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Atağ G, Kaptan D, Yüncü E, Başak Vural K, Mereu P, Pirastru M, Barbato M, Leoni GG, Güler MN, Er T, Eker E, Yazıcı TD, Kılıç MS, Altınışık NE, Çelik EA, Morell Miranda P, Dehasque M, Floridia V, Götherström A, Bilgin CC, Togan İ, Günther T, Özer F, Hadjisterkotis E, Somel M. Population Genomic History of the Endangered Anatolian and Cyprian Mouflons in Relation to Worldwide Wild, Feral, and Domestic Sheep Lineages. Genome Biol Evol 2024; 16:evae090. [PMID: 38670119 PMCID: PMC11109821 DOI: 10.1093/gbe/evae090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 04/09/2024] [Accepted: 04/22/2024] [Indexed: 04/28/2024] Open
Abstract
Once widespread in their homelands, the Anatolian mouflon (Ovis gmelini anatolica) and the Cyprian mouflon (Ovis gmelini ophion) were driven to near extinction during the 20th century and are currently listed as endangered populations by the International Union for Conservation of Nature. While the exact origins of these lineages remain unclear, they have been suggested to be close relatives of domestic sheep or remnants of proto-domestic sheep. Here, we study whole genome sequences of n = 5 Anatolian mouflons and n = 10 Cyprian mouflons in terms of population history and diversity, comparing them with eight other extant sheep lineages. We find reciprocal genetic affinity between Anatolian and Cyprian mouflons and domestic sheep, higher than all other studied wild sheep genomes, including the Iranian mouflon (O. gmelini). Studying diversity indices, we detect a considerable load of short runs of homozygosity blocks (<2 Mb) in both Anatolian and Cyprian mouflons, reflecting small effective population size (Ne). Meanwhile, Ne and mutation load estimates are lower in Cyprian compared with Anatolian mouflons, suggesting the purging of recessive deleterious variants in Cyprian sheep under a small long-term Ne, possibly attributable to founder effects, island isolation, introgression from domestic lineages, or differences in their bottleneck dynamics. Expanding our analyses to worldwide wild and feral Ovis genomes, we observe varying viability metrics among different lineages and a limited consistency between viability metrics and International Union for Conservation of Nature conservation status. Factors such as recent inbreeding, introgression, and unique population dynamics may have contributed to the observed disparities.
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Affiliation(s)
- Gözde Atağ
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Damla Kaptan
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Eren Yüncü
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Kıvılcım Başak Vural
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Paolo Mereu
- Department of Biochemical Sciences, University of Sassari, Sassari, Italy
| | - Monica Pirastru
- Department of Biochemical Sciences, University of Sassari, Sassari, Italy
| | - Mario Barbato
- Department of Veterinary Sciences, University of Messina, Messina, Italy
| | | | - Merve Nur Güler
- Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, Ankara, Turkey
| | - Tuğçe Er
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Elifnaz Eker
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Tunca Deniz Yazıcı
- Graduate School for Evolution, Ecology and Systematics, Ludwig Maximillian University of Munich, Munich, Germany
| | - Muhammed Sıddık Kılıç
- Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, Ankara, Turkey
| | | | - Ecem Ayşe Çelik
- Department of Settlement Archeology, Middle East Technical University, Ankara, Turkey
| | - Pedro Morell Miranda
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Marianne Dehasque
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Viviana Floridia
- Department of Veterinary Sciences, University of Messina, Messina, Italy
| | - Anders Götherström
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
- Centre for Palaeogenetics, Stockholm University, Stockholm, Sweden
| | - Cemal Can Bilgin
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - İnci Togan
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Torsten Günther
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Füsun Özer
- Department of Anthropology, Hacettepe University, Ankara, Turkey
| | - Eleftherios Hadjisterkotis
- Agricultural Research Institute, Ministry of Agriculture, Rural Development and Environment, Nicosia, Cyprus
| | - Mehmet Somel
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
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2
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Judson JM, Hoekstra LA, Janzen FJ. Demographic history and genomic signatures of selection in a widespread vertebrate ectotherm. Mol Ecol 2024; 33:e17269. [PMID: 38234254 PMCID: PMC10922411 DOI: 10.1111/mec.17269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 12/20/2023] [Accepted: 01/08/2024] [Indexed: 01/19/2024]
Abstract
Environmental conditions vary greatly across large geographic ranges, and yet certain species inhabit entire continents. In such species, genomic sequencing can inform our understanding of colonization history and the impact of selection on the genome as populations experience diverse local environments. As ectothermic vertebrates are among the most vulnerable to environmental change, it is critical to understand the contributions of local adaptation to population survival. Widespread ectotherms offer an opportunity to explore how species can successfully inhabit such differing environments and how future climatic shifts will impact species' survival. In this study, we investigated the widespread painted turtle (Chrysemys picta) to assess population genomic structure, demographic history, and genomic signatures of selection in the western extent of the range. We found support for a substantial role of serial founder effects in shaping population genomic structure: demographic analysis and runs of homozygosity were consistent with bottlenecks of increasing severity from eastern to western populations during and following the Last Glacial Maximum, and edge populations were more strongly diverged and had less genetic diversity than those from the centre of the range. We also detected outlier loci, but allelic patterns in many loci could be explained by either genetic surfing or selection. While range expansion complicates the identification of loci under selection, we provide candidates for future study of local adaptation in a long-lived, widespread ectotherm that faces an uncertain future as the global climate continues to rapidly change.
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Affiliation(s)
- Jessica M. Judson
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
- Current Address: W. K. Kellogg Biological Station, Departments of Fisheries and Wildlife & Integrative Biology, Michigan State University, Hickory Corners, MI 49060, USA
| | - Luke A. Hoekstra
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
- Current Address: Department of Integrative Biology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Fredric J. Janzen
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
- Current Address: W. K. Kellogg Biological Station, Departments of Fisheries and Wildlife & Integrative Biology, Michigan State University, Hickory Corners, MI 49060, USA
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3
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Kellner FL, Le Moullec M, Ellegaard MR, Rosvold J, Peeters B, Burnett HA, Pedersen ÅØ, Brealey JC, Dussex N, Bieker VC, Hansen BB, Martin MD. A palaeogenomic investigation of overharvest implications in an endemic wild reindeer subspecies. Mol Ecol 2024; 33:e17274. [PMID: 38279681 DOI: 10.1111/mec.17274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 12/11/2023] [Accepted: 01/09/2024] [Indexed: 01/28/2024]
Abstract
Overharvest can severely reduce the abundance and distribution of a species and thereby impact its genetic diversity and threaten its future viability. Overharvest remains an ongoing issue for Arctic mammals, which due to climate change now also confront one of the fastest changing environments on Earth. The high-arctic Svalbard reindeer (Rangifer tarandus platyrhynchus), endemic to Svalbard, experienced a harvest-induced demographic bottleneck that occurred during the 17-20th centuries. Here, we investigate changes in genetic diversity, population structure, and gene-specific differentiation during and after this overharvesting event. Using whole-genome shotgun sequencing, we generated the first ancient and historical nuclear (n = 11) and mitochondrial (n = 18) genomes from Svalbard reindeer (up to 4000 BP) and integrated these data with a large collection of modern genome sequences (n = 90) to infer temporal changes. We show that hunting resulted in major genetic changes and restructuring in reindeer populations. Near-extirpation followed by pronounced genetic drift has altered the allele frequencies of important genes contributing to diverse biological functions. Median heterozygosity was reduced by 26%, while the mitochondrial genetic diversity was reduced only to a limited extent, likely due to already low pre-harvest diversity and a complex post-harvest recolonization process. Such genomic erosion and genetic isolation of populations due to past anthropogenic disturbance will likely play a major role in metapopulation dynamics (i.e., extirpation, recolonization) under further climate change. Our results from a high-arctic case study therefore emphasize the need to understand the long-term interplay of past, current, and future stressors in wildlife conservation.
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Affiliation(s)
- Fabian L Kellner
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Mathilde Le Moullec
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Department of Mammals and Birds, Greenland Institute of Natural Resources (GINR), Nuuk, Greenland
| | - Martin R Ellegaard
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Jørgen Rosvold
- Department of Terrestrial Biodiversity, Norwegian Institute for Nature Research (NINA), Trondheim, Norway
| | - Bart Peeters
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Hamish A Burnett
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | | | - Jaelle C Brealey
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Nicolas Dussex
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Vanessa C Bieker
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Brage B Hansen
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Department of Terrestrial Ecology, Norwegian Institute for Nature Research (NINA), Trondheim, Norway
| | - Michael D Martin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
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4
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Burnett HA, Bieker VC, Le Moullec M, Peeters B, Rosvold J, Pedersen ÅØ, Dalén L, Loe LE, Jensen H, Hansen BB, Martin MD. Contrasting genomic consequences of anthropogenic reintroduction and natural recolonization in high-arctic wild reindeer. Evol Appl 2023; 16:1531-1548. [PMID: 37752961 PMCID: PMC10519417 DOI: 10.1111/eva.13585] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 07/27/2023] [Accepted: 08/01/2023] [Indexed: 09/28/2023] Open
Abstract
Anthropogenic reintroduction can supplement natural recolonization in reestablishing a species' distribution and abundance. However, both reintroductions and recolonizations can give rise to founder effects that reduce genetic diversity and increase inbreeding, potentially causing the accumulation of genetic load and reduced fitness. Most current populations of the endemic high-arctic Svalbard reindeer (Rangifer tarandus platyrhynchus) originate from recent reintroductions or recolonizations following regional extirpations due to past overharvesting. We investigated and compared the genomic consequences of these two paths to reestablishment using whole-genome shotgun sequencing of 100 Svalbard reindeer across their range. We found little admixture between reintroduced and natural populations. Two reintroduced populations, each founded by 12 individuals around four decades (i.e. 8 reindeer generations) ago, formed two distinct genetic clusters. Compared to the source population, these populations showed only small decreases in genome-wide heterozygosity and increases in inbreeding and lengths of runs of homozygosity. In contrast, the two naturally recolonized populations without admixture possessed much lower heterozygosity, higher inbreeding and longer runs of homozygosity, possibly caused by serial population founder effects and/or fewer or more genetically related founders than in the reintroduction events. Naturally recolonized populations can thus be more vulnerable to the accumulation of genetic load than reintroduced populations. This suggests that in some organisms even small-scale reintroduction programs based on genetically diverse source populations can be more effective than natural recolonization in establishing genetically diverse populations. These findings warrant particular attention in the conservation and management of populations and species threatened by habitat fragmentation and loss.
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Affiliation(s)
- Hamish A. Burnett
- Centre for Biodiversity Dynamics, Department of BiologyNorwegian University of Science and Technology (NTNU)TrondheimNorway
- Department of Natural History, NTNU University MuseumNorwegian University of Science and Technology (NTNU)TrondheimNorway
| | - Vanessa C. Bieker
- Centre for Biodiversity Dynamics, Department of BiologyNorwegian University of Science and Technology (NTNU)TrondheimNorway
- Department of Natural History, NTNU University MuseumNorwegian University of Science and Technology (NTNU)TrondheimNorway
| | - Mathilde Le Moullec
- Centre for Biodiversity Dynamics, Department of BiologyNorwegian University of Science and Technology (NTNU)TrondheimNorway
| | - Bart Peeters
- Centre for Biodiversity Dynamics, Department of BiologyNorwegian University of Science and Technology (NTNU)TrondheimNorway
| | - Jørgen Rosvold
- Department of Terrestrial BiodiversityNorwegian Institute for Nature Research (NINA)TrondheimNorway
| | | | - Love Dalén
- Centre for PalaeogeneticsStockholmSweden
- Department of Bioinformatics and GeneticsSwedish Museum of Natural HistoryStockholmSweden
- Department of ZoologyStockholm UniversityStockholmSweden
| | - Leif Egil Loe
- Faculty of Environmental Sciences and Natural Resource ManagementNorwegian University of Life SciencesAasNorway
| | - Henrik Jensen
- Centre for Biodiversity Dynamics, Department of BiologyNorwegian University of Science and Technology (NTNU)TrondheimNorway
| | - Brage B. Hansen
- Centre for Biodiversity Dynamics, Department of BiologyNorwegian University of Science and Technology (NTNU)TrondheimNorway
- Department of Terrestrial EcologyNorwegian Institute for Nature Research (NINA)TrondheimNorway
| | - Michael D. Martin
- Centre for Biodiversity Dynamics, Department of BiologyNorwegian University of Science and Technology (NTNU)TrondheimNorway
- Department of Natural History, NTNU University MuseumNorwegian University of Science and Technology (NTNU)TrondheimNorway
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5
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Kastelic M, Gregurić Gračner G, Tomažič I, Kvapil P, Harej M, Dovč A. Comparison of Cortisol Concentrations in Different Matrices in Alpine Ibex ( Capra ibex) at the Zoo. Animals (Basel) 2023; 13:2491. [PMID: 37570299 PMCID: PMC10417618 DOI: 10.3390/ani13152491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 07/31/2023] [Accepted: 08/01/2023] [Indexed: 08/13/2023] Open
Abstract
The usefulness of blood collection using venipuncture versus kissing bugs or medicinal leeches and the collection of saliva, faeces, hair, urine, and tears for measuring "immunoreactive" C (iC) concentration in Alpine ibexes was verified using commercial enzyme immunoassays. The mean value of serum C was highest in serum collected using venipuncture and lowest in serums collected using kissing bugs. Statistically significant differences were observed between venipuncture and kissing bugs and between leeches and kissing bugs. However, no statistically significant difference was found in C concentrations between samples collected with venipuncture and those collected with leeches. The highest mean value of C concentration was measured in serum (all three methods), followed by that in hair and faeces, and the lowest mean value was found in saliva. Statistically significant differences were found between saliva and faeces samples and between saliva and hair samples. The difference between the concentrations for faeces and hair was not statistically significant. A significant difference in C concentration between males and females was found in saliva. A significant difference in C concentration among different ages was measured in serum obtained using venipuncture in all three groups and in faeces between the groups older than ten years and younger than 10 months. Highly significant differences in C concentrations were also found between hair sampled in summer and hair sampled in autumn. Collecting tear and urine samples is a laborious procedure and is therefore less acceptable for C determination. Due to the small number of samples, statistical values are not given for these two matrices.
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Affiliation(s)
- Marjan Kastelic
- Zoo Ljubljana, Večna Pot 70, 1000 Ljubljana, Slovenia; (M.K.); (P.K.); (M.H.)
- Institute for Poultry, Birds, Small Mammals and Reptiles, Veterinary Faculty, University of Ljubljana, Gerbičeva 60, 1000 Ljubljana, Slovenia
| | - Gordana Gregurić Gračner
- Department of Animal Hygiene, Behaviour and Animal Welfare, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10000 Zagreb, Croatia;
| | - Iztok Tomažič
- The Group for Biological Education, Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna Pot 111, 1000 Ljubljana, Slovenia;
| | - Pavel Kvapil
- Zoo Ljubljana, Večna Pot 70, 1000 Ljubljana, Slovenia; (M.K.); (P.K.); (M.H.)
| | - Mojca Harej
- Zoo Ljubljana, Večna Pot 70, 1000 Ljubljana, Slovenia; (M.K.); (P.K.); (M.H.)
| | - Alenka Dovč
- Institute for Poultry, Birds, Small Mammals and Reptiles, Veterinary Faculty, University of Ljubljana, Gerbičeva 60, 1000 Ljubljana, Slovenia
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Martin CA, Sheppard EC, Illera JC, Suh A, Nadachowska-Brzyska K, Spurgin LG, Richardson DS. Runs of homozygosity reveal past bottlenecks and contemporary inbreeding across diverging populations of an island-colonizing bird. Mol Ecol 2023; 32:1972-1989. [PMID: 36704917 DOI: 10.1111/mec.16865] [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: 09/27/2022] [Revised: 01/11/2023] [Accepted: 01/20/2023] [Indexed: 01/28/2023]
Abstract
Genomes retain evidence of the demographic history and evolutionary forces that have shaped populations and drive speciation. Across island systems, contemporary patterns of genetic diversity reflect population demography, including colonization events, bottlenecks, gene flow and genetic drift. Here, we investigate genome-wide diversity and the distribution of runs of homozygosity (ROH) using whole-genome resequencing of individuals (>22× coverage) from six populations across three archipelagos of Berthelot's pipit (Anthus berthelotii)-a passerine that has recently undergone island speciation. We show the most dramatic reduction in diversity occurs between the mainland sister species (the tawny pipit) and Berthelot's pipit and is lowest in the populations that have experienced sequential bottlenecks (i.e., the Madeiran and Selvagens populations). Pairwise sequential Markovian coalescent (PSMC) analyses estimated that Berthelot's pipit diverged from its sister species ~2 million years ago, with the Madeiran archipelago founded 50,000 years ago, and the Selvagens colonized 8000 years ago. We identify many long ROH (>1 Mb) in these most recently colonized populations. Population expansion within the last 100 years may have eroded long ROH in the Madeiran archipelago, resulting in a prevalence of short ROH (<1 Mb). However, the extensive long and short ROH detected in the Selvagens suggest strong recent inbreeding and bottleneck effects, with as much as 38% of the autosomes consisting of ROH >250 kb. These findings highlight the importance of demographic history, as well as selection and genetic drift, in shaping contemporary patterns of genomic diversity across diverging populations.
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Affiliation(s)
- Claudia A Martin
- School of Biological Sciences, University of East Anglia, Norfolk, UK.,Terrestrial Ecology Unit, Biology Department, Ghent University, Ghent, Belgium
| | | | - Juan Carlos Illera
- Biodiversity Research Institute (CSIC-Oviedo University-Principality of Asturias), University of Oviedo, Mieres, Asturias, Spain
| | - Alexander Suh
- School of Biological Sciences, University of East Anglia, Norfolk, UK.,Department of Organismal Biology - Systematic Biology, Evolutionary Biology Centre (EBC), Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | | | - Lewis G Spurgin
- School of Biological Sciences, University of East Anglia, Norfolk, UK
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7
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Duntsch L, Whibley A, de Villemereuil P, Brekke P, Bailey S, Ewen JG, Santure AW. Genomic signatures of inbreeding depression for a threatened Aotearoa New Zealand passerine. Mol Ecol 2023; 32:1893-1907. [PMID: 36655901 DOI: 10.1111/mec.16855] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 11/19/2022] [Accepted: 01/16/2023] [Indexed: 01/20/2023]
Abstract
For small and isolated populations, the increased chance of mating between related individuals can result in a substantial reduction in individual and population fitness. Despite the increasing availability of genomic data to measure inbreeding accurately across the genome, inbreeding depression studies for threatened species are still scarce due to the difficulty of measuring fitness in the wild. Here, we investigate inbreeding and inbreeding depression for the extensively monitored Tiritiri Mātangi island population of a threatened Aotearoa New Zealand passerine, the hihi (Notiomystis cincta). First, using a custom 45 k single nucleotide polymorphism (SNP) array, we explore genomic inbreeding patterns by inferring homozygous segments across the genome. Although all individuals have similar levels of ancient inbreeding, highly inbred individuals are affected by recent inbreeding, which can probably be explained by bottleneck effects such as habitat loss after European arrival and their translocation to the island in the 1990s. Second, we investigate genomic inbreeding effects on fitness, measured as lifetime reproductive success, and its three components, juvenile survival, adult annual survival and annual reproductive success, in 363 hihi. We find that global inbreeding significantly affects juvenile survival but none of the remaining fitness traits. Finally, we employ a genome-wide association approach to test the locus-specific effects of inbreeding on fitness, and identify 13 SNPs significantly associated with lifetime reproductive success. Our findings suggest that inbreeding depression does impact hihi, but at different genomic scales for different traits, and that purging has therefore failed to remove all variants with deleterious effects from this population of conservation concern.
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Affiliation(s)
- Laura Duntsch
- Centre for Biodiversity and Biosecurity (CBB), School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Annabel Whibley
- Centre for Biodiversity and Biosecurity (CBB), School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Pierre de Villemereuil
- Institut de Systématique, Évolution, Biodiversité (ISYEB), École Pratique des Hautes Études, PSL, MNHN, CNRS, SU, UA, Paris, France
| | - Patricia Brekke
- Institute of Zoology, Zoological Society of London, London, UK
| | - Sarah Bailey
- Centre for Biodiversity and Biosecurity (CBB), School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - John G Ewen
- Institute of Zoology, Zoological Society of London, London, UK
| | - Anna W Santure
- Centre for Biodiversity and Biosecurity (CBB), School of Biological Sciences, University of Auckland, Auckland, New Zealand
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8
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Sundell T, Kammonen JI, Mustanoja E, Biard V, Kunnasranta M, Niemi M, Nykänen M, Nyman T, Palo JU, Valtonen M, Paulin L, Jernvall J, Auvinen P. Genomic evidence uncovers inbreeding and supports translocations in rescuing the genetic diversity of a landlocked seal population. CONSERV GENET 2023. [DOI: 10.1007/s10592-022-01497-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
AbstractFragmentation of isolated populations increases the risk of inbreeding and loss of genetic diversity. The endemic Saimaa ringed seal (Pusa hispida saimensis) is one of the most endangered pinnipeds in the world with a population of only ~ 400 individuals. The current genetic diversity of this subspecies, isolated in Lake Saimaa in Finland for ca. 1000 generations, is alarmingly low. We performed whole-genome sequencing on Saimaa ringed seals (N = 30) and analyzed the level of homozygosity and genetic composition across the individual genomes. Our results show that the Saimaa ringed seal population has a high number of runs of homozygosity (RoH) compared with the neighboring Baltic ringed seal (Pusa hispida botnica) reference population (p < 0.001). There is also a tendency for stillborn seal pups to have more pronounced RoH. Since the population is divided into semi-isolated subpopulations within the Lake Saimaa exposing the population to deleterious genomic effects, our results support augmented gene flow as a genetic conservation action. Based on our results suggesting inbreeding depression in the population, we recommend Pihlajavesi as a potential source and Southern Saimaa as a potential recipient subpopulation for translocating individuals. The Saimaa ringed seal is a recognized subspecies and therefore translocations should be considered only within the lake to avoid an unpredictable risk of disease, the introduction of deleterious alleles, and severe ecological issues for the population.
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Introduced, Mixed, and Peripheral: Conservation of Mitochondrial-DNA Lineages in the Wild Boar (Sus scrofa L.) Population in the Urals. DIVERSITY 2022. [DOI: 10.3390/d14110916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Translocations and introductions are important events that allow organisms to overcome natural barriers. The genetic background of colonization success and genetic consequences of the establishment of populations in new environments are of great interest for predicting species’ colonization success. The wild boar has been introduced into many parts of the world. We analyzed sequences of the mitochondrial-DNA control region in the wild boars introduced into the Ural region and compared them with sequences from founder populations (from Europe, the Caucasus, Central Asia, and the Far East). We found that the introduced population has high genetic diversity. Haplotypes from all the major phylogenetic clades were detected in the analyzed group of the animals from the Urals. In this group, no haplotypes identical to Far Eastern sequences were detectable despite a large number of founders from that region. The contribution of lineages originating from Eastern Europe was greater than expected from the proportions (%) of European and Asian animals in the founder populations. This is the first study on the genetic diversity and structure of a wild boar population of mixed origin at the northern periphery of this species’ geographical range.
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Marshall IR, Brauer CJ, Wedderburn SD, Whiterod NS, Hammer MP, Barnes TC, Attard CRM, Möller LM, Beheregaray LB. Longitudinal monitoring of neutral and adaptive genomic diversity in a reintroduction. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2022; 36:e13889. [PMID: 35023224 DOI: 10.1111/cobi.13889] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 12/16/2021] [Accepted: 12/28/2021] [Indexed: 06/14/2023]
Abstract
Restoration programs in the form of ex-situ breeding combined with reintroductions are becoming critical to counteract demographic declines and species losses. Such programs are increasingly using genetic management to improve conservation outcomes. However, the lack of long-term monitoring of genetic indicators following reintroduction prevents assessments of the trajectory and persistence of reintroduced populations. We carried out an extensive monitoring program in the wild for a threatened small-bodied fish (southern pygmy perch, Nannoperca australis) to assess the long-term genomic effects of its captive breeding and reintroduction. The species was rescued prior to its extirpation from the terminal lakes of Australia's Murray-Darling Basin, and then used for genetically informed captive breeding and reintroductions. Subsequent annual or biannual monitoring of abundance, fitness, and occupancy over a period of 11 years, combined with postreintroduction genetic sampling, revealed survival and recruitment of reintroduced fish. Genomic analyses based on data from the original wild rescued, captive born, and reintroduced cohorts revealed low inbreeding and strong maintenance of neutral and candidate adaptive genomic diversity across multiple generations. An increasing trend in the effective population size of the reintroduced population was consistent with field monitoring data in demonstrating successful re-establishment of the species. This provides a rare empirical example that the adaptive potential of a locally extinct population can be maintained during genetically informed ex-situ conservation breeding and reintroduction into the wild. Strategies to improve biodiversity restoration via ex-situ conservation should include genetic-based captive breeding and longitudinal monitoring of standing genomic variation in reintroduced populations.
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Affiliation(s)
- Imogen R Marshall
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
| | - Chris J Brauer
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
| | - Scotte D Wedderburn
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Nick S Whiterod
- Aquasave-Nature Glenelg Trust, Victor Harbor, South Australia, Australia
| | - Michael P Hammer
- Natural Sciences, Museum and Art Gallery of the Northern Territory, Darwin, Northern Territory, Australia
| | - Thomas C Barnes
- New South Wales Department of Primary Industries, Port Stephens Fisheries Institute, Nelson Bay, New South Wales, Australia
- Institute of Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, Australia
| | - Catherine R M Attard
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
| | - Luciana M Möller
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
| | - Luciano B Beheregaray
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
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11
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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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12
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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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13
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Brockett B, Banks S, Neaves LE, Gordon IJ, Pierson JC, Manning AD. Establishment, persistence and the importance of longitudinal monitoring in multi‐source reintroductions. Anim Conserv 2022. [DOI: 10.1111/acv.12764] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- B. Brockett
- Fenner School of Environment and Society The Australian National University Canberra ACT Australia
| | - S. Banks
- College of Engineering, IT and the Environment Charles Darwin University Darwin NT Australia
| | - L. E. Neaves
- Fenner School of Environment and Society The Australian National University Canberra ACT Australia
| | - I. J. Gordon
- Fenner School of Environment and Society The Australian National University Canberra ACT Australia
- James Hutton Institute Dundee UK
- Central Queensland University Townsville QLD Australia
- Land & Water CSIRO Townsville QLD Australia
- Protected Places Mission NERP2, Reef and Rainforest Research Center Cairns QLD Australia
| | - J. C. Pierson
- ACT Parks and Conservation Service Canberra Australia
| | - A. D. Manning
- Fenner School of Environment and Society The Australian National University Canberra ACT Australia
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14
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Ferrari G, Atmore LM, Jentoft S, Jakobsen KS, Makowiecki D, Barrett JH, Star B. An accurate assignment test for extremely low-coverage whole-genome sequence data. Mol Ecol Resour 2021; 22:1330-1344. [PMID: 34779123 DOI: 10.1111/1755-0998.13551] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 10/28/2021] [Accepted: 11/02/2021] [Indexed: 11/28/2022]
Abstract
Genomic assignment tests can provide important diagnostic biological characteristics, such as population of origin or ecotype. Yet, assignment tests often rely on moderate- to high-coverage sequence data that can be difficult to obtain for fields such as molecular ecology and ancient DNA. We have developed a novel approach that efficiently assigns biologically relevant information (i.e., population identity or structural variants such as inversions) in extremely low-coverage sequence data. First, we generate databases from existing reference data using a subset of diagnostic single nucleotide polymorphisms (SNPs) associated with a biological characteristic. Low-coverage alignment files are subsequently compared to these databases to ascertain allelic state, yielding a joint probability for each association. To assess the efficacy of this approach, we assigned haplotypes and population identity in Heliconius butterflies, Atlantic herring, and Atlantic cod using chromosomal inversion sites and whole-genome data. We scored both modern and ancient specimens, including the first whole-genome sequence data recovered from ancient Atlantic herring bones. The method accurately assigns biological characteristics, including population membership, using extremely low-coverage data (as low as 0.0001x) based on genome-wide SNPs. This approach will therefore increase the number of samples in evolutionary, ecological and archaeological research for which relevant biological information can be obtained.
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Affiliation(s)
- Giada Ferrari
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Lane M Atmore
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Kjetill S Jakobsen
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Daniel Makowiecki
- Department of Environmental Archaeology and Human Paleoecology, Institute of Archaeology, Nicolaus Copernicus University, Torun, Poland
| | - James H Barrett
- McDonald Institute for Archaeological Research, Department of Archaeology, University of Cambridge, Cambridge, UK.,Department of Archaeology and Cultural History, NTNU University Museum, Trondheim, Norway
| | - Bastiaan Star
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
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15
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Cardoso TF, Luigi‐Sierra MG, Castelló A, Cabrera B, Noce A, Mármol‐Sánchez E, García‐González R, Fernández‐Arias A, Alabart JL, López‐Olvera JR, Mentaberre G, Granados‐Torres JE, Cardells‐Peris J, Molina A, Sànchez A, Clop A, Amills M. Assessing the levels of intraspecific admixture and interspecific hybridization in Iberian wild goats ( Capra pyrenaica). Evol Appl 2021; 14:2618-2634. [PMID: 34815743 PMCID: PMC8591326 DOI: 10.1111/eva.13299] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 06/07/2021] [Accepted: 08/02/2021] [Indexed: 01/11/2023] Open
Abstract
Iberian wild goats (Capra pyrenaica, also known as Iberian ibex, Spanish ibex, and Spanish wild goat) underwent strong genetic bottlenecks during the 19th and 20th centuries due to overhunting and habitat destruction. From the 1970s to 1990s, augmentation translocations were frequently carried out to restock Iberian wild goat populations (very often with hunting purposes), but they were not systematically planned or recorded. On the other hand, recent data suggest the occurrence of hybridization events between Iberian wild goats and domestic goats (Capra hircus). Augmentation translocations and interspecific hybridization might have contributed to increase the diversity of Iberian wild goats. With the aim of investigating this issue, we have genotyped 118 Iberian wild goats from Tortosa-Beceite, Sierra Nevada, Muela de Cortes, Gredos, Batuecas, and Ordesa and Monte Perdido by using the Goat SNP50 BeadChip (Illumina). The analysis of genotypic data indicated that Iberian wild goat populations are strongly differentiated and display low diversity. Only three Iberian wild goats out from 118 show genomic signatures of mixed ancestry, a result consistent with a scenario in which past augmentation translocations have had a limited impact on the diversity of Iberian wild goats. Besides, we have detected eight Iberian wild goats from Tortosa-Beceite with signs of domestic goat introgression. Although rare, hybridization with domestic goats could become a potential threat to the genetic integrity of Iberian wild goats; hence, measures should be taken to avoid the presence of uncontrolled herds of domestic or feral goats in mountainous areas inhabited by this iconic wild ungulate.
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Affiliation(s)
- Tainã Figueiredo Cardoso
- Department of Animal GeneticsCentre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UBCampus de la Universitat Autònoma de BarcelonaBellaterraSpain
| | - María Gracia Luigi‐Sierra
- Department of Animal GeneticsCentre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UBCampus de la Universitat Autònoma de BarcelonaBellaterraSpain
| | - Anna Castelló
- Department of Animal GeneticsCentre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UBCampus de la Universitat Autònoma de BarcelonaBellaterraSpain
- Departament de Ciència Animal i dels AlimentsUniversitat Autònoma de BarcelonaBellaterraSpain
| | - Betlem Cabrera
- Department of Animal GeneticsCentre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UBCampus de la Universitat Autònoma de BarcelonaBellaterraSpain
- Departament de Ciència Animal i dels AlimentsUniversitat Autònoma de BarcelonaBellaterraSpain
| | - Antonia Noce
- Leibniz‐Institute for Farm Animal Biology (FBN)DummerstorfGermany
| | - Emilio Mármol‐Sánchez
- Department of Animal GeneticsCentre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UBCampus de la Universitat Autònoma de BarcelonaBellaterraSpain
| | | | - Alberto Fernández‐Arias
- Servicio de Caza y PescaDepartamento de Agricultura, Ganadería y Medio AmbienteGobierno de AragónZaragozaSpain
| | - José Luis Alabart
- Unidad de Producción y Sanidad AnimalCentro de Investigación y Tecnología Agroalimentaria de Aragón (CITA)Instituto Agroalimentario de Aragón ‐ IA2 (CITA‐Universidad de Zaragoza)Gobierno de AragónZaragozaSpain
| | - Jorge Ramón López‐Olvera
- Wildlife Ecology & Health Group and Servei d’Ecopatologia de Fauna Salvatge (SEFaS)Departament de Medicina i Cirurgia AnimalsUniversitat Autònoma de BarcelonaBellaterraSpain
| | - Gregorio Mentaberre
- Wildlife Ecology & Health Group and Departament de Ciència AnimalEscola Tècnica Superior d’Enginyeria Agraria (ETSEA)Universitat de Lleida (UdL)LleidaSpain
| | | | - Jesús Cardells‐Peris
- SAIGAS (Servicio de Análisis, Investigación y Gestión de Animales Silvestres) and Wildlife Ecology & Health Group, Faculty of VeterinaryUniversidad Cardenal Herrera‐CEU, CEU UniversitiesValenciaSpain
| | - Antonio Molina
- Departamento de GenéticaUniversidad de CórdobaCórdobaSpain
| | - Armand Sànchez
- Department of Animal GeneticsCentre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UBCampus de la Universitat Autònoma de BarcelonaBellaterraSpain
- Departament de Ciència Animal i dels AlimentsUniversitat Autònoma de BarcelonaBellaterraSpain
| | - Alex Clop
- Department of Animal GeneticsCentre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UBCampus de la Universitat Autònoma de BarcelonaBellaterraSpain
| | - Marcel Amills
- Department of Animal GeneticsCentre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UBCampus de la Universitat Autònoma de BarcelonaBellaterraSpain
- Departament de Ciència Animal i dels AlimentsUniversitat Autònoma de BarcelonaBellaterraSpain
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16
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Foster Y, Dutoit L, Grosser S, Dussex N, Foster BJ, Dodds KG, Brauning R, Van Stijn T, Robertson F, McEwan JC, Jacobs JME, Robertson BC. Genomic signatures of inbreeding in a critically endangered parrot, the kākāpō. G3 (BETHESDA, MD.) 2021; 11:jkab307. [PMID: 34542587 PMCID: PMC8527487 DOI: 10.1093/g3journal/jkab307] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 08/23/2021] [Indexed: 02/06/2023]
Abstract
Events of inbreeding are inevitable in critically endangered species. Reduced population sizes and unique life-history traits can increase the severity of inbreeding, leading to declines in fitness and increased risk of extinction. Here, we investigate levels of inbreeding in a critically endangered flightless parrot, the kākāpō (Strigops habroptilus), wherein a highly inbred island population and one individual from the mainland of New Zealand founded the entire extant population. Genotyping-by-sequencing (GBS), and a genotype calling approach using a chromosome-level genome assembly, identified a filtered set of 12,241 single-nucleotide polymorphisms (SNPs) among 161 kākāpō, which together encompass the total genetic potential of the extant population. Multiple molecular-based estimates of inbreeding were compared, including genome-wide estimates of heterozygosity (FH), the diagonal elements of a genomic-relatedness matrix (FGRM), and runs of homozygosity (RoH, FRoH). In addition, we compared levels of inbreeding in chicks from a recent breeding season to examine if inbreeding is associated with offspring survival. The density of SNPs generated with GBS was sufficient to identify chromosomes that were largely homozygous with RoH distributed in similar patterns to other inbred species. Measures of inbreeding were largely correlated and differed significantly between descendants of the two founding populations. However, neither inbreeding nor ancestry was found to be associated with reduced survivorship in chicks, owing to unexpected mortality in chicks exhibiting low levels of inbreeding. Our study highlights important considerations for estimating inbreeding in critically endangered species, such as the impacts of small population sizes and admixture between diverse lineages.
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Affiliation(s)
- Yasmin Foster
- Department of Zoology, University of Otago, Dunedin 9054, New Zealand
| | - Ludovic Dutoit
- Department of Zoology, University of Otago, Dunedin 9054, New Zealand
| | - Stefanie Grosser
- Department of Zoology, University of Otago, Dunedin 9054, New Zealand
| | - Nicolas Dussex
- Centre for Palaeogenetics, SE-106 91 Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-104 05 Stockholm, Sweden
- Department of Zoology, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Brodie J Foster
- Department of Zoology, University of Otago, Dunedin 9054, New Zealand
| | - Ken G Dodds
- AgResearch Invermay Agricultural Centre, Mosgiel 9053, New Zealand
| | - Rudiger Brauning
- AgResearch Invermay Agricultural Centre, Mosgiel 9053, New Zealand
| | - Tracey Van Stijn
- AgResearch Invermay Agricultural Centre, Mosgiel 9053, New Zealand
| | - Fiona Robertson
- Department of Zoology, University of Otago, Dunedin 9054, New Zealand
| | - John C McEwan
- AgResearch Invermay Agricultural Centre, Mosgiel 9053, New Zealand
| | | | - Bruce C Robertson
- Department of Zoology, University of Otago, Dunedin 9054, New Zealand
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17
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Gallego-García N, Caballero S, Shaffer HB. Are genomic updates of well-studied species worth the investment for conservation? A case study of the Critically Endangered Magdalena River turtle. J Hered 2021; 112:575-589. [PMID: 34628509 DOI: 10.1093/jhered/esab063] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 10/08/2021] [Indexed: 11/13/2022] Open
Abstract
As genomic-scale data sets become economically feasible for most organisms, a key question for conservation biology is whether the increased resolution offered by new genomic approaches justifies repeating earlier studies based on traditional markers, rather than investing those same time and monetary resources in less-known species. Genomic studies offer clear advantages when the objective is to identify adaptive loci that may be critical to conservation policy-makers. However, the answer is far less certain for the population and landscape studies based on neutral loci that dominate the conservation genetics research agenda. We used RADseq to revisit earlier molecular studies of the IUCN Critically Endangered Magdalena River turtle (Podocnemis lewyana), documenting the conservation insights gained by increasing the number of neutral markers by several orders of magnitude. Earlier research indicated that P. lewyana has the lowest genetic diversity known for any chelonian, and little or no population differentiation among independent rivers. In contrast, the RADseq data revealed discrete population structure with isolation-by-distance within river segments and identified precise population breaks clearly delineating management units. It also confirmed that the species does not have extremely low heterozygosity and that effective population sizes are probably sufficient to maintain long-term evolutionary potential. Contrary to earlier inferences from more limited population genetic markers, our genomic data suggest that management strategies should shift from active genetic rescue to more passive protection without extreme interventions. We conclude with a list of examples of conservation studies in other vertebrates indicating that for many systems a genomic update is worth the investment.
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Affiliation(s)
- Natalia Gallego-García
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA.,Departamento de Ciencias Biológicas, Laboratorio de Ecología Molecular de Vertebrados Acuáticos LEMVA, Universidad de los Andes, Bogotá, Colombia
| | - Susana Caballero
- Departamento de Ciencias Biológicas, Laboratorio de Ecología Molecular de Vertebrados Acuáticos LEMVA, Universidad de los Andes, Bogotá, Colombia
| | - H Bradley Shaffer
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA.,La Kretz Center for California Conservation Science, and Institute of the Environment and Sustainability, University of California, Los Angeles, CA, USA
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18
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Duntsch L, Whibley A, Brekke P, Ewen JG, Santure AW. Genomic data of different resolutions reveal consistent inbreeding estimates but contrasting homozygosity landscapes for the threatened Aotearoa New Zealand hihi. Mol Ecol 2021; 30:6006-6020. [PMID: 34242449 DOI: 10.1111/mec.16068] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 07/01/2021] [Indexed: 12/19/2022]
Abstract
Inbreeding can lead to a loss of heterozygosity in a population and when combined with genetic drift may reduce the adaptive potential of a species. However, there is uncertainty about whether resequencing data can provide accurate and consistent inbreeding estimates. Here, we performed an in-depth inbreeding analysis for hihi (Notiomystis cincta), an endemic and nationally vulnerable passerine bird of Aotearoa New Zealand. We first focused on subsampling variants from a reference genome male, and found that low-density data sets tend to miss runs of homozygosity (ROH) in some places and overestimate ROH length in others, resulting in contrasting homozygosity landscapes. Low-coverage resequencing and 50 K SNP array densities can yield comparable inbreeding results to high-coverage resequencing approaches, but the results for all data sets are highly dependent on the software settings employed. Second, we extended our analysis to 10 hihi where low-coverage whole genome resequencing, RAD-seq and SNP array genotypes are available. We inferred ROH and individual inbreeding to evaluate the relative effects of sequencing depth versus SNP density on estimating inbreeding coefficients and found that high rates of missingness downwardly bias both the number and length of ROH. In summary, when using genomic data to evaluate inbreeding, studies must consider that ROH estimates are heavily dependent on analysis parameters, data set density and individual sequencing depth.
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Affiliation(s)
- Laura Duntsch
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Annabel Whibley
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Patricia Brekke
- Institute of Zoology, Zoological Society of London, London, UK
| | - John G Ewen
- Institute of Zoology, Zoological Society of London, London, UK
| | - Anna W Santure
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
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19
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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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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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21
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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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Zecherle LJ, Nichols HJ, Bar‐David S, Brown RP, Hipperson H, Horsburgh GJ, Templeton AR. Subspecies hybridization as a potential conservation tool in species reintroductions. Evol Appl 2021; 14:1216-1224. [PMID: 34025762 PMCID: PMC8127701 DOI: 10.1111/eva.13191] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 12/11/2020] [Accepted: 12/27/2020] [Indexed: 11/30/2022] Open
Abstract
Reintroductions are a powerful tool for the recovery of endangered species. However, their long-term success is strongly influenced by the genetic diversity of the reintroduced population. The chances of population persistence can be improved by enhancing the population's adaptive ability through the mixing of individuals from different sources. However, where source populations are too diverse the reintroduced population could also suffer from outbreeding depression or unsuccessful admixture due to behavioural or genetic barriers. For the reintroduction of Asiatic wild ass Equus hemionus ssp. in Israel, a breeding core was created from individuals of two different subspecies (E. h. onager & E. h. kulan). Today the population comprises approximately 300 individuals and displays no signs of outbreeding depression. The aim of this study was a population genomic evaluation of this conservation reintroduction protocol. We used maximum likelihood methods and genetic clustering analyses to investigate subspecies admixture and test for spatial autocorrelation based on subspecies ancestry. Further, we analysed heterozygosity and effective population sizes in the breeding core prior to release and the current wild population. We discovered high levels of subspecies admixture in the breeding core and wild population, consistent with a significant heterozygote excess in the breeding core. Furthermore, we found no signs of spatial autocorrelation associated with subspecies ancestry in the wild population. Inbreeding and variance effective population size estimates were low. Our results indicate no genetic or behavioural barriers to admixture between the subspecies and suggest that their hybridization has led to greater genetic diversity in the reintroduced population. The study provides rare empirical evidence of the successful application of subspecies hybridization in a reintroduction. It supports use of intraspecific hybridization as a tool to increase genetic diversity in conservation translocations.
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Affiliation(s)
- Lilith J. Zecherle
- School of Biological and Environmental SciencesLiverpool John Moores UniversityLiverpoolUK
- Mitrani Department of Desert EcologyJacob Blaustein Institutes for Desert ResearchBen‐Gurion University of the NegevMidreshet Ben‐GurionIsrael
- NERC Biomolecular Analysis FacilityDepartment of Animal and Plant SciencesUniversity of SheffieldSheffieldUK
| | | | - Shirli Bar‐David
- Mitrani Department of Desert EcologyJacob Blaustein Institutes for Desert ResearchBen‐Gurion University of the NegevMidreshet Ben‐GurionIsrael
| | - Richard P. Brown
- School of Biological and Environmental SciencesLiverpool John Moores UniversityLiverpoolUK
| | - Helen Hipperson
- NERC Biomolecular Analysis FacilityDepartment of Animal and Plant SciencesUniversity of SheffieldSheffieldUK
| | - Gavin J. Horsburgh
- NERC Biomolecular Analysis FacilityDepartment of Animal and Plant SciencesUniversity of SheffieldSheffieldUK
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23
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García NC, Robinson WD. Current and Forthcoming Approaches for Benchmarking Genetic and Genomic Diversity. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.622603] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The current attrition of biodiversity extends beyond loss of species and unique populations to steady loss of a vast genomic diversity that remains largely undescribed. Yet the accelerating development of new techniques allows us to survey entire genomes ever faster and cheaper, to obtain robust samples from a diversity of sources including degraded DNA and residual DNA in the environment, and to address conservation efforts in new and innovative ways. Here we review recent studies that highlight the importance of carefully considering where to prioritize collection of genetic samples (e.g., organisms in rapidly changing landscapes or along edges of geographic ranges) and what samples to collect and archive (e.g., from individuals of little-known subspecies or populations, even of species not currently considered endangered). Those decisions will provide the sample infrastructure to detect the disappearance of certain genotypes or gene complexes, increases in inbreeding levels, and loss of genomic diversity as environmental conditions change. Obtaining samples from currently endangered, protected, and rare species can be particularly difficult, thus we also focus on studies that use new, non-invasive ways of obtaining genomic samples and analyzing them in these cases where other sampling options are highly constrained. Finally, biological collections archiving such samples face an inherent contradiction: their main goal is to preserve biological material in good shape so it can be used for scientific research for centuries to come, yet the technologies that can make use of such materials are advancing faster than collections can change their standardized practices. Thus, we also discuss current and potential new practices in biological collections that might bolster their usefulness for future biodiversity conservation research.
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24
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Forcina G, Woutersen K, Sánchez-Ramírez S, Angelone S, Crampe JP, Pérez JM, Fandos P, Granados JE, Jowers MJ. Demography reveals populational expansion of a recently extinct Iberian ungulate. ZOOSYST EVOL 2021. [DOI: 10.3897/zse.97.61854] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Reconstructing the demographic history of endangered taxa is paramount to predict future fluctuations and disentangle the contributing factors. Extinct taxa or populations might also provide key insights in this respect by means of the DNA extracted from museum specimens. Nevertheless, the degraded status of biological material and the limited number of records may pose some constraints. For this reason, identifying all available sources, including private and public biological collections, is a crucial step forward. In this study, we reconstructed the demographic history based on cytochrome-b sequence data of the Pyrenean ibex (Capra pyrenaica pyrenaica), a charismatic taxon of the European wildlife that became extinct in the year 2000. Moreover, we built a database of the museum specimens available in public biological collections worldwide and genotyped a privately owned 140-year-old trophy from the Spanish Pyrenees to confirm its origin. We found that the population of the Pyrenean ibex underwent a recent expansion approximately 20,000 years ago, after which trophy hunting and epizootics triggered a relentless population decline. Our interpretations, based on the genetic information currently available in public repositories, provide a solid basis for more exhaustive analyses relying on all the new sources identified. In particular, the adoption of a genome-wide approach appears a fundamental prerequisite to disentangle the multiple contributing factors associated with low genetic diversity, including inbreeding depression, acting as extinction drivers.
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25
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Luikart G, Antao T, Hand BK, Muhlfeld CC, Boyer MC, Cosart T, Trethewey B, Al-Chockhachy R, Waples RS. Detecting population declines via monitoring the effective number of breeders (N b ). Mol Ecol Resour 2020; 21:379-393. [PMID: 32881365 DOI: 10.1111/1755-0998.13251] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 06/10/2020] [Accepted: 06/12/2020] [Indexed: 12/16/2022]
Abstract
Estimating the effective population size and effective number of breeders per year (Nb ) can facilitate early detection of population declines. We used computer simulations to quantify bias and precision of the one-sample LDNe estimator of Nb in age-structured populations using a range of published species life history types, sample sizes, and DNA markers. Nb estimates were biased by ~5%-10% when using SNPs or microsatellites in species ranging from fishes to mosquitoes, frogs, and seaweed. The bias (high or low) was similar for different life history types within a species suggesting that life history variation in populations will not influence Nb estimation. Precision was higher for 100 SNPs (H ≈ 0.30) than for 15 microsatellites (H ≈ 0.70). Confidence intervals (CIs) were occasionally too narrow, and biased high when Nb was small (Nb < 50); however, the magnitude of bias would unlikely influence management decisions. The CIs (from LDNe) were sufficiently narrow to achieve high statistical power (≥0.80) to reject the null hypothesis that Nb = 50 when the true Nb = 30 and when sampling 50 individuals and 200 SNPs. Similarly, CIs were sufficiently narrow to reject Nb = 500 when the true Nb = 400 and when sampling 200 individuals and 5,000 loci. Finally, we present a linear regression method that provides high power to detect a decline in Nb when sampling at least five consecutive cohorts. This study provides guidelines and tools to simulate and estimate Nb for age structured populations (https://github.com/popgengui/agestrucnb/), which should help biologists develop sensitive monitoring programmes for early detection of changes in Nb and population declines.
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Affiliation(s)
- Gordon Luikart
- Flathead Lake Biological Station, Montana Conservation Genomics Laboratory, Division of Biological Sciences, University of Montana, Polson, MT, USA
| | - Tiago Antao
- The Welcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Brian K Hand
- Flathead Lake Biological Station, Montana Conservation Genomics Laboratory, Division of Biological Sciences, University of Montana, Polson, MT, USA
| | - Clint C Muhlfeld
- Northern Rocky Mountain Science Center, U.S. Geological Survey, Glacier National Park, Northern Rocky Mountain Science Center, West Glacier, MT, USA
| | | | - Ted Cosart
- Flathead Lake Biological Station, Montana Conservation Genomics Laboratory, Division of Biological Sciences, University of Montana, Polson, MT, USA
| | - Brian Trethewey
- Flathead Lake Biological Station, Montana Conservation Genomics Laboratory, Division of Biological Sciences, University of Montana, Polson, MT, USA
| | - Robert Al-Chockhachy
- U.S. Geological Survey, Northern Rocky Mountain Science Center, Bozeman, MT, USA
| | - Robin S Waples
- Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA, USA
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26
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Hohenlohe PA, Funk WC, Rajora OP. Population genomics for wildlife conservation and management. Mol Ecol 2020; 30:62-82. [PMID: 33145846 PMCID: PMC7894518 DOI: 10.1111/mec.15720] [Citation(s) in RCA: 158] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 10/02/2020] [Accepted: 10/29/2020] [Indexed: 12/21/2022]
Abstract
Biodiversity is under threat worldwide. Over the past decade, the field of population genomics has developed across nonmodel organisms, and the results of this research have begun to be applied in conservation and management of wildlife species. Genomics tools can provide precise estimates of basic features of wildlife populations, such as effective population size, inbreeding, demographic history and population structure, that are critical for conservation efforts. Moreover, population genomics studies can identify particular genetic loci and variants responsible for inbreeding depression or adaptation to changing environments, allowing for conservation efforts to estimate the capacity of populations to evolve and adapt in response to environmental change and to manage for adaptive variation. While connections from basic research to applied wildlife conservation have been slow to develop, these connections are increasingly strengthening. Here we review the primary areas in which population genomics approaches can be applied to wildlife conservation and management, highlight examples of how they have been used, and provide recommendations for building on the progress that has been made in this field.
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Affiliation(s)
- Paul A Hohenlohe
- Department of Biological Sciences and Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, USA
| | - W Chris Funk
- Department of Biology, Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado, USA
| | - Om P Rajora
- Faculty of Forestry and Environmental Management, University of New Brunswick, Fredericton, New Brunswick, Canada
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27
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Genetic diversity of cytochrome b in Iberian ibex from Andalusia. Mamm Biol 2020. [DOI: 10.1007/s42991-020-00077-z] [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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28
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de Jong JF, van Hooft P, Megens HJ, Crooijmans RPMA, de Groot GA, Pemberton JM, Huisman J, Bartoš L, Iacolina L, van Wieren SE, Ydenberg RC, Prins HHT. Fragmentation and Translocation Distort the Genetic Landscape of Ungulates: Red Deer in the Netherlands. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.535715] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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29
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An 85K SNP Array Uncovers Inbreeding and Cryptic Relatedness in an Antarctic Fur Seal Breeding Colony. G3-GENES GENOMES GENETICS 2020; 10:2787-2799. [PMID: 32540866 PMCID: PMC7407454 DOI: 10.1534/g3.120.401268] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
High density single nucleotide polymorphism (SNP) arrays allow large numbers of individuals to be rapidly and cost-effectively genotyped at large numbers of genetic markers. However, despite being widely used in studies of humans and domesticated plants and animals, SNP arrays are lacking for most wild organisms. We developed a custom 85K Affymetrix Axiom array for an intensively studied pinniped, the Antarctic fur seal (Arctocephalus gazella). SNPs were discovered from a combination of genomic and transcriptomic resources and filtered according to strict criteria. Out of a total of 85,359 SNPs tiled on the array, 75,601 (88.6%) successfully converted and were polymorphic in 270 animals from a breeding colony at Bird Island in South Georgia. Evidence was found for inbreeding, with three genomic inbreeding coefficients being strongly intercorrelated and the proportion of the genome in runs of homozygosity being non-zero in all individuals. Furthermore, analysis of genomic relatedness coefficients identified previously unknown first-degree relatives and multiple second-degree relatives among a sample of ostensibly unrelated individuals. Such “cryptic relatedness” within fur seal breeding colonies may increase the likelihood of consanguineous matings and could therefore have implications for understanding fitness variation and mate choice. Finally, we demonstrate the cross-amplification potential of the array in three related pinniped species. Overall, our SNP array will facilitate future studies of Antarctic fur seals and has the potential to serve as a more general resource for the wider pinniped research community.
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30
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Brambilla A, Von Hardenberg A, Nelli L, Bassano B. Distribution, status, and recent population dynamics of Alpine ibexCapra ibexin Europe. Mamm Rev 2020. [DOI: 10.1111/mam.12194] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Alice Brambilla
- Department of Evolutionary Biology and Environmental Studies University of Zurich Winterthurerstrasse 1908057Zurich ZH Switzerland
- Alpine Wildlife Research Centre Gran Paradiso National Park Frazione Jamonin 510080Noasca TO Italy
| | - Achaz Von Hardenberg
- Conservation Biology Research Group Department of Biological Sciences University of Chester Parkgate RoadCH2 4BJChester UK
| | - Luca Nelli
- Institute of Biodiversity, Animal Health and Comparative Medicine University of Glasgow Graham Kerr BuildingG12 8QQGlasgow UK
| | - Bruno Bassano
- Alpine Wildlife Research Centre Gran Paradiso National Park Frazione Jamonin 510080Noasca TO Italy
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31
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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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32
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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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Ponsart C, Riou M, Locatelli Y, Jacques I, Fadeau A, Jay M, Simon R, Perrot L, Freddi L, Breton S, Chaumeil T, Blanc B, Ortiz K, Vion C, Rioult D, Quéméré E, Sarradin P, Chollet JY, Garin-Bastuji B, Rossi S. Brucella melitensis Rev.1 vaccination generates a higher shedding risk of the vaccine strain in Alpine ibex (Capra ibex) compared to the domestic goat (Capra hircus). Vet Res 2019; 50:100. [PMID: 31775863 PMCID: PMC6882340 DOI: 10.1186/s13567-019-0717-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 10/25/2019] [Indexed: 12/12/2022] Open
Abstract
Epidemiological investigations implemented in wild and domestic ruminants evidenced a reservoir for Brucella in Capra ibex in the French Alps. Vaccination was considered as a possible way to control Brucella infection in this wildlife population. Twelve ibexes and twelve goats were allocated into four groups housed separately, each including six males or six non-pregnant females. Four to five animals were vaccinated and one or two animals were contact animals. Half of the animals were necropsied 45 days post-vaccination (pv), and the remaining ones at 90 days pv. Additional samples were collected 20 and 68 days pv to explore bacterial distribution in organs and humoral immunity. Neither clinical signs nor Brucella-specific lesions were observed and all vaccinated animals seroconverted. Brucella distribution and antibody profiles were highly contrasted between both species. Proportion of infected samples was significantly higher in ibex compared to goats and decreased between 45 and 90 days pv. Two male ibex presented urogenital excretion at 20 or 45 days pv. The bacterial load was higher 45 days in ibexes compared to goats, whereas it remained moderate to low 90 days pv in both species with large variability between animals. In this experiment, differences between species remained the main source of variation, with low impact of other individual factors. To conclude, multiplicative and shedding capacity of Rev.1 was much higher in ibex compared to goats within 90 days. These results provide initial information on the potential use in natura of a commercial vaccine.
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Affiliation(s)
- Claire Ponsart
- EU/OIE/FAO & National Reference Laboratory for Animal Brucellosis, Animal Health Laboratory, ANSES/Paris-Est University, 94706, Maisons-Alfort, France
| | - Mickaël Riou
- UE-1277 Plateforme d'Infectiologie expérimentale (PFIE), INRA Centre Val de Loire, 37380, Nouzilly, France.
| | - Yann Locatelli
- Réserve Zoologique de la Haute Touche, Muséum National d'Histoire Naturelle (MNHN), 36290, Obterre, France
| | - Isabelle Jacques
- Département Génie Biologique, Institut Universitaire Technologique (IUT), Université de Tours, 29 Rue du Pont Volant, 37082, Tours Cedex 2, France
- UMR-1282 Infectiologie et Santé Publique (ISP), INRA Centre Val de Loire - Université de Tours, 37380, Nouzilly, France
| | - Alain Fadeau
- Laboratoire de Touraine, Conseil départemental d'Indre-et-Loire, B.P. 67357, 37073, Tours Cedex 02, France
| | - Maryne Jay
- EU/OIE/FAO & National Reference Laboratory for Animal Brucellosis, Animal Health Laboratory, ANSES/Paris-Est University, 94706, Maisons-Alfort, France
| | - Roland Simon
- Réserve Zoologique de la Haute Touche, Muséum National d'Histoire Naturelle (MNHN), 36290, Obterre, France
| | - Ludivine Perrot
- EU/OIE/FAO & National Reference Laboratory for Animal Brucellosis, Animal Health Laboratory, ANSES/Paris-Est University, 94706, Maisons-Alfort, France
| | - Luca Freddi
- EU/OIE/FAO & National Reference Laboratory for Animal Brucellosis, Animal Health Laboratory, ANSES/Paris-Est University, 94706, Maisons-Alfort, France
| | - Sylvain Breton
- UE-1277 Plateforme d'Infectiologie expérimentale (PFIE), INRA Centre Val de Loire, 37380, Nouzilly, France
| | - Thierry Chaumeil
- UE-1277 Plateforme d'Infectiologie expérimentale (PFIE), INRA Centre Val de Loire, 37380, Nouzilly, France
| | - Barbara Blanc
- Réserve Zoologique de la Haute Touche, Muséum National d'Histoire Naturelle (MNHN), 36290, Obterre, France
| | - Katia Ortiz
- Réserve Zoologique de la Haute Touche, Muséum National d'Histoire Naturelle (MNHN), 36290, Obterre, France
| | - Colin Vion
- Réserve Zoologique de la Haute Touche, Muséum National d'Histoire Naturelle (MNHN), 36290, Obterre, France
| | - Damien Rioult
- Université de Reims Champagne-Ardenne, 9 Boulevard de la Paix, 51100, Reims, France
| | - Erwan Quéméré
- Unité Comportement et Écologie de la Faune Sauvage (CEFS), INRA, 24 chemin de Borde-Rouge-Auzeville CS 52627, 31326, Castanet-Tolosan Cedex, France
| | - Pierre Sarradin
- UE-1277 Plateforme d'Infectiologie expérimentale (PFIE), INRA Centre Val de Loire, 37380, Nouzilly, France
| | - Jean-Yves Chollet
- Unité sanitaire de la Faune, Direction de la Recherche et de l'Expertise (DRE), Office National de la Chasse et de la Faune Sauvage (ONCFS), 5 rue de Saint-Thibaud, Saint-Benoît, 78610, Auffargis, France
| | - Bruno Garin-Bastuji
- European and International Affairs Department, ANSES, 94701, Maisons-Alfort, France
| | - Sophie Rossi
- Unité sanitaire de la Faune, Direction de la Recherche et de l'Expertise (DRE), Office National de la Chasse et de la Faune Sauvage (ONCFS), 5 rue de Saint-Thibaud, Saint-Benoît, 78610, Auffargis, France
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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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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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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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38
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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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39
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Luikart G, Kardos M, Hand BK, Rajora OP, Aitken SN, Hohenlohe PA. Population Genomics: Advancing Understanding of Nature. POPULATION GENOMICS 2018. [DOI: 10.1007/13836_2018_60] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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40
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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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