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Subramanian S, Kumar M. Genomic footprints of bottleneck in landlocked salmon population. Sci Rep 2023; 13:6706. [PMID: 37185620 PMCID: PMC10130149 DOI: 10.1038/s41598-023-34076-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 04/24/2023] [Indexed: 05/17/2023] Open
Abstract
At the end of the last ice age, several Atlantic salmon populations got caught up in the lakes and ponds of the Northern Hemisphere. Occasionally, the populations also got locked when the flow of rivers terminated from reaching the sea due to land upheaval. Therefore, the pattern of evolution shaping the landlocked salmon populations is different from the other anadromous salmons, which migrate between the sea and rivers. According to the theories of population genetics, the effect of genetic drift is expected to be more pronounced in the former compared to the latter. Here we examined this using the whole genome data of landlocked and anadromous salmon populations of Norway. Our results showed a 50-80% reduction in the genomic heterozygosity in the landlocked compared to anadromous salmon populations. The number and total size of the runs of homozygosity (RoH) segments of landlocked salmons were two to eightfold higher than those of their anadromous counterparts. We found the former had a higher ratio of nonsynonymous-to-synonymous diversities than the latter. The investigation also revealed a significant elevation of homozygous deleterious Single Nucleotide Variants (SNVs) in the landlocked salmon compared to the anadromous populations. All these results point to a significant reduction in the population size of the landlocked salmons. This process of reduction might have started recently as the phylogeny revealed a recent separation of the landlocked from the anadromous population. Previous studies on terrestrial vertebrates observed similar signatures of a bottleneck when the populations from Island and the mainland were compared. Since landlocked waterbody such as ponds and lakes are geographically analogous to Islands for fish populations, the findings of this study suggest the similarity in the patterns of evolution between the two.
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Affiliation(s)
- Sankar Subramanian
- Centre for Bioinnovation, School of Science, Technology, and Engineering, The University of the Sunshine Coast, 1 Moreton Parade, Petrie, Moreton Bay, QLD, 4502, Australia.
| | - Manoharan Kumar
- Centre for Bioinnovation, School of Science, Technology, and Engineering, The University of the Sunshine Coast, 1 Moreton Parade, Petrie, Moreton Bay, QLD, 4502, Australia
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2
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Devillard S, Jacquier M, Vandel JM, Léger F, Duhayer J, Pardonnet S, Say L, Ruette S. Genetic variability and population size covary positively across nine badgers (Meles meles) populations in France. MAMMAL RES 2022. [DOI: 10.1007/s13364-021-00614-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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3
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4
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De Kort H, Prunier JG, Ducatez S, Honnay O, Baguette M, Stevens VM, Blanchet S. Life history, climate and biogeography interactively affect worldwide genetic diversity of plant and animal populations. Nat Commun 2021; 12:516. [PMID: 33483517 PMCID: PMC7822833 DOI: 10.1038/s41467-021-20958-2] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 01/04/2021] [Indexed: 01/30/2023] Open
Abstract
Understanding how biological and environmental factors interactively shape the global distribution of plant and animal genetic diversity is fundamental to biodiversity conservation. Genetic diversity measured in local populations (GDP) is correspondingly assumed representative for population fitness and eco-evolutionary dynamics. For 8356 populations across the globe, we report that plants systematically display much lower GDP than animals, and that life history traits shape GDP patterns both directly (animal longevity and size), and indirectly by mediating core-periphery patterns (animal fecundity and plant dispersal). Particularly in some plant groups, peripheral populations can sustain similar GDP as core populations, emphasizing their potential conservation value. We further find surprisingly weak support for general latitudinal GDP trends. Finally, contemporary rather than past climate contributes to the spatial distribution of GDP, suggesting that contemporary environmental changes affect global patterns of GDP. Our findings generate new perspectives for the conservation of genetic resources at worldwide and taxonomic-wide scales.
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Affiliation(s)
- H De Kort
- Plant Conservation and Population Biology, Department of Biology, University of Leuven, Heverlee, Belgium.
| | - J G Prunier
- Centre National de la Recherche Scientifique, SETE Station d'Ecologie Théorique et Expérimentale, UMR 5321, Moulis, France
| | - S Ducatez
- Department of Earth Sciences, University of Cambridge, Cambridge, UK
| | - O Honnay
- Plant Conservation and Population Biology, Department of Biology, University of Leuven, Heverlee, Belgium
| | - M Baguette
- Centre National de la Recherche Scientifique, SETE Station d'Ecologie Théorique et Expérimentale, UMR 5321, Moulis, France
- Institut Systématique, Evolution, Biodiversité (ISYEB), UMR 7205 Museum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - V M Stevens
- Centre National de la Recherche Scientifique, SETE Station d'Ecologie Théorique et Expérimentale, UMR 5321, Moulis, France
| | - S Blanchet
- Centre National de la Recherche Scientifique, SETE Station d'Ecologie Théorique et Expérimentale, UMR 5321, Moulis, France
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Pitirri MK, Vermeulen E, Komza K, Begun DR. Mandibular shape variation in mainland and insular hylobatids. Am J Primatol 2020; 82:e23175. [DOI: 10.1002/ajp.23175] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 06/15/2020] [Accepted: 07/03/2020] [Indexed: 12/17/2022]
Affiliation(s)
- M. Kathleen Pitirri
- Department of Anthropology University of Toronto Toronto Canada
- Department of Anthropology Pennsylvania State University State College Pennsylvania
| | - Erin Vermeulen
- Department of Anthropology University of Toronto Toronto Canada
| | - Klara Komza
- Department of Anthropology University of Toronto Toronto Canada
| | - David R. Begun
- Department of Anthropology University of Toronto Toronto Canada
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6
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Locally Fixed Alleles: A method to localize gene drive to island populations. Sci Rep 2019; 9:15821. [PMID: 31676762 PMCID: PMC6825234 DOI: 10.1038/s41598-019-51994-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 10/11/2019] [Indexed: 01/08/2023] Open
Abstract
Invasive species pose a major threat to biodiversity on islands. While successes have been achieved using traditional removal methods, such as toxicants aimed at rodents, these approaches have limitations and various off-target effects on island ecosystems. Gene drive technologies designed to eliminate a population provide an alternative approach, but the potential for drive-bearing individuals to escape from the target release area and impact populations elsewhere is a major concern. Here we propose the “Locally Fixed Alleles” approach as a novel means for localizing elimination by a drive to an island population that exhibits significant genetic isolation from neighboring populations. Our approach is based on the assumption that in small island populations of rodents, genetic drift will lead to alleles at multiple genomic loci becoming fixed. In contrast, multiple alleles are likely to be maintained in larger populations on mainlands. Utilizing the high degree of genetic specificity achievable using homing drives, for example based on the CRISPR/Cas9 system, our approach aims at employing one or more locally fixed alleles as the target for a gene drive on a particular island. Using mathematical modeling, we explore the feasibility of this approach and the degree of localization that can be achieved. We show that across a wide range of parameter values, escape of the drive to a neighboring population in which the target allele is not fixed will at most lead to modest transient suppression of the non-target population. While the main focus of this paper is on elimination of a rodent pest from an island, we also discuss the utility of the locally fixed allele approach for the goals of population suppression or population replacement. Our analysis also provides a threshold condition for the ability of a gene drive to invade a partially resistant population.
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7
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Igawa T, Sugawara H, Honda M, Tominaga A, Oumi S, Katsuren S, Ota H, Matsui M, Sumida M. Detecting inter- and intra-island genetic diversity: population structure of the endangered crocodile newt, Echinotriton andersoni, in the Ryukyus. CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01219-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Hardouin EA, Baltazar‐Soares M, Schilling A, Butler H, García‐Rodríguez O, Crowley E, Liang W, Meredith A, Lurz PWW, Forster J, Kenward RE, Hodder KH. Conservation of genetic uniqueness in remaining populations of red squirrels ( Sciurus vulgaris L.) in the South of England. Ecol Evol 2019; 9:6547-6558. [PMID: 31236243 PMCID: PMC6580283 DOI: 10.1002/ece3.5233] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 04/04/2019] [Accepted: 04/09/2019] [Indexed: 11/21/2022] Open
Abstract
The Eurasian red squirrel (Sciurus vulgaris) is an emblematic species for conservation, and its decline in the British Isles exemplifies the impact that alien introductions can have on native ecosystems. Indeed, red squirrels in this region have declined dramatically over the last 60 years due to the spread of squirrelpox virus following the introduction of the gray squirrel (Sciurus carolinensis). Currently, red squirrel populations in Britain are fragmented and need to be closely monitored in order to assess their viability and the effectiveness of conservation efforts. The situation is even more dramatic in the South of England, where S. vulgaris survives only on islands (Brownsea Island, Furzey Island, and the Isle of Wight). Using the D-loop, we investigated the genetic diversity and putative ancestry of the squirrels from Southern England and compared them to a European dataset composed of 1,016 samples from 54 populations. We found that our three populations were more closely related to other squirrels from the British Isles than squirrels from Europe, showed low genetic diversity, and also harbored several private haplotypes. Our study demonstrates how genetically unique the Southern English populations are in comparison with squirrels from the continental European range. We report the presence of four private haplotypes, suggesting that these populations may potentially harbor distinct genetic lineages. Our results emphasize the importance of preserving these isolated red squirrel populations for the conservation of the species.
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Affiliation(s)
- Emilie A. Hardouin
- Department of Life and Environmental Sciences, Faculty of Science and TechnologyBournemouth UniversityDorsetUK
| | - Miguel Baltazar‐Soares
- Department of Life and Environmental Sciences, Faculty of Science and TechnologyBournemouth UniversityDorsetUK
| | - Anna‐Katarina Schilling
- Royal (Dick) School of Veterinary Sciences, Easter Bush CampusUniversity of EdinburghMidlothianUK
- Moredun Research InstitutePentlands Science ParkPenicuikUK
| | | | - Oxala García‐Rodríguez
- Department of Life and Environmental Sciences, Faculty of Science and TechnologyBournemouth UniversityDorsetUK
| | - Eloise Crowley
- Department of Life and Environmental Sciences, Faculty of Science and TechnologyBournemouth UniversityDorsetUK
| | - Wei‐Jun Liang
- Department of Life and Environmental Sciences, Faculty of Science and TechnologyBournemouth UniversityDorsetUK
| | - Anna Meredith
- Royal (Dick) School of Veterinary Sciences, Easter Bush CampusUniversity of EdinburghMidlothianUK
- Faculty of Veterinary and Agricultural Sciences, Parkville CampusThe University of MelbourneMelbourneVictoriaAustralia
| | - Peter W. W. Lurz
- Royal (Dick) School of Veterinary Sciences, Easter Bush CampusUniversity of EdinburghMidlothianUK
| | - Jane Forster
- WISH Lab, Academic Unit of Cancer Sciences, Faculty of MedicineUniversity of SouthamptonSouthamptonUK
| | | | - Kathy H. Hodder
- Department of Life and Environmental Sciences, Faculty of Science and TechnologyBournemouth UniversityDorsetUK
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Costanzi J, Steifetten Ø. Island biogeography theory explains the genetic diversity of a fragmented rock ptarmigan ( Lagopus muta) population. Ecol Evol 2019; 9:3837-3849. [PMID: 31015970 PMCID: PMC6468070 DOI: 10.1002/ece3.5007] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 01/31/2019] [Accepted: 02/04/2019] [Indexed: 01/20/2023] Open
Abstract
The island biogeography theory is one of the major theories in ecology, and its applicability to natural systems is well documented. The core model of the theory, the equilibrium model of island biogeography, predicts that species diversity on an island is positively related to the size of the island, but negatively related by the island's distance to the mainland. In recent years, ecologists have begun to apply this model when investigating genetic diversity, arguing that genetic and species diversity might be influenced by similar ecological processes. However, most studies have focused on oceanic islands, but knowledge on how the theory applies to islands located on the mainland (e.g., mountain islands, forest islands) is scarce. In this study, we examined how the size and degree of isolation of mountain islands would affect the genetic diversity of an alpine bird, the rock ptarmigan (Lagopus muta). Within our study area, we defined the largest contiguous mountain area as the mainland, while smaller mountains surrounding the mainland were defined as islands. We found that the observed heterozygosity (H o) was significantly higher, and the inbreeding coefficient (F is) significantly lower, on the mainland compared to islands. There was a positive significant relationship between the unbiased expected heterozygosity (H n.b.) and island size (log km2), but a negative significant relationship between H o and the cost distance to the mainland. Our results are consistent with the equilibrium model of island biogeography and show that the model is well suited for investigating genetic diversity among islands, but also on islands located on the mainland.
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Affiliation(s)
- Jean‐Marc Costanzi
- Department of Natural Sciences and Environmental HealthUniversity of South‐Eastern NorwayBø i TelemarkNorway
| | - Øyvind Steifetten
- Department of Natural Sciences and Environmental HealthUniversity of South‐Eastern NorwayBø i TelemarkNorway
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10
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Jenkins DA, Yannic G, Schaefer JA, Conolly J, Lecomte N. Population structure of caribou in an ice-bound archipelago. DIVERS DISTRIB 2018. [DOI: 10.1111/ddi.12748] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Affiliation(s)
- Deborah. A. Jenkins
- Environmental and Life Sciences Graduate Program; Trent University; Peterborough ON Canada
- Canada Research Chair in Polar and Boreal Ecology and Centre d'Études Nordiques; University of Moncton; Moncton NB Canada
| | - Glenn Yannic
- University of Grenoble Alpes; University of Savoie Mont Blanc; CNRS; LECA (Laboratoire d'Ecologie Alpine); Le Bourget-du-Lac France
| | | | - James Conolly
- Department of Anthropology; Trent University; Peterborough ON Canada
| | - Nicolas Lecomte
- Canada Research Chair in Polar and Boreal Ecology and Centre d'Études Nordiques; University of Moncton; Moncton NB Canada
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11
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Wang S, Liu C, Wilson AB, Zhao N, Li X, Zhu W, Gao X, Liu X, Li Y. Pathogen richness and abundance predict patterns of adaptive major histocompatibility complex variation in insular amphibians. Mol Ecol 2017; 26:4671-4685. [PMID: 28734069 DOI: 10.1111/mec.14242] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Revised: 06/01/2017] [Accepted: 06/19/2017] [Indexed: 12/26/2022]
Abstract
The identification of the factors responsible for genetic variation and differentiation at adaptive loci can provide important insights into the evolutionary process and is crucial for the effective management of threatened species. We studied the impact of environmental viral richness and abundance on functional diversity and differentiation of the MHC class Ia locus in populations of the black-spotted pond frog (Pelophylax nigromaculatus), an IUCN-listed species, on 24 land-bridge islands of the Zhoushan Archipelago and three nearby mainland sites. We found a high proportion of private MHC alleles in mainland and insular populations, corresponding to 32 distinct functional supertypes, and strong positive selection on MHC antigen-binding sites in all populations. Viral pathogen diversity and abundance were reduced at island sites relative to the mainland, and islands housed distinctive viral communities. Standardized MHC diversity at island sites exceeded that found at neutral microsatellites, and the representation of key functional supertypes was positively correlated with the abundance of specific viruses in the environment (Frog virus 3 and Ambystoma tigrinum virus). These results indicate that pathogen-driven diversifying selection can play an important role in maintaining functionally important MHC variation following island isolation, highlighting the importance of considering functionally important genetic variation and host-pathogen associations in conservation planning and management.
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Affiliation(s)
- Supen Wang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Conghui Liu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Anthony B Wilson
- Department of Biology, Brooklyn College and The Graduate Center, City University of New York, Brooklyn, NY, USA
| | - Na Zhao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xianping Li
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Wei Zhu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xu Gao
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xuan Liu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yiming Li
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
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12
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Villanova VL, Hughes PT, Hoffman EA. Combining genetic structure and demographic analyses to estimate persistence in endangered Key deer (Odocoileus virginianus clavium). CONSERV GENET 2017. [DOI: 10.1007/s10592-017-0958-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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13
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Sato JJ, Tasaka Y, Tasaka R, Gunji K, Yamamoto Y, Takada Y, Uematsu Y, Sakai E, Tateishi T, Yamaguchi Y. Effects of Isolation by Continental Islands in the Seto Inland Sea, Japan, on Genetic Diversity of the Large Japanese Field Mouse, Apodemus speciosus (Rodentia: Muridae), Inferred from the Mitochondrial Dloop Region. Zoolog Sci 2017; 34:112-121. [DOI: 10.2108/zs160113] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Jun J. Sato
- Laboratory of Animal Cell Technology, Faculty of Life Science and Technology, Fukuyama University, Higashimura-cho, Aza, Sanzo, 985, Fukuyama 729-0292, Japan
| | - Yurina Tasaka
- Laboratory of Animal Cell Technology, Faculty of Life Science and Technology, Fukuyama University, Higashimura-cho, Aza, Sanzo, 985, Fukuyama 729-0292, Japan
| | - Ryoya Tasaka
- Laboratory of Animal Cell Technology, Faculty of Life Science and Technology, Fukuyama University, Higashimura-cho, Aza, Sanzo, 985, Fukuyama 729-0292, Japan
| | - Kentaro Gunji
- Laboratory of Animal Cell Technology, Faculty of Life Science and Technology, Fukuyama University, Higashimura-cho, Aza, Sanzo, 985, Fukuyama 729-0292, Japan
| | - Yuya Yamamoto
- Laboratory of Animal Cell Technology, Faculty of Life Science and Technology, Fukuyama University, Higashimura-cho, Aza, Sanzo, 985, Fukuyama 729-0292, Japan
| | - Yasushi Takada
- Department of Anatomy, School of Dentistry, Aichi-Gakuin University, Kusumoto-cho, Chikusa-ku, Nagoya 464-8650, Japan
| | - Yasushi Uematsu
- Department of Anatomy, School of Dentistry, Aichi-Gakuin University, Kusumoto-cho, Chikusa-ku, Nagoya 464-8650, Japan
| | - Eiichi Sakai
- Department of Dental Hygiene, Aichi-Gakuin University, Kusumoto-cho, Chikusa-ku, Nagoya 464-8650, Japan
| | | | - Yasunori Yamaguchi
- Laboratory of Animal Cell Technology, Faculty of Life Science and Technology, Fukuyama University, Higashimura-cho, Aza, Sanzo, 985, Fukuyama 729-0292, Japan
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14
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Cantos M, Arroyo-García R, García JL, Lara M, Morales R, López MÁ, Gallardo A, Ocete CA, Rodríguez Á, Valle JM, Vaca R, González-Maestro M, Bánáti H, Ocete R. Current distribution and characterization of the wild grapevine populations in Andalusia (Spain). C R Biol 2017; 340:164-177. [PMID: 28256414 DOI: 10.1016/j.crvi.2017.01.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 01/25/2017] [Accepted: 01/26/2017] [Indexed: 10/20/2022]
Abstract
For decades, human activities have gradually destroyed the natural habitats of wild grapevine, Vitis vinifera L. subsp. sylvestris (Gmelin) Hegi, and nowadays this species is endangered in southern Europe. In this paper, 94 populations of this species have been localized and characterized in the Andalusian region in the Iberian Peninsula between 1989 and 2013. Location, ecological aspects, and sanitary characteristics are described. Must properties and in vitro tolerance to calcareous conditions were also checked. The paper also contains a global description of female and male individuals. Two hundred individuals from six river basin populations have been sampled, and their genetic structure analyzed by using 25 nuclear microsatellites loci to investigate the gene diversity of wild grape populations in Andalusia at two levels: total individuals and at river basin populations. Also, the genetic relationship of wild and cultivated accessions has been tested. Wild grapevine is considered the ancestor of the cultivated varieties and should be preserved as this material could be used to start breeding programs of cultivated varieties and also to restore riverbank forests, which constitute one of the worst preserved ecosystems in the area.
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Affiliation(s)
- Manuel Cantos
- Instituto de Recursos Naturales y Agrobiología de Sevilla (CSIC), avenue Reina Mercedes 10, 41012 Sevilla, Spain.
| | - Rosa Arroyo-García
- Centro de Biotecnología y Genómica de Plantas, UPM-INIA, Campus de Montegancedo, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - José Luis García
- Instituto de Recursos Naturales y Agrobiología de Sevilla (CSIC), avenue Reina Mercedes 10, 41012 Sevilla, Spain
| | - Miguel Lara
- IFAPA Rancho de la Merced, Ctra. de Trebujena km. 3.2, 11431 Jerez de la Frontera, Cádiz, Spain
| | - Ramón Morales
- Real Jardín Botánico (CSIC), Plaza de Murillo 2, 28014 Madrid, Spain
| | - María Ángeles López
- Laboratorio Entomología Aplicada, Universidad de Sevilla, avenue Reina Mercedes 6, 41012 Sevilla, Spain
| | - Antonio Gallardo
- Laboratorio Entomología Aplicada, Universidad de Sevilla, avenue Reina Mercedes 6, 41012 Sevilla, Spain
| | - Carlos Alvar Ocete
- Laboratorio Entomología Aplicada, Universidad de Sevilla, avenue Reina Mercedes 6, 41012 Sevilla, Spain
| | - Álvaro Rodríguez
- Escuela Universitaria de Ingeniería, Universidad del País Vasco, Vitoria-Gasteiz, Spain
| | - José Manuel Valle
- Escuela Universitaria de Ingeniería, Universidad del País Vasco, Vitoria-Gasteiz, Spain
| | - Ramón Vaca
- Macià Batle Wineries, 07320 Santa María del Camí, Illes Balears, Spain
| | - Magdalena González-Maestro
- Instituto de Recursos Naturales y Agrobiología de Sevilla (CSIC), avenue Reina Mercedes 10, 41012 Sevilla, Spain
| | - Hajnalka Bánáti
- Department of Ecotoxicology, Central Environmental and Food Science Research Institute, Herman Ottó út 15, 1022 Budapest, Hungary
| | - Rafael Ocete
- Laboratorio Entomología Aplicada, Universidad de Sevilla, avenue Reina Mercedes 6, 41012 Sevilla, Spain
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15
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Trujillo AL, Hoffman EA. Uncovering discordance between taxonomy and evolutionary history in Florida raccoons. SYST BIODIVERS 2016. [DOI: 10.1080/14772000.2016.1214190] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Alexa L. Trujillo
- University of Central Florida, 4000 Central Florida Blvd, Orlando, FL, 32816, USA
| | - Eric A. Hoffman
- University of Central Florida, 4000 Central Florida Blvd, Orlando, FL, 32816, USA
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16
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Harradine EL, Andrew ME, Thomas JW, How RA, Schmitt LH, Spencer PBS. Importance of dispersal routes that minimize open-ocean movement to the genetic structure of island populations. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2015; 29:1704-1714. [PMID: 26171679 DOI: 10.1111/cobi.12555] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 04/23/2015] [Indexed: 06/04/2023]
Abstract
Islands present a unique scenario in conservation biology, offering refuge yet imposing limitations on insular populations. The Kimberley region of northwestern Australia has more than 2500 islands that have recently come into focus as substantial conservation resources. It is therefore of great interest for managers to understand the driving forces of genetic structure of species within these island archipelagos. We used the ubiquitous bar-shouldered skink (Ctenotus inornatus) as a model species to represent the influence of landscape factors on genetic structure across the Kimberley islands. On 41 islands and 4 mainland locations in a remote area of Australia, we genotyped individuals across 18 nuclear (microsatellite) markers. Measures of genetic differentiation and diversity were used in two complementary analyses. We used circuit theory and Mantel tests to examine the influence of the landscape matrix on population connectivity and linear regression and model selection based on Akaike's information criterion to investigate landscape controls on genetic diversity. Genetic differentiation between islands was best predicted with circuit-theory models that accounted for the large difference in resistance to dispersal between land and ocean. In contrast, straight-line distances were unrelated to either resistance distances or genetic differentiation. Instead, connectivity was determined by island-hopping routes that allow organisms to minimize the distance of difficult ocean passages. Island populations of C. inornatus retained varying degrees of genetic diversity (NA = 1.83 - 7.39), but it was greatest on islands closer to the mainland, in terms of resistance-distance units. In contrast, genetic diversity was unrelated to island size. Our results highlight the potential for islands to contribute to both theoretical and applied conservation, provide strong evidence of the driving forces of population structure within undisturbed landscapes, and identify the islands most valuable for conservation based on their contributions to gene flow and genetic diversity.
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Affiliation(s)
- E L Harradine
- School of Veterinary and Life Sciences, Murdoch University, 90 South Street, Western Australia, 6150, Australia
| | - M E Andrew
- School of Veterinary and Life Sciences, Murdoch University, 90 South Street, Western Australia, 6150, Australia
| | - J W Thomas
- School of Veterinary and Life Sciences, Murdoch University, 90 South Street, Western Australia, 6150, Australia
| | - R A How
- School of Anatomy, Physiology & Human Biology, The University of Western Australia, Crawley, WA, 6009, Australia
| | - L H Schmitt
- School of Anatomy, Physiology & Human Biology, The University of Western Australia, Crawley, WA, 6009, Australia
| | - P B S Spencer
- School of Veterinary and Life Sciences, Murdoch University, 90 South Street, Western Australia, 6150, Australia
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García-Verdugo C, Sajeva M, La Mantia T, Harrouni C, Msanda F, Caujapé-Castells J. Do island plant populations really have lower genetic variation than mainland populations? Effects of selection and distribution range on genetic diversity estimates. Mol Ecol 2015; 24:726-41. [PMID: 25580539 DOI: 10.1111/mec.13060] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Revised: 12/16/2014] [Accepted: 12/30/2014] [Indexed: 01/17/2023]
Abstract
Ecological and evolutionary studies largely assume that island populations display low levels of neutral genetic variation. However, this notion has only been formally tested in a few cases involving plant taxa, and the confounding effect of selection on genetic diversity (GD) estimates based on putatively neutral markers has typically been overlooked. Here, we generated nuclear microsatellite and plastid DNA sequence data in Periploca laevigata, a plant taxon with an island-mainland distribution area, to (i) investigate whether selection affects GD estimates of populations across contrasting habitats; and (ii) test the long-standing idea that island populations have lower GD than their mainland counterparts. Plastid data showed that colonization of the Canary Islands promoted strong lineage divergence within P. laevigata, which was accompanied by selective sweeps at several nuclear microsatellite loci. Inclusion of loci affected by strong divergent selection produced a significant downward bias in the GD estimates of the mainland lineage, but such underestimates were substantial (>14%) only when more than one loci under selection were included in the computations. When loci affected by selection were removed, we did not find evidence that insular Periploca populations have less GD than their mainland counterparts. The analysis of data obtained from a comprehensive literature survey reinforced this result, as overall comparisons of GD estimates between island and mainland populations were not significant across plant taxa (N = 66), with the only exception of island endemics with narrow distributions. This study suggests that identification and removal of markers potentially affected by selection should be routinely implemented in estimates of GD, particularly if different lineages are compared. Furthermore, it provides compelling evidence that the expectation of low GD cannot be generalized to island plant populations.
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Affiliation(s)
- C García-Verdugo
- Departamento de Biodiversidad Molecular y Banco de ADN, Jardín Botánico Canario 'Viera y Clavijo' - Unidad Asociada CSIC, Cabildo de Gran Canaria, Camino del Palmeral 15 de Tafira Alta, 35017, Las Palmas de Gran Canaria, Spain
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A comparative study on genetic effects of artificial and natural habitat fragmentation on Loropetalum chinense (Hamamelidaceae) in Southeast China. Heredity (Edinb) 2014; 114:544-51. [PMID: 25515015 DOI: 10.1038/hdy.2014.114] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Revised: 11/06/2014] [Accepted: 11/10/2014] [Indexed: 11/08/2022] Open
Abstract
Elucidating the demographic and landscape features that determine the genetic effects of habitat fragmentation has become fundamental to research in conservation and evolutionary biology. Land-bridge islands provide ideal study areas for investigating the genetic effects of habitat fragmentation at different temporal and spatial scales. In this context, we compared patterns of nuclear microsatellite variation between insular populations of a shrub of evergreen broad-leaved forest, Loropetalum chinense, from the artificially created Thousand-Island Lake (TIL) and the Holocene-dated Zhoushan Archipelago of Southeast China. Populations from the TIL region harboured higher levels of genetic diversity than those from the Zhoushan Archipelago, but these differences were not significant. There was no correlation between genetic diversity and most island features, excepting a negative effect of mainland-island distance on allelic richness and expected heterozygosity in the Zhoushan Archipelago. In general, levels of gene flow among island populations were moderate to high, and tests of alternative models of population history strongly favoured a gene flow-drift model over a pure drift model in each region. In sum, our results showed no obvious genetic effects of habitat fragmentation due to recent (artificial) or past (natural) island formation. Rather, they highlight the importance of gene flow (most likely via seed) in maintaining genetic variation and preventing inter-population differentiation in the face of habitat 'insularization' at different temporal and spatial scales.
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Espindola S, Cuarón AD, Gaggiotti OE, Vázquez-Domínguez E. High genetic structure of the Cozumel Harvest mice, a critically endangered island endemic: conservation implications. CONSERV GENET 2014. [DOI: 10.1007/s10592-014-0625-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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20
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Sato JJ, Kawakami T, Tasaka Y, Tamenishi M, Yamaguchi Y. A Few Decades of Habitat Fragmentation has Reduced Population Genetic Diversity: A Case Study of Landscape Genetics of the Large Japanese Field Mouse,Apodemus speciosus. MAMMAL STUDY 2014. [DOI: 10.3106/041.039.0102] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Wang S, Zhu W, Gao X, Li X, Yan S, Liu X, Yang J, Gao Z, Li Y. Population size and time since island isolation determine genetic diversity loss in insular frog populations. Mol Ecol 2014; 23:637-48. [PMID: 24351057 DOI: 10.1111/mec.12634] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2013] [Revised: 12/05/2013] [Accepted: 12/11/2013] [Indexed: 12/01/2022]
Affiliation(s)
- Supen Wang
- Key Laboratory of Animal Ecology and Conservation Biology; Institute of Zoology; The Chinese Academy of Sciences; 1 Datun Beichen West Road Chaoyang Beijing 100101 China
- University of Chinese Academy of Sciences; 19 Yuquan Road Shijingshan Beijing 100049 China
| | - Wei Zhu
- Key Laboratory of Animal Ecology and Conservation Biology; Institute of Zoology; The Chinese Academy of Sciences; 1 Datun Beichen West Road Chaoyang Beijing 100101 China
- University of Chinese Academy of Sciences; 19 Yuquan Road Shijingshan Beijing 100049 China
| | - Xu Gao
- Key Laboratory of Animal Ecology and Conservation Biology; Institute of Zoology; The Chinese Academy of Sciences; 1 Datun Beichen West Road Chaoyang Beijing 100101 China
- University of Chinese Academy of Sciences; 19 Yuquan Road Shijingshan Beijing 100049 China
| | - Xianping Li
- Key Laboratory of Animal Ecology and Conservation Biology; Institute of Zoology; The Chinese Academy of Sciences; 1 Datun Beichen West Road Chaoyang Beijing 100101 China
- University of Chinese Academy of Sciences; 19 Yuquan Road Shijingshan Beijing 100049 China
| | - Shaofei Yan
- Key Laboratory of Animal Ecology and Conservation Biology; Institute of Zoology; The Chinese Academy of Sciences; 1 Datun Beichen West Road Chaoyang Beijing 100101 China
- University of Chinese Academy of Sciences; 19 Yuquan Road Shijingshan Beijing 100049 China
| | - Xuan Liu
- Key Laboratory of Animal Ecology and Conservation Biology; Institute of Zoology; The Chinese Academy of Sciences; 1 Datun Beichen West Road Chaoyang Beijing 100101 China
| | - Ji Yang
- Key Laboratory of Animal Ecology and Conservation Biology; Institute of Zoology; The Chinese Academy of Sciences; 1 Datun Beichen West Road Chaoyang Beijing 100101 China
| | - Zengxiang Gao
- College of Environmental Science and Engineering; Ocean University of China; 5 Yushan Road Lao Shan Qingdao 266003 China
| | - Yiming Li
- Key Laboratory of Animal Ecology and Conservation Biology; Institute of Zoology; The Chinese Academy of Sciences; 1 Datun Beichen West Road Chaoyang Beijing 100101 China
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Martínková N, Barnett R, Cucchi T, Struchen R, Pascal M, Pascal M, Fischer MC, Higham T, Brace S, Ho SYW, Quéré JP, O'Higgins P, Excoffier L, Heckel G, Hoelzel AR, Dobney KM, Searle JB. Divergent evolutionary processes associated with colonization of offshore islands. Mol Ecol 2013; 22:5205-20. [PMID: 23998800 PMCID: PMC4159590 DOI: 10.1111/mec.12462] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2013] [Revised: 07/02/2013] [Accepted: 07/09/2013] [Indexed: 11/25/2022]
Abstract
Oceanic islands have been a test ground for evolutionary theory, but here, we focus on the possibilities for evolutionary study created by offshore islands. These can be colonized through various means and by a wide range of species, including those with low dispersal capabilities. We use morphology, modern and ancient sequences of cytochrome b (cytb) and microsatellite genotypes to examine colonization history and evolutionary change associated with occupation of the Orkney archipelago by the common vole (Microtus arvalis), a species found in continental Europe but not in Britain. Among possible colonization scenarios, our results are most consistent with human introduction at least 5100 bp (confirmed by radiocarbon dating). We used approximate Bayesian computation of population history to infer the coast of Belgium as the possible source and estimated the evolutionary timescale using a Bayesian coalescent approach. We showed substantial morphological divergence of the island populations, including a size increase presumably driven by selection and reduced microsatellite variation likely reflecting founder events and genetic drift. More surprisingly, our results suggest that a recent and widespread cytb replacement event in the continental source area purged cytb variation there, whereas the ancestral diversity is largely retained in the colonized islands as a genetic ‘ark’. The replacement event in the continental M. arvalis was probably triggered by anthropogenic causes (land‐use change). Our studies illustrate that small offshore islands can act as field laboratories for studying various evolutionary processes over relatively short timescales, informing about the mainland source area as well as the island.
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Affiliation(s)
- Natália Martínková
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK; Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Květná 8, Brno, 603 65, Czech Republic
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23
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Jensen H, Moe R, Hagen IJ, Holand AM, Kekkonen J, Tufto J, Saether BE. Genetic variation and structure of house sparrow populations: is there an island effect? Mol Ecol 2013; 22:1792-805. [PMID: 23379682 DOI: 10.1111/mec.12226] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2011] [Revised: 12/04/2012] [Accepted: 12/11/2012] [Indexed: 11/30/2022]
Abstract
Population genetic structure and intrapopulation levels of genetic variation have important implications for population dynamics and evolutionary processes. Habitat fragmentation is one of the major threats to biodiversity. It leads to smaller population sizes and reduced gene flow between populations and will thus also affect genetic structure. We use a natural system of island and mainland populations of house sparrows along the coast of Norway to characterize the different population genetic properties of fragmented populations. We genotyped 636 individuals distributed across 14 populations at 15 microsatellite loci. The level of genetic differentiation was estimated using F-statistics and specially designed Mantel tests were conducted to study the influence of population type (i.e. mainland or island) and geographic distance on the genetic population structure. Furthermore, the effects of population type, population size and latitude on the level of genetic variation within populations were examined. Our results suggest that genetic processes on islands and mainland differed in two important ways. First, the intrapopulation level of genetic variation tended to be lower and the occurrence of population bottlenecks more frequent on islands than the mainland. Second, although the general level of genetic differentiation was low to moderate, it was higher between island populations than between mainland populations. However, differentiation increased in mainland populations somewhat faster with geographical distance. These results suggest that population bottleneck events and genetic drift have been more important in shaping the genetic composition of island populations compared with populations on the mainland. Such knowledge is relevant for a better understanding of evolutionary processes and conservation of threatened populations.
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Affiliation(s)
- Henrik Jensen
- Department of Biology, Centre for Conservation Biology, Norwegian University of Science and Technology, Trondheim, Norway.
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24
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Pelletier A, Obbard M, Mills K, Howe E, Burrows F, White B, Kyle C. Delineating genetic groupings in continuously distributed species across largely homogeneous landscapes: a study of American black bears (Ursus americanus) in Ontario, Canada. CAN J ZOOL 2012. [DOI: 10.1139/z2012-068] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
There is a crucial need to understand the genetic consequences of landscape modifications on continuous populations that could become fragmented, and to evaluate the degree of differentiation of isolated populations that were historically part of the core. Using 15 microsatellite loci, we evaluated the genetic structure of American black bears ( Ursus americanus Pallas, 1780) across a vast, contiguous Ontario landscape (>1 × 106 km2) that largely represents their pre-European settlement distribution. Because geographic barriers are absent, we predicted that isolation by distance would drive genetic structure. We identified three genetic clusters (Northwest, Southeast, and Bruce Peninsula) that were less differentiated than when assessed with mtDNA, suggesting the influence of male-biased dispersal on large-scale genetic differentiation. Isolation by distance (r = 0.552, P = 0.001) was supported by a weak, clinal variation between Northwest and Southeast, illustrating the challenges to delineate populations in wide-ranging taxa. The Bruce Peninsula cluster, confined to a small area under strong anthropogenic pressures, was more differentiated from neighbouring clusters (FST > 0.13, P < 0.0001), with a genetic diversity corresponding to disjunct populations of black bears. Our results could be used in landscape genetics models to project the evolution of population differentiation based on upcoming landscape modifications in northern regions of North America.
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Affiliation(s)
- A. Pelletier
- Environmental and Life Sciences Program, Environmental Science Building, Trent University, 1600 West Bank Drive, Peterborough, ON K9J 7B8, Canada
| | - M.E. Obbard
- Wildlife Research and Development Section, ON Ministry of Natural Resources, DNA Building, Trent University, 2140 East Bank Drive, Peterborough, ON K9J 7B8, Canada
| | - K. Mills
- Biology Section, Centre of Forensic Sciences, Ministry of Community Safety and Correctional Services, 25 Grosvenor Street, Toronto, ON M7A 2G8, Canada
| | - E.J. Howe
- Wildlife Research and Development Section, ON Ministry of Natural Resources, DNA Building, Trent University, 2140 East Bank Drive, Peterborough, ON K9J 7B8, Canada
| | - F.G. Burrows
- Bruce Peninsula National Park and Fathom Five National Marine Park, Parks Canada, P.O. Box 189, 248 Big Tub Road, Tobermory, ON N0H 2R0, Canada
| | - B.N. White
- Natural Resources DNA Profiling and Forensic Centre, DNA Building, Trent University, 2140 East Bank Drive, Peterborough, ON K9J 7B8, Canada
| | - C.J. Kyle
- Forensic Science Department, DNA Building, Trent University, 2140 East Bank Drive, Peterborough, ON K9J 7B8, Canada
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25
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Habitat fragmentation sensitivity in mammals: a target selection for landscape planning comparing two different approaches (bibliographic review and expert based). RENDICONTI LINCEI 2012. [DOI: 10.1007/s12210-012-0184-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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26
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Ploshnitsa AI, Goltsman ME, Macdonald DW, Kennedy LJ, Sommer S. Impact of historical founder effects and a recent bottleneck on MHC variability in Commander Arctic foxes (Vulpes lagopus). Ecol Evol 2012; 2:165-80. [PMID: 22408734 PMCID: PMC3297186 DOI: 10.1002/ece3.42] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Revised: 08/24/2011] [Accepted: 08/26/2011] [Indexed: 11/11/2022] Open
Abstract
Populations of Arctic foxes (Vulpes lagopus) have been isolated on two of the Commander Islands (Bering and Mednyi) from the circumpolar distributed mainland population since the Pleistocene. In 1970-1980, an epizootic outbreak of mange caused a severe population decline on Mednyi Island. Genes of the major histocompatibility complex (MHC) play a primary role in infectious disease resistance. The main objectives of our study were to compare contemporary variation of MHC class II in mainland and island Arctic foxes, and to document the effects of the isolation and the recent bottleneck on MHC polymorphism by analyzing samples from historical and contemporary Arctic foxes. In 184 individuals, we found 25 unique MHC class II DRB and DQB alleles, and identified evidence of balancing selection maintaining allelic lineages over time at both loci. Twenty different MHC alleles were observed in mainland foxes and eight in Bering Island foxes. The historical Mednyi population contained five alleles and all contemporary individuals were monomorphic at both DRB and DQB. Our data indicate that despite positive and diversifying selection leading to elevated rates of amino acid replacement in functionally important antigen-binding sites, below a certain population size, balancing selection may not be strong enough to maintain genetic diversity in functionally important genes. This may have important fitness consequences and might explain the high pathogen susceptibility in some island populations. This is the first study that compares MHC diversity before and after a bottleneck in a wild canid population using DNA from museum samples.
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De Andrés MT, Benito A, Pérez-Rivera G, Ocete R, Lopez MA, Gaforio L, Muñoz G, Cabello F, Martínez Zapater JM, Arroyo-García R. Genetic diversity of wild grapevine populations in Spain and their genetic relationships with cultivated grapevines. Mol Ecol 2011; 21:800-16. [PMID: 22151598 DOI: 10.1111/j.1365-294x.2011.05395.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The wild grapevine, Vitis vinifera L. ssp. sylvestris (Gmelin) Hegi, considered as the ancestor of the cultivated grapevine, is native from Eurasia. In Spain, natural populations of V. vinifera ssp. sylvestris can still be found along river banks. In this work, we have performed a wide search of wild grapevine populations in Spain and characterized the amount and distribution of their genetic diversity using 25 nuclear SSR loci. We have also analysed the possible coexistence in the natural habitat of wild grapevines with naturalized grapevine cultivars and rootstocks. In this way, phenotypic and genetic analyses identified 19% of the collected samples as derived from cultivated genotypes, being either naturalized cultivars or hybrid genotypes derived from spontaneous crosses between wild and cultivated grapevines. The genetic diversity of wild grapevine populations was similar than that observed in the cultivated group. The molecular analysis showed that cultivated germplasm and wild germplasm are genetically divergent with low level of introgression. Using a model-based approach implemented in the software structure, we identified four genetic groups, with two of them fundamentally represented among cultivated genotypes and two among wild accessions. The analyses of genetic relationships between wild and cultivated grapevines could suggest a genetic contribution of wild accessions from Spain to current Western cultivars.
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Affiliation(s)
- M T De Andrés
- Departamento de Investigación Agroalimentaria, IMIDRA, Finca El Encín, Apto 127, 28800 Alcalá de Henares, Madrid, Spain
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28
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Devillard S, Santin-Janin H, Say L, Pontier D. Linking genetic diversity and temporal fluctuations in population abundance of the introduced feral cat (Felis silvestris catus) on the Kerguelen archipelago. Mol Ecol 2011; 20:5141-53. [PMID: 22098605 DOI: 10.1111/j.1365-294x.2011.05329.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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29
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Polyakov AV, White TA, Jones RM, Borodin PM, Searle JB. Natural hybridization between extremely divergent chromosomal races of the common shrew (Sorex araneus, Soricidae, Soricomorpha): hybrid zone in Siberia. J Evol Biol 2011; 24:1393-402. [PMID: 21507114 DOI: 10.1111/j.1420-9101.2011.02266.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Chromosomal races of the common shrew differ in sets of metacentric chromosomes and on contact may produce hybrids with extraordinarily complex configurations at meiosis I that are associated with reduced fertility. There is an expectation that these may be some of the most extreme tension zones available for study and therefore are of interest as potential sites for reproductive isolation. Here, we analyse one of these zones, between the Novosibirsk race (characterized by metacentrics go, hn, ik, jl, mp and qr) and the Tomsk race (metacentrics gk, hi, jl and mn and acrocentrics o, p, q and r), which form hybrids with a chain-of-nine (CIX) and a chain-of-three (CIII) configuration at meiosis I. At the Novosibirsk-Tomsk hybrid zone, the CIX chromosomes form clines of 8.53 km standardized width on average, whereas the cline for the CIII chromosomes was 52.83 km wide. The difference in these cline widths fits with the difference in meiotic errors expected with the CIX and CIII configuration, and we produce estimates of selection against hybrids with these types of configurations, which we relate to dispersal and age of the hybrid zone. The hybrid zone is located at the isocline at 200 m altitude above sea level; this relationship between the races and altitude is suggested at both coarse and fine scales. This indicates adaptive differences between the races that may in turn have been promoted by the chromosome differences. Thus, the extreme chromosomal divergence between the Novosibirsk and Tomsk may be associated with genic differentiation, but it is still striking that, despite the large chromosomal differences, reproductive isolation between the Novosibirsk and Tomsk races has not occurred.
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Affiliation(s)
- A V Polyakov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
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Moska M, Wierzbicki H, Macierzyńska A, Strzała T, Maślak R, Warchałowski M. A microsatellite study in the Łęgucki Młyn/Popielno hybrid zone reveals no genetic differentiation between two chromosome races of the common shrew (Sorex araneus). ACTA THERIOLOGICA 2011; 56:117-122. [PMID: 21475705 PMCID: PMC3061409 DOI: 10.1007/s13364-011-0029-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2010] [Accepted: 11/08/2010] [Indexed: 10/26/2022]
Abstract
This study investigated a chromosome hybrid zone between two chromosomal races of the common shrew (Sorex araneus). Gene flow and genetic structure of the hybrid zone, located in the northeast of Poland, were studied using seven polymorphic autosomal microsatellite loci (L9, L14, L33, L45, L67, L68, L97) and a Y-linked microsatellite locus (L8Y). Seventy-five animals (46 of the Łęgucki Młyn race and 29 of the Popielno race) from nine different localities were examined and the data were analyzed using hierarchical AMOVA and F-statistic. The studied microsatellite loci and races (divided into nine geographical populations) were characterized by observed heterozygosity (H(O)), expected heterozygosities within (H(S)), and between (H(T)) populations, inbreeding coefficient (F(IS)), fixation index (F(ST)), and average allelic richness (A). We found that genetic structuring within and between the two chromosome races were weak and non-significant. This finding and unconstrained gene flow between the races indicates a high level of migration within the Łęgucki Młyn/Popielno hybrid zone, suggesting that evolutionarily important genetic structuring does not occur in interracial zones where races which are not genetically distinct come into contact.
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Affiliation(s)
- Magdalena Moska
- Department of Genetics and Animal Breeding, Wrocław University of Environmental and Life Sciences, Kożuchowska 7, 51-631 Wrocław, Poland
| | - Heliodor Wierzbicki
- Department of Genetics and Animal Breeding, Wrocław University of Environmental and Life Sciences, Kożuchowska 7, 51-631 Wrocław, Poland
| | - Anna Macierzyńska
- Department of Genetics and Animal Breeding, Wrocław University of Environmental and Life Sciences, Kożuchowska 7, 51-631 Wrocław, Poland
| | - Tomasz Strzała
- Department of Genetics and Animal Breeding, Wrocław University of Environmental and Life Sciences, Kożuchowska 7, 51-631 Wrocław, Poland
| | - Robert Maślak
- Institute of Zoology, Wrocław University, Sienkiewicza 21, 50-335 Wrocław, Poland
| | - Marcin Warchałowski
- Department of Genetics and Animal Breeding, Wrocław University of Environmental and Life Sciences, Kożuchowska 7, 51-631 Wrocław, Poland
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Ortego J, Yannic G, Shafer ABA, Mainguy J, Festa-Bianchet M, Coltman DW, Côté SD. Temporal dynamics of genetic variability in a mountain goat (Oreamnos americanus) population. Mol Ecol 2011; 20:1601-11. [PMID: 21366746 DOI: 10.1111/j.1365-294x.2011.05022.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The association between population dynamics and genetic variability is of fundamental importance for both evolutionary and conservation biology. We combined long-term population monitoring and molecular genetic data from 123 offspring and their parents at 28 microsatellite loci to investigate changes in genetic diversity over 14 cohorts in a small and relatively isolated population of mountain goats (Oreamnos americanus) during a period of demographic increase. Offspring heterozygosity decreased while parental genetic similarity and inbreeding coefficients (F(IS) ) increased over the study period (1995-2008). Immigrants introduced three novel alleles into the population and matings between residents and immigrants produced more heterozygous offspring than local crosses, suggesting that immigration can increase population genetic variability. The population experienced genetic drift over the study period, reflected by a reduced allelic richness over time and an 'isolation-by-time' pattern of genetic structure. The temporal decline of individual genetic diversity despite increasing population size probably resulted from a combination of genetic drift due to small effective population size, inbreeding and insufficient counterbalancing by immigration. This study highlights the importance of long-term genetic monitoring to understand how demographic processes influence temporal changes of genetic diversity in long-lived organisms.
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Affiliation(s)
- Joaquín Ortego
- Département de biologie and Centre d'études nordiques, Université Laval, 1045 avenue de Médecine, Québec, Canada.
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32
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Population genetic structure and history of fragmented remnant populations of the New England cottontail (Sylvilagus transitionalis). CONSERV GENET 2011. [DOI: 10.1007/s10592-011-0197-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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33
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Genetic variation and effective population size in isolated populations of coastal cutthroat trout. CONSERV GENET 2010. [DOI: 10.1007/s10592-010-0083-y] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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34
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MUNSHI-SOUTH JASON, KHARCHENKO KATERINA. Rapid, pervasive genetic differentiation of urban white-footed mouse (Peromyscus leucopus) populations in New York City. Mol Ecol 2010; 19:4242-54. [DOI: 10.1111/j.1365-294x.2010.04816.x] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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35
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Gortat T, Gryczyńska-Siemiątkowska A, Rutkowski R, Kozakiewicz A, Mikoszewski A, Kozakiewicz M. Landscape pattern and genetic structure of a yellow-necked mouse Apodemus flavicollis population in north-eastern Poland. ACTA ACUST UNITED AC 2010. [DOI: 10.4098/j.at.0001-7051.102.2009] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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36
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Genetic erosion in a stenotopic heathland ground beetle (Coleoptera: Carabidae): a matter of habitat size? CONSERV GENET 2009. [DOI: 10.1007/s10592-009-9994-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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MCDEVITT ALLAND, RAMBAU RAMUGONDOV, O'BRIEN JOHN, MCDEVITT CDAMIEN, HAYDEN THOMASJ, SEARLE JEREMYB. Genetic variation in Irish pygmy shrews Sorex minutus (Soricomorpha: Soricidae): implications for colonization history. Biol J Linn Soc Lond 2009. [DOI: 10.1111/j.1095-8312.2009.01218.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Detecting bottlenecks using BOTTLENECK 1.2.02 in wild populations: the importance of the microsatellite structure. CONSERV GENET 2009. [DOI: 10.1007/s10592-009-9949-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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39
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Lucas ZL, McLoughlin PD, Coltman DW, Barber C. Multiscale analysis reveals restricted gene flow and a linear gradient in heterozygosity for an island population of feral horses. CAN J ZOOL 2009. [DOI: 10.1139/z09-019] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We studied the genetic (microsatellite) diversity of a feral population of horses ( Equus caballus L., 1758) on Sable Island, Nova Scotia, Canada (1983–2003), at two spatial scales: (1) for the island as a whole and (2) at the level of four equally sized subdivisions along the length of Sable Island, which is a long (42 km) and narrow (1.5 km) vegetated sand bar. At the island scale (n = 264 horses), observed heterozygosity over 10 loci was 0.647 ± 0.035 (mean ± 1 SE), while expected heterozygosity was 0.696 ± 0.029; we observed significant heterozygote deficiency with all loci considered (P < 0.0001). At the subdivision scale, observed heterozygosity ranged from 0.589 to 0.694 in a gradient from west to east. We observed a corresponding gradient in effective number of alleles and allelic richness. Pairwise values of FST were significant for most subdivision pairs, ranging as high as 0.067 from west to east. Western areas showed highest levels of inbreeding (FIS = 0.113) with outbreeding indicated in the east (FIS = –0.008). Our results suggest that for a large mammal that lives in polygynous social groups, like the feral horse, gene flow along linear habitats (corridors) may be restricted (relative to the dispersal capabilities of the species), even over short distances.
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Affiliation(s)
- Z. L. Lucas
- Sable Island Green Horse Society, P.O. Box 64, Halifax CRO, Halifax, NS B3J 2L4, Canada
- Department of Biology, University of Saskatchewan, 112 Science Place, Saskatoon, SK S7N 5E2, Canada
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
- Department of Biology, Saint Mary's University, 923 Robie Street, Halifax, NS B3H 3C3, Canada
| | - P. D. McLoughlin
- Sable Island Green Horse Society, P.O. Box 64, Halifax CRO, Halifax, NS B3J 2L4, Canada
- Department of Biology, University of Saskatchewan, 112 Science Place, Saskatoon, SK S7N 5E2, Canada
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
- Department of Biology, Saint Mary's University, 923 Robie Street, Halifax, NS B3H 3C3, Canada
| | - D. W. Coltman
- Sable Island Green Horse Society, P.O. Box 64, Halifax CRO, Halifax, NS B3J 2L4, Canada
- Department of Biology, University of Saskatchewan, 112 Science Place, Saskatoon, SK S7N 5E2, Canada
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
- Department of Biology, Saint Mary's University, 923 Robie Street, Halifax, NS B3H 3C3, Canada
| | - C. Barber
- Sable Island Green Horse Society, P.O. Box 64, Halifax CRO, Halifax, NS B3J 2L4, Canada
- Department of Biology, University of Saskatchewan, 112 Science Place, Saskatoon, SK S7N 5E2, Canada
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
- Department of Biology, Saint Mary's University, 923 Robie Street, Halifax, NS B3H 3C3, Canada
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Whiteley AR, Gende SM, Gharrett AJ, Tallmon DA. Background matching and color-change plasticity in colonizing freshwater sculpin populations following rapid deglaciation. Evolution 2009; 63:1519-29. [PMID: 19154389 DOI: 10.1111/j.1558-5646.2009.00627.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Anthropogenic-induced change is forcing organisms to shift their distributions and colonize novel habitats at an increasing rate, which leads to complex interactions among evolutionary processes. Coastrange sculpin (Cottus aleuticus) have colonized recently deglaciated streams of Glacier Bay in Alaska within the last 220 years. We examined divergence among populations in background matching coloration and tested the hypothesis that observed variation is due to morphological color plasticity. To examine how color-change plasticity has interacted with other evolutionary processes, we also determined the influence of colonization on neutral genetic diversity. We observed clinal variation in substrate-matching fish color along the chronological continuum of streams. Microsatellites provided little evidence of genetic subdivision among sculpin populations. Fish color was significantly correlated to substrate color, but was not correlated to neutral population genetic structure. Furthermore, a laboratory experiment revealed that morphological color plasticity could explain much, but not all, of the observed fish color divergence. Our study demonstrates that sculpin in Glacier Bay have colonized and adapted to recently deglaciated habitat and suggests that color change plasticity has aided in this process. This research, therefore, highlights the important role phenotypic plasticity may play in the adaptation of species to rapid climate change.
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Affiliation(s)
- Andrew R Whiteley
- Biology and Marine Biology Programs, University of Alaska Southeast, 11120 Glacier Highway, Juneau, Alaska 99801, USA.
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41
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Firman RC, Simmons LW. The frequency of multiple paternity predicts variation in testes size among island populations of house mice. J Evol Biol 2008; 21:1524-33. [PMID: 18811664 DOI: 10.1111/j.1420-9101.2008.01612.x] [Citation(s) in RCA: 115] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Polyandry generates selection on males through sperm competition, which has broad implications for the evolution of ejaculates and male reproductive anatomy. Comparative analyses across species and competitive mating trials within species have suggested that sperm competition can influence the evolution of testes size, sperm production and sperm form and function. Surprisingly, the intraspecific approach of comparing among population variation for investigating the selective potential of sperm competition has rarely been explored. We sampled seven island populations of house mice and determined the frequency of multiple paternity within each population. Applying the frequency of multiple paternity as an index of the risk of sperm competition, we looked for selective responses in male reproductive traits. We found that the risk of sperm competition predicted testes size across the seven island populations of house mice. However, variation in sperm traits was not explained by sperm competition risk. We discuss these findings in relation to sperm competition theory, and other intrinsic and extrinsic factors that might influence ejaculate quality.
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Affiliation(s)
- R C Firman
- Centre for Evolutionary Biology, School of Animal Biology M092, The University of Western Australia, Nedlands, WA, Australia.
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42
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Ortego J, Aparicio JM, Cordero PJ, Calabuig G. Individual genetic diversity correlates with the size and spatial isolation of natal colonies in a bird metapopulation. Proc Biol Sci 2008; 275:2039-47. [PMID: 18505717 PMCID: PMC2596367 DOI: 10.1098/rspb.2008.0475] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2008] [Revised: 05/06/2008] [Accepted: 05/08/2008] [Indexed: 11/12/2022] Open
Abstract
The genetic consequences of small population size and isolation are of central concern in both population and conservation biology. Organisms with a metapopulation structure generally show effective population sizes that are much smaller than the number of mature individuals and this can reduce genetic diversity especially in small sized and isolated subpopulations. Here, we examine the association between heterozygosity and the size and spatial isolation of natal colonies in a metapopulation of lesser kestrels (Falco naumanni). For this purpose, we used capture-mark-recapture data to determine the patterns of immigration into the studied colonies, and 11 highly polymorphic microsatellite markers that allowed us to estimate genetic diversity of locally born individuals. We found that individuals born in smaller and more isolated colonies were genetically less diverse. These colonies received a lower number of immigrants, supporting the idea that both reduced gene flow and small population size are responsible for the genetic pattern observed. Our results are particularly intriguing because the lesser kestrel is a vagile and migratory species with great movement capacity and dispersal potential. Overall, this study provides evidence of the association between individual heterozygosity and the size and spatial isolation of natal colonies in a highly mobile vertebrate showing relatively frequent dispersal and low genetic differentiation among local subpopulations.
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Affiliation(s)
- Joaquín Ortego
- Grupo de Investigación de la Biodiversidad Genética y Cultural, Instituto de Investigación en Recursos Cinegéticos, Ronda de Toledo s/n, Ciudad Real, Spain.
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WHITE THOMASA, SEARLE JEREMYB. The colonization of Scottish islands by the common shrew, Sorex araneus (Eulipotyphla: Soricidae). Biol J Linn Soc Lond 2008. [DOI: 10.1111/j.1095-8312.2008.01019.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Wilson A, Arcese P, Keller LF, Pruett CL, Winker K, Patten MA, Chan Y. The contribution of island populations to in situ genetic conservation. CONSERV GENET 2008. [DOI: 10.1007/s10592-008-9612-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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45
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White TA, Searle JB. Mandible asymmetry and genetic diversity in island populations of the common shrew, Sorex araneus. J Evol Biol 2008; 21:636-41. [PMID: 18194233 DOI: 10.1111/j.1420-9101.2007.01481.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Mandibles from 13 island and six mainland populations of common shrews from the west coast of Scotland were subjected to geometric morphometric analysis in order to investigate the relationship between genetic diversity and fluctuating asymmetry. Although population mean shape fluctuating asymmetry (FA) and size FA were significantly inversely correlated with population genetic diversity this result was substantially due to one island. Sanda, the smallest island with by far the lowest genetic diversity, also had the highest FA. When Sanda was removed from the analysis, the relationship was not significant. There was no relationship between genetic diversity and FA at the individual level, whether measured as mean locus heterozygosity or d(2). In general, if genetic variation affects FA at all, the effect is weak and may only be of biological interest in very small populations.
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Affiliation(s)
- T A White
- Department of Biology, University of York, Heslington, York, UK.
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