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Walter WD, Fameli A, Russo‐Petrick K, Edson JE, Rosenberry CS, Schuler KL, Tonkovich MJ. Large-scale assessment of genetic structure to assess risk of populations of a large herbivore to disease. Ecol Evol 2024; 14:e11347. [PMID: 38774134 PMCID: PMC11106048 DOI: 10.1002/ece3.11347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 03/28/2024] [Accepted: 04/12/2024] [Indexed: 05/24/2024] Open
Abstract
Chronic wasting disease (CWD) can spread among cervids by direct and indirect transmission, the former being more likely in emerging areas. Identifying subpopulations allows the delineation of focal areas to target for intervention. We aimed to assess the population structure of white-tailed deer (Odocoileus virginianus) in the northeastern United States at a regional scale to inform managers regarding gene flow throughout the region. We genotyped 10 microsatellites in 5701 wild deer samples from Maryland, New York, Ohio, Pennsylvania, and Virginia. We evaluated the distribution of genetic variability through spatial principal component analysis and inferred genetic structure using non-spatial and spatial Bayesian clustering algorithms (BCAs). We simulated populations representing each inferred wild cluster, wild deer in each state and each physiographic province, total wild population, and a captive population. We conducted genetic assignment tests using these potential sources, calculating the probability of samples being correctly assigned to their origin. Non-spatial BCA identified two clusters across the region, while spatial BCA suggested a maximum of nine clusters. Assignment tests correctly placed deer into captive or wild origin in most cases (94%), as previously reported, but performance varied when assigning wild deer to more specific origins. Assignments to clusters inferred via non-spatial BCA performed well, but efficiency was greatly reduced when assigning samples to clusters inferred via spatial BCA. Differences between spatial BCA clusters are not strong enough to make assignment tests a reliable method for inferring the geographic origin of deer using 10 microsatellites. However, the genetic distinction between clusters may indicate natural and anthropogenic barriers of interest for management.
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Affiliation(s)
- W. David Walter
- U.S. Geological Survey, Pennsylvania Cooperative Fish and Wildlife Research UnitThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
| | - Alberto Fameli
- Pennsylvania Cooperative Fish and Wildlife Research UnitThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
| | - Kelly Russo‐Petrick
- Pennsylvania Cooperative Fish and Wildlife Research UnitThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
| | - Jessie E. Edson
- Pennsylvania Cooperative Fish and Wildlife Research UnitThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
| | | | - Krysten L. Schuler
- Cornell Wildlife Health Lab, New York State Wildlife Health ProgramIthacaNew YorkUSA
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2
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Briones C, Nuñez JJ, Pérez M, Garrido O, Campos B, Godoy K, Hartley R, Oyarzún PA, Guiñez R. Linking Acrosome Size and Genetic Divergence in an Inter-Oceanic Mussel from the Pacific and Atlantic Coasts: A Case of Incipient Speciation? Animals (Basel) 2024; 14:674. [PMID: 38473058 DOI: 10.3390/ani14050674] [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: 01/11/2024] [Revised: 02/14/2024] [Accepted: 02/19/2024] [Indexed: 03/14/2024] Open
Abstract
In recent years, advances in analyses of the sperm morphology and genetics of Perumytilus purpuratus have allowed to two evolutionary scenarios for this mussel to be suggested: (1) the scenario of cryptic species and (2) the scenario of incipient or in progress speciation. For a better understanding of the evolutionary history of P. purpuratus, we performed extensive sampling along a latitudinal gradient of ca. 7180 km of coastline-from the Southern Pacific Ocean to the Atlantic Ocean-and we delved deeper into the sperm morphology of P. purpuratus, exploring its association with the phylogeny and population genetics to determine whether the variability in sperm traits between the northern and southern regions was a signal of cryptic or incipient species. Overall, our results showed that sperm sizes were strongly correlated with the genetic structure in males of P. purpuratus. We identified at 37° S on the Pacific coast a coincident break of both sperm size and genetic disruption that can be explained by historical events and postglacial recolonization as causal phenomena for the observed divergences. Furthermore, evidence of genetic admixture between lineages was found at 38° S, suggesting the presence of an introgressive hybridization zone and incomplete reproductive isolation in an in fraganti or incipient speciation process.
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Affiliation(s)
- Carolina Briones
- Instituto de Ciencias Naturales Alexander von Humbodt, Facultad de Ciencias del Mar y de Recursos Biológicos, Universidad de Antofagasta, Angamos 601, Antofagasta 1270300, Chile
| | - José J Nuñez
- Instituto de Ciencias Marinas y Limnológicas, Facultad de Ciencias, Universidad Austral de Chile, Casilla 567, Valdivia 5090000, Chile
| | - Montse Pérez
- AquaCOV, Centro Oceanográfico de Vigo, Instituto Español de Oceanografía, Consejo Superior de Investigaciones Científicas (IEO, CSIC), 36390 Vigo, Spain
| | - Orlando Garrido
- Instituto de Ciencias Marinas y Limnológicas, Facultad de Ciencias, Universidad Austral de Chile, Casilla 567, Valdivia 5090000, Chile
| | | | - Karina Godoy
- Núcleo Científico y Tecnológico de Biorecursos (BIOREN), Universidad de La Frontera, Temuco 4811230, Chile
| | - Ricardo Hartley
- Instituto de Investigación y Postgrado, Facultad de Medicina y Ciencias de la Salud, Universidad Central de Chile, Santiago 8330507, Chile
| | - Pablo A Oyarzún
- Centro de Investigación Marina Quintay (CIMARQ), Universidad Andrés Bello, Quintay 2340000, Chile
| | - Ricardo Guiñez
- Instituto de Ciencias Naturales Alexander von Humbodt, Facultad de Ciencias del Mar y de Recursos Biológicos, Universidad de Antofagasta, Angamos 601, Antofagasta 1270300, Chile
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3
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Plis K, Niedziałkowska M, Borowik T, Lang J, Heddergott M, Tiainen J, Bunevich A, Šprem N, Paule L, Danilkin A, Kholodova M, Zvychaynaya E, Kashinina N, Pokorny B, Flajšman K, Paulauskas A, Djan M, Ristić Z, Novák L, Kusza S, Miller C, Tsaparis D, Stoyanov S, Shkvyria M, Suchentrunk F, Kutal M, Lavadinović V, Šnjegota D, Krapal AM, Dănilă G, Veeroja R, Dulko E, Jędrzejewska B. Mitochondrial DNA diversity and the population genetic structure of contemporary roe deer (Capreolus capreolus) in Europe. Mamm Biol 2022. [DOI: 10.1007/s42991-022-00274-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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4
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Bourgeois YXC, Warren BH. An overview of current population genomics methods for the analysis of whole-genome resequencing data in eukaryotes. Mol Ecol 2021; 30:6036-6071. [PMID: 34009688 DOI: 10.1111/mec.15989] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 04/26/2021] [Accepted: 05/11/2021] [Indexed: 01/01/2023]
Abstract
Characterizing the population history of a species and identifying loci underlying local adaptation is crucial in functional ecology, evolutionary biology, conservation and agronomy. The constant improvement of high-throughput sequencing techniques has facilitated the production of whole genome data in a wide range of species. Population genomics now provides tools to better integrate selection into a historical framework, and take into account selection when reconstructing demographic history. However, this improvement has come with a profusion of analytical tools that can confuse and discourage users. Such confusion limits the amount of information effectively retrieved from complex genomic data sets, and impairs the diffusion of the most recent analytical tools into fields such as conservation biology. It may also lead to redundancy among methods. To address these isssues, we propose an overview of more than 100 state-of-the-art methods that can deal with whole genome data. We summarize the strategies they use to infer demographic history and selection, and discuss some of their limitations. A website listing these methods is available at www.methodspopgen.com.
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Affiliation(s)
| | - Ben H Warren
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, UA, CP 51, Paris, France
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5
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Clear phylogeographic pattern and genetic structure of wild boar Sus scrofa population in Central and Eastern Europe. Sci Rep 2021; 11:9680. [PMID: 33958636 PMCID: PMC8102581 DOI: 10.1038/s41598-021-88991-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 04/19/2021] [Indexed: 11/15/2022] Open
Abstract
The wild boar Sus scrofa is one of the widely spread ungulate species in Europe, yet the origin and genetic structure of the population inhabiting Central and Eastern Europe are not well recognized. We analysed 101 newly obtained sequences of complete mtDNA genomes and 548 D-loop sequences of the species and combined them with previously published data. We identified five phylogenetic clades in Europe with clear phylogeographic pattern. Two of them occurred mainly in western and central part of the continent, while the range of the third clade covered North-Eastern, Central and South-Eastern Europe. The two other clades had rather restricted distribution. In Central Europe, we identified a contact zone of three mtDNA clades. Population genetic structure reflected clear phylogeographic pattern of wild boar in this part of Europe. The contribution of lineages originating from the southern (Dinaric-Balkan) and eastern (northern cost of the Black Sea) areas to the observed phylogeographic pattern of the species in Central and Eastern Europe was larger than those from the regions located in southern France, Iberian, and Italian Peninsulas. The present work was the first mitogenomic analysis conducted in Central and Eastern Europe to study genetic diversity and structure of wild boar population.
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Tolley KA, Hopkins KP, da Silva JM. Genetic structure associated with habitat diversification supports the independent evolution of ecomorphs inBradypodion pumilum. AFR J HERPETOL 2019. [DOI: 10.1080/21564574.2019.1646324] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Krystal A Tolley
- South African National Biodiversity Institute, Cape Town, South Africa
- Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Johannesburg, South Africa
| | - Kevin P Hopkins
- South African National Biodiversity Institute, Cape Town, South Africa
| | - Jessica M da Silva
- South African National Biodiversity Institute, Cape Town, South Africa
- Department of Botany and Zoology, Stellenbosch University, Stellenbosch, South Africa
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7
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Distribution, fine-scale subdivision, and population size of San Joaquin kit foxes in the Ciervo-Panoche Natural Area, California. CONSERV GENET 2019. [DOI: 10.1007/s10592-018-1122-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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8
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Do roads act as a barrier to gene flow of subterranean small mammals? A case study with Ctenomys minutus. CONSERV GENET 2019. [DOI: 10.1007/s10592-018-01139-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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9
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Recolonizing lost habitat—how European beavers (Castor fiber) return to south-western Germany. MAMMAL RES 2018. [DOI: 10.1007/s13364-018-0360-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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10
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Gene-flow in the clouds: landscape genetics of a viviparous, montane grassland toad in the tropics. CONSERV GENET 2017. [DOI: 10.1007/s10592-017-1029-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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11
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Parnassius apollo nevadensis: identification of recent population structure and source–sink dynamics. CONSERV GENET 2017. [DOI: 10.1007/s10592-017-0931-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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12
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Cousseau L, Husemann M, Foppen R, Vangestel C, Lens L. A longitudinal genetic survey identifies temporal shifts in the population structure of Dutch house sparrows. Heredity (Edinb) 2016; 117:259-67. [PMID: 27273323 PMCID: PMC5026754 DOI: 10.1038/hdy.2016.38] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 04/05/2016] [Accepted: 04/06/2016] [Indexed: 11/08/2022] Open
Abstract
Dutch house sparrow (Passer domesticus) densities dropped by nearly 50% since the early 1980s, and similar collapses in population sizes have been reported across Europe. Whether, and to what extent, such relatively recent demographic changes are accompanied by concomitant shifts in the genetic population structure of this species needs further investigation. Therefore, we here explore temporal shifts in genetic diversity, genetic structure and effective sizes of seven Dutch house sparrow populations. To allow the most powerful statistical inference, historical populations were resampled at identical locations and each individual bird was genotyped using nine polymorphic microsatellites. Although the demographic history was not reflected by a reduction in genetic diversity, levels of genetic differentiation increased over time, and the original, panmictic population (inferred from the museum samples) diverged into two distinct genetic clusters. Reductions in census size were supported by a substantial reduction in effective population size, although to a smaller extent. As most studies of contemporary house sparrow populations have been unable to identify genetic signatures of recent population declines, results of this study underpin the importance of longitudinal genetic surveys to unravel cryptic genetic patterns.
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Affiliation(s)
- L Cousseau
- Terrestrial Ecology Unit, Department of Biology, Ghent University, Ghent, Belgium
| | - M Husemann
- General Zoology, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - R Foppen
- Sovon, Dutch Centre for Field Ornithology, Nijmegen, The Netherlands
- Radboud University, Institute for Water and Wetland Research, Department of Animal Ecology and Ecophysiology, Nijmegen, The Netherlands
| | - C Vangestel
- Terrestrial Ecology Unit, Department of Biology, Ghent University, Ghent, Belgium
- Taxonomy and Phylogeny Unit, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - L Lens
- Terrestrial Ecology Unit, Department of Biology, Ghent University, Ghent, Belgium
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13
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Goldsmith EW, Renshaw B, Clement CJ, Himschoot EA, Hundertmark KJ, Hueffer K. Population structure of two rabies hosts relative to the known distribution of rabies virus variants in Alaska. Mol Ecol 2016; 25:675-88. [PMID: 26661691 DOI: 10.1111/mec.13509] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Revised: 11/26/2015] [Accepted: 11/27/2015] [Indexed: 01/18/2023]
Abstract
For pathogens that infect multiple species, the distinction between reservoir hosts and spillover hosts is often difficult. In Alaska, three variants of the arctic rabies virus exist with distinct spatial distributions. We tested the hypothesis that rabies virus variant distribution corresponds to the population structure of the primary rabies hosts in Alaska, arctic foxes (Vulpes lagopus) and red foxes (Vulpes vulpes) to possibly distinguish reservoir and spillover hosts. We used mitochondrial DNA (mtDNA) sequence and nine microsatellites to assess population structure in those two species. mtDNA structure did not correspond to rabies virus variant structure in either species. Microsatellite analyses gave varying results. Bayesian clustering found two groups of arctic foxes in the coastal tundra region, but for red foxes it identified tundra and boreal types. Spatial Bayesian clustering and spatial principal components analysis identified 3 and 4 groups of arctic foxes, respectively, closely matching the distribution of rabies virus variants in the state. Red foxes, conversely, showed eight clusters comprising two regions (boreal and tundra) with much admixture. These results run contrary to previous beliefs that arctic fox show no fine-scale spatial population structure. While we cannot rule out that the red fox is part of the maintenance host community for rabies in Alaska, the distribution of virus variants appears to be driven primarily by the arctic fox. Therefore, we show that host population genetics can be utilized to distinguish between maintenance and spillover hosts when used in conjunction with other approaches.
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Affiliation(s)
- Elizabeth W Goldsmith
- Department of Biology and Wildlife, University of Alaska Fairbanks, PO Box 756100, Fairbanks, AK, 99775, USA
| | - Benjamin Renshaw
- Department of Biology and Wildlife, University of Alaska Fairbanks, PO Box 756100, Fairbanks, AK, 99775, USA
| | - Christopher J Clement
- Department of Biology and Wildlife, University of Alaska Fairbanks, PO Box 756100, Fairbanks, AK, 99775, USA
| | - Elizabeth A Himschoot
- Department of Biology and Wildlife, University of Alaska Fairbanks, PO Box 756100, Fairbanks, AK, 99775, USA
| | - Kris J Hundertmark
- Department of Biology and Wildlife, University of Alaska Fairbanks, PO Box 756100, Fairbanks, AK, 99775, USA.,Institute of Arctic Biology, University of Alaska Fairbanks, PO Box 757000, Fairbanks, AK, 99775, USA
| | - Karsten Hueffer
- Department of Veterinary Medicine, University of Alaska Fairbanks, PO Box 755940, Fairbanks, AK, 99775, USA
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14
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Victoriano PF, Muñoz-Mendoza C, Sáez PA, Salinas HF, Muñoz-Ramírez C, Sallaberry M, Fibla P, Méndez MA. Evolution and Conservation on Top of the World: Phylogeography of the Marbled Water Frog (Telmatobius marmoratus Species Complex; Anura, Telmatobiidae) in Protected Areas of Chile. J Hered 2015; 106 Suppl 1:546-59. [PMID: 26245789 DOI: 10.1093/jhered/esv039] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The Andean Altiplano has served as a complex setting throughout its history, driving dynamic processes of diversification in several taxa. We investigated phylogeographic processes in the Telmatobius marmoratus species complex occurring in this region by studying the geographic patterns of genetic variability, genealogies, and historical migration, using the cytochrome b (cyt-b) gene as a marker. DNA sequences from Telmatobius gigas and Telmatobius culeus, Bolivian species with an uncertain taxonomic status, were also included. Additionally, we evaluated the phylogenetic diversity (PD) represented within Chilean protected areas and the complementary contribution from unprotected populations. Phylogenetic reconstructions from 148 cyt-b sequences revealed 4 main clades, one of which corresponded to T. culeus. T. gigas was part of T. marmoratus clade indicating paraphyletic relationships. Haplotypes from Chilean and Bolivian sites were not reciprocally monophyletic. Geographic distribution of lineages, spatial Bayesian analysis, and migration patterns indicated that T. marmoratus displays a weaker geographic structure than expected based on habitat distribution and physiological requirements. Demographic and statistical phylogeography analyses pointed out to a scenario of recent population expansion and high connectivity events of a more recent age than the post Last Glacial Maximum, probably associated to more humid events in Altiplano. PD of T. marmoratus populations within protected areas represents 55.6% of the total estimated PD. The unprotected populations that would contribute the most to PD are Caquena and Quebe (21%). Recent evolutionary processes and paleoclimatic changes, potentially driving shifts in habitat connectivity levels and population sizes, could explain the phylogeographic patterns recovered herein.
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Affiliation(s)
- Pedro F Victoriano
- From the Depto. de Zoología, Fac. de Cs. Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile (Victoriano and Muñoz-Mendoza); Laboratorio de Genética y Evolución, Facultad de Ciencias, Universidad de Chile, Santiago, Chile (Sáez, Salinas, Sallaberry, Fibla, and Méndez); Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA (Muñoz-Ramírez).
| | - Carla Muñoz-Mendoza
- From the Depto. de Zoología, Fac. de Cs. Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile (Victoriano and Muñoz-Mendoza); Laboratorio de Genética y Evolución, Facultad de Ciencias, Universidad de Chile, Santiago, Chile (Sáez, Salinas, Sallaberry, Fibla, and Méndez); Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA (Muñoz-Ramírez)
| | - Paola A Sáez
- From the Depto. de Zoología, Fac. de Cs. Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile (Victoriano and Muñoz-Mendoza); Laboratorio de Genética y Evolución, Facultad de Ciencias, Universidad de Chile, Santiago, Chile (Sáez, Salinas, Sallaberry, Fibla, and Méndez); Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA (Muñoz-Ramírez)
| | - Hugo F Salinas
- From the Depto. de Zoología, Fac. de Cs. Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile (Victoriano and Muñoz-Mendoza); Laboratorio de Genética y Evolución, Facultad de Ciencias, Universidad de Chile, Santiago, Chile (Sáez, Salinas, Sallaberry, Fibla, and Méndez); Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA (Muñoz-Ramírez)
| | - Carlos Muñoz-Ramírez
- From the Depto. de Zoología, Fac. de Cs. Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile (Victoriano and Muñoz-Mendoza); Laboratorio de Genética y Evolución, Facultad de Ciencias, Universidad de Chile, Santiago, Chile (Sáez, Salinas, Sallaberry, Fibla, and Méndez); Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA (Muñoz-Ramírez)
| | - Michel Sallaberry
- From the Depto. de Zoología, Fac. de Cs. Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile (Victoriano and Muñoz-Mendoza); Laboratorio de Genética y Evolución, Facultad de Ciencias, Universidad de Chile, Santiago, Chile (Sáez, Salinas, Sallaberry, Fibla, and Méndez); Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA (Muñoz-Ramírez)
| | - Pablo Fibla
- From the Depto. de Zoología, Fac. de Cs. Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile (Victoriano and Muñoz-Mendoza); Laboratorio de Genética y Evolución, Facultad de Ciencias, Universidad de Chile, Santiago, Chile (Sáez, Salinas, Sallaberry, Fibla, and Méndez); Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA (Muñoz-Ramírez)
| | - Marco A Méndez
- From the Depto. de Zoología, Fac. de Cs. Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile (Victoriano and Muñoz-Mendoza); Laboratorio de Genética y Evolución, Facultad de Ciencias, Universidad de Chile, Santiago, Chile (Sáez, Salinas, Sallaberry, Fibla, and Méndez); Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA (Muñoz-Ramírez)
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15
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Edwards T, Berry KH, Inman RD, Esque TC, Nussear KE, Jones CA, Culver M. Testing Taxon Tenacity of Tortoises: evidence for a geographical selection gradient at a secondary contact zone. Ecol Evol 2015; 5:2095-114. [PMID: 26045959 PMCID: PMC4449762 DOI: 10.1002/ece3.1500] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 03/10/2015] [Accepted: 03/11/2015] [Indexed: 11/30/2022] Open
Abstract
We examined a secondary contact zone between two species of desert tortoise, Gopherus agassizii and G. morafkai. The taxa were isolated from a common ancestor during the formation of the Colorado River (4–8 mya) and are a classic example of allopatric speciation. However, an anomalous population of G. agassizii comes into secondary contact with G. morafkai east of the Colorado River in the Black Mountains of Arizona and provides an opportunity to examine reinforcement of species' boundaries under natural conditions. We sampled 234 tortoises representing G. agassizii in California (n - 103), G. morafkai in Arizona (n - 78), and 53 individuals of undetermined assignment in the contact zone including and surrounding the Black Mountains. We genotyped individuals for 25 STR loci and determined maternal lineage using mtDNA sequence data. We performed multilocus genetic clustering analyses and used multiple statistical methods to detect levels of hybridization. We tested hypotheses about habitat use between G. agassizii and G. morafkai in the region where they co-occur using habitat suitability models. Gopherus agassizii and G. morafkai maintain independent taxonomic identities likely due to ecological niche partitioning, and the maintenance of the hybrid zone is best described by a geographical selection gradient model.
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Affiliation(s)
- Taylor Edwards
- School of Natural Resources and the Environment, The University of Arizona Tucson, Arizona, 85721 ; University of Arizona Genetics Core, University of Arizona 1657 E. Helen Street, Tucson, Arizona, 85721
| | - Kristin H Berry
- Western Ecological Research Center, U.S. Geological Survey Falcon Business Park, 21803 Cactus Avenue, Suite F, Riverside, California, 92518
| | - Richard D Inman
- Western Ecological Research Center, U.S. Geological Survey 160 North Stephanie St., Henderson, Nevada, 89074
| | - Todd C Esque
- Western Ecological Research Center, U.S. Geological Survey 160 North Stephanie St., Henderson, Nevada, 89074
| | - Kenneth E Nussear
- Western Ecological Research Center, U.S. Geological Survey 160 North Stephanie St., Henderson, Nevada, 89074
| | - Cristina A Jones
- School of Natural Resources and the Environment, The University of Arizona Tucson, Arizona, 85721 ; Arizona Game and Fish Department, Nongame Wildlife Branch Phoenix, Arizona, 85086
| | - Melanie Culver
- School of Natural Resources and the Environment, The University of Arizona Tucson, Arizona, 85721 ; Arizona Cooperative Fish and Wildlife Research Unit, U.S. Geological Survey, University of Arizona Tucson, Arizona, 85721
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16
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Matute DR, Ayroles JF. Hybridization occurs between Drosophila simulans
and D. sechellia
in the Seychelles archipelago. J Evol Biol 2014; 27:1057-68. [DOI: 10.1111/jeb.12391] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 02/12/2014] [Accepted: 03/20/2014] [Indexed: 01/30/2023]
Affiliation(s)
- D. R. Matute
- Department of Human Genetics; University of Chicago; Chicago IL USA
| | - J. F. Ayroles
- Department of Molecular Biology and Genetics; Cornell University; Ithaca NY USA
- Department of Organismic and Evolutionary Biology; Harvard University; Cambridge MA USA
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17
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Dellicour S, Mardulyn P. spads 1.0: a toolbox to perform spatial analyses on DNA sequence data sets. Mol Ecol Resour 2013; 14:647-51. [PMID: 24215429 DOI: 10.1111/1755-0998.12200] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Revised: 10/21/2013] [Accepted: 11/07/2013] [Indexed: 11/27/2022]
Abstract
SPADS 1.0 (for 'Spatial and Population Analysis of DNA Sequences') is a population genetic toolbox for characterizing genetic variability within and among populations from DNA sequences. In view of the drastic increase in genetic information available through sequencing methods, spads was specifically designed to deal with multilocus data sets of DNA sequences. It computes several summary statistics from populations or groups of populations, performs input file conversions for other population genetic programs and implements locus-by-locus and multilocus versions of two clustering algorithms to study the genetic structure of populations. The toolbox also includes two MATLAB and r functions, GDISPAL and GDIVPAL, to display differentiation and diversity patterns across landscapes. These functions aim to generate interpolating surfaces based on multilocus distance and diversity indices. In the case of multiple loci, such surfaces can represent a useful alternative to multiple pie charts maps traditionally used in phylogeography to represent the spatial distribution of genetic diversity. These coloured surfaces can also be used to compare different data sets or different diversity and/or distance measures estimated on the same data set.
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Affiliation(s)
- Simon Dellicour
- Evolutionary Biology and Ecology, Université Libre de Bruxelles, av. FD Roosevelt 50, Brussels, 1050, Belgium
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Fitzpatrick BM. Alternative forms for genomic clines. Ecol Evol 2013; 3:1951-66. [PMID: 23919142 PMCID: PMC3728937 DOI: 10.1002/ece3.609] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Revised: 04/22/2013] [Accepted: 04/24/2013] [Indexed: 11/30/2022] Open
Abstract
Understanding factors regulating hybrid fitness and gene exchange is a major research challenge for evolutionary biology. Genomic cline analysis has been used to evaluate alternative patterns of introgression, but only two models have been used widely and the approach has generally lacked a hypothesis testing framework for distinguishing effects of selection and drift. I propose two alternative cline models, implement multivariate outlier detection to identify markers associated with hybrid fitness, and simulate hybrid zone dynamics to evaluate the signatures of different modes of selection. Analysis of simulated data shows that previous approaches are prone to false positives (multinomial regression) or relatively insensitive to outlier loci affected by selection (Barton's concordance). The new, theory-based logit-logistic cline model is generally best at detecting loci affecting hybrid fitness. Although some generalizations can be made about different modes of selection, there is no one-to-one correspondence between pattern and process. These new methods will enhance our ability to extract important information about the genetics of reproductive isolation and hybrid fitness. However, much remains to be done to relate statistical patterns to particular evolutionary processes. The methods described here are implemented in a freely available package “HIest” for the R statistical software (CRAN; http://cran.r-project.org/).
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Affiliation(s)
- Benjamin M Fitzpatrick
- Department of Ecology and Evolutionary Biology, University of Tennessee Knoxville, Tennessee, 37996
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Černá K, Straka J, Munclinger P. Population structure of pioneer specialist solitary bee Andrena vaga (Hymenoptera: Andrenidae) in central Europe: the effect of habitat fragmentation or evolutionary history? CONSERV GENET 2013. [DOI: 10.1007/s10592-013-0482-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Sá-Pinto A, Branco MS, Alexandrino PB, Fontaine MC, Baird SJE. Barriers to gene flow in the marine environment: insights from two common intertidal limpet species of the Atlantic and Mediterranean. PLoS One 2012; 7:e50330. [PMID: 23239977 PMCID: PMC3519802 DOI: 10.1371/journal.pone.0050330] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Accepted: 10/17/2012] [Indexed: 11/25/2022] Open
Abstract
Knowledge of the scale of dispersal and the mechanisms governing gene flow in marine environments remains fragmentary despite being essential for understanding evolution of marine biota and to design management plans. We use the limpets Patella ulyssiponensis and Patella rustica as models for identifying factors affecting gene flow in marine organisms across the North-East Atlantic and the Mediterranean Sea. A set of allozyme loci and a fragment of the mitochondrial gene cytochrome C oxidase subunit I were screened for genetic variation through starch gel electrophoresis and DNA sequencing, respectively. An approach combining clustering algorithms with clinal analyses was used to test for the existence of barriers to gene flow and estimate their geographic location and abruptness. Sharp breaks in the genetic composition of individuals were observed in the transitions between the Atlantic and the Mediterranean and across southern Italian shores. An additional break within the Atlantic cluster separates samples from the Alboran Sea and Atlantic African shores from those of the Iberian Atlantic shores. The geographic congruence of the genetic breaks detected in these two limpet species strongly supports the existence of transpecific barriers to gene flow in the Mediterranean Sea and Northeastern Atlantic. This leads to testable hypotheses regarding factors restricting gene flow across the study area.
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Affiliation(s)
- Alexandra Sá-Pinto
- Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO/UP), Campus Agrário de Vairão, Vairão, Portugal
- * E-mail: (ASP); (MCF)
| | - Madalena S. Branco
- Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO/UP), Campus Agrário de Vairão, Vairão, Portugal
| | - Paulo B. Alexandrino
- Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO/UP), Campus Agrário de Vairão, Vairão, Portugal
- Departamento de Zoologia-Antropologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
- * E-mail: (ASP); (MCF)
| | - Michaël C. Fontaine
- Ecologie, Systématique et Evolution, Université Paris-Sud, Orsay, France
- CNRS, Orsay, France
- Ecoanthropology and Ethnobiology UMR 5145 CNRS-MNHN-Université Paris 7 Musée de l'Homme, Paris, France
| | - Stuart J. E. Baird
- Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO/UP), Campus Agrário de Vairão, Vairão, Portugal
- Centre de Biologie et de Gestion des Populations (CBGP), Campus International de Baillarguet, CS 30 016, Montpelier/Lez, France
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