1
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Nistelberger HM, Roycroft E, Macdonald AJ, McArthur S, White LC, Grady PGS, Pierson J, Sims C, Cowen S, Moseby K, Tuft K, Moritz C, Eldridge MDB, Byrne M, Ottewell K. Genetic mixing in conservation translocations increases diversity of a keystone threatened species, Bettongia lesueur. Mol Ecol 2023. [PMID: 37715549 DOI: 10.1111/mec.17119] [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: 04/10/2023] [Revised: 07/11/2023] [Accepted: 08/17/2023] [Indexed: 09/17/2023]
Abstract
Translocation programmes are increasingly being informed by genetic data to monitor and enhance conservation outcomes for both natural and established populations. These data provide a window into contemporary patterns of genetic diversity, structure and relatedness that can guide managers in how to best source animals for their translocation programmes. The inclusion of historical samples, where possible, strengthens monitoring by allowing assessment of changes in genetic diversity over time and by providing a benchmark for future improvements in diversity via management practices. Here, we used reduced representation sequencing (ddRADseq) data to report on the current genetic health of three remnant and seven translocated boodie (Bettongia lesueur) populations, now extinct on the Australian mainland. In addition, we used exon capture data from seven historical mainland specimens and a subset of contemporary samples to compare pre-decline and current diversity. Both data sets showed the significant impact of population founder source (whether multiple or single) on the genetic diversity of translocated populations. Populations founded by animals from multiple sources showed significantly higher genetic diversity than the natural remnant and single-source translocation populations, and we show that by mixing the most divergent populations, exon capture heterozygosity was restored to levels close to that observed in pre-decline mainland samples. Relatedness estimates were surprisingly low across all contemporary populations and there was limited evidence of inbreeding. Our results show that a strategy of genetic mixing has led to successful conservation outcomes for the species in terms of increasing genetic diversity and provides strong rationale for mixing as a management strategy.
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Affiliation(s)
- Heidi M Nistelberger
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Kensington, Western Australia, Australia
| | - Emily Roycroft
- Division of Ecology & Evolution, Research School of Biology, ANU College of Science, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Anna J Macdonald
- Division of Ecology & Evolution, Research School of Biology, ANU College of Science, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Shelley McArthur
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Kensington, Western Australia, Australia
| | - Lauren C White
- Department of Environment, Land, Water and Planning, Arthur Rylah Institute for Environmental Research, Heidelberg, Victoria, Australia
| | - Patrick G S Grady
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Jennifer Pierson
- Australian Wildlife Conservancy, Subiaco, Western Australia, Australia
| | - Colleen Sims
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Kensington, Western Australia, Australia
| | - Saul Cowen
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Kensington, Western Australia, Australia
| | - Katherine Moseby
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | | | - Craig Moritz
- Division of Ecology & Evolution, Research School of Biology, ANU College of Science, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Mark D B Eldridge
- Terrestrial Vertebrates, Australian Museum Research Institute, Sydney, New South Wales, Australia
| | - Margaret Byrne
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Kensington, Western Australia, Australia
| | - Kym Ottewell
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Kensington, Western Australia, Australia
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2
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Tidière M, Portanier E, Jacquet S, Goodman SM, Monnier G, Beuneux G, Desmet J, Kaerle C, Queney G, Barataud M, Pontier D. Species delineation and genetic structure of two
Chaerephon
species (
C. pusillus
and
C. leucogaster
) on Madagascar and the Comoro archipelago. Ecol Evol 2022; 12:e9566. [DOI: 10.1002/ece3.9566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 11/03/2022] [Accepted: 11/14/2022] [Indexed: 12/04/2022] Open
Affiliation(s)
- Morgane Tidière
- LabEx ECOFECT Université de Lyon Lyon France
- LBBE UMR5558 CNRS Université de Lyon 1 Villeurbanne France
| | | | - Stéphanie Jacquet
- LabEx ECOFECT Université de Lyon Lyon France
- LBBE UMR5558 CNRS Université de Lyon 1 Villeurbanne France
| | - Steven M. Goodman
- Field Museum of Natural History Chicago Illinois USA
- Association Vahatra Antananarivo Madagascar
| | | | - Gregory Beuneux
- Société Française pour l'Etude et la Protection des Mammifères Bourges France
| | | | | | | | - Michel Barataud
- Société Française pour l'Etude et la Protection des Mammifères Bourges France
| | - Dominique Pontier
- LabEx ECOFECT Université de Lyon Lyon France
- LBBE UMR5558 CNRS Université de Lyon 1 Villeurbanne France
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3
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Zhang S, Lin M, Liu J, Chen J, Liu D, Zhao J, Yao M. A centenary tale: population genetic insights into the introduction history of the oriental fire-bellied toad (Bombina orientalis) in Beijing. BMC Ecol Evol 2022; 22:117. [PMID: 36241967 PMCID: PMC9569074 DOI: 10.1186/s12862-022-02072-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: 06/01/2022] [Accepted: 09/02/2022] [Indexed: 11/06/2022] Open
Abstract
Background The successful establishment of a species population following a single introduction of a few individuals to a non-native area has been limited. Nevertheless, the oriental fire-bellied toad (Bombina orientalis) population in Beijing is purportedly descended from a single introduction of about 200 individuals translocated from Yantai, Shandong Province, China, in 1927. Results To resolve the introduction process and to understand the genetic consequences since that introduction approximately 90 years ago, we investigated the population’s genetic diversity and structure using 261 toads from Beijing and two native Shandong populations and inferred the species’ introduction history using simulation-based approaches. Analysis of mitochondrial DNA (mtDNA) sequences showed the two haplotypes found in Beijing nested within Yantai haplotypes, thus corroborating the historical record of the translocation source. The mtDNA and 11 nuclear microsatellite markers revealed both considerably lower genetic diversity in Beijing than in the source population and strong genetic differentiation between them. Although the current census population in Beijing may be in the range of a few thousand, the effective population size was estimated at only 20–57. Simulations also suggest that this population may have descended from 40–60 founders. Conclusions The Beijing population’s genetic patterns were consistent with the consequences of a severe bottleneck during introduction followed by genetic drift. The introduction trajectory constructed for this B. orientalis population reveals the genetic footprints of a small population sustained in isolation for nearly a century. Our results provide an intriguing example of establishment success from limited founders and may inform ex situ conservation efforts as well as the management of biological invasions. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-022-02072-z.
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Affiliation(s)
- Shan Zhang
- grid.11135.370000 0001 2256 9319School of Life Sciences, Peking University, R312, School of Life Sciences Bldg., 100871 Beijing, China ,grid.11135.370000 0001 2256 9319Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, 100871 China
| | - Meixi Lin
- grid.11135.370000 0001 2256 9319School of Life Sciences, Peking University, R312, School of Life Sciences Bldg., 100871 Beijing, China ,grid.19006.3e0000 0000 9632 6718Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, CA 90095 USA
| | - Jiawei Liu
- grid.11135.370000 0001 2256 9319School of Life Sciences, Peking University, R312, School of Life Sciences Bldg., 100871 Beijing, China ,grid.170205.10000 0004 1936 7822Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637 USA
| | - Jiangce Chen
- grid.63054.340000 0001 0860 4915Mechanical Engineering Department, University of Connecticut, Storrs, CT 06269 USA
| | - Dong Liu
- grid.263817.90000 0004 1773 1790Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055 China
| | - Jindong Zhao
- grid.11135.370000 0001 2256 9319School of Life Sciences, Peking University, R312, School of Life Sciences Bldg., 100871 Beijing, China ,grid.11135.370000 0001 2256 9319Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, 100871 China
| | - Meng Yao
- grid.11135.370000 0001 2256 9319School of Life Sciences, Peking University, R312, School of Life Sciences Bldg., 100871 Beijing, China ,grid.11135.370000 0001 2256 9319Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, 100871 China
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4
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Robin M, Ferrari G, Akgül G, Münger X, von Seth J, Schuenemann VJ, Dalén L, Grossen C. Ancient mitochondrial and modern whole genomes unravel massive genetic diversity loss during near extinction of Alpine ibex. Mol Ecol 2022; 31:3548-3565. [PMID: 35560856 PMCID: PMC9328357 DOI: 10.1111/mec.16503] [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: 11/15/2021] [Revised: 04/13/2022] [Accepted: 05/04/2022] [Indexed: 11/27/2022]
Abstract
Population bottlenecks can have dramatic consequences for the health and long-term survival of a species. Understanding of historic population size and standing genetic variation prior to a contraction allows estimating the impact of a bottleneck on the species genetic diversity. Although historic population sizes can be modelled based on extant genomics, uncertainty is high for the last 10-20 millenia. Hence, integrating ancient genomes provides a powerful complement to retrace the evolution of genetic diversity through population fluctuations. Here, we recover 15 high-quality mitogenomes of the once nearly extinct Alpine ibex spanning 8601 BP to 1919 CE and combine these with 60 published modern whole genomes. Coalescent demography simulations based on modern whole genomes indicate population fluctuations coinciding with the last major glaciation period. Using our ancient and historic mitogenomes, we investigate the more recent demographic history of the species and show that mitochondrial haplotype diversity was reduced to a fifth of the pre-bottleneck diversity with several highly differentiated mitochondrial lineages having co-existed historically. The main collapse of mitochondrial diversity coincides with elevated human population growth during the last 1-2 kya. After recovery, one lineage was spread and nearly fixed across the Alps due to recolonization efforts. Our study highlights that a combined approach integrating genomic data of ancient, historic and extant populations unravels major long-term population fluctuations from the emergence of a species through its near extinction up to the recent past.
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Affiliation(s)
- Mathieu Robin
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland.,Institute of Evolutionary Medicine, University of Zurich, Zürich, Switzerland
| | - Giada Ferrari
- Institute of Evolutionary Medicine, University of Zurich, Zürich, Switzerland
| | - Gülfirde Akgül
- Institute of Evolutionary Medicine, University of Zurich, Zürich, Switzerland
| | - Xenia Münger
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - Johanna von Seth
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Centre for Palaeogenetics, Stockholm, Sweden
| | | | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Centre for Palaeogenetics, Stockholm, Sweden
| | - Christine Grossen
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
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5
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Moroni B, Brambilla A, Rossi L, Meneguz PG, Bassano B, Tizzani P. Hybridization between Alpine Ibex and Domestic Goat in the Alps: A Sporadic and Localized Phenomenon? Animals (Basel) 2022; 12:ani12060751. [PMID: 35327148 PMCID: PMC8944563 DOI: 10.3390/ani12060751] [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: 01/14/2022] [Revised: 02/12/2022] [Accepted: 02/14/2022] [Indexed: 12/04/2022] Open
Abstract
Simple Summary The Alpine ibex (Capra ibex) is a protected wild ungulate. The species is known to have a low genetic variability and to occasionally suffer from local population decline as a consequence of epidemic diseases. Another, less investigated, threat for the species’ long-term conservation is represented by the hybridization with feral domestic goats that may breed with ibex if abandoned in the mountain at the end of the summer pasture. Further reproduction and the spread of hybrids may jeopardize the genetic integrity of wild Alpine ibex. By means of an online survey and using a network of experts, we mapped unpublished evidence on observed hybridization events between Alpine ibex and feral domestic goats. The results of this study suggested that hybrids are currently distributed in several countries, and their presence is not a rare event, with some clusters including 4–20 probable hybrids. This calls for more studies clearly quantifying hybrids in Alpine ibex colonies, but also highlights the need for conservation actions aimed at controlling this phenomenon, such as the effective management of domestic herds grazing in Alpine ibex core areas and clear guidelines on hybrid management. Abstract The Alpine ibex (Capra ibex) is a mountain ungulate living in the European Alps. Although being currently classified as a species of Least Concern (LC) by the IUCN, a potential threat for its long-term conservation is introgression following hybridization with domestic goats (Capra hircus). Hybridization has been documented in Switzerland in captive and free ranging animals, although accurate data to assess the extent of this phenomenon in natural conditions in the Alps are lacking. Using an online survey and a network of experts, we collected and mapped unpublished evidence of hybridization events that occurred between Alpine ibex and feral domestic goats from 2000 to 2021. The results of this study showed that hybrids are distributed in most of the Alpine countries, and their presence is not a sporadic event, with some clusters including 4–20 probable hybrids. Our results illustrated the need for establishing a standardized and effective protocol to identify hybrids in the field (such as a formal description of the morphological traits characterizing hybrids), as well as clear guidelines for hybrid management. Even more importantly, this study also highlighted the need for actions aimed at avoiding hybridization, such as the effective management of domestic herds grazing in Alpine ibex core areas.
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Affiliation(s)
- Barbara Moroni
- Department of Veterinary Sciences, University of Turin, Largo Braccini 2, 10095 Grugliasco, Italy; (L.R.); (P.G.M.); (P.T.)
- Correspondence:
| | - Alice Brambilla
- Alpine Wildlife Research Centre, Gran Paradiso National Park, 10080 Noasca, Italy; (A.B.); (B.B.)
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8057 Zurich, Switzerland
| | - Luca Rossi
- Department of Veterinary Sciences, University of Turin, Largo Braccini 2, 10095 Grugliasco, Italy; (L.R.); (P.G.M.); (P.T.)
| | - Pier Giuseppe Meneguz
- Department of Veterinary Sciences, University of Turin, Largo Braccini 2, 10095 Grugliasco, Italy; (L.R.); (P.G.M.); (P.T.)
| | - Bruno Bassano
- Alpine Wildlife Research Centre, Gran Paradiso National Park, 10080 Noasca, Italy; (A.B.); (B.B.)
| | - Paolo Tizzani
- Department of Veterinary Sciences, University of Turin, Largo Braccini 2, 10095 Grugliasco, Italy; (L.R.); (P.G.M.); (P.T.)
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6
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Vasiljevic N, Morf NV, Senn J, Pérez‐Espona S, Mattucci F, Mucci N, Moore‐Jones G, Pisano SRR, Kratzer A, Ogden R. Phylogeography and population genetic structure of the European roe deer in Switzerland following recent recolonization. Ecol Evol 2022; 12:e8626. [PMID: 35222977 PMCID: PMC8858214 DOI: 10.1002/ece3.8626] [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: 09/30/2021] [Revised: 01/03/2022] [Accepted: 01/26/2022] [Indexed: 11/12/2022] Open
Abstract
In the early 1800s, the European roe deer (Capreolus capreolus) was probably extirpated from Switzerland, due to overhunting and deforestation. After a federal law was enacted in 1875 to protect lactating females and young, and limiting the hunting season, the roe deer successfully recovered and recolonized Switzerland. In this study, we use mitochondrial DNA and nuclear DNA markers to investigate the recolonization and assess contemporary genetic structure in relation to broad topographic features, in order to understand underlying ecological processes, inform future roe deer management strategies, and explore the opportunity for development of forensic traceability tools. The results concerning the recolonization origin support natural, multidirectional immigration from neighboring countries. We further demonstrate that there is evidence of weak genetic differentiation within Switzerland among topographic regions. Finally, we conclude that the genetic data support the recognition of a single roe deer management unit within Switzerland, within which there is a potential for broad‐scale geographic origin assignment using nuclear markers to support law enforcement.
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Affiliation(s)
- Nina Vasiljevic
- Zurich Institute of Forensic Medicine University of Zurich Switzerland
| | - Nadja V. Morf
- Zurich Institute of Forensic Medicine University of Zurich Switzerland
| | - Josef Senn
- Swiss Federal Research Institute WSL Birmensdorf Switzerland
| | - Sílvia Pérez‐Espona
- Royal (Dick) School of Veterinary Studies and the Roslin Institute University of Edinburgh Midlothian UK
| | - Federica Mattucci
- ISPRA‐Istituto Superiore per la Protezione e la Ricerca Ambientale Area per la Genetica della Conservazione BIO‐CGE Bologna Italy
| | - Nadia Mucci
- ISPRA‐Istituto Superiore per la Protezione e la Ricerca Ambientale Area per la Genetica della Conservazione BIO‐CGE Bologna Italy
| | - Gaia Moore‐Jones
- Institute for Fish and Wildlife Health (FIWI), Department of Infectious Diseases and Pathobiology, Vetsuisse‐Faculty University of Bern Bern Switzerland
| | - Simone Roberto Rolando Pisano
- Institute for Fish and Wildlife Health (FIWI), Department of Infectious Diseases and Pathobiology, Vetsuisse‐Faculty University of Bern Bern Switzerland
| | - Adelgunde Kratzer
- Zurich Institute of Forensic Medicine University of Zurich Switzerland
| | - Rob Ogden
- Royal (Dick) School of Veterinary Studies and the Roslin Institute University of Edinburgh Midlothian UK
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7
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New insights into the past and recent evolutionary history of the Corsican mouflon (Ovis gmelini musimon) to inform its conservation. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01399-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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8
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OCCURRENCE OF FOOTROT IN FREE-RANGING ALPINE IBEX (CAPRA IBEX) COLONIES IN SWITZERLAND. J Wildl Dis 2021; 57:327-337. [PMID: 33822150 DOI: 10.7589/jwd-d-20-00050] [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: 04/03/2020] [Accepted: 10/09/2020] [Indexed: 11/20/2022]
Abstract
Footrot is a worldwide economically important, debilitating disease caused by Dichelobacter nodosus. In sheep (Ovis aries), it is characterized by lesions of varying severity, depending on the strain, whereas Alpine ibex (Capra ibex) seem to develop severe lesions, whatever the strain. Healthy carriers occur in livestock but are rare in wild ruminants. Using a triangulation approach (retrospective questionnaire survey, necropsy database screening, and pathogen prevalence estimation in selected ibex colonies with and without footrot), we aimed at evaluating the importance of footrot in the ibex population, identifying potential risk factors for disease occurrence in this species, and defining the epidemiological role of ibex. Our study revealed that footrot occurs throughout the entire ibex territory (34% of the Swiss ibex colonies affected) but only as a sporadic disease (mostly one case per disease event), although the situation differed among footrot-positive colonies because half of them had experienced outbreak recurrences. Risk factor analysis for the occurrence of footrot in ibex colonies suggested an absence of an effect of meteorologic conditions, region, contacts with sheep or cattle (known to be very common healthy carriers of D. nodosus) and existing local disease control program. We found a significant effect only of contacts with sheep having footrot. Pathogen prevalence was very low in all investigated colonies. In conclusion, our results support previous data suggesting that ibex are susceptible spillover hosts, likely infected mainly by sympatric sheep displaying clinical signs.
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9
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Kessler C, Brambilla A, Waldvogel D, Camenisch G, Biebach I, Leigh DM, Grossen C, Croll D. A robust sequencing assay of a thousand amplicons for the high-throughput population monitoring of Alpine ibex immunogenetics. Mol Ecol Resour 2021; 22:66-85. [PMID: 34152681 PMCID: PMC9292246 DOI: 10.1111/1755-0998.13452] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 06/10/2021] [Accepted: 06/14/2021] [Indexed: 11/27/2022]
Abstract
Polymorphism for immune functions can explain significant variation in health and reproductive success within species. Drastic loss in genetic diversity at such loci constitutes an extinction risk and should be monitored in species of conservation concern. However, effective implementations of genome‐wide immune polymorphism sets into high‐throughput genotyping assays are scarce. Here, we report the design and validation of a microfluidics‐based amplicon sequencing assay to comprehensively capture genetic variation in Alpine ibex (Capra ibex). This species represents one of the most successful large mammal restorations recovering from a severely depressed census size and a massive loss in diversity at the major histocompatibility complex (MHC). We analysed 65 whole‐genome sequencing sets of the Alpine ibex and related species to select the most representative markers and to prevent primer binding failures. In total, we designed ~1,000 amplicons densely covering the MHC, further immunity‐related genes as well as randomly selected genome‐wide markers for the assessment of neutral population structure. Our analysis of 158 individuals shows that the genome‐wide markers perform equally well at resolving population structure as RAD‐sequencing or low‐coverage genome sequencing data sets. Immunity‐related loci show unexpectedly high degrees of genetic differentiation within the species. Such information can now be used to define highly targeted individual translocations. Our design strategy can be realistically implemented into genetic surveys of a large range of species. In conclusion, leveraging whole‐genome sequencing data sets to design targeted amplicon assays allows the simultaneous monitoring of multiple genetic risk factors and can be translated into species conservation recommendations.
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Affiliation(s)
- Camille Kessler
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Alice Brambilla
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland.,Alpine Wildlife Research Center, Gran Paradiso National Park, Italy
| | - Dominique Waldvogel
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
| | - Glauco Camenisch
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
| | - Iris Biebach
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
| | - Deborah M Leigh
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland.,WSL Swiss Federal Research Institute, Birmensdorf, Switzerland
| | - Christine Grossen
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
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10
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Naito‐Liederbach AM, Sato Y, Nakajima N, Maeda T, Inoue T, Yamazaki T, Ogden R, Inoue‐Murayama M. Genetic diversity of the endangered Japanese golden eagle at neutral and functional loci. Ecol Res 2021. [DOI: 10.1111/1440-1703.12246] [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]
Affiliation(s)
| | - Yu Sato
- Wildlife Research Center Kyoto University Kyoto Japan
- Royal (Dick) School of Veterinary Studies and the Roslin Institute University of Edinburgh Roslin UK
| | - Nobuyoshi Nakajima
- Center for Environmental Biology and Ecosystem Studies National Institute for Environmental Studies Tsukuba Japan
| | - Taku Maeda
- Iwate Prefectural Research Institute for Environmental Sciences and Public Health Morioka Japan
| | - Takehiko Inoue
- Asian Raptor Research and Conservation Network Yasu Japan
| | - Toru Yamazaki
- Asian Raptor Research and Conservation Network Yasu Japan
| | - Rob Ogden
- Royal (Dick) School of Veterinary Studies and the Roslin Institute University of Edinburgh Roslin UK
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11
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Leigh DM, Lischer HEL, Guillaume F, Grossen C, Günther T. Disentangling adaptation from drift in bottlenecked and reintroduced populations of Alpine ibex. Mol Ecol Resour 2021; 21:2350-2363. [PMID: 34097819 PMCID: PMC8518545 DOI: 10.1111/1755-0998.13442] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 05/27/2021] [Accepted: 06/01/2021] [Indexed: 01/25/2023]
Abstract
Identifying local adaptation in bottlenecked species is essential for conservation management. Selection detection methods have an important role in species management plans, assessments of adaptive capacity, and looking for responses to climate change. Yet, the allele frequency changes exploited in selection detection methods are similar to those caused by the strong neutral genetic drift expected during a bottleneck. Consequently, it is often unclear what accuracy selection detection methods have across bottlenecked populations. In this study, simulations were used to explore if signals of selection could be confidently distinguished from genetic drift across 23 bottlenecked and reintroduced populations of Alpine ibex (Capra ibex). The meticulously recorded demographic history of the Alpine ibex was used to generate comprehensive simulated SNP data. The simulated SNPs were then used to benchmark the confidence we could place in outliers identified in empirical Alpine ibex RADseq derived SNP data. Within the simulated data set, the false positive rates were high for all selection detection methods (FST outlier scans and Genetic‐Environment Association analyses) but fell substantially when two or more methods were combined. True positive rates were consistently low and became negligible with increased stringency. Despite finding many outlier loci in the empirical Alpine ibex SNPs, none could be distinguished from genetic drift‐driven false positives. Unfortunately, the low true positive rate also prevents the exclusion of recent local adaptation within the Alpine ibex. The baselines and stringent approach outlined here should be applied to other bottlenecked species to ensure the risk of false positive, or negative, signals of selection are accounted for in conservation management plans.
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Affiliation(s)
- Deborah M Leigh
- WSL Swiss Federal Research Institute, Birmensdorf, Switzerland
| | - Heidi E L Lischer
- Interfaculty Bioinformatics Unit, University of Bern, Bern, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Frédéric Guillaume
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Christine Grossen
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Torsten Günther
- Human Evolution, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
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12
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Zanet S, Ferroglio E, Orlandini F, Bassano B, Battisti E, Brambilla A. Bronchopulmonary Nematodes in Alpine Ibex: Shedding of First Stage Larvae Analyzed at the Individual Host Level. Front Vet Sci 2021; 8:663268. [PMID: 33996985 PMCID: PMC8116586 DOI: 10.3389/fvets.2021.663268] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 04/06/2021] [Indexed: 12/03/2022] Open
Abstract
Pneumonia is the most frequent cause of death for Alpine ibex (Capra ibex) in Gran Paradiso National Park, (Italy). The etiology of this form of pneumonia is currently unknown and the identification of the primary etiological agent remains difficult due to biological and logistic constraints. Uncovering individual differences in Protostrongylid prevalence and intensity is important to further investigate the epidemiology of respiratory diseases and their relationship to heterozygosity and inbreeding in a once almost extinct population like C. ibex. In a group of 21 individually recognizable adult male we monitored monthly prevalence and intensity of Protostrongylid first-stage larvae using Baerman's technique from June to September 2019. First-stage larvae of 5 genera were detected. Muellerius (P = 100%, CI95% = 84–100) and Protostrongylus (P = 86%, CI95%:71–100) were two dominant genera according to Bush's importance index. Neostrongylus (P = 38%,CI95%: 17–59), Cystocaulus (P = 33%,CI95% = 13–53) were classified as co-dominant genera while Dictyocaulus filaria (P = 0.05%, CI95% = 0.04–0.13) was detected, for the first time in Alpine ibex, in one subject. Protostrongylidae larval excretion varied significantly over time, with minimum L1 excretion in July. Individual median larval intensity ranged from 4.4 lpg to 82.2 lpg with Poulin's discrepancy index showing highly aggregated distribution patterns for Muellerius spp. (D = 0.283, CI95% = 0.760–0.895) and Protostrongylus spp. (D = 0.635, CI95% = 0.580–0.705). Presented data provide the necessary base point to further investigate how lungworm infection account for the different rates of progression of pneumonia in C. ibex. Individual aggregation of larval intensity must be further evaluated to determine whether these differences mirror different levels of parasitic infection related to individual differences in immune response, hormonal-states or genetic fitness.
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Affiliation(s)
- Stefania Zanet
- Department Veterinary Sciences, University of Turin, Turin, Italy
| | - Ezio Ferroglio
- Department Veterinary Sciences, University of Turin, Turin, Italy
| | | | - Bruno Bassano
- Gran Paradiso National Park, Alpine Wildlife Research Center, Noasca, Italy
| | - Elena Battisti
- Department Veterinary Sciences, University of Turin, Turin, Italy
| | - Alice Brambilla
- Gran Paradiso National Park, Alpine Wildlife Research Center, Noasca, Italy.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
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13
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Flesch EP, Graves TA, Thomson JM, Proffitt KM, White PJ, Stephenson TR, Garrott RA. Evaluating wildlife translocations using genomics: A bighorn sheep case study. Ecol Evol 2020; 10:13687-13704. [PMID: 33391673 PMCID: PMC7771163 DOI: 10.1002/ece3.6942] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 08/12/2020] [Accepted: 09/25/2020] [Indexed: 01/10/2023] Open
Abstract
Wildlife restoration often involves translocation efforts to reintroduce species and supplement small, fragmented populations. We examined the genomic consequences of bighorn sheep (Ovis canadensis) translocations and population isolation to enhance understanding of evolutionary processes that affect population genetics and inform future restoration strategies. We conducted a population genomic analysis of 511 bighorn sheep from 17 areas, including native and reintroduced populations that received 0-10 translocations. Using the Illumina High Density Ovine array, we generated datasets of 6,155 to 33,289 single nucleotide polymorphisms and completed clustering, population tree, and kinship analyses. Our analyses determined that natural gene flow did not occur between most populations, including two pairs of native herds that had past connectivity. We synthesized genomic evidence across analyses to evaluate 24 different translocation events and detected eight successful reintroductions (i.e., lack of signal for recolonization from nearby populations) and five successful augmentations (i.e., reproductive success of translocated individuals) based on genetic similarity with the source populations. A single native population founded six of the reintroduced herds, suggesting that environmental conditions did not need to match for populations to persist following reintroduction. Augmentations consisting of 18-57 animals including males and females succeeded, whereas augmentations of two males did not result in a detectable genetic signature. Our results provide insight on genomic distinctiveness of native and reintroduced herds, information on the relative success of reintroduction and augmentation efforts and their associated attributes, and guidance to enhance genetic contribution of augmentations and reintroductions to aid in bighorn sheep restoration.
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Affiliation(s)
- Elizabeth P. Flesch
- Fish and Wildlife Ecology and Management ProgramEcology DepartmentMontana State UniversityBozemanMTUSA
| | - Tabitha A. Graves
- Northern Rocky Mountain Science CenterU.S. Geological SurveyWest GlacierMTUSA
| | | | | | - P. J. White
- Yellowstone Center for ResourcesNational Park ServiceMammothWYUSA
| | - Thomas R. Stephenson
- Sierra Nevada Bighorn Sheep Recovery ProgramCalifornia Department of Fish and WildlifeBishopCAUSA
| | - Robert A. Garrott
- Fish and Wildlife Ecology and Management ProgramEcology DepartmentMontana State UniversityBozemanMTUSA
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14
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White LC, Thomson VA, West R, Ruykys L, Ottewell K, Kanowski J, Moseby KE, Byrne M, Donnellan SC, Copley P, Austin JJ. Genetic monitoring of the greater stick-nest rat meta-population for strategic supplementation planning. CONSERV GENET 2020. [DOI: 10.1007/s10592-020-01299-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
AbstractTranslocation is an increasingly common component of species conservation efforts. However, translocated populations often suffer from loss of genetic diversity and increased inbreeding, and thus may require active management to establish gene flow across isolated populations. Assisted gene flow can be laborious and costly, so recipient and source populations should be carefully chosen to maximise genetic diversity outcomes. The greater stick-nest rat (GSNR, Leporillus conditor), a threatened Australian rodent, has been the focus of a translocation program since 1985, resulting in five extant translocated populations (St Peter Island, Reevesby Island, Arid Recovery, Salutation Island and Mt Gibson), all derived from a remnant wild population on the East and West Franklin Islands. We evaluated the genetic diversity in all extant GSNR populations using a large single nucleotide polymorphism dataset with the explicit purpose of informing future translocation planning. Our results show varying levels of genetic divergence, inbreeding and loss of genetic diversity in all translocated populations relative to the remnant source on the Franklin Islands. All translocated populations would benefit from supplementation to increase genetic diversity, but two—Salutation Island and Mt Gibson—are of highest priority. We recommend a targeted admixture approach, in which animals for supplementation are sourced from populations that have low relatedness to the recipient population. Subject to assessment of contemporary genetic diversity, St Peter Island and Arid Recovery are the most appropriate source populations for genetic supplementation. Our study demonstrates an effective use of genetic surveys for data-driven management of threatened species.
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15
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Quéméré E, Rossi S, Petit E, Marchand P, Merlet J, Game Y, Galan M, Gilot-Fromont E. Genetic epidemiology of the Alpine ibex reservoir of persistent and virulent brucellosis outbreak. Sci Rep 2020; 10:4400. [PMID: 32157133 PMCID: PMC7064506 DOI: 10.1038/s41598-020-61299-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 02/25/2020] [Indexed: 01/23/2023] Open
Abstract
While it is now broadly accepted that inter-individual variation in the outcomes of host-pathogen interactions is at least partially genetically controlled, host immunogenetic characteristics are rarely investigated in wildlife epidemiological studies. Furthermore, most immunogenetic studies in the wild focused solely on the major histocompatibility complex (MHC) diversity despite it accounts for only a fraction of the genetic variation in pathogen resistance. Here, we investigated immunogenetic diversity of the Alpine ibex (Capra ibex) population of the Bargy massif, reservoir of a virulent outbreak of brucellosis. We analysed the polymorphism and associations with disease resistance of the MHC Class II Drb gene and several non-MHC genes (Toll-like receptor genes, Slc11A1) involved in the innate immune response to Brucella in domestic ungulates. We found a very low neutral genetic diversity and a unique MHC Drb haplotype in this population founded few decades ago from a small number of individuals. By contrast, other immunity-related genes have maintained polymorphism and some showed significant associations with the brucellosis infection status hence suggesting a predominant role of pathogen-mediated selection in their recent evolutionary trajectory. Our results highlight the need to monitor immunogenetic variation in wildlife epidemiological studies and to look beyond the MHC.
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Affiliation(s)
- Erwan Quéméré
- CEFS, INRAE, Université de Toulouse, Castanet-Tolosan, France.
- ESE, Ecology and Ecosystems Health, Agrocampus Ouest, INRAE, 35042 Rennes, France.
| | - Sophie Rossi
- Office Français de la Biodiversité, Unité Sanitaire de la Faune, Gap, France
| | - Elodie Petit
- Office Français de la Biodiversité, Unité Ongulés sauvages, Gières, France
| | - Pascal Marchand
- Office Français de la Biodiversité, Unité Ongulés sauvages, Gières, France
| | - Joël Merlet
- CEFS, INRAE, Université de Toulouse, Castanet-Tolosan, France
| | - Yvette Game
- Laboratoire Départemental d'Analyses Vétérinaires de Savoie, Chambéry, France
| | - Maxime Galan
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Emmanuelle Gilot-Fromont
- Université de Lyon, VetAgro Sup - Campus vétérinaire de Lyon, Marcy l'Étoile, France
- Université de Lyon 1, UMR CNRS 5558 Laboratoire de Biométrie et Biologie Evolutive (LBBE), Villeurbanne, France
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16
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Purging of highly deleterious mutations through severe bottlenecks in Alpine ibex. Nat Commun 2020; 11:1001. [PMID: 32081890 PMCID: PMC7035315 DOI: 10.1038/s41467-020-14803-1] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 02/05/2020] [Indexed: 12/14/2022] Open
Abstract
Human activity has caused dramatic population declines in many wild species. The resulting bottlenecks have a profound impact on the genetic makeup of a species with unknown consequences for health. A key genetic factor for species survival is the evolution of deleterious mutation load, but how bottleneck strength and mutation load interact lacks empirical evidence. We analyze 60 complete genomes of six ibex species and the domestic goat. We show that historic bottlenecks rather than the current conservation status predict levels of genome-wide variation. By analyzing the exceptionally well-characterized population bottlenecks of the once nearly extinct Alpine ibex, we find genomic evidence of concurrent purging of highly deleterious mutations but accumulation of mildly deleterious mutations. This suggests that recolonization bottlenecks induced both relaxed selection and purging, thus reshaping the landscape of deleterious mutation load. Our findings highlight that even populations of ~1000 individuals can accumulate mildly deleterious mutations. Conservation efforts should focus on preventing population declines below such levels to ensure long-term survival of species. Although there is extensive theory predicting the effects of population bottlenecks on mutation load, there is little empirical evidence from recent bottlenecks. Here, Grossen et al. compare the consequences of population bottlenecks in six ibex species for genome-wide variation and mutation load.
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Fuller J, Ferchaud A, Laporte M, Le Luyer J, Davis TB, Côté SD, Bernatchez L. Absence of founder effect and evidence for adaptive divergence in a recently introduced insular population of white‐tailed deer (
Odocoileus virginianus
). Mol Ecol 2019; 29:86-104. [DOI: 10.1111/mec.15317] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 10/25/2019] [Accepted: 10/29/2019] [Indexed: 12/16/2022]
Affiliation(s)
- Jérémie Fuller
- Département de Biologie Université Laval Québec QC Canada
- Natural Sciences and Engineering Research Council of Canada (NSERC) Research Chair in Integrated Management of the Resources of Anticosti Island and Centre d'Études Nordiques (CEN) Québec QC Canada
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| | - Anne‐Laure Ferchaud
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| | - Martin Laporte
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| | - Jérémy Le Luyer
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| | | | - Steeve D. Côté
- Département de Biologie Université Laval Québec QC Canada
- Natural Sciences and Engineering Research Council of Canada (NSERC) Research Chair in Integrated Management of the Resources of Anticosti Island and Centre d'Études Nordiques (CEN) Québec QC Canada
| | - Louis Bernatchez
- Département de Biologie Université Laval Québec QC Canada
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
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18
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Cullingham CI, Moehrenschlager A. Genetics of a reintroduced swift fox population highlights the need for integrated conservation between neighbouring countries. Anim Conserv 2019. [DOI: 10.1111/acv.12508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- C. I. Cullingham
- Department of Biological Sciences University of Alberta Edmonton Alberta Canada
| | - A. Moehrenschlager
- Centre for Conservation Research Calgary Zoological Society Calgary Alberta Canada
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19
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Inbreeding reduces long-term growth of Alpine ibex populations. Nat Ecol Evol 2019; 3:1359-1364. [PMID: 31477848 DOI: 10.1038/s41559-019-0968-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 07/26/2019] [Indexed: 11/08/2022]
Abstract
Many studies document negative inbreeding effects on individuals, and conservation efforts to preserve rare species routinely employ strategies to reduce inbreeding. Despite this, there are few clear examples in nature of inbreeding decreasing the growth rates of populations, and the extent of population-level effects of inbreeding in the wild remains controversial. Here, we take advantage of a long-term dataset of 26 reintroduced Alpine ibex (Capra ibex ibex) populations spanning nearly 100 years to show that inbreeding substantially reduced per capita population growth rates, particularly for populations in harsher environments. Populations with high average inbreeding (F ≈ 0.2) had population growth rates reduced by 71% compared with populations with no inbreeding. Our results show that inbreeding can have long-term demographic consequences even when environmental variation is large and deleterious alleles may have been purged during bottlenecks. Thus, efforts to guard against inbreeding effects in populations of endangered species have not been misplaced.
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20
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Jahner JP, Matocq MD, Malaney JL, Cox M, Wolff P, Gritts MA, Parchman TL. The genetic legacy of 50 years of desert bighorn sheep translocations. Evol Appl 2019; 12:198-213. [PMID: 30697334 PMCID: PMC6346675 DOI: 10.1111/eva.12708] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 08/16/2018] [Accepted: 08/18/2018] [Indexed: 12/20/2022] Open
Abstract
Conservation biologists have increasingly used translocations to mitigate population declines and restore locally extirpated populations. Genetic data can guide the selection of source populations for translocations and help evaluate restoration success. Bighorn sheep (Ovis canadensis) are a managed big game species that suffered widespread population extirpations across western North America throughout the early 1900s. Subsequent translocation programs have successfully re-established many formally extirpated bighorn herds, but most of these programs pre-date genetically informed management practices. The state of Nevada presents a particularly well-documented case of decline followed by restoration of extirpated herds. Desert bighorn sheep (O. c. nelsoni) populations declined to less than 3,000 individuals restricted to remnant herds in the Mojave Desert and a few locations in the Great Basin Desert. Beginning in 1968, the Nevada Department of Wildlife translocated ~2,000 individuals from remnant populations to restore previously extirpated areas, possibly establishing herds with mixed ancestries. Here, we examined genetic diversity and structure among remnant herds and the genetic consequences of translocation from these herds using a genotyping-by-sequencing approach to genotype 17,095 loci in 303 desert bighorn sheep. We found a signal of population genetic structure among remnant Mojave Desert populations, even across geographically proximate mountain ranges. Further, we found evidence of a genetically distinct, potential relict herd from a previously hypothesized Great Basin lineage of desert bighorn sheep. The genetic structure of source herds was clearly reflected in translocated populations. In most cases, herds retained genetic evidence of multiple translocation events and subsequent admixture when founded from multiple remnant source herds. Our results add to a growing literature on how population genomic data can be used to guide and monitor restoration programs.
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Affiliation(s)
| | - Marjorie D. Matocq
- Department of Natural Resources and Environmental Science, and Program in Ecology, Evolution, and Conservation BiologyUniversity of NevadaRenoNevada
| | - Jason L. Malaney
- Department of BiologyAustin Peay State UniversityClarksvilleTennessee
| | - Mike Cox
- Nevada Department of Wildlife, and Wild Sheep Working GroupWestern Association of Fish and Wildlife AgenciesRenoNevada
| | | | | | - Thomas L. Parchman
- Department of Biology, and Program in Ecology, Evolution, and Conservation BiologyUniversity of NevadaRenoNevada
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21
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Bhattacharyya S, Dawson DA, Hipperson H, Ishtiaq F. A diet rich in C 3 plants reveals the sensitivity of an alpine mammal to climate change. Mol Ecol 2019; 28:250-265. [PMID: 30136323 PMCID: PMC6391869 DOI: 10.1111/mec.14842] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 07/17/2018] [Accepted: 08/03/2018] [Indexed: 02/06/2023]
Abstract
Plant-herbivore interactions provide critical insights into the mechanisms that govern the spatiotemporal distributions of organisms. These interactions are crucial to understanding the impacts of climate change, which are likely to have an effect on the population dynamics of alpine herbivores. The Royle's pika (Ochotona roylei, hereafter pika) is a lagomorph found in the western Himalaya and is dependent on alpine plants that are at risk from climate change. As the main prey of many carnivores in the region, the pika plays a crucial role in trophic interactions. We examined topographical features, plant genera presence and seasonal dynamics as drivers of the plant richness in the pika's diet across an elevational gradient (2,600-4,450 m). We identified 79 plant genera in the faecal pellets of pikas, of which 89% were forbs, >60% were endemic to the Himalaya, and 97.5% of the diet plant genera identified followed the C3 photosynthetic pathway. We found that, during the premonsoon season, the number of genera in the pika's diet decreased with increasing elevation. We demonstrate that a large area of talus supports greater plant diversity and, not surprisingly, results in higher species richness in the pika's diet. However, in talus habitat with deep crevices, pikas consumed fewer plant genera suggesting they may be foraging suboptimally due to predation risk. The continued increase in global temperature is expected to have an effect on the distribution dynamics of C3 plants and consequently influence pika diet and distribution, resulting in a significant negative cascading effect on the Himalayan ecosystem.
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Affiliation(s)
- Sabuj Bhattacharyya
- Centre for Ecological SciencesIndian Institute of ScienceBangaloreIndia
- Department of Animal and Plant SciencesWestern BankUniversity of SheffieldSheffieldUK
| | - Deborah A. Dawson
- Department of Animal and Plant SciencesWestern BankUniversity of SheffieldSheffieldUK
| | - Helen Hipperson
- Department of Animal and Plant SciencesWestern BankUniversity of SheffieldSheffieldUK
| | - Farah Ishtiaq
- Centre for Ecological SciencesIndian Institute of ScienceBangaloreIndia
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22
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Bullock JM, Bonte D, Pufal G, da Silva Carvalho C, Chapman DS, García C, García D, Matthysen E, Delgado MM. Human-Mediated Dispersal and the Rewiring of Spatial Networks. Trends Ecol Evol 2018; 33:958-970. [PMID: 30314915 DOI: 10.1016/j.tree.2018.09.008] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 09/03/2018] [Accepted: 09/12/2018] [Indexed: 12/13/2022]
Abstract
Humans fundamentally affect dispersal, directly by transporting individuals and indirectly by altering landscapes and natural vectors. This human-mediated dispersal (HMD) modifies long-distance dispersal, changes dispersal paths, and overall benefits certain species or genotypes while disadvantaging others. HMD is leading to radical changes in the structure and functioning of spatial networks, which are likely to intensify as human activities increase in scope and extent. Here, we provide an overview to guide research into HMD and the resulting rewiring of spatial networks, making predictions about the ecological and evolutionary consequences and how these vary according to spatial scale and the traits of species. Future research should consider HMD holistically, assessing the range of direct and indirect processes to understand the complex impacts on eco-evolutionary dynamics.
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Affiliation(s)
| | - Dries Bonte
- Department of Biology, Ghent University, Ghent, Belgium
| | - Gesine Pufal
- Department of Nature Conservation and Landscape Ecology, University of Freiburg, Freiburg, Germany
| | | | | | - Cristina García
- Centre for Research on Biodiversity and Genetic Resources, University of Porto, Porto, Portugal; Institute of Integrative Biology, Department of Evolution, Ecology and Behaviour, University of Liverpool, Liverpool, UK
| | - Daniel García
- Department of Biology of Organisms and Systems and Biodiversity Research Unit, University of Oviedo, Oviedo, Spain
| | - Erik Matthysen
- Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Maria Mar Delgado
- Department of Biology of Organisms and Systems and Biodiversity Research Unit, University of Oviedo, Oviedo, Spain
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23
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Hassan LMA, Arends D, Rahmatalla SA, Reissmann M, Reyer H, Wimmers K, Abukashawa SMA, Brockmann GA. Genetic diversity of Nubian ibex in comparison to other ibex and domesticated goat species. EUR J WILDLIFE RES 2018. [DOI: 10.1007/s10344-018-1212-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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24
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Brambilla A, Keller L, Bassano B, Grossen C. Heterozygosity-fitness correlation at the major histocompatibility complex despite low variation in Alpine ibex ( Capra ibex). Evol Appl 2018; 11:631-644. [PMID: 29875807 PMCID: PMC5979623 DOI: 10.1111/eva.12575] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 10/30/2017] [Indexed: 01/06/2023] Open
Abstract
Crucial for the long-term survival of wild populations is their ability to fight diseases. Disease outbreaks can lead to severe population size reductions, which makes endangered and reintroduced species especially vulnerable. In vertebrates, the major histocompatibility complex (MHC) plays an important role in determining the immune response. Species that went through severe bottlenecks often show very low levels of genetic diversity at the MHC. Due to the known link between the MHC and immune response, such species are expected to be at particular risk in case of disease outbreaks. However, so far, only few studies have shown that low MHC diversity is correlated with increased disease susceptibility in species after severe bottlenecks. We investigated genetic variation at the MHC and its correlations with disease resistance and other fitness-related traits in Alpine ibex (Capra ibex), a wild goat species that underwent a strong bottleneck in the last century and that is known to have extremely low genetic variability, both genome-wide and at the MHC. We studied MHC variation in male ibex of Gran Paradiso National Park, the population used as a source for all postbottleneck reintroductions. We found that individual MHC heterozygosity (based on six microsatellites) was not correlated with genome-wide neutral heterozygosity. MHC heterozygosity, but not genome-wide heterozygosity, was positively correlated with resistance to infectious keratoconjunctivitis and with body mass. Our results show that genetic variation at the MHC plays an important role in disease resistance and, hence, should be taken into account for successfully managing species conservation.
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Affiliation(s)
- Alice Brambilla
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZurich (ZH)Switzerland
- Alpine Wildlife Research CentreGran Paradiso National ParkNoasca (TO)Italy
| | - Lukas Keller
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZurich (ZH)Switzerland
| | - Bruno Bassano
- Alpine Wildlife Research CentreGran Paradiso National ParkNoasca (TO)Italy
| | - Christine Grossen
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZurich (ZH)Switzerland
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25
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Büntgen U, Galván JD, Mysterud A, Krusic PJ, Hülsmann L, Jenny H, Senn J, Bollmann K. Horn growth variation and hunting selection of the Alpine ibex. J Anim Ecol 2018; 87:1069-1079. [DOI: 10.1111/1365-2656.12839] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 03/21/2018] [Indexed: 11/30/2022]
Affiliation(s)
- Ulf Büntgen
- Department of Geography; University of Cambridge; Cambridge UK
- Swiss Federal Research Institute WSL; Birmensdorf Switzerland
- Global Change Research Centre and Masaryk University; Brno Czech Republic
| | - Juan D. Galván
- Swiss Federal Research Institute WSL; Birmensdorf Switzerland
| | - Atle Mysterud
- Centre for Ecological and Evolutionary Synthesis (CEES); Department of Biosciences; University of Oslo; Oslo Norway
| | - Paul J. Krusic
- Department of Geography; University of Cambridge; Cambridge UK
- Department of Physical Geography; Stockholm University; Stockholm Sweden
| | - Lisa Hülsmann
- Swiss Federal Research Institute WSL; Birmensdorf Switzerland
- Forest Ecology; Institute of Terrestrial Ecosystems; Department of Environmental Sciences; ETH Zurich; Zurich Switzerland
- Department of Theoretical Ecology; University of Regensburg; Regensburg Germany
| | - Hannes Jenny
- Department of Wildlife and Fishery Service Grisons; Chur Switzerland
| | - Josef Senn
- Swiss Federal Research Institute WSL; Birmensdorf Switzerland
| | - Kurt Bollmann
- Swiss Federal Research Institute WSL; Birmensdorf Switzerland
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26
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Leigh DM, Lischer HEL, Grossen C, Keller LF. Batch effects in a multiyear sequencing study: False biological trends due to changes in read lengths. Mol Ecol Resour 2018; 18:778-788. [DOI: 10.1111/1755-0998.12779] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 02/27/2018] [Accepted: 03/01/2018] [Indexed: 12/11/2022]
Affiliation(s)
- D. M. Leigh
- Department of Evolutionary Biology and Environmental Studies University of Zurich Zurich Switzerland
- Swiss Institute of Bioinformatics Quartier Sorge ‐ Batiment Genopode Lausanne Switzerland
- Department of Biology Queen's University Kingston ON Canada
| | - H. E. L. Lischer
- Department of Evolutionary Biology and Environmental Studies University of Zurich Zurich Switzerland
- Swiss Institute of Bioinformatics Quartier Sorge ‐ Batiment Genopode Lausanne Switzerland
| | - C. Grossen
- Department of Evolutionary Biology and Environmental Studies University of Zurich Zurich Switzerland
| | - L. F. Keller
- Department of Evolutionary Biology and Environmental Studies University of Zurich Zurich Switzerland
- Zoological Museum University of Zurich Zurich Switzerland
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27
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Russo IRM, Hoban S, Bloomer P, Kotzé A, Segelbacher G, Rushworth I, Birss C, Bruford MW. ‘Intentional Genetic Manipulation’ as a conservation threat. CONSERV GENET RESOUR 2018. [DOI: 10.1007/s12686-018-0983-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Portanier E, Garel M, Devillard S, Marchand P, Andru J, Maillard D, Bourgoin G. Introduction history overrides social factors in explaining genetic structure of females in Mediterranean mouflon. Ecol Evol 2017; 7:9580-9591. [PMID: 29187991 PMCID: PMC5696436 DOI: 10.1002/ece3.3433] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 08/15/2017] [Accepted: 08/15/2017] [Indexed: 11/25/2022] Open
Abstract
Fine‐scale spatial genetic structure of populations results from social and spatial behaviors of individuals such as sex‐biased dispersal and philopatry. However, the demographic history of a given population can override such socio‐spatial factors in shaping genetic variability when bottlenecks or founder events occurred in the population. Here, we investigated whether socio‐spatial organization determines the fine‐scale genetic structure for both sexes in a Mediterranean mouflon (Ovis gmelini musimon × Ovis sp.) population in southern France 60 years after its introduction. Based on multilocus genotypes at 16 loci of microsatellite DNA (n = 230 individuals), we identified three genetic groups for females and two for males, and concurrently defined the same number of socio‐spatial units using both GPS‐collared individuals (n = 121) and visual resightings of marked individuals (n = 378). The socio‐spatial and genetic structures did not match, indicating that the former was not the main driver of the latter for both sexes. Beyond this structural mismatch, we found significant, yet low, genetic differentiation among female socio‐spatial groups, and no genetic differentiation in males, with this suggesting female philopatry and male‐biased gene flow, respectively. Despite spatial disconnection, females from the north of the study area were genetically closer to females from the south, as indicated by the spatial analysis of the genetic variability, and this pattern was in accordance with the common genetic origin of their founders. To conclude, more than 14 generations later, genetic signatures of first introduction are not only still detectable among females, but they also represent the main factor shaping their present‐time genetic structure.
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Affiliation(s)
- Elodie Portanier
- Laboratoire de Biométrie et Biologie Evolutive CNRS Université Claude Bernard Lyon 1 Université de Lyon Villeurbanne France.,Unité Faune de Montagne Office National de la Chasse et de la Faune Sauvage Juvignac France.,VetAgro Sup - Campus Vétérinaire de Lyon Université de Lyon Marcy l'Etoile France
| | - Mathieu Garel
- Unité Faune de Montagne Office National de la Chasse et de la Faune Sauvage Juvignac France
| | - Sébastien Devillard
- Laboratoire de Biométrie et Biologie Evolutive CNRS Université Claude Bernard Lyon 1 Université de Lyon Villeurbanne France
| | - Pascal Marchand
- Unité Faune de Montagne Office National de la Chasse et de la Faune Sauvage Juvignac France
| | - Julie Andru
- Unité Faune de Montagne Office National de la Chasse et de la Faune Sauvage Juvignac France.,VetAgro Sup - Campus Vétérinaire de Lyon Université de Lyon Marcy l'Etoile France
| | - Daniel Maillard
- Unité Faune de Montagne Office National de la Chasse et de la Faune Sauvage Juvignac France
| | - Gilles Bourgoin
- Laboratoire de Biométrie et Biologie Evolutive CNRS Université Claude Bernard Lyon 1 Université de Lyon Villeurbanne France.,VetAgro Sup - Campus Vétérinaire de Lyon Université de Lyon Marcy l'Etoile France
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Grossen C, Biebach I, Angelone-Alasaad S, Keller LF, Croll D. Population genomics analyses of European ibex species show lower diversity and higher inbreeding in reintroduced populations. Evol Appl 2017; 11:123-139. [PMID: 29387150 PMCID: PMC5775499 DOI: 10.1111/eva.12490] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Accepted: 04/04/2017] [Indexed: 12/30/2022] Open
Abstract
Restoration of lost species ranges to their native distribution is key for the survival of endangered species. However, reintroductions often fail and long‐term genetic consequences are poorly understood. Alpine ibex (Capra ibex) are wild goats that recovered from <100 individuals to ~50,000 within a century by population reintroductions. We analyzed the population genomic consequences of the Alpine ibex reintroduction strategy. We genotyped 101,822 genomewide single nucleotide polymorphism loci in 173 Alpine ibex, the closely related Iberian ibex (Capra pyrenaica) and domestic goat (Capra hircus). The source population of all Alpine ibex maintained genetic diversity comparable to Iberian ibex, which experienced less severe bottlenecks. All reintroduced Alpine ibex populations had individually and combined lower levels of genetic diversity than the source population. The reintroduction strategy consisted of primary reintroductions from captive breeding and secondary reintroductions from established populations. This stepwise reintroduction strategy left a strong genomic footprint of population differentiation, which increased with subsequent rounds of reintroductions. Furthermore, analyses of genomewide runs of homozygosity showed recent inbreeding primarily in individuals of reintroduced populations. We showed that despite the rapid census recovery, Alpine ibex carry a persistent genomic signature of their reintroduction history. We discuss how genomic monitoring can serve as an early indicator of inbreeding.
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Affiliation(s)
- Christine Grossen
- Department of Evolutionary Biology and Environmental Studies University of Zürich Zürich Switzerland
| | - Iris Biebach
- Department of Evolutionary Biology and Environmental Studies University of Zürich Zürich Switzerland
| | - Samer Angelone-Alasaad
- Department of Evolutionary Biology and Environmental Studies University of Zürich Zürich Switzerland
| | - Lukas F Keller
- Department of Evolutionary Biology and Environmental Studies University of Zürich Zürich Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics Institute of Biology University of Neuchâtel Neuchâtel Switzerland
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Angelone-Alasaad S, Biebach I, Pérez JM, Soriguer RC, Granados JE. Molecular Analyses Reveal Unexpected Genetic Structure in Iberian Ibex Populations. PLoS One 2017; 12:e0170827. [PMID: 28135293 PMCID: PMC5279733 DOI: 10.1371/journal.pone.0170827] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2016] [Accepted: 01/11/2017] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Genetic differentiation in historically connected populations could be the result of genetic drift or adaptation, two processes that imply a need for differing strategies in population management. The aim of our study was to use neutral genetic markers to characterize C. pyrenaica populations genetically and examine results in terms of (i) demographic history, (ii) subspecific classification and (iii) the implications for the management of Iberian ibex. METHODOLOGY/PRINCIPAL FINDINGS We used 30 neutral microsatellite markers from 333 Iberian ibex to explore genetic diversity in the three main Iberian ibex populations in Spain corresponding to the two persisting subspecies (victoria and hispanica). Our molecular analyses detected recent genetic bottlenecks in all the studied populations, a finding that coincides with the documented demographic decline in C. pyrenaica in recent decades. Genetic divergence between the two C. pyrenaica subspecies (hispanica and victoriae) was substantial (FST between 0.39 and 0.47). Unexpectedly, we found similarly high genetic differentiation between two populations (Sierra Nevada and Maestrazgo) belonging to the subspecies hispanica. The genetic pattern identified in our study could be the result of strong genetic drift due to the severe genetic bottlenecks in the studied populations, caused in turn by the progressive destruction of natural habitat, disease epidemics and/or uncontrolled hunting. CONCLUSIONS Previous Capra pyrenaica conservation decision-making was based on the clear distinction between the two subspecies (victoriae and hispanica); yet our paper raises questions about the usefulness for conservation plans of the distinction between these subspecies.
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Affiliation(s)
- Samer Angelone-Alasaad
- Institute of Evolutionary Biology and Environmental Studies (IEU), University of Zürich, Winterthurerstrasse 190, Zürich, Switzerland
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Avda. Américo Vespucio s/n Sevilla, Spain
| | - Iris Biebach
- Institute of Evolutionary Biology and Environmental Studies (IEU), University of Zürich, Winterthurerstrasse 190, Zürich, Switzerland
| | - Jesús M. Pérez
- Departamento de Biología Animal, Biología Vegetal y Ecología, Universidad de Jaén, Campus Las Lagunillas, s/n, Jaén, Spain
| | - Ramón C. Soriguer
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Avda. Américo Vespucio s/n Sevilla, Spain
| | - José E. Granados
- Espacio Natural de Sierra Nevada, Carretera Antigua de Sierra Nevada, km 7, Pinos Genil, Granada, Spain
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31
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Bozzuto C, Hoeck PEA, Bagheri HC, Keller LF. Modelling different reintroduction strategies for the critically endangered Floreana mockingbird. Anim Conserv 2016. [DOI: 10.1111/acv.12299] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- C. Bozzuto
- Department of Evolutionary Biology and Environmental Studies; University of Zurich; Zurich Switzerland
| | - P. E. A. Hoeck
- Department of Evolutionary Biology and Environmental Studies; University of Zurich; Zurich Switzerland
| | - H. C. Bagheri
- Department of Evolutionary Biology and Environmental Studies; University of Zurich; Zurich Switzerland
| | - L. F. Keller
- Department of Evolutionary Biology and Environmental Studies; University of Zurich; Zurich Switzerland
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32
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Lenstra JA, Tigchelaar J, Biebach I, Hallsson JH, Kantanen J, Nielsen VH, Pompanon F, Naderi S, Rezaei HR, Saether N, Ertugrul O, Grossen C, Camenisch G, Vos-Loohuis M, van Straten M, de Poel EA, Windig J, Oldenbroek K. Microsatellite diversity of the Nordic type of goats in relation to breed conservation: how relevant is pure ancestry? J Anim Breed Genet 2016; 134:78-84. [PMID: 27339108 DOI: 10.1111/jbg.12226] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 05/24/2016] [Indexed: 11/25/2022]
Abstract
In the last decades, several endangered breeds of livestock species have been re-established effectively. However, the successful revival of the Dutch and Danish Landrace goats involved crossing with exotic breeds and the ancestry of the current populations is therefore not clear. We have generated genotypes for 27 FAO-recommended microsatellites of these landraces and three phenotypically similar Nordic-type landraces and compared these breeds with central European, Mediterranean and south-west Asian goats. We found decreasing levels of genetic diversity with increasing distance from the south-west Asian domestication site with a south-east-to-north-west cline that is clearly steeper than the Mediterranean east-to-west cline. In terms of genetic diversity, the Dutch Landrace comes next to the isolated Icelandic breed, which has an extremely low diversity. The Norwegian coastal goat and the Finnish and Icelandic landraces are clearly related. It appears that by a combination of mixed origin and a population bottleneck, the Dutch and Danish Land-races are separated from the other breeds. However, the current Dutch and Danish populations with the multicoloured and long-horned appearance effectively substitute for the original breed, illustrating that for conservation of cultural heritage, the phenotype of a breed is more relevant than pure ancestry and the genetic diversity of the original breed. More in general, we propose that for conservation, the retention of genetic diversity of an original breed and of the visual phenotype by which the breed is recognized and defined needs to be considered separately.
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Affiliation(s)
- J A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - J Tigchelaar
- Stichting Zeldzame Huisdierrassen, Wageningen, The Netherlands
| | - I Biebach
- Institute of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
| | | | - J H Hallsson
- Faculty of Land and Animal Resources, Agricultural University of Iceland, Reykjavik, Iceland
| | - J Kantanen
- Green Technology, Natural Resources Institute Finland, Jokioinen, Finland.,Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland
| | - V H Nielsen
- Research Centre Foulum, Aarhus University, Tjele, Denmark
| | - F Pompanon
- Université Grenoble Alpes, Grenoble, France
| | - S Naderi
- Environmental Sciences Department, Natural Resources Faculty, University of Guilan, Guilan, Iran
| | - H-R Rezaei
- Environmental Sciences Department, Gorgan University of Agriculture and Natural Resources, Gorgan, Iran
| | - N Saether
- Norwegian Genetic Resource Centre, Ås, Norway
| | - O Ertugrul
- Veterinary Faculty, Ankara University, Ankara, Turkey
| | - C Grossen
- Institute of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
| | - G Camenisch
- Institute of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
| | - M Vos-Loohuis
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - M van Straten
- Stichting Zeldzame Huisdierrassen, Wageningen, The Netherlands
| | - E A de Poel
- Stichting Zeldzame Huisdierrassen, Wageningen, The Netherlands
| | - J Windig
- Animal Sciences Group and Centre for Genetic Resources-Wageningen UR, Lelystad, The Netherlands
| | - K Oldenbroek
- Stichting Zeldzame Huisdierrassen, Wageningen, The Netherlands.,Animal Sciences Group and Centre for Genetic Resources-Wageningen UR, Lelystad, The Netherlands
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33
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Functional gene diversity and migration timing in reintroduced Chinook salmon. CONSERV GENET 2015. [DOI: 10.1007/s10592-015-0753-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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34
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Levý E, Putnová L, Štohl R, Svobodová K, Matoušková J, Robovský J, Lamka J, Vrtková I, Ernst M. Utility of several microsatellite markers for the genetic characterisation of three ex situ populations of threatened caprine taxa (<i>Capra aegagrus</i>, <i>C. cylindricornis</i> and <i>C. falconeri</i>). Arch Anim Breed 2015. [DOI: 10.5194/aab-58-365-2015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Abstract. Caprines belong to the most endangered group of mammals and artiodactyls suffering from many negative human impacts. Fortunately, many of them are protected and managed by national and international legislation and in situ and ex situ conservation actions. Although many microsatellite markers have been developed for wild and domestic caprines, they remain uninvestigated in respect of their utility for some taxa. We examined the utility of the International Society for Animal Genetics microsatellite set for genetic characterisations of three wild and one domestic Capra species from captive or semi-captive ex situ populations in Europe. Our data suggest the utility of this microsatellite set for detecting shared and species-specific alleles, characterising the genetic variability, and determining phylogenetic relationships and intraspecific structures in investigated taxa. We detected a depleted genetic variability in Capra falconeri and Capra cylindricornis in European ex situ populations; unrelated individuals are therefore needed for improving genetic variability parameters, as they are for the extralimital population of Capra aegagrus in the Vřísek game reserve (Czech Republic), for which we identified no genetic introgression from the domestic goat and great dissimilarity with some analysed individuals from European zoos. Current results here indicate some difficulties with the historical evidence, for example with respect to the origin and purity of particular individuals under breeding programmes.
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35
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Winton CL, Plante Y, Hind P, McMahon R, Hegarty MJ, McEwan NR, Davies-Morel MCG, Morgan CM, Powell W, Nash DM. Comparative genetic diversity in a sample of pony breeds from the U.K. and North America: a case study in the conservation of global genetic resources. Ecol Evol 2015; 5:3507-22. [PMID: 26380682 PMCID: PMC4569044 DOI: 10.1002/ece3.1562] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 05/14/2015] [Accepted: 05/18/2015] [Indexed: 11/09/2022] Open
Abstract
Most species exist as subdivided ex situ daughter population(s) derived from a single original group of individuals. Such subdivision occurs for many reasons both natural and manmade. Traditional British and Irish pony breeds were introduced to North America (U.S.A. and Canada) within the last 150 years, and subsequently equivalent breed societies were established. We have analyzed selected U.K. and North American equivalent pony populations as a case study for understanding the relationship between putative source and derived subpopulations. Diversity was measured using mitochondrial DNA and a panel of microsatellite markers. Genetic signatures differed between the North American subpopulations according to historical management processes. Founder effect and stochastic drift was apparent, particularly pronounced in some breeds, with evidence of admixture of imported mares of different North American breeds. This demonstrates the importance of analysis of subpopulations to facilitate understanding the genetic effects of past management practices and to lead to informed future conservation strategies.
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Affiliation(s)
- Clare L Winton
- IBERS, Aberystwyth University Aberystwyth, Ceredigion, SY23 3DA, U.K
| | - Yves Plante
- Agriculture and Agri-Food Canada Saskatoon, Saskatchewan, S7N 5A8, Canada
| | - Pamela Hind
- Agriculture and Agri-Food Canada Saskatoon, Saskatchewan, S7N 5A8, Canada
| | - Robert McMahon
- IBERS, Aberystwyth University Aberystwyth, Ceredigion, SY23 3DA, U.K
| | - Matthew J Hegarty
- IBERS, Aberystwyth University Aberystwyth, Ceredigion, SY23 3DA, U.K
| | - Neil R McEwan
- IBERS, Aberystwyth University Aberystwyth, Ceredigion, SY23 3DA, U.K
| | | | - Charly M Morgan
- IBERS, Aberystwyth University Aberystwyth, Ceredigion, SY23 3DA, U.K
| | | | - Deborah M Nash
- IBERS, Aberystwyth University Aberystwyth, Ceredigion, SY23 3DA, U.K
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36
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Brambilla A, Biebach I, Bassano B, Bogliani G, von Hardenberg A. Direct and indirect causal effects of heterozygosity on fitness-related traits in Alpine ibex. Proc Biol Sci 2015; 282:20141873. [PMID: 25392468 DOI: 10.1098/rspb.2014.1873] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Heterozygosity-fitness correlations (HFCs) are a useful tool to investigate the effects of inbreeding in wild populations, but are not informative in distinguishing between direct and indirect effects of heterozygosity on fitness-related traits. We tested HFCs in male Alpine ibex (Capra ibex) in a free-ranging population (which suffered a severe bottleneck at the end of the eighteenth century) and used confirmatory path analysis to disentangle the causal relationships between heterozygosity and fitness-related traits. We tested HFCs in 149 male individuals born between 1985 and 2009. We found that standardized multi-locus heterozygosity (MLH), calculated from 37 microsatellite loci, was related to body mass and horn growth, which are known to be important fitness-related traits, and to faecal egg counts (FECs) of nematode eggs, a proxy of parasite resistance. Then, using confirmatory path analysis, we were able to show that the effect of MLH on horn growth was not direct but mediated by body mass and FEC. HFCs do not necessarily imply direct genetic effects on fitness-related traits, which instead can be mediated by other traits in complex and unexpected ways.
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Affiliation(s)
- Alice Brambilla
- DSTA-Department of Earth and Environmental Science, University of Pavia, Via A. Ferrata 9, 27100 Pavia (PV), Italy
| | - Iris Biebach
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Bruno Bassano
- Alpine Wildlife Research Centre, Gran Paradiso National Park, Degioz 11, 11010 Valsavarenche, AO, Italy
| | - Giuseppe Bogliani
- DSTA-Department of Earth and Environmental Science, University of Pavia, Via A. Ferrata 9, 27100 Pavia (PV), Italy
| | - Achaz von Hardenberg
- Alpine Wildlife Research Centre, Gran Paradiso National Park, Degioz 11, 11010 Valsavarenche, AO, Italy
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37
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Mowry RA, Schneider TM, Latch EK, Gompper ME, Beringer J, Eggert LS. Genetics and the successful reintroduction of the Missouri river otter. Anim Conserv 2014. [DOI: 10.1111/acv.12159] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- R. A. Mowry
- Division of Biological Sciences; University of Missouri; Columbia MO USA
| | - T. M. Schneider
- Division of Biology; Kansas State University; Manhattan KS USA
| | - E. K. Latch
- Department of Biological Sciences; University of Wisconsin; Milwaukee WI USA
| | - M. E. Gompper
- Department of Fisheries and Wildlife Science; University of Missouri; Columbia MO USA
| | - J. Beringer
- Missouri Department of Conservation; Resource Science Center; Columbia MO USA
| | - L. S. Eggert
- Division of Biological Sciences; University of Missouri; Columbia MO USA
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38
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Grossen C, Keller L, Biebach I, Croll D. Introgression from domestic goat generated variation at the major histocompatibility complex of Alpine ibex. PLoS Genet 2014; 10:e1004438. [PMID: 24945814 PMCID: PMC4063738 DOI: 10.1371/journal.pgen.1004438] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 04/30/2014] [Indexed: 12/30/2022] Open
Abstract
The major histocompatibility complex (MHC) is a crucial component of the vertebrate immune system and shows extremely high levels of genetic polymorphism. The extraordinary genetic variation is thought to be ancient polymorphisms maintained by balancing selection. However, introgression from related species was recently proposed as an additional mechanism. Here we provide evidence for introgression at the MHC in Alpine ibex (Capra ibex ibex). At a usually very polymorphic MHC exon involved in pathogen recognition (DRB exon 2), Alpine ibex carried only two alleles. We found that one of these DRB alleles is identical to a DRB allele of domestic goats (Capra aegagrus hircus). We sequenced 2489 bp of the coding and non-coding regions of the DRB gene and found that Alpine ibex homozygous for the goat-type DRB exon 2 allele showed nearly identical sequences (99.8%) to a breed of domestic goats. Using Sanger and RAD sequencing, microsatellite and SNP chip data, we show that the chromosomal region containing the goat-type DRB allele has a signature of recent introgression in Alpine ibex. A region of approximately 750 kb including the DRB locus showed high rates of heterozygosity in individuals carrying one copy of the goat-type DRB allele. These individuals shared SNP alleles both with domestic goats and other Alpine ibex. In a survey of four Alpine ibex populations, we found that the region surrounding the DRB allele shows strong linkage disequilibria, strong sequence clustering and low diversity among haplotypes carrying the goat-type allele. Introgression at the MHC is likely adaptive and introgression critically increased MHC DRB diversity in the genetically impoverished Alpine ibex. Our finding contradicts the long-standing view that genetic variability at the MHC is solely a consequence of ancient trans-species polymorphism. Introgression is likely an underappreciated source of genetic diversity at the MHC and other loci under balancing selection. The major histocompatibility complex (MHC), a crucial component of the defense against pathogens, contains the most polymorphic functional genes in vertebrate genomes. The extraordinary genetic variation is generally considered to be ancient. We investigated whether a previously neglected mechanism, introgression from related species, provides an additional source of MHC variation. We show that introgression from domestic goat dramatically increased genetic variation at the MHC of Alpine ibex, a species that had nearly gone extinct during the 18th century, but has been restored to large numbers since. We show that Alpine ibex share one of only two alleles at a generally highly polymorphic MHC locus with domestic goats and that the chromosomal region containing the goat-type allele has a signature of recent introgression. Our finding contradicts the long-standing view that ancient trans-species polymorphism is the sole source of the extraordinary genetic variability at the MHC. Instead, we show that in Alpine ibex introgression generated genetic diversity at a MHC locus. Our study supports the view that loci favoring genetic polymorphism may be susceptible to adaptive introgression from related species and will encourage future research to identify unexpected signatures of introgression.
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Affiliation(s)
- Christine Grossen
- Institute of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
- Department of Zoology, University of British Columbia, Vancouver, Canada
- * E-mail:
| | - Lukas Keller
- Institute of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
| | - Iris Biebach
- Institute of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
| | - The International Goat Genome Consortium
- Kunming Institute of Zoology, Chinese Academy of Sciences, State Key Laboratory of Genetic Resources and Evolution, Kunming, China
- INRA, UMR444, Laboratoire de Génétique Cellulaire, Castanet-Tolosan, France
| | - Daniel Croll
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
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39
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Moreno E. Retrospective and prospective perspectives on zoonotic brucellosis. Front Microbiol 2014; 5:213. [PMID: 24860561 PMCID: PMC4026726 DOI: 10.3389/fmicb.2014.00213] [Citation(s) in RCA: 166] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2014] [Accepted: 04/23/2014] [Indexed: 11/13/2022] Open
Abstract
Members of the genus Brucella are pathogenic bacteria exceedingly well adapted to their hosts. The bacterium is transmitted by direct contact within the same host species or accidentally to secondary hosts, such as humans. Human brucellosis is strongly linked to the management of domesticated animals and ingestion of their products. Since the domestication of ungulates and dogs in the Fertile Crescent and Asia in 12000 and 33000 ya, respectively, a steady supply of well adapted emergent Brucella pathogens causing zoonotic disease has been provided. Likewise, anthropogenic modification of wild life may have also impacted host susceptibility and Brucella selection. Domestication and human influence on wild life animals are not neutral phenomena. Consequently, Brucella organisms have followed their hosts’ fate and have been selected under conditions that favor high transmission rate. The “arm race” between Brucella and their preferred hosts has been driven by genetic adaptation of the bacterium confronted with the evolving immune defenses of the host. Management conditions, such as clustering, selection, culling, and vaccination of Brucella preferred hosts have profound influences in the outcome of brucellosis and in the selection of Brucella organisms. Countries that have controlled brucellosis systematically used reliable smooth live vaccines, consistent immunization protocols, adequate diagnostic tests, broad vaccination coverage and sustained removal of the infected animals. To ignore and misuse tools and strategies already available for the control of brucellosis may promote the emergence of new Brucella variants. The unrestricted use of low-efficacy vaccines may promote a “false sense of security” and works towards selection of Brucella with higher virulence and transmission potential.
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Affiliation(s)
- Edgardo Moreno
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional Heredia, Costa Rica ; Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica San José, Costa Rica
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40
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Puckett EE, Kristensen TV, Wilton CM, Lyda SB, Noyce KV, Holahan PM, Leslie DM, Beringer J, Belant JL, White D, Eggert LS. Influence of drift and admixture on population structure of American black bears (Ursus americanus) in the Central Interior Highlands, USA, 50 years after translocation. Mol Ecol 2014; 23:2414-27. [PMID: 24712442 DOI: 10.1111/mec.12748] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 04/04/2014] [Accepted: 04/04/2014] [Indexed: 11/29/2022]
Affiliation(s)
- Emily E. Puckett
- Division of Biological Sciences; University of Missouri; 226 Tucker Hall Columbia MO 65211 USA
| | - Thea V. Kristensen
- Department of Biological Sciences; University of Arkansas; Science and Engineering 601 Fayetteville AR 72701 USA
| | - Clay M. Wilton
- Carnivore Ecology Laboratory; Forest and Wildlife Research Center; Mississippi State University; Box 9690 Mississippi State MS 39762 USA
| | - Sara B. Lyda
- Oklahoma Cooperative Fish and Wildlife Research Unit; Department of Natural Resource Ecology and Management; Oklahoma State University; 007 Agriculture Hall Stillwater OK 74078 USA
| | - Karen V. Noyce
- Forest Wildlife Populations and Research Group; Minnesota Department of Natural Resources; 1201 East Highway 2 Grand Rapids MN 55744 USA
| | - Paula M. Holahan
- University of Wisconsin Zoological Museum; 250 North Mills Street Madison WI 53706 USA
| | - David M. Leslie
- Oklahoma Cooperative Fish and Wildlife Research Unit; Department of Natural Resource Ecology and Management; U.S. Geological Survey; Oklahoma State University; 007 Agriculture Hall Stillwater OK 74078 USA
| | - Jeff Beringer
- Missouri Department of Conservation; Resource Science Center; 3500 Gans Creed Road Columbia MO 65201 USA
| | - Jerrold L. Belant
- Carnivore Ecology Laboratory; Forest and Wildlife Research Center; Mississippi State University; Box 9690 Mississippi State MS 39762 USA
| | - Don White
- Arkansas Forest Resources Center; University of Arkansas Agricultural Experiment Station; University of Arkansas-Monticello; 110 University Court Monticello AR 71656 USA
| | - Lori S. Eggert
- Division of Biological Sciences; University of Missouri; 226 Tucker Hall Columbia MO 65211 USA
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Wright DJ, Spurgin LG, Collar NJ, Komdeur J, Burke T, Richardson DS. The impact of translocations on neutral and functional genetic diversity within and among populations of the Seychelles warbler. Mol Ecol 2014; 23:2165-77. [PMID: 24689851 PMCID: PMC4237152 DOI: 10.1111/mec.12740] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Revised: 03/06/2014] [Accepted: 03/07/2014] [Indexed: 01/10/2023]
Abstract
Translocations are an increasingly common tool in conservation. The maintenance of genetic diversity through translocation is critical for both the short- and long-term persistence of populations and species. However, the relative spatio-temporal impacts of translocations on neutral and functional genetic diversity, and how this affects genetic structure among the conserved populations overall, have received little investigation. We compared the impact of translocating different numbers of founders on both microsatellite and major histocompatibility complex (MHC) class I diversity over a 23-year period in the Seychelles warbler (Acrocephalus sechellensis). We found low and stable microsatellite and MHC diversity in the source population and evidence for only a limited loss of either type of diversity in the four new populations. However, we found evidence of significant, but low to moderate, genetic differentiation between populations, with those populations established with fewer founders clustering separately. Stochastic genetic capture (as opposed to subsequent drift) was the main determinant of translocated population diversity. Furthermore, a strong correlation between microsatellite and MHC differentiation suggested that neutral processes outweighed selection in shaping MHC diversity in the new populations. These data provide important insights into how to optimize the use of translocation as a conservation tool.
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Affiliation(s)
- David J Wright
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK; NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
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Hoban SM, Gaggiotti OE, Bertorelle G. The number of markers and samples needed for detecting bottlenecks under realistic scenarios, with and without recovery: a simulation-based study. Mol Ecol 2014; 22:3444-50. [PMID: 23967455 DOI: 10.1111/mec.12258] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Detecting bottlenecks is a common task in molecular ecology. While several bottleneck detection method sexist, evaluations of their power have focused only on severe bottlenecks (e.g. to Ne ~10). As a component of a recent review, Peery et al. (2012) analysed the power of two approaches, the M-ratio and heterozygote excess tests, to detect moderate bottlenecks (e.g. to Ne ~100),which is realistic for many conservation situations. In this Comment, we address three important points relevant to but not considered in Peery et al. Under moderate bottleneck scenarios, we test the (i) relative advantage of sampling more markers vs. more individuals, (ii) potential power to detect the bottleneck when utilizing dozens of microsatellites (a realistic possibility for contemporary studies) and (iii) reduction in power when post bottle neck recovery has occurred. For the realistic situations examined,we show that (i) doubling the number of loci shows equal or better power than tripling the number of individuals,(ii) increasing the number of markers (up to 100) results in continued additive gains in power, and (iii)recovery after a moderate amount of time or gradual change in size reduces power, by up to one-half. Our results provide a practical supplement to Peery et al. and encourage the continued use of bottleneck detection methods in the genomic age, but also emphasize that the power under different sampling schemes should be estimated,using simulation modelling, as a routine component of molecular ecology studies.
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Büntgen U, Liebhold A, Jenny H, Mysterud A, Egli S, Nievergelt D, Stenseth NC, Bollmann K. European springtime temperature synchronises ibex horn growth across the eastern Swiss Alps. Ecol Lett 2013; 17:303-13. [PMID: 24341995 PMCID: PMC4257578 DOI: 10.1111/ele.12231] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Revised: 10/09/2013] [Accepted: 11/12/2013] [Indexed: 12/03/2022]
Abstract
Direct effects of climate change on animal physiology, and indirect impacts from disruption of seasonal synchrony and breakdown of trophic interactions are particularly severe in Arctic and Alpine ecosystems. Unravelling biotic from abiotic drivers, however, remains challenging because high-resolution animal population data are often limited in space and time. Here, we show that variation in annual horn growth (an indirect proxy for individual performance) of 8043 male Alpine ibex (Capra ibex) over the past four decades is well synchronised among eight disjunct colonies in the eastern Swiss Alps. Elevated March to May temperatures, causing premature melting of Alpine snowcover, earlier plant phenology and subsequent improvement of ibex food resources, fuelled annual horn growth. These results reveal dependency of local trophic interactions on large-scale climate dynamics, and provide evidence that declining herbivore performance is not a universal response to global warming even for high-altitude populations that are also harvested.
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Affiliation(s)
- Ulf Büntgen
- Swiss Federal Institute for Forest Snow and Landscape Research (WSL), Birmensdorf, CH-8903, Switzerland; Oeschger Centre for Climate Change Research (OCCR), University of Bern, Bern, CH-3012, Switzerland; Global Change Research Centre AS CR, v.v.i., Bělidla 986/4a, Brno, CZ-60300, Czech Republic
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Bristol RM, Tucker R, Dawson DA, Horsburgh G, Prys-Jones RP, Frantz AC, Krupa A, Shah NJ, Burke T, Groombridge JJ. Comparison of historical bottleneck effects and genetic consequences of re-introduction in a critically endangered island passerine. Mol Ecol 2013; 22:4644-62. [DOI: 10.1111/mec.12429] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Revised: 06/21/2013] [Accepted: 06/24/2013] [Indexed: 11/26/2022]
Affiliation(s)
- Rachel M. Bristol
- Durrell Institute of Conservation and Ecology; School of Anthropology and Conservation; University of Kent; Marlowe Building Canterbury CT2 7NR UK
- NERC Biomolecular Analysis Facility; Department of Animal and Plant Sciences; University of Sheffield; Western Bank; Alfred Denny Building Sheffield South Yorkshire S20 2TN UK
| | - Rachel Tucker
- Durrell Institute of Conservation and Ecology; School of Anthropology and Conservation; University of Kent; Marlowe Building Canterbury CT2 7NR UK
- NERC Biomolecular Analysis Facility; Department of Animal and Plant Sciences; University of Sheffield; Western Bank; Alfred Denny Building Sheffield South Yorkshire S20 2TN UK
- Imperial College London; Silwood Park Campus, Buckhurst Road Ascot Berkshire SL5 7PY UK
| | - Deborah A. Dawson
- NERC Biomolecular Analysis Facility; Department of Animal and Plant Sciences; University of Sheffield; Western Bank; Alfred Denny Building Sheffield South Yorkshire S20 2TN UK
| | - Gavin Horsburgh
- NERC Biomolecular Analysis Facility; Department of Animal and Plant Sciences; University of Sheffield; Western Bank; Alfred Denny Building Sheffield South Yorkshire S20 2TN UK
| | - Robert P. Prys-Jones
- Bird Group; Department of Life Sciences; Natural History Museum; Akeman St Tring Herts HP23 6AP UK
| | - Alain C. Frantz
- NERC Biomolecular Analysis Facility; Department of Animal and Plant Sciences; University of Sheffield; Western Bank; Alfred Denny Building Sheffield South Yorkshire S20 2TN UK
| | - Andy Krupa
- NERC Biomolecular Analysis Facility; Department of Animal and Plant Sciences; University of Sheffield; Western Bank; Alfred Denny Building Sheffield South Yorkshire S20 2TN UK
| | - Nirmal J. Shah
- Nature Seychelles; Centre for Environment and Education; Roche Caiman PO Box 1310 Mahé Seychelles
| | - Terry Burke
- NERC Biomolecular Analysis Facility; Department of Animal and Plant Sciences; University of Sheffield; Western Bank; Alfred Denny Building Sheffield South Yorkshire S20 2TN UK
| | - Jim J. Groombridge
- Durrell Institute of Conservation and Ecology; School of Anthropology and Conservation; University of Kent; Marlowe Building Canterbury CT2 7NR UK
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Simpson S, Blampied N, Peniche G, Dozières A, Blackett T, Coleman S, Cornish N, Groombridge JJ. Genetic structure of introduced populations: 120-year-old DNA footprint of historic introduction in an insular small mammal population. Ecol Evol 2013; 3:614-28. [PMID: 23532702 PMCID: PMC3605850 DOI: 10.1002/ece3.486] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Accepted: 12/24/2012] [Indexed: 11/06/2022] Open
Abstract
Wildlife populations have been introduced to new areas by people for centuries, but this human-mediated movement can disrupt natural patterns of genetic structure by altering patterns of gene flow. Insular populations are particularly prone to these influences due to limited opportunities for natural dispersal onto islands. Consequently, understanding how genetic patterns develop in island populations is important, particularly given that islands are frequently havens for protected wildlife. We examined the evolutionary origins and extent of genetic structure within the introduced island population of red squirrels (Sciurus vulgaris) on the Channel Island of Jersey using mitochondrial DNA (mtDNA) control region sequence and nuclear microsatellite genotypes. Our findings reveal two different genetic origins and a genetic architecture reflective of the introductions 120 years ago. Genetic structure is marked within the maternally inherited mtDNA, indicating slow dispersal of female squirrels. However, nuclear markers detected only weak genetic structure, indicating substantially greater male dispersal. Data from both mitochondrial and nuclear markers support historic records that squirrels from England were introduced to the west of the island and those from mainland Europe to the east. Although some level of dispersal and introgression across the island between the two introductions is evident, there has not yet been sufficient gene flow to erase this historic genetic "footprint." We also investigated if inbreeding has contributed to high observed levels of disease, but found no association. Genetic footprints of introductions can persist for considerable periods of time and beyond traditional timeframes of wildlife management.
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Affiliation(s)
- Siobhan Simpson
- Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, University of Kent Canterbury, CT2 7NR, United Kingdom
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Aeschbacher S, Futschik A, Beaumont MA. Approximate
B
ayesian computation for modular inference problems with many parameters: the example of migration rates. Mol Ecol 2013; 22:987-1002. [DOI: 10.1111/mec.12165] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2012] [Revised: 11/08/2012] [Accepted: 11/08/2012] [Indexed: 12/01/2022]
Affiliation(s)
- S. Aeschbacher
- Institute of Evolutionary Biology University of Edinburgh Edinburgh EH9 3JTUK
- Institute of Science and Technology Austria (IST Austria) 3400Klosterneuburg Austria
| | - A. Futschik
- Institute of Statistics and Decision Support Systems University of Vienna 1010Vienna Austria
| | - M. A. Beaumont
- Department of Mathematics and School of Biological Sciences University of Bristol Bristol BS8 1TWUK
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Baker KH, Rus Hoelzel A. Evolution of population genetic structure of the British roe deer by natural and anthropogenic processes (Capreolus capreolus). Ecol Evol 2012; 3:89-102. [PMID: 23403955 PMCID: PMC3568846 DOI: 10.1002/ece3.430] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Revised: 10/17/2012] [Accepted: 10/21/2012] [Indexed: 11/17/2022] Open
Abstract
Human influence typically impacts on natural populations of conservation interest. These interactions are varied and sometimes complex, and may be negative and unintended or associated with conservation and management strategy. Understanding the details of how these interactions influence and are influenced by natural evolutionary processes is essential to the development of effective conservation strategies. In this study, we investigate a species in Britain that has experienced both negative impact through overhunting in historical times and management efforts through culls and translocations. At the same time, there are regional populations that have been less affected by human influence. We use mtDNA and nuclear microsatellite DNA markers to investigate patterns of connectivity and diversity and find multiple insular populations in Britain that probably evolved within the Holocene (when the habitat was free of ice). We identify three concurrent processes. First, surviving indigenous populations show highly provincial patterns of philopatry, maintaining and generating population structure on a small geographic scale. Second, founder populations into habitat extirpated of native populations have expanded, but remained largely insular. Third, introductions into established populations generate some admixture. We discuss the implications for the evolution of diversity of the integration of natural processes with anthropogenic influences on population size and distribution.
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Affiliation(s)
- Karis H Baker
- School of Biological and Biomedical Sciences, Durham University South Road, Durham, DH1 3LE, UK
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Abstract
The choice of summary statistics is a crucial step in approximate Bayesian computation (ABC). Since statistics are often not sufficient, this choice involves a trade-off between loss of information and reduction of dimensionality. The latter may increase the efficiency of ABC. Here, we propose an approach for choosing summary statistics based on boosting, a technique from the machine-learning literature. We consider different types of boosting and compare them to partial least-squares regression as an alternative. To mitigate the lack of sufficiency, we also propose an approach for choosing summary statistics locally, in the putative neighborhood of the true parameter value. We study a demographic model motivated by the reintroduction of Alpine ibex (Capra ibex) into the Swiss Alps. The parameters of interest are the mean and standard deviation across microsatellites of the scaled ancestral mutation rate (θ(anc) = 4N(e)u) and the proportion of males obtaining access to matings per breeding season (ω). By simulation, we assess the properties of the posterior distribution obtained with the various methods. According to our criteria, ABC with summary statistics chosen locally via boosting with the L(2)-loss performs best. Applying that method to the ibex data, we estimate θ(anc)≈ 1.288 and find that most of the variation across loci of the ancestral mutation rate u is between 7.7 × 10(-4) and 3.5 × 10(-3) per locus per generation. The proportion of males with access to matings is estimated as ω≈ 0.21, which is in good agreement with recent independent estimates.
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Loss of genetic diversity means loss of geological information: the endangered Japanese crayfish exhibits remarkable historical footprints. PLoS One 2012; 7:e33986. [PMID: 22470505 PMCID: PMC3314697 DOI: 10.1371/journal.pone.0033986] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Accepted: 02/24/2012] [Indexed: 11/19/2022] Open
Abstract
Intra-specific genetic diversity is important not only because it influences population persistence and evolutionary potential, but also because it contains past geological, climatic and environmental information. In this paper, we show unusually clear genetic structure of the endangered Japanese crayfish that, as a sedentary species, provides many insights into lesser-known past environments in northern Japan. Over the native range, most populations consisted of unique 16S mtDNA haplotypes, resulting in significant genetic divergence (overall FST = 0.96). Owing to the simple and clear structure, a new graphic approach unraveled a detailed evolutionary history; regional crayfish populations were comprised of two distinct lineages that had experienced contrasting demographic processes (i.e. rapid expansion vs. slow stepwise range expansion) following differential drainage topologies and past climate events. Nuclear DNA sequences also showed deep separation between the lineages. Current ocean barriers to dispersal did not significantly affect the genetic structure of the freshwater crayfish, indicating the formation of relatively recent land bridges. This study provides one of the best examples of how phylogeographic analysis can unravel a detailed evolutionary history of a species and how this history contributes to the understanding of the past environment in the region. Ongoing local extinctions of the crayfish lead not only to loss of biodiversity but also to the loss of a significant information regarding past geological and climatic events.
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