ground over eight consecutive years. A high proportion of females (26%) were iteroparous and reproduced two to four times in their lifetime. A smaller proportion of males (9%) spawned at least twice in their lifetime. Sex-specific patterns of reproductive fitness were related to vgll3 genotype. Females showed a pattern of overdominance where vgll3*EL genotypes had three-fold more total offspring than homozygous females. In contrast, males demonstrated that late-maturing vgll3*LL individuals had two-fold more offspring than either vgll3*EE or vgll3*EL males. Taken together, these data suggest that balancing selection in females contributes to the maintenance of variation at this locus via increased fitness of iteroparous vgll3*EL females. This study demonstrates the utility of multigenerational pedigrees for uncovering complex patterns of reproduction, sex-specific selection and the maintenance of genetic variation.
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Affiliation(s)
- Kenyon B Mobley
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Department of Genetics, Norwegian College of Fishery Science, UiT the Arctic University of Norway, Tromsø, Norway
| | - Henry J Barton
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Mikko Ellmén
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Annukka Ruokolainen
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Olavi Guttorm
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Hans Pieski
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Panu Orell
- Natural Resources Institute Finland (Luke), Oulu, Finland
| | | | - Craig R Primmer
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Institute for Biotechnology, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
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6
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Hogg CJ. Translating genomic advances into biodiversity conservation. Nat Rev Genet 2024; 25:362-373. [PMID: 38012268 DOI: 10.1038/s41576-023-00671-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/12/2023] [Indexed: 11/29/2023]
Abstract
A key action of the new Global Biodiversity Framework is the maintenance of genetic diversity in all species to safeguard their adaptive potential. To achieve this goal, a translational mindset, which aims to convert results of basic research into direct practical benefits, needs to be applied to biodiversity conservation. Despite much discussion on the value of genomics to conservation, a disconnect between those generating genomic resources and those applying it to biodiversity management remains. As global efforts to generate reference genomes for non-model species increase, investment into practical biodiversity applications is critically important. Applications such as understanding population and multispecies diversity and longitudinal monitoring need support alongside education for policymakers on integrating the data into evidence-based decisions. Without such investment, the opportunity to revolutionize global biodiversity conservation using genomics will not be fully realized.
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Affiliation(s)
- Carolyn J Hogg
- School of Life & Environmental Sciences, The University of Sydney, Sydney, NSW, Australia.
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7
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Hewett AM, Johnston SE, Morris A, Morris S, Pemberton JM. Genetic architecture of inbreeding depression may explain its persistence in a population of wild red deer. Mol Ecol 2024; 33:e17335. [PMID: 38549143 DOI: 10.1111/mec.17335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 03/01/2024] [Accepted: 03/20/2024] [Indexed: 04/23/2024]
Abstract
Inbreeding depression is of major concern in declining populations, but relatively little is known about its genetic architecture in wild populations, such as the degree to which it is composed of large or small effect loci and their distribution throughout the genome. Here, we combine fitness and genomic data from a wild population of red deer to investigate the genomic distribution of inbreeding effects. Based on the runs of homozygosity (ROH)-based inbreeding coefficient, FROH, we use chromosome-specific inbreeding coefficients (FROHChr) to explore whether the effect of inbreeding varies between chromosomes. Under the assumption that within an individual the probability of being identical-by-descent is equal across all chromosomes, we used a multi-membership model to estimate the deviation of FROHChr from the average inbreeding effect. This novel approach ensures effect sizes are not overestimated whilst maximising the power of our available dataset of >3000 individuals genotyped on >35,000 autosomal SNPs. We find that most chromosomes confer a minor reduction in fitness-related traits, which when these effects are summed, results in the observed inbreeding depression in birth weight, survival and lifetime breeding success. However, no chromosomes had a significant detrimental effect compared to the overall effect of inbreeding, indicating no major effect loci. We conclude that in this population, inbreeding depression is likely the result of multiple mildly or moderately deleterious mutations spread across all chromosomes, which are difficult to detect with statistical confidence. Such mutations will be inefficiently purged, which may explain the persistence of inbreeding depression in this population.
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Affiliation(s)
- Anna M Hewett
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
- Department of Ecology and Evolution, University of Lausanne (UNIL), Lausanne, Switzerland
| | - Susan E Johnston
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Alison Morris
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Sean Morris
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Josephine M Pemberton
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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8
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O'Mahony ÉN, Sremba AL, Keen EM, Robinson N, Dundas A, Steel D, Wray J, Baker CS, Gaggiotti OE. Collecting baleen whale blow samples by drone: A minimally intrusive tool for conservation genetics. Mol Ecol Resour 2024:e13957. [PMID: 38576153 DOI: 10.1111/1755-0998.13957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 03/05/2024] [Accepted: 03/25/2024] [Indexed: 04/06/2024]
Abstract
In coastal British Columbia, Canada, marine megafauna such as humpback whales (Megaptera novaeangliae) and fin whales (Balaenoptera physalus velifera) have been subject to a history of exploitation and near extirpation. While their populations have been in recovery, significant threats are posed to these vulnerable species by proposed natural resource ventures in this region, in addition to the compounding effects of anthropogenic climate change. Genetic tools play a vital role in informing conservation efforts, but the associated collection of tissue biopsy samples can be challenging for the investigators and disruptive to the ongoing behaviour of the targeted whales. Here, we evaluate a minimally intrusive approach based on collecting exhaled breath condensate, or respiratory 'blow' samples, from baleen whales using an unoccupied aerial system (UAS), within Gitga'at First Nation territory for conservation genetics. Minimal behavioural responses to the sampling technique were observed, with no response detected 87% of the time (of 112 UAS deployments). DNA from whale blow (n = 88 samples) was extracted, and DNA profiles consisting of 10 nuclear microsatellite loci, sex identification and mitochondrial (mt) DNA haplotypes were constructed. An average of 7.5 microsatellite loci per individual were successfully genotyped. The success rates for mtDNA and sex assignment were 80% and 89% respectively. Thus, this minimally intrusive sampling method can be used to describe genetic diversity and generate genetic profiles for individual identification. The results of this research demonstrate the potential of UAS-collected whale blow for conservation genetics from a remote location.
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Affiliation(s)
- Éadin N O'Mahony
- Centre for Biological Diversity and Scottish Oceans Institute, School of Biology, University of St Andrews, St Andrews, Fife, UK
- North Coast Cetacean Society, Alert Bay, British Columbia, Canada
| | - Angela L Sremba
- Marine Mammal Institute, Hatfield Marine Science Centre, Oregon State University, Newport, Oregon, USA
- Cooperative Institute for Marine Ecosystem Resources, Oregon State University, Newport, Oregon, USA
| | - Eric M Keen
- North Coast Cetacean Society, Alert Bay, British Columbia, Canada
- Sewanee: The University of the South, Sewanee, Tennessee, USA
| | - Nicole Robinson
- Gitga'at Oceans and Lands Department, Hartley Bay, British Columbia, Canada
| | - Archie Dundas
- Gitga'at Oceans and Lands Department, Hartley Bay, British Columbia, Canada
| | - Debbie Steel
- Marine Mammal Institute, Hatfield Marine Science Centre, Oregon State University, Newport, Oregon, USA
| | - Janie Wray
- North Coast Cetacean Society, Alert Bay, British Columbia, Canada
| | - C Scott Baker
- Marine Mammal Institute, Hatfield Marine Science Centre, Oregon State University, Newport, Oregon, USA
| | - Oscar E Gaggiotti
- Centre for Biological Diversity and Scottish Oceans Institute, School of Biology, University of St Andrews, St Andrews, Fife, UK
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9
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Eriksson CE, Roffler GH, Allen JM, Lewis A, Levi T. The origin, connectivity, and individual specialization of island wolves after deer extirpation. Ecol Evol 2024; 14:e11266. [PMID: 38633525 PMCID: PMC11021858 DOI: 10.1002/ece3.11266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 03/28/2024] [Accepted: 03/30/2024] [Indexed: 04/19/2024] Open
Abstract
Wolves are assumed to be ungulate obligates, however, a recently described pack on Pleasant Island, Alaska USA, is persisting on sea otters and other marine resources without ungulate prey, violating this long-held assumption. We address questions about these wolves regarding their origin and fate, degree of isolation, risk of inbreeding depression, and diet specialization by individual and sex. We applied DNA metabarcoding and genotyping by amplicon sequencing using 957 scats collected from 2016 to 2022, and reduced representation sequencing of tissue samples to establish a detailed understanding of Pleasant Island wolf ecology and compare them with adjacent mainland wolves. Dietary overlap was higher among individual wolves on Pleasant Island (Pianka's index mean 0.95 ± 0.03) compared to mainland wolves (0.70 ± 0.21). The individual diets of island wolves were dominated by sea otter, ranging from 40.6% to 63.2% weighted percent of occurrence (wPOO) (mean 55.5 ± 8.7). In contrast, individual mainland wolves primarily fed on ungulates (42.2 ± 21.3) or voles during a population outbreak (31.2 ± 23.2). We traced the origin of the Pleasant Island pack to a mainland pair that colonized around 2013 and produced several litters. After this breeding pair was killed, their female offspring and an immigrant male became the new breeders in 2019. We detected 20 individuals of which 8 (40%) were trapped and killed while two died of natural causes during the 6-year study. Except for the new breeding male, the pedigree analysis and genotype results showed no additional movement to or from the island, indicating limited dispersal but no evidence of inbreeding. Our findings suggest wolves exhibit more flexible foraging behavior than previously believed, and hunting strategies can substantially differ between individuals within or between packs. Nevertheless, anthropogenic and natural mortality combined with limited connectivity to the mainland may inhibit the continued persistence of Pleasant Island wolves.
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Affiliation(s)
- Charlotte E. Eriksson
- Department of Fisheries, Wildlife, and Conservation SciencesOregon State UniversityCorvallisOregonUSA
| | - Gretchen H. Roffler
- Alaska Department of Fish and GameDivision of Wildlife ConservationDouglasAlaskaUSA
| | - Jennifer M. Allen
- Department of Fisheries, Wildlife, and Conservation SciencesOregon State UniversityCorvallisOregonUSA
| | - Alex Lewis
- Alaska Department of Fish and GameDivision of Wildlife ConservationDouglasAlaskaUSA
| | - Taal Levi
- Department of Fisheries, Wildlife, and Conservation SciencesOregon State UniversityCorvallisOregonUSA
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10
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James C, Pemberton JM, Navarro P, Knott S. Investigating pedigree- and SNP-associated components of heritability in a wild population of Soay sheep. Heredity (Edinb) 2024; 132:202-210. [PMID: 38341521 PMCID: PMC10997785 DOI: 10.1038/s41437-024-00673-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 01/19/2024] [Accepted: 01/24/2024] [Indexed: 02/12/2024] Open
Abstract
Estimates of narrow sense heritability derived from genomic data that contain related individuals may be biased due to the within-family effects such as dominance, epistasis and common environmental factors. However, for many wild populations, removal of related individuals from the data would result in small sample sizes. In 2013, Zaitlen et al. proposed a method to estimate heritability in populations that include close relatives by simultaneously fitting an identity-by-state (IBS) genomic relatedness matrix (GRM) and an identity-by-descent (IBD) GRM. The IBD GRM is identical to the IBS GRM, except relatedness estimates below a specified threshold are set to 0. We applied this method to a sample of 8557 wild Soay sheep from St. Kilda, with genotypic information for 419,281 single nucleotide polymorphisms. We aimed to see how this method would partition heritability into population-level (IBS) and family-associated (IBD) variance for a range of genetic architectures, and so we focused on a mixture of polygenic and monogenic traits. We also implemented a variant of the model in which the IBD GRM was replaced by a GRM constructed from SNPs with low minor allele frequency to examine whether any additive genetic variance is captured by rare alleles. Whilst the inclusion of the IBD GRM did not significantly improve the fit of the model for the monogenic traits, it improved the fit for some of the polygenic traits, suggesting that dominance, epistasis and/or common environment not already captured by the non-genetic random effects fitted in our models may influence these traits.
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Affiliation(s)
- Caelinn James
- Institute of Ecology and Evolution, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK.
- Scotland's Rural College (SRUC), The Roslin Institute Building, Easter Bush, Midlothian, UK.
| | - Josephine M Pemberton
- Institute of Ecology and Evolution, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
| | - Pau Navarro
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, UK
- MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
| | - Sara Knott
- Institute of Ecology and Evolution, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
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11
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Hooper R, Maher K, Moore K, McIvor G, Hosken D, Thornton A. Ultimate drivers of forced extra-pair copulations in birds lacking a penis: jackdaws as a case-study. ROYAL SOCIETY OPEN SCIENCE 2024; 11:231226. [PMID: 38545615 PMCID: PMC10966391 DOI: 10.1098/rsos.231226] [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: 08/18/2023] [Revised: 12/14/2023] [Accepted: 02/01/2024] [Indexed: 04/26/2024]
Abstract
Forced copulation is common, presumably because it can increase male reproductive success. Forced extra-pair copulation (FEPC) occurs in birds, even though most species lack a penis and are widely thought to require female cooperation for fertilization. How FEPC persists, despite a presumed lack of siring success and likely non-negligible costs to the male, is unknown. Using the jackdaw (Corvus monedula) as a case study, we use SNPs to quantify the extra-pair paternity rate through FEPC and evaluate explanations for the persistence of FEPC in species without a penis. We then collate evidence for FEPC across penis-lacking birds. Combining genetic and behavioural analyses, our study suggests that the most likely explanations for the maintenance of FEPC in jackdaws are that it provides a selective advantage to males or it is a relic. Our literature review shows that across birds lacking a penis, FEPC is taxonomically widespread, and yet, little is known about its evolution. A broader implementation of the approach used here, combining both genetic and behavioural data, may shed light on why this widespread sexual behaviour persists. Additional work is necessary to understand whether a penis is needed for paternity through forced copulation and to quantify the costs of FEPC.
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Affiliation(s)
- Rebecca Hooper
- Centre for Research in Animal Behaviour, University of Exeter, Exeter, UK
| | - Kathryn Maher
- NERC Environmental Omics Facility, School of Biosciences, The University of Sheffield, Sheffield, UK
| | - Karen Moore
- Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Guillam McIvor
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, UK
| | - David Hosken
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, UK
| | - Alex Thornton
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, UK
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12
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Schmidt TL, Thia JA, Hoffmann AA. How Can Genomics Help or Hinder Wildlife Conservation? Annu Rev Anim Biosci 2024; 12:45-68. [PMID: 37788416 DOI: 10.1146/annurev-animal-021022-051810] [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] [Indexed: 10/05/2023]
Abstract
Genomic data are becoming increasingly affordable and easy to collect, and new tools for their analysis are appearing rapidly. Conservation biologists are interested in using this information to assist in management and planning but are typically limited financially and by the lack of genomic resources available for non-model taxa. It is therefore important to be aware of the pitfalls as well as the benefits of applying genomic approaches. Here, we highlight recent methods aimed at standardizing population assessments of genetic variation, inbreeding, and forms of genetic load and methods that help identify past and ongoing patterns of genetic interchange between populations, including those subjected to recent disturbance. We emphasize challenges in applying some of these methods and the need for adequate bioinformatic support. We also consider the promises and challenges of applying genomic approaches to understand adaptive changes in natural populations to predict their future adaptive capacity.
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Affiliation(s)
- Thomas L Schmidt
- School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, Victoria, Australia;
| | - Joshua A Thia
- School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, Victoria, Australia;
| | - Ary A Hoffmann
- School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, Victoria, Australia;
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13
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Xia L, Shi M, Li H, Zhang W, Cheng Y, Xia XQ. PMSeeker: A Scheme Based on the Greedy Algorithm and the Exhaustive Algorithm to Screen Low-Redundancy Marker Sets for Large-Scale Parentage Assignment with Full Parental Genotyping. BIOLOGY 2024; 13:100. [PMID: 38392318 PMCID: PMC10886308 DOI: 10.3390/biology13020100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 01/30/2024] [Accepted: 01/31/2024] [Indexed: 02/24/2024]
Abstract
Parentage assignment is a genetic test that utilizes genetic characteristics, such as molecular markers, to identify the parental relationships within populations, which, in commercial fish farming, are almost always large and where full information on potential parents is known. To accurately find the true parents, the genotypes of all loci in the parentage marker set (PMS) are required for each individual being tested. With the same accuracy, a PMS containing a smaller number of markers will undoubtedly save experimental costs. Thus, this study established a scheme to screen low-redundancy PMSs using the exhaustive algorithm and greedy algorithm. When screening PMSs, the greedy algorithm selects markers based on the parental dispersity index (PDI), a uniquely defined metric that outperforms the probability of exclusion (PE). With the conjunctive use of the two algorithms, non-redundant PMSs were found for more than 99.7% of solvable cases in three groups of random sample experiments in this study. Then, a low-redundancy PMS can be composed using two or more of these non-redundant PMSs. This scheme effectively reduces the number of markers in PMSs, thus conserving human and experimental resources and laying the groundwork for the widespread implementation of parentage assignment technology in economic species breeding.
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Affiliation(s)
- Lei Xia
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture and Rural Affairs, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mijuan Shi
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture and Rural Affairs, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Heng Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture and Rural Affairs, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wanting Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture and Rural Affairs, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Yingyin Cheng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture and Rural Affairs, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Xiao-Qin Xia
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture and Rural Affairs, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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14
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Kar F, Nakagawa S, Noble DWA. Heritability and developmental plasticity of growth in an oviparous lizard. Heredity (Edinb) 2024; 132:67-76. [PMID: 37968348 PMCID: PMC10844306 DOI: 10.1038/s41437-023-00660-3] [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: 11/09/2022] [Revised: 10/28/2023] [Accepted: 10/29/2023] [Indexed: 11/17/2023] Open
Abstract
Selective processes act on phenotypic variation although the evolutionary potential of a trait relies on the underlying heritable variation. Developmental plasticity is an important source of phenotypic variation, but it can also promote changes in genetic variation, yet we have a limited understanding of how they are both impacted. Here, we quantified the influence of developmental temperature on growth in delicate skinks (Lampropholis delicata) and partitioned total phenotypic variance using an animal model fitted with a genomic relatedness matrix. We measured mass for 261 individuals (nhot = 125, ncold = 136) over 16 months (nobservations = 3002) and estimated heritability and maternal effects over time. Our results show that lizards reared in cold developmental temperatures had consistently higher mass across development compared to lizards that were reared in hot developmental temperatures. However, developmental temperature did not impact the rate of growth. On average, additive genetic variance, maternal effects and heritability were higher in the hot developmental temperature treatment; however, these differences were not statistically significant. Heritability increased with age, whereas maternal effects decreased upon hatching but increased again at a later age, which could be driven by social competition or intrinsic changes in the expression of variation as an individual's growth. Our work suggests that the evolutionary potential of growth is complex, age-dependent and not overtly affected by extremes in natural nest temperatures.
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Affiliation(s)
- Fonti Kar
- School of Biological Earth and Environmental Sciences, Ecology and Evolution Research Centre, University of New South Wales, Sydney, NSW, Australia
| | - Shinichi Nakagawa
- School of Biological Earth and Environmental Sciences, Ecology and Evolution Research Centre, University of New South Wales, Sydney, NSW, Australia
- Diabetes and Metabolism Division, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, Sydney, NSW, 2010, Australia
| | - Daniel W A Noble
- School of Biological Earth and Environmental Sciences, Ecology and Evolution Research Centre, University of New South Wales, Sydney, NSW, Australia.
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia.
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15
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Stroupe S, Derr JN. Development and evaluation of a novel single nucleotide polymorphism panel for North American bison. Evol Appl 2024; 17:e13658. [PMID: 38390379 PMCID: PMC10883761 DOI: 10.1111/eva.13658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 11/17/2023] [Accepted: 01/09/2024] [Indexed: 02/24/2024] Open
Abstract
Genome-wide single nucleotide polymorphism (SNP) genotyping platforms have become increasingly popular in characterizing livestock and wildlife populations, replacing traditional methods such as microsatellite fragment analysis. Herein, we report the development and evaluation of a novel bison SNP panel for population management and conservation. Initially, 2474 autosomal SNPs were selected from existing bison whole-genome sequences and variable sites among bison on the GGSP bovine 50K Chip, based on minor allele frequency, data completeness, and chromosome location. Additionally, 20 mitochondrial SNPs were chosen to identify known mitochondrial haplotypes in bison according to previous research. The SNPs were further evaluated using genotyping-by-sequencing with 190 bison, representing the historical lineages that survived the major population crash of the late 1800s. Variants with high potential for genotyping error were filtered out, and the remaining SNPs were placed on a custom Illumina™ array. The final panel consisting of 798 autosomal and 13 mitochondrial SNPs was used to establish baseline genetic parameters, compare populations, and assign mitochondrial haplotypes in 995 bison across ten populations. These SNPs were also found to be highly informative for individual animal identification and parentage assignment. This SNP panel provides a powerful new method to establish a baseline for estimating genetic health of bison populations and a new tool for bison managers to make informed management decisions based on genetic information specific to their populations.
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Affiliation(s)
- Sam Stroupe
- Department of Veterinary Pathobiology, College of Veterinary Medicine Texas A&M University System College Station Texas USA
| | - James N Derr
- Department of Veterinary Pathobiology, College of Veterinary Medicine Texas A&M University System College Station Texas USA
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16
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Jablonszky M, Canal D, Hegyi G, Herényi M, Laczi M, Markó G, Nagy G, Rosivall B, Szöllősi E, Török J, Garamszegi LZ. The estimation of additive genetic variance of body size in a wild passerine is sensitive to the method used to estimate relatedness among the individuals. Ecol Evol 2024; 14:e10981. [PMID: 38352200 PMCID: PMC10862163 DOI: 10.1002/ece3.10981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 01/17/2024] [Accepted: 01/23/2024] [Indexed: 02/16/2024] Open
Abstract
Assessing additive genetic variance is a crucial step in predicting the evolutionary response of a target trait. However, the estimated genetic variance may be sensitive to the methodology used, e.g., the way relatedness is assessed among the individuals, especially in wild populations where social pedigrees can be inaccurate. To investigate this possibility, we investigated the additive genetic variance in tarsus length, a major proxy of skeletal body size in birds. The model species was the collared flycatcher (Ficedula albicollis), a socially monogamous but genetically polygamous migratory passerine. We used two relatedness matrices to estimate the genetic variance: (1) based solely on social links and (2) a genetic similarity matrix based on a large array of single-nucleotide polymorphisms (SNPs). Depending on the relatedness matrix considered, we found moderate to high additive genetic variance and heritability estimates for tarsus length. In particular, the heritability estimates were higher when obtained with the genetic similarity matrix instead of the social pedigree. Our results confirm the potential for this crucial trait to respond to selection and highlight methodological concerns when calculating additive genetic variance and heritability in phenotypic traits. We conclude that using a social pedigree instead of a genetic similarity matrix to estimate relatedness among individuals in a genetically polygamous wild population may significantly deflate the estimates of additive genetic variation.
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Affiliation(s)
- Mónika Jablonszky
- Evolutionary Ecology Research GroupInstitute of Ecology and Botany, HUN_REN Centre for Ecological ResearchVácrátotHungary
- Behavioural Ecology Group, Department of Systematic Zoology and EcologyELTE Eötvös Loránd UniversityBudapestHungary
| | - David Canal
- Department of Evolutionary EcologyNational Museum of Natural Sciences (MNCN‐CSIC)MadridSpain
| | - Gergely Hegyi
- Behavioural Ecology Group, Department of Systematic Zoology and EcologyELTE Eötvös Loránd UniversityBudapestHungary
| | - Márton Herényi
- Behavioural Ecology Group, Department of Systematic Zoology and EcologyELTE Eötvös Loránd UniversityBudapestHungary
- Department of Zoology and EcologyHungarian University of Agriculture and Life SciencesGodolloHungary
| | - Miklós Laczi
- Behavioural Ecology Group, Department of Systematic Zoology and EcologyELTE Eötvös Loránd UniversityBudapestHungary
- HUN‐REN‐ELTE‐MTM Integrative Ecology Research GroupBudapestHungary
| | - Gábor Markó
- Department of Plant Pathology, Institute of Plant ProtectionHungarian University of Agriculture and Life SciencesBudapestHungary
| | - Gergely Nagy
- Evolutionary Ecology Research GroupInstitute of Ecology and Botany, HUN_REN Centre for Ecological ResearchVácrátotHungary
- Behavioural Ecology Group, Department of Systematic Zoology and EcologyELTE Eötvös Loránd UniversityBudapestHungary
| | - Balázs Rosivall
- Behavioural Ecology Group, Department of Systematic Zoology and EcologyELTE Eötvös Loránd UniversityBudapestHungary
| | - Eszter Szöllősi
- Behavioural Ecology Group, Department of Systematic Zoology and EcologyELTE Eötvös Loránd UniversityBudapestHungary
| | - János Török
- Behavioural Ecology Group, Department of Systematic Zoology and EcologyELTE Eötvös Loránd UniversityBudapestHungary
| | - László Zsolt Garamszegi
- Evolutionary Ecology Research GroupInstitute of Ecology and Botany, HUN_REN Centre for Ecological ResearchVácrátotHungary
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17
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Hayah I, Talbi C, Chafai N, Houaga I, Botti S, Badaoui B. Genetic diversity and breed-informative SNPs identification in domestic pig populations using coding SNPs. Front Genet 2023; 14:1229741. [PMID: 38034497 PMCID: PMC10687199 DOI: 10.3389/fgene.2023.1229741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 10/31/2023] [Indexed: 12/02/2023] Open
Abstract
Background: The use of breed-informative genetic markers, specifically coding Single Nucleotide Polymorphisms (SNPs), is crucial for breed traceability, authentication of meat and dairy products, and the preservation and improvement of pig breeds. By identifying breed informative markers, we aimed to gain insights into the genetic mechanisms that influence production traits, enabling informed decisions in animal management and promoting sustainable pig production to meet the growing demand for animal products. Methods: Our dataset consists of 300 coding SNPs genotyped from three Italian commercial pig populations: Landrace, Yorkshire, and Duroc. Firstly, we analyzed the genetic diversity among the populations. Then, we applied a discriminant analysis of principal components to identify the most informative SNPs for discriminating between these populations. Lastly, we conducted a functional enrichment analysis to identify the most enriched pathways related to the genetic variation observed in the pig populations. Results: The alpha diversity indexes revealed a high genetic diversity within the three breeds. The higher proportion of observed heterozygosity than expected revealed an excess of heterozygotes in the populations that was supported by negative values of the fixation index (FIS) and deviations from the Hardy-Weinberg equilibrium. The Euclidean distance, the pairwise FST, and the pairwise Nei's GST genetic distances revealed that Yorkshire and Landrace breeds are genetically the closest, with distance values of 2.242, 0.029, and 0.033, respectively. Conversely, Landrace and Duroc breeds showed the highest genetic divergence, with distance values of 2.815, 0.048, and 0.052, respectively. We identified 28 significant SNPs that are related to phenotypic traits and these SNPs were able to differentiate between the pig breeds with high accuracy. The Functional Enrichment Analysis of the informative SNPs highlighted biological functions related to DNA packaging, chromatin integrity, and the preparation of DNA into higher-order structures. Conclusion: Our study sheds light on the genetic underpinnings of phenotypic variation among three Italian pig breeds, offering potential insights into the mechanisms driving breed differentiation. By prioritizing breed-specific coding SNPs, our approach enables a more focused analysis of specific genomic regions relevant to the research question compared to analyzing the entire genome.
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Affiliation(s)
- Ichrak Hayah
- Laboratory of Biodiversity, Ecology, and Genome, Department of Biology, Faculty of Sciences, Mohammed V University in Rabat, Rabat, Morocco
| | - Chouhra Talbi
- Plant and Microbial Biotechnologies, Biodiversity, and Environment (BioBio), Mohammed V University in Rabat, Rabat, Morocco
| | - Narjice Chafai
- Laboratory of Biodiversity, Ecology, and Genome, Department of Biology, Faculty of Sciences, Mohammed V University in Rabat, Rabat, Morocco
| | - Isidore Houaga
- Centre for Tropical Livestock Genetics and Health, The Roslin Institute, Royal (Dick) School of Veterinary Medicine, The University of Edinburgh, Edinburgh, United Kingdom
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | | | - Bouabid Badaoui
- Laboratory of Biodiversity, Ecology, and Genome, Department of Biology, Faculty of Sciences, Mohammed V University in Rabat, Rabat, Morocco
- African Sustainable Agriculture Research Institute (ASARI), Mohammed VI Polytechnic University (UM6P), Laâyoune, Morocco
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18
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Delmé C, Jackson N, Class B, Strickland K, Potvin DA, Frère CH. Adaptive significance of affiliative behaviour differs between sexes in a wild reptile population. Proc Biol Sci 2023; 290:20230805. [PMID: 37339740 PMCID: PMC10281801 DOI: 10.1098/rspb.2023.0805] [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: 04/11/2023] [Accepted: 05/22/2023] [Indexed: 06/22/2023] Open
Abstract
In recent years, we have begun to appreciate that social behaviours might exhibit repeatable among-individual variation. Such behavioural traits may even covary and have critical evolutionary implications. Importantly, some social behaviours such as aggressiveness have been shown to provide fitness benefits, including higher reproductive success and survival. However, fitness consequences of affiliative behaviours, especially between or among sexes, can be more challenging to establish. Using a longitudinal behavioural dataset (2014-2021) collected on eastern water dragons (Intellagama lesueurii), we investigated whether various aspects of affiliative behaviour (i) were repeatable across years, (ii) covaried with each other at the among-individual level, and (iii) influenced individuals' fitness. In particular, we considered affiliative behaviours towards opposite-sex and same-sex conspecifics separately. We found that social traits were repeatable and covaried with each other similarly for both sexes. More notably, we found that male reproductive success was positively correlated with the number of female associates and the proportion of time spent with females, while females' reproductive success was not correlated with any of the measured social behaviour metrics. Overall, these findings suggest that selection may be acting differently on social behaviour of male and female eastern water dragons.
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Affiliation(s)
- C. Delmé
- School of Science, Technology and Engineering, University of the Sunshine Coast, Queensland, Australia
| | - N. Jackson
- School of Biological Sciences, University of Queensland, Brisbane, Queensland, Australia
| | - B. Class
- School of Science, Technology and Engineering, University of the Sunshine Coast, Queensland, Australia
- Ludwig-Maximilians-Universität München, Munich, Germany
| | - K. Strickland
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - D. A. Potvin
- School of Science, Technology and Engineering, University of the Sunshine Coast, Queensland, Australia
| | - C. H. Frère
- School of Biological Sciences, University of Queensland, Brisbane, Queensland, Australia
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19
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Johnsson M. Genomics in animal breeding from the perspectives of matrices and molecules. Hereditas 2023; 160:20. [PMID: 37149663 PMCID: PMC10163706 DOI: 10.1186/s41065-023-00285-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 05/03/2023] [Indexed: 05/08/2023] Open
Abstract
BACKGROUND This paper describes genomics from two perspectives that are in use in animal breeding and genetics: a statistical perspective concentrating on models for estimating breeding values, and a sequence perspective concentrating on the function of DNA molecules. MAIN BODY This paper reviews the development of genomics in animal breeding and speculates on its future from these two perspectives. From the statistical perspective, genomic data are large sets of markers of ancestry; animal breeding makes use of them while remaining agnostic about their function. From the sequence perspective, genomic data are a source of causative variants; what animal breeding needs is to identify and make use of them. CONCLUSION The statistical perspective, in the form of genomic selection, is the more applicable in contemporary breeding. Animal genomics researchers using from the sequence perspective are still working towards this the isolation of causative variants, equipped with new technologies but continuing a decades-long line of research.
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Affiliation(s)
- Martin Johnsson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, Uppsala, 75007, Sweden.
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20
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Chapman EG, Pilkington JG, Pemberton JM. Correlates of early reproduction and apparent fitness consequences in male Soay sheep. Ecol Evol 2023; 13:e10058. [PMID: 37168987 PMCID: PMC10164647 DOI: 10.1002/ece3.10058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 04/05/2023] [Accepted: 04/17/2023] [Indexed: 05/13/2023] Open
Abstract
Life history trade-offs are ubiquitous across species and place constraints on the timing of life history events, including the optimal age at first reproduction. However, studies on lifetime breeding success of male mammals are rare due to sex-biased dispersal and the requirement for genetic paternity inferences. We studied the correlates and apparent fitness consequences of early life reproduction among males in a free-living population of Soay sheep (Ovis aries) on St Kilda, Scotland. We investigated the factors associated with early breeding success and the apparent consequences of early success for survival and future reproduction. We used genetic paternity inferences, population data, and individual morphology measurements collected over 30 years. We found that individuals born in years with low-density population size had the highest early life breeding success and singletons were more likely to be successful than twins. Individuals that bred successfully at 7 months were more likely to survive their first winter. For individuals that survived their first winter, early breeding success was not associated with later breeding success. As individual heterogeneity affects breeding success, we believe that variation in individual quality masks the costs of early reproduction in this population. Our findings provide no evidence for selection for delayed age at reproduction in male Soay sheep.
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Affiliation(s)
- Elisabeth G. Chapman
- School of Biological Sciences, Institute of Ecology and EvolutionUniversity of EdinburghEdinburghUK
| | - Jill G. Pilkington
- School of Biological Sciences, Institute of Ecology and EvolutionUniversity of EdinburghEdinburghUK
| | - Josephine M. Pemberton
- School of Biological Sciences, Institute of Ecology and EvolutionUniversity of EdinburghEdinburghUK
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21
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Stojanovic D, McLennan E, Olah G, Cobden M, Heinsohn R, Manning AD, Alves F, Hogg C, Rayner L. Reproductive skew in a Vulnerable bird favors breeders that monopolize nest cavities. Anim Conserv 2023. [DOI: 10.1111/acv.12855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- D. Stojanovic
- Fenner School of Environment and Society Australian National University Canberra Australia
| | - E. McLennan
- School of Life & Environmental Sciences The University of Sydney Sydney New South Wales Australia
| | - G. Olah
- Fenner School of Environment and Society Australian National University Canberra Australia
| | - M. Cobden
- Fenner School of Environment and Society Australian National University Canberra Australia
| | - R. Heinsohn
- Fenner School of Environment and Society Australian National University Canberra Australia
| | - A. D. Manning
- Fenner School of Environment and Society Australian National University Canberra Australia
| | - F. Alves
- Fenner School of Environment and Society Australian National University Canberra Australia
| | - C. Hogg
- School of Life & Environmental Sciences The University of Sydney Sydney New South Wales Australia
| | - L. Rayner
- ACT Parks and Conservation Service, Australian Capital Territory Government Canberra Australia
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22
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Wanelik KM, Begon M, Bradley JE, Friberg IM, Jackson JA, Taylor CH, Paterson S. Effects of an IgE receptor polymorphism acting on immunity, susceptibility to infection, and reproduction in a wild rodent. eLife 2023; 12:77666. [PMID: 36645701 PMCID: PMC9842384 DOI: 10.7554/elife.77666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 12/22/2022] [Indexed: 01/17/2023] Open
Abstract
The genotype of an individual is an important predictor of their immune function, and subsequently, their ability to control or avoid infection and ultimately contribute offspring to the next generation. However, the same genotype, subjected to different intrinsic and/or extrinsic environments, can also result in different phenotypic outcomes, which can be missed in controlled laboratory studies. Natural wildlife populations, which capture both genotypic and environmental variability, provide an opportunity to more fully understand the phenotypic expression of genetic variation. We identified a synonymous polymorphism in the high-affinity Immunoglobulin E (IgE) receptor (GC and non-GC haplotypes) that has sex-dependent effects on immune gene expression, susceptibility to infection, and reproductive success of individuals in a natural population of field voles (Microtus agrestis). We found that the effect of the GC haplotype on the expression of immune genes differed between sexes. Regardless of sex, both pro-inflammatory and anti-inflammatory genes were more highly relatively expressed in individuals with the GC haplotype than individuals without the haplotype. However, males with the GC haplotype showed a stronger signal for pro-inflammatory genes, while females showed a stronger signal for anti-inflammatory genes. Furthermore, we found an effect of the GC haplotype on the probability of infection with a common microparasite, Babesia microti, in females - with females carrying the GC haplotype being more likely to be infected. Finally, we found an effect of the GC haplotype on reproductive success in males - with males carrying the GC haplotype having a lower reproductive success. This is a rare example of a polymorphism whose consequences we are able to follow across immunity, infection, and reproduction for both males and females in a natural population.
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Affiliation(s)
- Klara M Wanelik
- Institute of Infection, Veterinary and Ecological Sciences, University of LiverpoolLiverpoolUnited Kingdom
| | - Mike Begon
- Institute of Infection, Veterinary and Ecological Sciences, University of LiverpoolLiverpoolUnited Kingdom
| | - Janette E Bradley
- School of Life Sciences, University of NottinghamNottinghamUnited Kingdom
| | - Ida M Friberg
- School of Environment and Life Sciences, University of SalfordSalfordUnited Kingdom
| | - Joseph A Jackson
- School of Environment and Life Sciences, University of SalfordSalfordUnited Kingdom
| | | | - Steve Paterson
- Institute of Infection, Veterinary and Ecological Sciences, University of LiverpoolLiverpoolUnited Kingdom
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23
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Pedigree reconstruction and population structure using SNP markers in Gir cattle. J Appl Genet 2023; 64:329-340. [PMID: 36645582 DOI: 10.1007/s13353-023-00747-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 11/24/2022] [Accepted: 01/03/2023] [Indexed: 01/17/2023]
Abstract
Our objective was to establish a SNPs panel for pedigree reconstruction using microarrays of different densities and evaluate the genomic relationship coefficient of the inferred pedigree, in addition to analyzing the population structure based on genomic analyses in Gir cattle. For parentage analysis and genomic relationship, 16,205 genotyped Gir animals (14,458 females and 1747 males) and 1810 common markers to the four SNP microarrays were used. For population structure analyses, including linkage disequilibrium, effective population size, and runs of homozygosity (ROH), genotypes from 21,656 animals were imputed. Likelihood ratio (LR) approach was used to reconstruct the pedigree, deepening the pedigree and showing it is well established in terms of recent information. Coefficients for each relationship category of the inferred pedigree were adequate. Linkage disequilibrium showed rapid decay. We detected a decrease in the effective population size over the last 50 generations, with the average generation interval around 9.08 years. Higher ROH-based inbreeding coefficient in a class of short ROH segments, with moderate to high values, was also detected, suggesting bottlenecks in the Gir genome. Breeding strategies to minimize inbreeding and avoid massive use of few proven sires with high genetic value are suggested to maintain genetic variability in future generations. In addition, we recommend reducing the generation interval to maximize genetic progress and increase effective population size.
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24
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Gervais L, Mouginot P, Gibert A, Salles O, Latutrie M, Piquet J, Archambeau J, Pujol B. Wild snapdragon plant pedigree sheds light on limited connectivity enhanced by higher migrant reproductive success in a fragmented landscape. OPEN RESEARCH EUROPE 2023; 1:145. [PMID: 37645181 PMCID: PMC10446054 DOI: 10.12688/openreseurope.14281.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 12/16/2022] [Indexed: 08/31/2023]
Abstract
Background: In contrast with historical knowledge, a recent view posits that a non-negligible proportion of populations thrive in a fragmented landscape. One underlying mechanism is the maintenance of functional connectivity, i.e., the net flow of individuals or their genes moving among suitable habitat patches. Alternatively, functional connectivity might be typically limited but enhanced by a higher reproductive success of migrants. Methods: We tested for this hypothesis in wild snapdragon plants inhabiting six patches separated by seawater in a fragmented Mediterranean scrubland landscape. We reconstructed their pedigree by using a parentage assignment method based on microsatellite genetic markers. We then estimated functional connectivity and the reproductive success of plants resulting from between-patch dispersal events. Results: We found that wild snapdragon plants thrived in this fragmented landscape, although functional connectivity between habitat patches was low (i.e. 2.9%). The progeny resulting from between-patch dispersal events had a higher reproductive success than residents. Conclusion: Our findings imply that low functional connectivity in a fragmented landscapes may have been enhanced by higher reproductive success after migration. This original mechanisms might be partly compensating the negative impact of fragmentation.
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Affiliation(s)
- Laura Gervais
- CRIOBE PSL Université Paris : EHPE-UPVD-CNRS, Université de Perpignan, USR 3278, CNRS, Perpignan, France
| | - Pierick Mouginot
- CRIOBE PSL Université Paris : EHPE-UPVD-CNRS, Université de Perpignan, USR 3278, CNRS, Perpignan, France
| | - Anais Gibert
- CRIOBE PSL Université Paris : EHPE-UPVD-CNRS, Université de Perpignan, USR 3278, CNRS, Perpignan, France
| | - Oceane Salles
- CRIOBE PSL Université Paris : EHPE-UPVD-CNRS, Université de Perpignan, USR 3278, CNRS, Perpignan, France
| | - Mathieu Latutrie
- CRIOBE PSL Université Paris : EHPE-UPVD-CNRS, Université de Perpignan, USR 3278, CNRS, Perpignan, France
| | - Jesaelle Piquet
- CRIOBE PSL Université Paris : EHPE-UPVD-CNRS, Université de Perpignan, USR 3278, CNRS, Perpignan, France
| | | | - Benoit Pujol
- CRIOBE PSL Université Paris : EHPE-UPVD-CNRS, Université de Perpignan, USR 3278, CNRS, Perpignan, France
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25
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Small effects of family size on sociality despite strong kin preferences in female bottlenose dolphins. Anim Behav 2023. [DOI: 10.1016/j.anbehav.2022.10.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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26
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Abstract
We organized this special issue to highlight new work and review recent advances at the cutting edge of 'wild quantitative genomics'. In this editorial, we will present some history of wild quantitative genetic and genomic studies, before discussing the main themes in the papers published in this special issue and highlighting the future outlook of this dynamic field.
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Affiliation(s)
- Susan E Johnston
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, Edinburgh EH9 3FL, UK
| | - Nancy Chen
- Department of Biology, University of Rochester, Rochester, 14627, NY, USA
| | - Emily B Josephs
- Department of Plant Biology and Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, 48824, MI, USA
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27
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DeLeo DM, Morrison CL, Sei M, Salamone V, Demopoulos AWJ, Quattrini AM. Genetic diversity and connectivity of chemosynthetic cold seep mussels from the U.S. Atlantic margin. BMC Ecol Evol 2022; 22:76. [PMID: 35715723 PMCID: PMC9204967 DOI: 10.1186/s12862-022-02027-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 05/18/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Deep-sea mussels in the subfamily Bathymodiolinae have unique adaptations to colonize hydrothermal-vent and cold-seep environments throughout the world ocean. These invertebrates function as important ecosystem engineers, creating heterogeneous habitat and promoting biodiversity in the deep sea. Despite their ecological significance, efforts to assess the diversity and connectivity of this group are extremely limited. Here, we present the first genomic-scale diversity assessments of the recently discovered bathymodioline cold-seep communities along the U.S. Atlantic margin, dominated by Gigantidas childressi and Bathymodiolus heckerae.
Results
A Restriction-site Associated DNA Sequencing (RADSeq) approach was used on 177 bathymodiolines to examine genetic diversity and population structure within and between seep sites. Assessments of genetic differentiation using single-nucleotide polymorphism (SNP) data revealed high gene flow among sites, with the shallower and more northern sites serving as source populations for deeper occurring G. childressi. No evidence was found for genetic diversification across depth in G. childressi, likely due to their high dispersal capabilities. Kinship analyses indicated a high degree of relatedness among individuals, and at least 10–20% of local recruits within a particular site. We also discovered candidate adaptive loci in G. childressi and B. heckerae that suggest differences in developmental processes and depth-related and metabolic adaptations to chemosynthetic environments.
Conclusions
These results highlight putative source communities for an important ecosystem engineer in the deep sea that may be considered in future conservation efforts. Our results also provide clues into species-specific adaptations that enable survival and potential speciation within chemosynthetic ecosystems.
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Pemberton JM, Kruuk LE, Clutton-Brock T. The Unusual Value of Long-Term Studies of Individuals: The Example of the Isle of Rum Red Deer Project. ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS 2022. [DOI: 10.1146/annurev-ecolsys-012722-024041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Long-term studies of individuals enable incisive investigations of questions across ecology and evolution. Here, we illustrate this claim by reference to our long-term study of red deer on the Isle of Rum, Scotland. This project has established many of the characteristics of social organization, selection, and population ecology typical of large, polygynous, seasonally breeding mammals, with wider implications for our understanding of sexual selection and the evolution of sex differences, as well as for their population dynamics and population management. As molecular genetic techniques have developed, the project has pivoted to investigate evolutionary genetic questions, also breaking new ground in this field. With ongoing advances in genomics and statistical approaches and the development of increasingly sophisticated ways to assay new phenotypic traits, the questions that long-term studies such as the red deer study can answer become both broader and ever more sophisticated. They also offer powerful means of understanding the effects of ongoing climate change on wild populations.
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Affiliation(s)
- Josephine M. Pemberton
- Institute of Ecology and Evolution, School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom
| | - Loeske E.B. Kruuk
- Institute of Ecology and Evolution, School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom
| | - Tim Clutton-Brock
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
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29
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Gauzere J, Pemberton JM, Kruuk LEB, Morris A, Morris S, Walling CA. Maternal effects do not resolve the paradox of stasis in birth weight in a wild red deer populaton. Evolution 2022; 76:2605-2617. [PMID: 36111977 PMCID: PMC9828841 DOI: 10.1111/evo.14622] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 08/14/2022] [Indexed: 01/22/2023]
Abstract
In natural populations, quantitative traits seldom show short-term evolution at the rate predicted by evolutionary models. Resolving this "paradox of stasis" is a key goal in evolutionary biology, as it directly challenges our capacity to predict evolutionary change. One particularly promising hypothesis to explain the lack of evolutionary responses in a key offspring trait, body weight, is that positive selection on juveniles is counterbalanced by selection against maternal investment in offspring growth, given that reproduction is costly for the mothers. Here, we used data from one of the longest individual-based studies of a wild mammal population to test this hypothesis. We first showed that despite positive directional selection on birth weight, and heritable variation for this trait, no genetic change has been observed for birth weight over the past 47 years in the study population. Contrarily to our expectation, we found no evidence of selection against maternal investment in birth weight-if anything, selection favors mothers that produce large calves. Accordingly, we show that genetic change in birth weight over the study period is actually lower than that predicted from models including selection on maternal performance; ultimately our analysis here only deepens rather than resolves the paradox of stasis.
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Affiliation(s)
- Julie Gauzere
- Institute of Evolutionary Biology, School of Biological SciencesUniversity of EdinburghEdinburghEH9 3FLUK
| | - Josephine M. Pemberton
- Institute of Evolutionary Biology, School of Biological SciencesUniversity of EdinburghEdinburghEH9 3FLUK
| | - Loeske E. B. Kruuk
- Institute of Evolutionary Biology, School of Biological SciencesUniversity of EdinburghEdinburghEH9 3FLUK,Research School of BiologyThe Australian National UniversityCanberraACT 0200Australia
| | - Alison Morris
- Institute of Evolutionary Biology, School of Biological SciencesUniversity of EdinburghEdinburghEH9 3FLUK
| | - Sean Morris
- Institute of Evolutionary Biology, School of Biological SciencesUniversity of EdinburghEdinburghEH9 3FLUK
| | - Craig A. Walling
- Institute of Evolutionary Biology, School of Biological SciencesUniversity of EdinburghEdinburghEH9 3FLUK
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30
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Carrier A, Prunier J, Poisson W, Trottier-Lavoie M, Gilbert I, Cavedon M, Pokharel K, Kantanen J, Musiani M, Côté SD, Albert V, Taillon J, Bourret V, Droit A, Robert C. Design and validation of a 63K genome-wide SNP-genotyping platform for caribou/reindeer (Rangifer tarandus). BMC Genomics 2022; 23:687. [PMID: 36199020 PMCID: PMC9533608 DOI: 10.1186/s12864-022-08899-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 09/15/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Development of large single nucleotide polymorphism (SNP) arrays can make genomic data promptly available for conservation problematic. Medium and high-density panels can be designed with sufficient coverage to offer a genome-wide perspective and the generated genotypes can be used to assess different genetic metrics related to population structure, relatedness, or inbreeding. SNP genotyping could also permit sexing samples with unknown associated metadata as it is often the case when using non-invasive sampling methods favored for endangered species. Genome sequencing of wild species provides the necessary information to design such SNP arrays. We report here the development of a SNP-array for endangered Rangifer tarandus using a multi-platform sequencing approach from animals found in diverse populations representing the entire circumpolar distribution of the species. RESULTS From a very large comprehensive catalog of SNPs detected over the entire sample set (N = 894), a total of 63,336 SNPs were selected. SNP selection accounted for SNPs evenly distributed across the entire genome (~ every 50Kb) with known minor alleles across populations world-wide. In addition, a subset of SNPs was selected to represent rare and local alleles found in Eastern Canada which could be used for ecotype and population assignments - information urgently needed for conservation planning. In addition, heterozygosity from SNPs located in the X-chromosome and genotyping call-rate of SNPs located into the SRY gene of the Y-chromosome yielded an accurate and robust sexing assessment. All SNPs were validated using a high-throughput SNP-genotyping chip. CONCLUSION This design is now integrated into the first genome-wide commercially available genotyping platform for Rangifer tarandus. This platform would pave the way to future genomic investigation of populations for this endangered species, including estimation of genetic diversity parameters, population assignments, as well as animal sexing from genetic SNP data for non-invasive samples.
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Affiliation(s)
- Alexandra Carrier
- Département de sciences animales, Faculté de l'agriculture et d'alimentation, Université Laval, Quebec City, Québec, Canada.,Centre de recherche en reproduction, développement et santé intergénérationnelle (CRDSI), Quebec City, Québec, Canada.,Réseau Québécois en reproduction (RQR), Saint-Hyacinthe, Québec, Canada
| | - Julien Prunier
- Département de médecine moléculaire, Faculté de médecine, Université Laval, Quebec City, Québec, Canada
| | - William Poisson
- Département de sciences animales, Faculté de l'agriculture et d'alimentation, Université Laval, Quebec City, Québec, Canada.,Centre de recherche en reproduction, développement et santé intergénérationnelle (CRDSI), Quebec City, Québec, Canada.,Réseau Québécois en reproduction (RQR), Saint-Hyacinthe, Québec, Canada
| | - Mallorie Trottier-Lavoie
- Département de sciences animales, Faculté de l'agriculture et d'alimentation, Université Laval, Quebec City, Québec, Canada.,Centre de recherche en reproduction, développement et santé intergénérationnelle (CRDSI), Quebec City, Québec, Canada.,Réseau Québécois en reproduction (RQR), Saint-Hyacinthe, Québec, Canada
| | - Isabelle Gilbert
- Département de sciences animales, Faculté de l'agriculture et d'alimentation, Université Laval, Quebec City, Québec, Canada.,Centre de recherche en reproduction, développement et santé intergénérationnelle (CRDSI), Quebec City, Québec, Canada.,Réseau Québécois en reproduction (RQR), Saint-Hyacinthe, Québec, Canada
| | - Maria Cavedon
- Department of biological sciences, Faculty of Science, University of Calgary, Calgary, Canada
| | | | - Juha Kantanen
- Natural Resources Institute Finland, Jokioinen, Finland
| | - Marco Musiani
- Department of Biological, Geological and Environmental Sciences (BiGeA), University of Bologna, Bologna, Italy
| | - Steeve D Côté
- Département de biologie - Faculté de sciences et génie, Caribou Ungava, Université Laval, Quebec City, Québec, Canada
| | - Vicky Albert
- Ministère des Forêts, de la Faune et des Parcs du Québec (MFFP), Quebec City, Québec, Canada
| | - Joëlle Taillon
- Ministère des Forêts, de la Faune et des Parcs du Québec (MFFP), Quebec City, Québec, Canada
| | - Vincent Bourret
- Ministère des Forêts, de la Faune et des Parcs du Québec (MFFP), Quebec City, Québec, Canada
| | - Arnaud Droit
- Département de médecine moléculaire, Faculté de médecine, Université Laval, Quebec City, Québec, Canada
| | - Claude Robert
- Département de sciences animales, Faculté de l'agriculture et d'alimentation, Université Laval, Quebec City, Québec, Canada. .,Centre de recherche en reproduction, développement et santé intergénérationnelle (CRDSI), Quebec City, Québec, Canada. .,Réseau Québécois en reproduction (RQR), Saint-Hyacinthe, Québec, Canada.
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31
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Reproductive timing as an explanation for skewed parentage assignment ratio in a bisexually philopatric population. Behav Ecol Sociobiol 2022. [DOI: 10.1007/s00265-022-03233-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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32
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Vianney TJ, Berger DJ, Doyle SR, Sankaranarayanan G, Serubanja J, Nakawungu PK, Besigye F, Sanya RE, Holroyd N, Allan F, Webb EL, Elliott AM, Berriman M, Cotton JA. Genome-wide analysis of Schistosoma mansoni reveals limited population structure and possible praziquantel drug selection pressure within Ugandan hot-spot communities. PLoS Negl Trop Dis 2022; 16:e0010188. [PMID: 35981002 PMCID: PMC9426917 DOI: 10.1371/journal.pntd.0010188] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 08/30/2022] [Accepted: 07/05/2022] [Indexed: 12/23/2022] Open
Abstract
Populations within schistosomiasis control areas, especially those in Africa, are recommended to receive regular mass drug administration (MDA) with praziquantel (PZQ) as the main strategy for controlling the disease. The impact of PZQ treatment on schistosome genetics remains poorly understood, and is limited by a lack of high-resolution genetic data on the population structure of parasites within these control areas. We generated whole-genome sequence data from 174 individual miracidia collected from both children and adults from fishing communities on islands in Lake Victoria in Uganda that had received either annual or quarterly MDA with PZQ over four years, including samples collected immediately before and four weeks after treatment. Genome variation within and between samples was characterised and we investigated genomic signatures of natural selection acting on these populations that could be due to PZQ treatment. The parasite population on these islands was more diverse than found in nearby villages on the lake shore. We saw little or no genetic differentiation between villages, or between the groups of villages with different treatment intensity, but slightly higher genetic diversity within the pre-treatment compared to post-treatment parasite populations. We identified classes of genes significantly enriched within regions of the genome with evidence of recent positive selection among post-treatment and intensively treated parasite populations. The differential selection observed in post-treatment and pre-treatment parasite populations could be linked to any reduced susceptibility of parasites to praziquantel treatment.
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Affiliation(s)
- Tushabe John Vianney
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, United Kingdom
- Immunomodulation and Vaccines Programme, Medical Research Council/Uganda Virus Research Institute and the London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda
| | - Duncan J. Berger
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Stephen R. Doyle
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, United Kingdom
| | | | - Joel Serubanja
- Immunomodulation and Vaccines Programme, Medical Research Council/Uganda Virus Research Institute and the London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda
| | - Prossy Kabuubi Nakawungu
- Immunomodulation and Vaccines Programme, Medical Research Council/Uganda Virus Research Institute and the London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda
| | - Fred Besigye
- Immunomodulation and Vaccines Programme, Medical Research Council/Uganda Virus Research Institute and the London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda
| | - Richard E. Sanya
- Immunomodulation and Vaccines Programme, Medical Research Council/Uganda Virus Research Institute and the London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda
- Health and Systems for Health Unit, African Population and Health Research Center, Nairobi, Kenya
| | - Nancy Holroyd
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Fiona Allan
- Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Emily L. Webb
- MRC International Statistics and Epidemiology Group, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Alison M. Elliott
- Immunomodulation and Vaccines Programme, Medical Research Council/Uganda Virus Research Institute and the London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda
- Department of Clinical Research, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Matthew Berriman
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - James A. Cotton
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, United Kingdom
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33
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Nishiyama S, Sato K, Tao R. Integer programming for selecting set of informative markers in paternity inference. BMC Bioinformatics 2022; 23:265. [PMID: 35804290 PMCID: PMC9264695 DOI: 10.1186/s12859-022-04801-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 06/09/2022] [Indexed: 11/24/2022] Open
Abstract
Background Parentage information is fundamental to various life sciences. Recent advances in sequencing technologies have made it possible to accurately infer parentage even in non-model species. The optimization of sets of genome-wide markers is valuable for cost-effective applications but requires extremely large amounts of computation, which presses for the development of new efficient algorithms. Results Here, for a closed half-sib population, we generalized the process of marker loci selection as a binary integer programming problem. The proposed systematic formulation considered marker localization and the family structure of the potential parental population, resulting in an accurate assignment with a small set of markers. We also proposed an efficient heuristic approach, which effectively improved the number of markers, localization, and tolerance to missing data of the set. Applying this method to the actual genotypes of apple (Malus × domestica) germplasm, we identified a set of 34 SNP markers that distinguished 300 potential parents crossed to a particular cultivar with a greater than 99% accuracy. Conclusions We present a novel approach for selecting informative markers based on binary integer programming. Since the data generated by high-throughput sequencing technology far exceeds the requirement for parentage assignment, a combination of the systematic marker selection with targeted SNP genotyping, such as KASP, allows flexibly enlarging the analysis up to a scale that has been unrealistic in various species. The method developed in this study can be directly applied to unsolved large-scale problems in breeding, reproduction, and ecological research, and is expected to lead to novel knowledge in various biological fields. The implementation is available at https://github.com/SoNishiyama/IP-SIMPAT. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04801-z.
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Affiliation(s)
| | - Kengo Sato
- School of System Design and Technology, Tokyo Denki University, Tokyo, Japan
| | - Ryutaro Tao
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
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34
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Bonnet T, Morrissey MB, de Villemereuil P, Alberts SC, Arcese P, Bailey LD, Boutin S, Brekke P, Brent LJN, Camenisch G, Charmantier A, Clutton-Brock TH, Cockburn A, Coltman DW, Courtiol A, Davidian E, Evans SR, Ewen JG, Festa-Bianchet M, de Franceschi C, Gustafsson L, Höner OP, Houslay TM, Keller LF, Manser M, McAdam AG, McLean E, Nietlisbach P, Osmond HL, Pemberton JM, Postma E, Reid JM, Rutschmann A, Santure AW, Sheldon BC, Slate J, Teplitsky C, Visser ME, Wachter B, Kruuk LEB. Genetic variance in fitness indicates rapid contemporary adaptive evolution in wild animals. Science 2022; 376:1012-1016. [PMID: 35617403 DOI: 10.1126/science.abk0853] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The rate of adaptive evolution, the contribution of selection to genetic changes that increase mean fitness, is determined by the additive genetic variance in individual relative fitness. To date, there are few robust estimates of this parameter for natural populations, and it is therefore unclear whether adaptive evolution can play a meaningful role in short-term population dynamics. We developed and applied quantitative genetic methods to long-term datasets from 19 wild bird and mammal populations and found that, while estimates vary between populations, additive genetic variance in relative fitness is often substantial and, on average, twice that of previous estimates. We show that these rates of contemporary adaptive evolution can affect population dynamics and hence that natural selection has the potential to partly mitigate effects of current environmental change.
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Affiliation(s)
- Timothée Bonnet
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | | | - Pierre de Villemereuil
- Institut de Systématique, Évolution, Biodiversité (ISYEB), École Pratique des Hautes Études, PSL, MNHN, CNRS, SU, UA, Paris, France.,School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Susan C Alberts
- Departments of Biology and Evolutionary Anthropology, Duke University, Durham, NC, USA
| | - Peter Arcese
- Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Liam D Bailey
- Departments of Evolutionary Ecology and Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Stan Boutin
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Patricia Brekke
- Institute of Zoology, Zoological Society of London, Regents Park, London, UK
| | - Lauren J N Brent
- Centre for Research in Animal Behaviour, University of Exeter, Penryn, UK
| | - Glauco Camenisch
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Anne Charmantier
- Centre d'Écologie Fonctionnelle et Évolutive, Université de Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Tim H Clutton-Brock
- Department of Zoology, University of Cambridge, Cambridge, UK.,Mammal Research Institute, University of Pretoria, Pretoria, South Africa
| | - Andrew Cockburn
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - David W Coltman
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Alexandre Courtiol
- Departments of Evolutionary Ecology and Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Eve Davidian
- Departments of Evolutionary Ecology and Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Simon R Evans
- Edward Grey Institute, Department of Zoology, University of Oxford, Oxford, UK.,Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden.,Centre for Ecology and Conservation, University of Exeter, Penryn, UK
| | - John G Ewen
- Institute of Zoology, Zoological Society of London, Regents Park, London, UK
| | | | - Christophe de Franceschi
- Centre d'Écologie Fonctionnelle et Évolutive, Université de Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Lars Gustafsson
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Oliver P Höner
- Departments of Evolutionary Ecology and Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Thomas M Houslay
- Department of Zoology, University of Cambridge, Cambridge, UK.,Centre for Ecology and Conservation, University of Exeter, Penryn, UK
| | - Lukas F Keller
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.,Zoological Museum, University of Zurich,, Zurich, Switzerland
| | - Marta Manser
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.,Mammal Research Institute, University of Pretoria, Pretoria, South Africa
| | - Andrew G McAdam
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Emily McLean
- Biology Department, Oxford College, Emory University, Oxford, GA, USA
| | - Pirmin Nietlisbach
- School of Biological Sciences, Illinois State University, Normal, IL, USA
| | - Helen L Osmond
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | | | - Erik Postma
- Centre for Ecology and Conservation, University of Exeter, Penryn, UK
| | - Jane M Reid
- Centre for Biodiversity Dynamics, Norwegian University of Science and Technology (NTNU), Trondheim, Norway.,School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - Alexis Rutschmann
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Anna W Santure
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Ben C Sheldon
- Edward Grey Institute, Department of Zoology, University of Oxford, Oxford, UK
| | - Jon Slate
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield, UK
| | - Céline Teplitsky
- Centre d'Écologie Fonctionnelle et Évolutive, Université de Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Marcel E Visser
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - Bettina Wachter
- Departments of Evolutionary Ecology and Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Loeske E B Kruuk
- Research School of Biology, Australian National University, Canberra, ACT, Australia.,Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
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35
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Levine BA, Hill RL, Mendelson JR, Booth W. Parentage assignment reveals multiple paternity in the critically-endangered Guatemalan beaded lizard (Heloderma charlesbogerti). CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01448-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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36
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Abecia JE, King AJ, Luiz OJ, Crook DA, Wedd D, Banks SC. Diverse parentage relationships in paternal mouthbrooding fishes. Biol Lett 2022; 18:20210576. [PMID: 35506241 PMCID: PMC9065974 DOI: 10.1098/rsbl.2021.0576] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
While mouthbrooding is not an uncommon parental care strategy in fishes, paternal mouthbrooding only occurs in eight fish families and is little studied. The high cost of paternal mouthbrooding to the male implies a low risk of investment in another male's offspring but genetic parentage patterns are poorly known for paternal mouthbrooders. Here, we used single-nucleotide polymorphism genetic data to investigate parentage relationships of broods of two mouthbrooders of northern Australian rivers, mouth almighty Glossamia aprion and blue catfish Neoarius graeffei. For N. graeffei, we found that the parentage pattern was largely monogamous with the brooder male as the sire. For G. aprion, the parentage pattern was more heterogeneous including observations of monogamous broods with the brooder male as the sire (73%), polygyny (13%), cuckoldry (6%) and a brood genetically unrelated to the brooder male (6%). Findings demonstrate the potential for complex interrelationships of male care, paternity confidence and mating behaviour in mouthbrooding fishes.
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Affiliation(s)
- Janine E Abecia
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Ellengowan Drive, Casuarina, NT 0810, Australia
| | - Alison J King
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Ellengowan Drive, Casuarina, NT 0810, Australia.,Centre for Freshwater Ecosystems, La Trobe University, Albury/Wodonga Campus, Vic 3690, Australia
| | - Osmar J Luiz
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Ellengowan Drive, Casuarina, NT 0810, Australia
| | - David A Crook
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Ellengowan Drive, Casuarina, NT 0810, Australia.,Centre for Freshwater Ecosystems, La Trobe University, Albury/Wodonga Campus, Vic 3690, Australia
| | - Dion Wedd
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Ellengowan Drive, Casuarina, NT 0810, Australia
| | - Sam C Banks
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Ellengowan Drive, Casuarina, NT 0810, Australia
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37
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Steele CA, Delomas TA, Campbell MR, Powell JH. Single‐parentage assignments reveal negative‐assortative mating in an endangered salmonid. Ecol Evol 2022; 12:e8846. [PMID: 35494502 PMCID: PMC9036198 DOI: 10.1002/ece3.8846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 04/05/2022] [Indexed: 11/22/2022] Open
Abstract
Understanding reproductive patterns in endangered species is critical for supporting their recovery efforts. In this study we use a combination of paired‐parent and single‐parent assignments to examine the reproductive patterns in an endangered population of sockeye salmon (Oncorhynchus nerka) that uses Redfish Lake in central Idaho as a spawning and nursery lake. Recovery efforts include the release of maturing adults into the lake for volitional spawning. The lake is also inhabited by a population of resident O. nerka that is genetically indistinguishable, but phenotypically smaller, to the maturing adults released into the lake. The resident population is difficult to sample and the reproductive patterns between the two groups are unknown. We used results of paired‐ and single‐parentage assignments to specifically examine the reproductive patterns of male fish released into the lake under an equal sex ratio and a male‐biased sex ratio. Assignment results of offspring leaving the lake indicated a reproductive shift by males under the two scenarios. Males displayed an assortative mating pattern under an equal sex ratio and spawned almost exclusively with the released females. Under a male‐biased sex ratio most males shifted to a negative‐assortative mating pattern and spawned with smaller females from the resident population. These males were younger and smaller than males that spawned with released females suggesting they were unable to compete with larger males for spawning opportunities with the larger, released females. The results provided insights into the reproductive behavior of this endangered population and has implications for recovery efforts.
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Affiliation(s)
- Craig A. Steele
- Pacific States Marine Fisheries Commission Eagle Fish Genetics Lab Eagle Idaho USA
| | - Thomas A. Delomas
- Pacific States Marine Fisheries Commission Eagle Fish Genetics Lab Eagle Idaho USA
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38
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Valenza-Troubat N, Montanari S, Ritchie P, Wellenreuther M. Unraveling the complex genetic basis of growth in New Zealand silver trevally ( Pseudocaranx georgianus). G3 GENES|GENOMES|GENETICS 2022; 12:6512062. [PMID: 35100394 PMCID: PMC8896004 DOI: 10.1093/g3journal/jkac016] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 01/06/2022] [Indexed: 11/13/2022]
Abstract
Abstract
Growth directly influences production rate and therefore is one of the most important and well-studied traits in animal breeding. However, understanding the genetic basis of growth has been hindered by its typically complex polygenic architecture. Here, we performed quantitative trait locus mapping and genome-wide association studies for 10 growth traits that were observed over 2 years in 1,100 F1 captive-bred trevally (Pseudocaranx georgianus). We constructed the first high-density linkage map for trevally, which included 19,861 single nucleotide polymorphism markers, and discovered 8 quantitative trait loci for height, length, and weight on linkage groups 3, 14, and 18. Using genome-wide association studies, we further identified 113 single nucleotide polymorphism-trait associations, uncovering 10 genetic hot spots involved in growth. Two of the markers found in the genome-wide association studies colocated with the quantitative trait loci previously mentioned, demonstrating that combining quantitative trait locus mapping and genome-wide association studies represents a powerful approach for the identification and validation of loci controlling complex traits. This is the first study of its kind for trevally. Our findings provide important insights into the genetic architecture of growth in this species and supply a basis for fine mapping quantitative trait loci, genomic selection, and further detailed functional analysis of the genes underlying growth in trevally.
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Affiliation(s)
- Noemie Valenza-Troubat
- Seafood Production Group, The New Zealand Institute for Plant & Food Research Ltd , Nelson 7010, New Zealand
| | - Sara Montanari
- Seafood Production Group, The New Zealand Institute for Plant & Food Research Ltd , Nelson 7010, New Zealand
| | - Peter Ritchie
- School of Biological Sciences, Victoria University of Wellington , Wellington 6140, New Zealand
| | - Maren Wellenreuther
- Seafood Production Group, The New Zealand Institute for Plant & Food Research Ltd , Nelson 7010, New Zealand
- School of Biological Sciences, The University of Auckland , Auckland 1010, New Zealand
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39
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Al Rawahi Q, Mijangos JL, Khatkar MS, Al Abri MA, AlJahdhami MH, Kaden J, Senn H, Brittain K, Gongora J. Rescued back from extinction in the wild: past, present and future of the genetics of the Arabian oryx in Oman. ROYAL SOCIETY OPEN SCIENCE 2022; 9:210558. [PMID: 35308631 PMCID: PMC8924751 DOI: 10.1098/rsos.210558] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 02/02/2022] [Indexed: 06/14/2023]
Abstract
The Arabian oryx was the first species to be rescued from extinction in the wild by the concerted efforts of captive programmes in zoos and private collections around the world. Reintroduction efforts have used two main sources: the 'World Herd', established at the Phoenix Zoo, and private collections in Saudi Arabia. The breeding programme at the Al-Wusta Wildlife Reserve (WWR) in Oman has played a central role in the rescue of the oryx. Individuals from the 'World Herd' and the United Arab Emirates have been the main source for the WWR programme. However, no breeding strategies accounting for genetic diversity have been implemented. To address this, we investigated the diversity of the WWR population and historical samples using mitochondrial DNA (mtDNA) and single nucleotide polymorphisms (SNPs). We found individuals at WWR contain 58% of the total mtDNA diversity observed globally. Inference of ancestry and spatial patterns of SNP variation shows the presence of three ancestral sources and three different groups of individuals. Similar levels of diversity and low inbreeding were observed between groups. We identified individuals and groups that could most effectively contribute to maximizing genetic diversity. Our results will be valuable to guide breeding and reintroduction programmes at WWR.
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Affiliation(s)
- Qais Al Rawahi
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, NSW 2006, Australia
- Office for Conservation of the Environment, Diwan of Royal Court, PO Box 246, P.C. 100, Muscat, Oman
- College of Applied Sciences, A'Sharqiyah University, PO Box 42, Postal Code 400, Ibra, Sultanate of Oman
| | - Jose Luis Mijangos
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, NSW 2006, Australia
- Centre for Conservation Ecology and Genomics, Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2617, Australia
| | - Mehar S. Khatkar
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, NSW 2006, Australia
| | - Mohammed A. Al Abri
- Department of Animal and Veterinary Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Muscat, Oman
| | - Mansoor H. AlJahdhami
- Office for Conservation of the Environment, Diwan of Royal Court, PO Box 246, P.C. 100, Muscat, Oman
| | - Jennifer Kaden
- RZSSWildGenes Laboratory, Royal Zoological Society of Scotland, Edinburgh EH12 6TS, UK
| | - Helen Senn
- RZSSWildGenes Laboratory, Royal Zoological Society of Scotland, Edinburgh EH12 6TS, UK
| | - Katherine Brittain
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, NSW 2006, Australia
| | - Jaime Gongora
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, NSW 2006, Australia
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40
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Quantitative multidimensional phenotypes improve genetic analysis of laterality traits. Transl Psychiatry 2022; 12:68. [PMID: 35184143 PMCID: PMC8858319 DOI: 10.1038/s41398-022-01834-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 02/03/2022] [Accepted: 02/03/2022] [Indexed: 01/10/2023] Open
Abstract
Handedness is the most commonly investigated lateralised phenotype and is usually measured as a binary left/right category. Its links with psychiatric and neurodevelopmental disorders prompted studies aimed at understanding the underlying genetics, while other measures and side preferences have been less studied. We investigated the heritability of hand, as well as foot, and eye preference by assessing parental effects (n ≤ 5028 family trios) and SNP-based heritability (SNP-h2, n ≤ 5931 children) in the Avon Longitudinal Study of Parents and Children (ALSPAC). An independent twin cohort from Hong Kong (n = 358) was used to replicate results from structural equation modelling (SEM). Parental left-side preference increased the chance of an individual to be left-sided for the same trait, with stronger maternal than paternal effects for footedness. By regressing out the effects of sex, age, and ancestry, we transformed laterality categories into quantitative measures. The SNP-h2 for quantitative handedness and footedness was 0.21 and 0.23, respectively, which is higher than the SNP-h2 reported in larger genetic studies using binary handedness measures. The heritability of the quantitative measure of handedness increased (0.45) compared to a binary measure for writing hand (0.27) in the Hong Kong twins. Genomic and behavioural SEM identified a shared genetic factor contributing to handedness, footedness, and eyedness, but no independent effects on individual phenotypes. Our analysis demonstrates how quantitative multidimensional laterality phenotypes are better suited to capture the underlying genetics than binary traits.
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41
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Genomic Predictions of Phenotypes and Pseudo-Phenotypes for Viral Nervous Necrosis Resistance, Cortisol Concentration, Antibody Titer and Body Weight in European Sea Bass. Animals (Basel) 2022; 12:ani12030367. [PMID: 35158690 PMCID: PMC8833701 DOI: 10.3390/ani12030367] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/27/2022] [Accepted: 01/30/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Selective breeding programs based on genomic data are still not a common practice in aquaculture, although genomic selection has been widely demonstrated to be advantageous when trait phenotyping is a difficult task. In this study, we investigated the accuracy of predicting the phenotype and the estimated breeding value (EBV) of three Bayesian models and a Random Forest algorithm exploiting the information of a genome-wide SNP panel for European sea bass. The genomic predictions were developed for mortality caused by viral nervous necrosis, post-stress cortisol concentration, antibody titer against nervous necrosis virus and body weight. Selective breeding based on genomic data is a possible option for improving these traits while overcoming difficulties related to individual phenotyping of the investigated traits. Our results evidenced that the EBV used as a pseudo-phenotype enhances the predictive performances of genomic models, and that EBV can be predicted with satisfactory accuracy. The genomic prediction of the EBV for mortality might also be used to classify the phenotype for the same trait. Abstract In European sea bass (Dicentrarchus labrax L.), the viral nervous necrosis mortality (MORT), post-stress cortisol concentration (HC), antibody titer (AT) against nervous necrosis virus and body weight (BW) show significant heritability, which makes selective breeding a possible option for their improvement. An experimental population (N = 650) generated by a commercial broodstock was phenotyped for the aforementioned traits and genotyped with a genome-wide SNP panel (16,075 markers). We compared the predictive accuracies of three Bayesian models (Bayes B, Bayes C and Bayesian Ridge Regression) and a machine-learning method (Random Forest). The prediction accuracy of the EBV for MORT was approximately 0.90, whereas the prediction accuracies of the EBV and the phenotype were 0.86 and 0.21 for HC, 0.79 and 0.26 for AT and 0.71 and 0.38 for BW. The genomic prediction of the EBV for MORT used to classify the phenotype for the same trait showed moderate classification performance. Genome-wide association studies confirmed the polygenic nature of MORT and demonstrated a complex genetic structure for HC and AT. Genomic predictions of the EBV for MORT could potentially be used to classify the phenotype of the same trait, though further investigations on a larger experimental population are needed.
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42
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Hogg CJ, Ottewell K, Latch P, Rossetto M, Biggs J, Gilbert A, Richmond S, Belov K. Threatened Species Initiative: Empowering conservation action using genomic resources. Proc Natl Acad Sci U S A 2022; 119:e2115643118. [PMID: 35042806 PMCID: PMC8795520 DOI: 10.1073/pnas.2115643118] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Globally, 15,521 animal species are listed as threatened by the International Union for the Conservation of Nature, and of these less than 3% have genomic resources that can inform conservation management. To combat this, global genome initiatives are developing genomic resources, yet production of a reference genome alone does not conserve a species. The reference genome allows us to develop a suite of tools to understand both genome-wide and functional diversity within and between species. Conservation practitioners can use these tools to inform their decision-making. But, at present there is an implementation gap between the release of genome information and the use of genomic data in applied conservation by conservation practitioners. In May 2020, we launched the Threatened Species Initiative and brought a consortium of genome biologists, population biologists, bioinformaticians, population geneticists, and ecologists together with conservation agencies across Australia, including government, zoos, and nongovernment organizations. Our objective is to create a foundation of genomic data to advance our understanding of key Australian threatened species, and ultimately empower conservation practitioners to access and apply genomic data to their decision-making processes through a web-based portal. Currently, we are developing genomic resources for 61 threatened species from a range of taxa, across Australia, with more than 130 collaborators from government, academia, and conservation organizations. Developed in direct consultation with government threatened-species managers and other conservation practitioners, herein we present our framework for meeting their needs and our systematic approach to integrating genomics into threatened species recovery.
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Affiliation(s)
- Carolyn J Hogg
- School of Life & Environmental Science, University of Sydney, Sydney, NSW 2006, Australia;
| | - Kym Ottewell
- Conservation Science Centre, Department of Biodiversity, Conservation, & Attractions, Kensington, WA 6151, Australia
| | - Peter Latch
- Australian Government Department of Agriculture, Water & Environment, Canberra, ACT 2600, Australia
| | - Maurizio Rossetto
- Research Centre for Ecosystem Resilience, Australian Institute of Botanical Science, The Royal Botanic Garden Sydney, Sydney, NSW 2000, Australia
| | - James Biggs
- Zoo and Aquarium Association Australasia, Mosman, NSW 2088, Australia
| | | | | | - Katherine Belov
- School of Life & Environmental Science, University of Sydney, Sydney, NSW 2006, Australia
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43
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Huang W, Dicks KL, Hadfield JD, Johnston SE, Ballingall KT, Pemberton JM. Contemporary selection on MHC genes in a free-living ruminant population. Ecol Lett 2022; 25:828-838. [PMID: 35050541 PMCID: PMC9306867 DOI: 10.1111/ele.13957] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 10/21/2021] [Accepted: 12/08/2021] [Indexed: 11/27/2022]
Abstract
Genes within the major histocompatibility complex (MHC) are the most variable identified in vertebrates. Pathogen-mediated selection is believed to be the main force maintaining MHC diversity. However, relatively few studies have demonstrated contemporary selection on MHC genes. Here, we examine associations between MHC variation and several fitness measurements including total fitness and five fitness components, in 3400 wild Soay sheep (Ovis aries) monitored between 1989 and 2012. In terms of total fitness, measured as lifetime breeding success of all individuals born, we found haplotypes named C and D were associated with decreased and increased male total fitness respectively. In terms of fitness components, juvenile survival was associated with haplotype divergence while individual haplotypes (C, D and F) were associated with adult fitness components. Consistent with the increased male total fitness, the rarest haplotype D has increased in frequency throughout the study period more than expected under neutral expectations. Our results demonstrate contemporary natural selection is acting on MHC class II genes in Soay sheep and the mode of selection on specific fitness components can be different mode from selection on total fitness.
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Affiliation(s)
- Wei Huang
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Kara L Dicks
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.,Royal Zoological Society of Scotland, Edinburgh, UK
| | - Jarrod D Hadfield
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Susan E Johnston
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | | - Josephine M Pemberton
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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44
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McLennan EA, Belov K, Hogg CJ, Grueber CE. How much is enough? Sampling intensity influences estimates of reproductive variance in an introduced population. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2022; 32:e02462. [PMID: 34614257 DOI: 10.1002/eap.2462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 05/14/2021] [Indexed: 06/13/2023]
Abstract
Conservation introductions to islands and fenced enclosures are increasing as in situ mitigations fail to keep pace with population declines. Few studies consider the potential loss of genetic diversity and increased inbreeding if released individuals breed disproportionately. As funding is limited and post-release monitoring expensive for conservation programs, understanding how sampling effort influences estimates of reproductive variance is useful. To investigate this relationship, we used a well-studied population of Tasmanian devils (Sarcophilus harrisii) introduced to Maria Island, Tasmania, Australia. Pedigree reconstruction based on molecular data revealed high variance in number of offspring per breeder and high proportions of unsuccessful individuals. Computational subsampling of 20%, 40%, 60%, and 80% of observed offspring resulted in inaccurate estimates of reproductive variance compared to the pedigree reconstructed with all sampled individuals. With decreased sampling effort, the proportion of inferred unsuccessful individuals was overestimated and the variance in number of offspring per breeder was underestimated. To accurately estimate reproductive variance, we recommend sampling as many individuals as logistically possible during the early stages of population establishment. Further, we recommend careful selection of colonizing individuals as they may be disproportionately represented in subsequent generations. Within the conservation management context, our results highlight important considerations for sample collection and post-release monitoring during population establishment.
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Affiliation(s)
- Elspeth A McLennan
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, 2006, Australia
| | - Katherine Belov
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, 2006, Australia
| | - Carolyn J Hogg
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, 2006, Australia
| | - Catherine E Grueber
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, 2006, Australia
- San Diego Zoo Global, PO BOX 120551, San Diego, California, 92112, USA
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45
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Pemberton J, Johnston SE, Fletcher TJ. The genome sequence of the red deer, Cervus elaphus Linnaeus 1758. Wellcome Open Res 2021. [DOI: 10.12688/wellcomeopenres.17493.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We present a genome assembly from an individual female Cervus elaphus (the red deer; Chordata; Mammalia; Artiodactyla; Cervidae). The genome sequence is 2,887 megabases in span. The majority of the assembly is scaffolded into 34 chromosomal pseudomolecules, with the X sex chromosome assembled.
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46
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Peters L, Huisman J, Kruuk LEB, Pemberton JM, Johnston SE. Genomic analysis reveals a polygenic architecture of antler morphology in wild red deer (Cervus elaphus). Mol Ecol 2021; 31:1281-1298. [PMID: 34878674 DOI: 10.1111/mec.16314] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 11/26/2021] [Accepted: 12/01/2021] [Indexed: 11/28/2022]
Abstract
Sexually selected traits show large variation and rapid evolution across the animal kingdom, yet genetic variation often persists within populations despite apparent directional selection. A key step in solving this long-standing paradox is to determine the genetic architecture of sexually selected traits to understand evolutionary drivers and constraints at the genomic level. Antlers are a form of sexual weaponry in male red deer (Cervus elaphus). On the island of Rum, Scotland, males with larger antlers have increased breeding success, yet there has been no evidence of any response to selection at the genetic level. To try and understand the mechanisms underlying this observation, we investigate the genetic architecture of ten antler traits and their principal components using genomic data from >38,000 SNPs. We estimate the heritabilities and genetic correlations of the antler traits using a genomic relatedness approach. We then use genome-wide association and haplotype-based regional heritability to identify regions of the genome underlying antler morphology, and an empirical Bayes approach to estimate the underlying distributions of allele effect sizes. We show that antler morphology is highly repeatable over an individual's lifetime, heritable and has a polygenic architecture and that almost all antler traits are positively genetically correlated with some loci identified as having pleiotropic effects. Our findings suggest that a large mutational target and genetic covariances among antler traits, in part maintained by pleiotropy, are likely to contribute to the maintenance of genetic variation in antler morphology in this population.
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Affiliation(s)
- Lucy Peters
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Jisca Huisman
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Loeske E B Kruuk
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.,Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Josephine M Pemberton
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Susan E Johnston
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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48
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Jewett EM, McManus KF, Freyman WA, Auton A, Auton A. Bonsai: An efficient method for inferring large human pedigrees from genotype data. Am J Hum Genet 2021; 108:2052-2070. [PMID: 34739834 PMCID: PMC8595950 DOI: 10.1016/j.ajhg.2021.09.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 09/24/2021] [Indexed: 11/29/2022] Open
Abstract
Pedigree inference from genotype data is a challenging problem, particularly when pedigrees are sparsely sampled and individuals may be distantly related to their closest genotyped relatives. We present a method that infers small pedigrees of close relatives and then assembles them into larger pedigrees. To assemble large pedigrees, we introduce several formulas and tools including a likelihood for the degree separating two small pedigrees, a generalization of the fast DRUID point estimate of the degree separating two pedigrees, a method for detecting individuals who share background identity-by-descent (IBD) that does not reflect recent common ancestry, and a method for identifying the ancestral branches through which distant relatives are connected. Our method also takes several approaches that help to improve the accuracy and efficiency of pedigree inference. In particular, we incorporate age information directly into the likelihood rather than using ages only for consistency checks and we employ a heuristic branch-and-bound-like approach to more efficiently explore the space of possible pedigrees. Together, these approaches make it possible to construct large pedigrees that are challenging or intractable for current inference methods.
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49
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Levine BA, Yackel Adams AA, Douglas MR, Douglas ME, Nafus MG. Female persistence during toxicant treatment predicts survival probability of offspring in invasive brown treesnakes (Boiga irregularis). Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2021.e01827] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Martins FB, Moraes ACL, Aono AH, Ferreira RCU, Chiari L, Simeão RM, Barrios SCL, Santos MF, Jank L, do Valle CB, Vigna BBZ, de Souza AP. A Semi-Automated SNP-Based Approach for Contaminant Identification in Biparental Polyploid Populations of Tropical Forage Grasses. FRONTIERS IN PLANT SCIENCE 2021; 12:737919. [PMID: 34745171 PMCID: PMC8569613 DOI: 10.3389/fpls.2021.737919] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 09/20/2021] [Indexed: 06/13/2023]
Abstract
Artificial hybridization plays a fundamental role in plant breeding programs since it generates new genotypic combinations that can result in desirable phenotypes. Depending on the species and mode of reproduction, controlled crosses may be challenging, and contaminating individuals can be introduced accidentally. In this context, the identification of such contaminants is important to avoid compromising further selection cycles, as well as genetic and genomic studies. The main objective of this work was to propose an automated multivariate methodology for the detection and classification of putative contaminants, including apomictic clones (ACs), self-fertilized individuals, half-siblings (HSs), and full contaminants (FCs), in biparental polyploid progenies of tropical forage grasses. We established a pipeline to identify contaminants in genotyping-by-sequencing (GBS) data encoded as allele dosages of single nucleotide polymorphism (SNP) markers by integrating principal component analysis (PCA), genotypic analysis (GA) measures based on Mendelian segregation, and clustering analysis (CA). The combination of these methods allowed for the correct identification of all contaminants in all simulated progenies and the detection of putative contaminants in three real progenies of tropical forage grasses, providing an easy and promising methodology for the identification of contaminants in biparental progenies of tetraploid and hexaploid species. The proposed pipeline was made available through the polyCID Shiny app and can be easily coupled with traditional genetic approaches, such as linkage map construction, thereby increasing the efficiency of breeding programs.
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Affiliation(s)
- Felipe Bitencourt Martins
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), São Paulo, Brazil
| | - Aline Costa Lima Moraes
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), São Paulo, Brazil
| | - Alexandre Hild Aono
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), São Paulo, Brazil
| | | | - Lucimara Chiari
- Embrapa Gado de Corte, Brazilian Agricultural Research Corporation, Campo Grande, Brazil
| | - Rosangela Maria Simeão
- Embrapa Gado de Corte, Brazilian Agricultural Research Corporation, Campo Grande, Brazil
| | | | | | - Liana Jank
- Embrapa Gado de Corte, Brazilian Agricultural Research Corporation, Campo Grande, Brazil
| | | | | | - Anete Pereira de Souza
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), São Paulo, Brazil
- Department of Plant Biology, Biology Institute, University of Campinas (UNICAMP), São Paulo, Brazil
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