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León F, Pizarro EJ, Noll D, Pertierra LR, Gonzalez BA, Johnson WE, Marín JC, Vianna JA. History of Diversification and Adaptation from North to South Revealed by Genomic Data: Guanacos from the Desert to Sub-Antarctica. Genome Biol Evol 2024; 16:evae085. [PMID: 38761112 PMCID: PMC11102080 DOI: 10.1093/gbe/evae085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/21/2024] [Indexed: 05/20/2024] Open
Abstract
The increased availability of quality genomic data has greatly improved the scope and resolution of our understanding of the recent evolutionary history of wild species adapted to extreme environments and their susceptibility to anthropogenic impacts. The guanaco (Lama guanicoe), the largest wild ungulate in South America, is a good example. The guanaco is well adapted to a wide range of habitats, including the Sechura Desert, the high Andes Mountains to the north, and the extreme temperatures and conditions of Navarino Island to the south. Guanacos also have a long history of overexploitation by humans. To assess the evolutionary impact of these challenging habitats on the genomic diversity, we analyzed 38 genomes (∼10 to 16×) throughout their extensive latitudinal distribution from the Sechura and Atacama Desert to southward into Tierra del Fuego Island. These included analyses of patterns of unique differentiation in the north and geographic region further south with admixture among L. g. cacsilensis and L. g. guanicoe. Our findings provide new insights on the divergence of the subspecies ∼800,000 yr BP and document two divergent demographic trajectories and to the initial expansion of guanaco into the more southern portions of the Atacama Desert. Patagonian guanacos have experienced contemporary reductions in effective population sizes, likely the consequence of anthropogenic impacts. The lowest levels of genetic diversity corresponded to their northern and western limits of distribution and some varying degrees of genetic differentiation. Adaptive genomic diversity was strongly linked with environmental variables and was linked with colonization toward the south followed by adaptation.
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Affiliation(s)
- Fabiola León
- Pontificia Universidad Católica de Chile, Facultad de Ciencias Biológicas, Instituto para el Desarrollo Sustentable, Santiago, Chile
- Millennium Institute Center for Genome Regulation (CRG), Santiago, Chile
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago, Chile
- Millennium Nucleus of Patagonian Limit of Life (LiLi), Santiago, Chile
| | - Eduardo J Pizarro
- Pontificia Universidad Católica de Chile, Facultad de Ciencias Biológicas, Instituto para el Desarrollo Sustentable, Santiago, Chile
- Millennium Institute Center for Genome Regulation (CRG), Santiago, Chile
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago, Chile
- Millennium Nucleus of Patagonian Limit of Life (LiLi), Santiago, Chile
| | - Daly Noll
- Pontificia Universidad Católica de Chile, Facultad de Ciencias Biológicas, Instituto para el Desarrollo Sustentable, Santiago, Chile
- Millennium Institute Center for Genome Regulation (CRG), Santiago, Chile
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago, Chile
- Millennium Nucleus of Patagonian Limit of Life (LiLi), Santiago, Chile
| | - Luis R Pertierra
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago, Chile
| | - Benito A Gonzalez
- Laboratorio de Ecología de Vida Silvestre, Facultad de Ciencias Forestales y de la Conservación de la Naturaleza, Universidad de Chile, Santigo, Chile
| | | | - Juan Carlos Marín
- Laboratorio de Genómica y Biodiversidad, Departamento de Ciencias Básicas, Universidad del Bio-Bío, Chillán, Chile
| | - Juliana A Vianna
- Pontificia Universidad Católica de Chile, Facultad de Ciencias Biológicas, Instituto para el Desarrollo Sustentable, Santiago, Chile
- Millennium Institute Center for Genome Regulation (CRG), Santiago, Chile
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago, Chile
- Millennium Nucleus of Patagonian Limit of Life (LiLi), Santiago, Chile
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Guo K, Zhong J, Xie F, Zhu L, Qu Y, Ji X. Climate warming will increase chances of hybridization and introgression between two Takydromus lizards (Lacertidae). Ecol Evol 2021; 11:8573-8584. [PMID: 34257917 PMCID: PMC8258214 DOI: 10.1002/ece3.7671] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 04/23/2021] [Accepted: 04/27/2021] [Indexed: 11/06/2022] Open
Abstract
Coexisting species may experience population and range changes alone or jointly in response to environmental change. Here, we used six climate variables and ten modeling algorithms to predict the distribution of two Takydromus species (T. septentrionalis and T. sexlineatus) in China. We identified the sympatric and allopatric areas by comparing projections between the two species based on habitat suitability under present and future climate scenarios. We constructed the hypervolumes of six climate variables for the two species and then evaluated overlaps between hypervolumes. From this study, we know the following. First, minimum temperature of coldest month contributes the most to the prediction of habitat suitability. Second, habitats suitable for the two species will shift northward in response to climate warming. Third, the range of T. sexlineatus will expand across the four future time intervals before 2,100, namely the 2021-2040, 2041-2060, 2061-2080, and 2081-2100 intervals, under both Shared socioeconomic pathway (SSP) 245 and SSP585 scenarios, and the range of T. septentrionalis will also expand in the future except at the 2081-2100 interval under the SSP585 scenario. Fourth, the sympatric areas will contract or expand under the SSP245 scenario and expand across the four future time intervals before 2,100 under the SSP585 scenario. Fifth, the niche hypervolumes of the two species partially overlapped, and the differences in niche centroid show some degree of niche differentiation between the two species. These results allow to conclude that climate warming will not only drive the northward drift of sympatric areas but also increase the size of these areas if nothing is done to limit the emission of greenhouse gases. Given the existence of hybridization and introgression between T. septentrionalis and T. sexlineatus in the field where they coexist, we also conclude that climate warming will increase chances of hybridization and introgression between the two species.
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Affiliation(s)
- Kun Guo
- Jiangsu Key Laboratory for Biodiversity and BiotechnologyCollege of Life SciencesNanjing Normal UniversityNanjingChina
- College of Life and Environmental SciencesWenzhou UniversityWenzhouChina
| | - Jun Zhong
- Jiangsu Key Laboratory for Biodiversity and BiotechnologyCollege of Life SciencesNanjing Normal UniversityNanjingChina
- College of Life and Environmental SciencesWenzhou UniversityWenzhouChina
| | - Fan Xie
- Jiangsu Key Laboratory for Biodiversity and BiotechnologyCollege of Life SciencesNanjing Normal UniversityNanjingChina
| | - Lin Zhu
- Jiangsu Key Laboratory for Biodiversity and BiotechnologyCollege of Life SciencesNanjing Normal UniversityNanjingChina
| | - Yan‐Fu Qu
- Jiangsu Key Laboratory for Biodiversity and BiotechnologyCollege of Life SciencesNanjing Normal UniversityNanjingChina
| | - Xiang Ji
- Jiangsu Key Laboratory for Biodiversity and BiotechnologyCollege of Life SciencesNanjing Normal UniversityNanjingChina
- College of Life and Environmental SciencesWenzhou UniversityWenzhouChina
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Influence of Habitat Structure and Prey Abundance on Occupancy and Abundance of Two Anole Ecomorphs, Anolis cristatellus and Anolis krugi, in Secondary Karst Forests in Northern Puerto Rico. J HERPETOL 2020. [DOI: 10.1670/19-009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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4
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Afonso Silva AC, Bragg JG, Potter S, Fernandes C, Coelho MM, Moritz C. Tropical specialist vs. climate generalist: Diversification and demographic history of sister species of
Carlia
skinks from northwestern Australia. Mol Ecol 2017; 26:4045-4058. [DOI: 10.1111/mec.14185] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 04/29/2016] [Accepted: 05/02/2017] [Indexed: 01/05/2023]
Affiliation(s)
- Ana C. Afonso Silva
- Research School of Biology and Centre for Biodiversity Analysis Australian National University Acton ACT Australia
- cE3c ‐ Centre for Ecology, Evolution and Environmental Changes Departamento de Biologia Animal Faculdade de Ciências Universidade de Lisboa Lisboa Portugal
| | - Jason G. Bragg
- Research School of Biology and Centre for Biodiversity Analysis Australian National University Acton ACT Australia
- Royal Botanic Garden Sydney NSW Australia
| | - Sally Potter
- Research School of Biology and Centre for Biodiversity Analysis Australian National University Acton ACT Australia
| | - Carlos Fernandes
- cE3c ‐ Centre for Ecology, Evolution and Environmental Changes Departamento de Biologia Animal Faculdade de Ciências Universidade de Lisboa Lisboa Portugal
| | - Maria Manuela Coelho
- cE3c ‐ Centre for Ecology, Evolution and Environmental Changes Departamento de Biologia Animal Faculdade de Ciências Universidade de Lisboa Lisboa Portugal
| | - Craig Moritz
- Research School of Biology and Centre for Biodiversity Analysis Australian National University Acton ACT Australia
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5
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Niche overlap of mountain hare subspecies and the vulnerability of their ranges to invasion by the European hare; the (bad) luck of the Irish. Biol Invasions 2016. [DOI: 10.1007/s10530-016-1330-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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6
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Gómez Fernández MJ, Boston ESM, Gaggiotti OE, Kittlein MJ, Mirol PM. Influence of environmental heterogeneity on the distribution and persistence of a subterranean rodent in a highly unstable landscape. Genetica 2016; 144:711-722. [DOI: 10.1007/s10709-016-9937-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 11/04/2016] [Indexed: 11/24/2022]
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Vernesi C, Hoban SM, Pecchioli E, Crestanello B, Bertorelle G, Rosà R, Hauffe HC. Ecology, environment and evolutionary history influence genetic structure in five mammal species from the Italian Alps. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12651] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Cristiano Vernesi
- Department of Biodiversity and Molecular Ecology; Research and Innovation Centre; Fondazione Edmund Mach; 38010 S. Michele all'Adige (TN) Italy
| | - Sean M. Hoban
- National Institute for Mathematical and Biological Synthesis; University of Tennessee; 1122 Volunteer Blvd. Suite 106 Knoxville TN 37996-3410 USA
| | - Elena Pecchioli
- Department of Biodiversity and Molecular Ecology; Research and Innovation Centre; Fondazione Edmund Mach; 38010 S. Michele all'Adige (TN) Italy
| | - Barbara Crestanello
- Department of Biodiversity and Molecular Ecology; Research and Innovation Centre; Fondazione Edmund Mach; 38010 S. Michele all'Adige (TN) Italy
| | - Giorgio Bertorelle
- Department of Biology and Evolution; University of Ferrara; 44100 Ferrara Italy
| | - Roberto Rosà
- Department of Biodiversity and Molecular Ecology; Research and Innovation Centre; Fondazione Edmund Mach; 38010 S. Michele all'Adige (TN) Italy
| | - Heidi C. Hauffe
- Department of Biodiversity and Molecular Ecology; Research and Innovation Centre; Fondazione Edmund Mach; 38010 S. Michele all'Adige (TN) Italy
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Barker BS, Rodríguez-Robles JA, Cook JA. Climate as a driver of tropical insular diversity: comparative phylogeography of two ecologically distinctive frogs in Puerto Rico. ECOGRAPHY 2015; 38:769-781. [PMID: 26508809 PMCID: PMC4620057 DOI: 10.1111/ecog.01327] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/04/2014] [Indexed: 06/05/2023]
Abstract
The effects of late Quaternary climate on distributions and evolutionary dynamics of insular species are poorly understood in most tropical archipelagoes. We used ecological niche models under past and current climate to derive hypotheses regarding how stable climatic conditions shaped genetic diversity in two ecologically distinctive frogs in Puerto Rico. Whereas the Mountain Coquí, Eleutherodactylus portoricensis, is restricted to montane forest in the Cayey and Luquillo Mountains, the Red-eyed Coquí, E. antillensis, is a habitat generalist distributed across the entire Puerto Rican Bank (Puerto Rico and the Virgin Islands, excluding St. Croix). To test our hypotheses, we conducted phylogeographic and population genetic analyses based on mitochondrial and nuclear loci of each species across their range in Puerto Rico. Patterns of population differentiation in E. portoricensis, but not in E. antillensis, supported our hypotheses. For E. portoricensis, these patterns include: individuals isolated by long-term unsuitable climate in the Río Grande de Loíza Basin in eastern Puerto Rico belong to different genetic clusters; past and current climate strongly predicted genetic differentiation; and Cayey and Luquillo Mountains populations split prior to the last interglacial. For E. antillensis, these patterns include: genetic clusters did not fully correspond to predicted long-term unsuitable climate; and past and current climate weakly predicted patterns of genetic differentiation. Genetic signatures in E. antillensis are consistent with a recent range expansion into western Puerto Rico, possibly resulting from climate change and anthropogenic influences. As predicted, regions with a large area of long-term suitable climate were associated with higher genetic diversity in both species, suggesting larger and more stable populations. Finally, we discussed the implications of our findings for developing evidence-based management decisions for E. portoricensis, a taxon of special concern. Our findings illustrate the role of persistent suitable climatic conditions in promoting the persistence and diversification of tropical island organisms.
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Affiliation(s)
- Brittany S. Barker
- Department of Biology, University of New Mexico, Albuquerque, New Mexico 87131-0001, USA
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA
| | - Javier A. Rodríguez-Robles
- School of Life Sciences, University of Nevada, Las Vegas, 4505 Maryland Parkway, Las Vegas, NV 89154-4004, USA
| | - Joseph A. Cook
- Department of Biology, University of New Mexico, Albuquerque, New Mexico 87131-0001, USA
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico 87131-0001, USA
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Phillips JG, Deitloff J, Guyer C, Huetteman S, Nicholson KE. Biogeography and evolution of a widespread Central American lizard species complex: Norops humilis, (Squamata: Dactyloidae). BMC Evol Biol 2015; 15:143. [PMID: 26187158 PMCID: PMC4506609 DOI: 10.1186/s12862-015-0391-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 05/26/2015] [Indexed: 11/15/2022] Open
Abstract
Background Caribbean anole lizards (Dactyloidae) have frequently been used as models to study questions regarding biogeography and adaptive radiations, but the evolutionary history of Central American anoles (particularly those of the genus Norops) has not been well studied. Previous work has hypothesized a north-to-south dispersal pattern of Central American Norops, but no studies have examined dispersal within any Norops lineages. Here we test two major hypotheses for the dispersal of the N. humilis/quaggulus complex (defined herein, forming a subset within Savage and Guyer’s N. humilis group). Results Specimens of the N. humilis group were collected in Central America, from eastern Mexico to the Canal Zone of Panama. Major nodes were dated for comparison to the geologic history of Central America, and ancestral ranges were estimated for the N. humilis/quaggulus complex to test hypothesized dispersal patterns. These lineages displayed a northward dispersal pattern. We also demonstrate that the N. humilis/quaggulus complex consists of a series of highly differentiated mitochondrial lineages, with more conserved nuclear evolution. The paraphyly of the N. humilis species group is confirmed. A spatial analysis of molecular variance suggests that current populations are genetically distinct from one another, with limited mitochondrial gene flow occurring among sites. Conclusions The observed south-to-north colonization route within the Norops humilis/quaggulus complex represents the first evidence of a Norops lineage colonizing in a south-to-north pattern, (opposite to the previously held hypothesis for mainland Norops). One previously described taxon (N. quaggulus) was nested within N. humilis, demonstrating the paraphyly of this species; while our analyses also reject the monophyly of the Norops humilis species group (sensu Savage and Guyer), with N. tropidonotus, N. uniformis, and N. marsupialis being distantly related to/highly divergent from the N. humilis/quaggulus complex. Our work sheds light on mainland anole biogeography and past dispersal events, providing a pattern to test against other groups of mainland anoles. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0391-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- John G Phillips
- Department of Biology, Central Michigan University, Mt. Pleasant, MI, 48859, USA. .,Present address: Department of Biological Sciences, University of Tulsa, Tulsa, OK, 74104, USA.
| | - Jennifer Deitloff
- Department of Biological Sciences, Auburn University, Auburn, AL, 36849, USA.,Present address: Department of Biological Sciences, Lock Haven University, Lock Haven, PA, 17745, USA
| | - Craig Guyer
- Department of Biological Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Sara Huetteman
- Department of Biology, Central Michigan University, Mt. Pleasant, MI, 48859, USA
| | - Kirsten E Nicholson
- Department of Biology, Central Michigan University, Mt. Pleasant, MI, 48859, USA
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10
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Heikkinen ME, Ruokonen M, Alexander M, Aspi J, Pyhäjärvi T, Searle JB. Relationship between wild greylag and European domestic geese based on mitochondrial DNA. Anim Genet 2015; 46:485-97. [PMID: 26096191 DOI: 10.1111/age.12319] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/27/2015] [Indexed: 11/30/2022]
Abstract
The origins of the European domestic goose are uncertain. The available information comes from archaeological findings and historical literature, but genetic evidence has hitherto been scarce. The domestic goose in Europe is derived from the greylag goose (Anser anser), but it is not known where the initial domestication took place and which of the two subspecies of greylag goose was ancestral. We aimed to determine the amount and geographical distribution of genetic diversity in modern populations of greylag geese as well as in different breeds of the domestic goose to make inferences about goose domestication. We studied DNA sequence variation in the mitochondrial control region of greylag geese from multiple populations across Europe and western Asia as well as specimens of domestic geese representing 18 modern breeds and individuals not belonging to any recognised breed. Our results show notable differences in genetic diversity between different greylag goose populations and the presence of six mitochondrial haplogroups which show a degree of geographical partitioning. The genetic diversity of the domestic goose is low, with 84% of sampled individuals having one of two major closely related haplotypes, suggesting that modern European domestic geese may derive from a narrow genetic base. The site of domestication remains unresolved, but domestic geese in Turkey were unusually diverse, indicating the importance of further sampling in the vicinity of the eastern Mediterranean and the Near East. There appears to be past or ongoing hybridisation between greylags and domestic geese in particular areas, consistent with field observations.
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Affiliation(s)
- M E Heikkinen
- Genetics and Physiology Unit, University of Oulu, Oulu, 90014, Finland
| | - M Ruokonen
- Genetics and Physiology Unit, University of Oulu, Oulu, 90014, Finland
| | - M Alexander
- Department of Archaeology, University of York, York, YO10 5DD, United Kingdom
| | - J Aspi
- Genetics and Physiology Unit, University of Oulu, Oulu, 90014, Finland
| | - T Pyhäjärvi
- Genetics and Physiology Unit, University of Oulu, Oulu, 90014, Finland
| | - J B Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, 14853, USA
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11
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Kolanowska M, Konowalik K. Niche Conservatism and Future Changes in the Potential Area Coverage ofArundina graminifolia, an Invasive Orchid Species from Southeast Asia. Biotropica 2014. [DOI: 10.1111/btp.12089] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Marta Kolanowska
- Department of Plant Taxonomy and Nature Conservation; University of Gdańsk; ul. Wita Stwosza 59 80-308 Gdańsk Poland
| | - Kamil Konowalik
- Institute of Botany; University of Regensburg; Universitätsstr. 31 D-93053 Regensburg Bavaria
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12
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Niche conservatism and the future potential range of Epipactis helleborine (Orchidaceae). PLoS One 2013; 8:e77352. [PMID: 24143222 PMCID: PMC3797094 DOI: 10.1371/journal.pone.0077352] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Accepted: 09/02/2013] [Indexed: 11/19/2022] Open
Abstract
The aim of the present study was to evaluate the current distribution of suitable niches for the invasive orchid species, Epipactis helleborine, and to estimate the possibility of its further expansion. Moreover, niche modeling tools were used to explain its rapid expansion in North America and to test the niche conservatism of the species. The maximum entropy method was used to create models of the suitable niche distribution. A database of E. helleborine localities was prepared based on the examination of herbarium specimens, information from electronic databases as well as data gathered during field works. The differences between the niches occupied by native and invasive populations were evaluated using the niche overlap and niche identity test indexes. Moreover, the coverage of the most suitable habitats for the species was measured for three future scenarios as well as for the present time model. Populations of E. helleborine occupy North American west coast habitats very similar to those preferred by native, Eurasian populations, while the expansion in the east coast is related to the niche shift. The created models of suitable niche distribution indicate that the species does not realize its potential niche in the native range. The total surface of the habitats potentially available for E. helleborine will decrease in all climate change scenarios created for 2080.
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Gartner GEA, Gamble T, Jaffe AL, Harrison A, Losos JB. Left-right dewlap asymmetry and phylogeography ofAnolis lineatuson Aruba and Curaçao. Biol J Linn Soc Lond 2013. [DOI: 10.1111/bij.12131] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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14
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Falk BG, Perkins SL. Host specificity shapes population structure of pinworm parasites in Caribbean reptiles. Mol Ecol 2013; 22:4576-90. [DOI: 10.1111/mec.12410] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Revised: 05/14/2013] [Accepted: 05/16/2013] [Indexed: 11/30/2022]
Affiliation(s)
- Bryan G. Falk
- Division of Invertebrate Zoology; Sackler Institute for Comparative Genomics; American Museum of Natural History; Central Park West at 79 Street New York NY 10024 USA
| | - Susan L. Perkins
- Division of Invertebrate Zoology; Sackler Institute for Comparative Genomics; American Museum of Natural History; Central Park West at 79 Street New York NY 10024 USA
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15
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Puente-Rolón AR, Reynolds RG, Revell LJ. Preliminary genetic analysis supports cave populations as targets for conservation in the endemic endangered Puerto Rican boa (Boidae: Epicrates inornatus). PLoS One 2013; 8:e63899. [PMID: 23691110 PMCID: PMC3655012 DOI: 10.1371/journal.pone.0063899] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Accepted: 04/09/2013] [Indexed: 11/18/2022] Open
Abstract
The endemic Puerto Rican boa (Epicrates inornatus) has spent 42 years on the Endangered Species List with little evidence for recovery. One significant impediment to effective conservation planning has been a lack of knowledge of the distribution of genetic variability in the species. It has previously been suggested that boas might best be protected around caves that harbor large populations of bats. Prior study has found Puerto Rican boas at relatively high densities in and around bat caves, which they use both to feed and seek shelter. However, it is unknown whether these behaviorally distinctive populations represent a distinct evolutionary lineage, or (conversely) whether caves harbor representative genetic diversity for the species across the island. We provide the first genetic study of the Puerto Rican boa, and we examine and compare genetic diversity and divergence among two cave populations and two surface populations of boas. We find three haplogroups and an apparent lack of phylogeographic structure across the island. In addition, we find that the two cave populations appear no less diverse than the two surface populations, and harbor multiple mtDNA lineages. We discuss the conservation implications of these findings, including a call for the immediate protection of the remaining cave-associated populations of boas.
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Affiliation(s)
- Alberto R. Puente-Rolón
- Departamento de Ciencias y Tecnología, Universidad Interamericana de Puerto Rico, Recinto de Arecibo, Arecibo, Puerto Rico
| | - R. Graham Reynolds
- Department of Biology, University of Massachusetts Boston, Boston, Massachusetts, United States of America
- * E-mail:
| | - Liam J. Revell
- Department of Biology, University of Massachusetts Boston, Boston, Massachusetts, United States of America
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Jezkova T, Leal M, Rodríguez-Robles JA. Genetic drift or natural selection? Hybridization and asymmetric mitochondrial introgression in two Caribbean lizards (Anolis pulchellus and Anolis krugi). J Evol Biol 2013; 26:1458-71. [PMID: 23663090 DOI: 10.1111/jeb.12149] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Revised: 02/20/2013] [Accepted: 02/21/2013] [Indexed: 11/28/2022]
Abstract
Hybridization and gene introgression can occur frequently between closely related taxa, but appear to be rare phenomena among members of the species-rich West Indian radiation of Anolis lizards. We investigated the pattern and possible mechanism of introgression between two sister species from Puerto Rico, Anolis pulchellus and Anolis krugi, using mitochondrial (ND2) and nuclear (DNAH3, NKTR) DNA sequences. Our findings demonstrated extensive introgression of A. krugi mtDNA (k-mtDNA) into the genome of A. pulchellus in western Puerto Rico, to the extent that k-mtDNA has mostly or completely replaced the native mtDNA of A. pulchellus on this part of the island. We proposed two not mutually exclusive scenarios to account for the interspecific matings between A. pulchellus and A. krugi. We inferred that hybridization events occurred independently in several populations, and determined that k-mtDNA haplotypes harboured in individuals of A. pulchellus can be assigned to four of the five major mtDNA clades of A. krugi. Further, the spatial distribution of k-mtDNA clades in the two species is largely congruent. Based on this evidence, we concluded that natural selection was the probable driving mechanism for the extensive k-mtDNA introgression into A. pulchellus. Our two nuclear data sets yielded different results. DNAH3 showed reciprocal monophyly of A. pulchellus and A. krugi, indicating no effect of hybridization on this marker. In contrast, the two species shared nine NKTR alleles, probably due to incomplete lineage sorting. Our study system will provide an excellent opportunity to experimentally assess the behavioural and ecological mechanisms that can lead to hybridization in closely related taxa.
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Affiliation(s)
- T Jezkova
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV 89154-4004, USA
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Antoniou A, Magoulas A, Platis P, Kotoulas G. Assessing the genetic landscape of a contact zone: the case of European hare in northeastern Greece. Genetica 2013; 141:23-40. [PMID: 23381134 DOI: 10.1007/s10709-013-9703-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Accepted: 01/30/2013] [Indexed: 12/28/2022]
Abstract
The European hare populations of the Balkan Peninsula comprise two divergent phylogenetic lineages with discrete geographical distribution slightly overlapping in the area of northeastern Greece and Bulgaria. Here we elucidate their contact zone, by defining the spatial distributional pattern of the two highly divergent groups, detecting individuals of hybrid origin, and identifying genetic barriers present in the area of their co-existence. Specimens from northeastern Greece were assayed for lineage assignment and population genetic inference based on a 511 bp fragment of mitochondrial DNA control region and allelic data from 10 microsatellite loci. Bayesian analyses on original and simulated genotypes were performed allowing for the contact zone delineation. Our results indicate high genetic diversity in both nuclear and mitochondrial DNA, strong population structure and non random spatial distribution of the differentiated gene pools. The information provided by the two types of molecular markers yielded consistent results. This study comprises a fine scale analysis of the contact zone between the two evolutionary lineages of European brown hares in northeastern Greece. Specific questions on the spatial patterns where addressed for the first time. Furthermore, hypotheses regarding the presence of hybrids were also tested. As a result, interpretive power to the diversity patterns observed today in the Balkans was added and previously overlooked aspects of the species biology were highlighted.
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Affiliation(s)
- Aglaia Antoniou
- Department of Biology, University of Crete, Herakleio, Crete, Greece.
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Lawson LP. Diversification in a biodiversity hot spot: landscape correlates of phylogeographic patterns in the African spotted reed frog. Mol Ecol 2013; 22:1947-60. [DOI: 10.1111/mec.12229] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Revised: 12/05/2012] [Accepted: 12/20/2012] [Indexed: 12/25/2022]
Affiliation(s)
- Lucinda P. Lawson
- Committee on Evolutionary Biology; University of Chicago; Chicago IL 60637 USA
- Zoology Department; Field Museum of Natural History; Chicago IL 60605 USA
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Barker BS, Rodríguez-Robles JA, Aran VS, Montoya A, Waide RB, Cook JA. Sea level, topography and island diversity: phylogeography of the Puerto Rican Red-eyed Coquí, Eleutherodactylus antillensis. Mol Ecol 2012; 21:6033-52. [PMID: 23163292 DOI: 10.1111/mec.12020] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Revised: 07/26/2012] [Accepted: 07/31/2012] [Indexed: 01/08/2023]
Abstract
Quaternary climatic oscillations caused changes in sea level that altered the size, number and degree of isolation of islands, particularly in land-bridge archipelagoes. Elucidating the demographic effects of these oscillations increases our understanding of the role of climate change in shaping evolutionary processes in archipelagoes. The Puerto Rican Bank (PRB) (Puerto Rico and the Eastern Islands, which comprise Vieques, Culebra, the Virgin Islands and associated islets) in the eastern Caribbean Sea periodically coalesced during glaciations and fragmented during interglacial periods of the quaternary. To explore population-level consequences of sea level changes, we studied the phylogeography of the frog Eleutherodactylus antillensis across the archipelago. We tested hypotheses encompassing vicariance and dispersal narratives by sequencing mtDNA (c. 552 bp) of 285 individuals from 58 localities, and four nuDNA introns (totalling c. 1633 bp) from 173 of these individuals. We found low support for a hypothesis of divergence of the Eastern Islands populations prior to the start of the penultimate interglacial c. 250 kya, and higher support for a hypothesis of colonization of the Eastern Islands from sources in eastern Puerto Rico during the penultimate and last glacial period, when a land bridge united the PRB. The Río Grande de Loíza Basin in eastern Puerto Rico delineates a phylogeographic break. Haplotypes shared between the PRB and St. Croix (an island c. 105 km south-east of this archipelago) likely represent human-mediated introductions. Our findings illustrate how varying degrees of connectivity and isolation influence the evolution of tropical island organisms.
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Affiliation(s)
- Brittany S Barker
- Department of Biology, University of New Mexico, Albuquerque, NM, 87131-0001, USA.
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Wang IJ, Glor RE, Losos JB. Quantifying the roles of ecology and geography in spatial genetic divergence. Ecol Lett 2012; 16:175-82. [DOI: 10.1111/ele.12025] [Citation(s) in RCA: 190] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Revised: 07/18/2012] [Accepted: 10/04/2012] [Indexed: 12/01/2022]
Affiliation(s)
- Ian J. Wang
- Department of Organismic and Evolutionary Biology; Harvard University; Cambridge; MA; 02138; USA
| | - Richard E. Glor
- Department of Biology; University of Rochester; Rochester; NY; 14627; USA
| | - Jonathan B. Losos
- Department of Organismic and Evolutionary Biology; Harvard University; Cambridge; MA; 02138; USA
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Ortego J, Riordan EC, Gugger PF, Sork VL. Influence of environmental heterogeneity on genetic diversity and structure in an endemic southern Californian oak. Mol Ecol 2012; 21:3210-23. [PMID: 22548448 DOI: 10.1111/j.1365-294x.2012.05591.x] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Understanding how specific environmental factors shape gene flow while disentangling their importance relative to the effects of geographical isolation is a major question in evolutionary biology and a specific goal of landscape genetics. Here, we combine information from nuclear microsatellite markers and ecological niche modelling to study the association between climate and spatial genetic structure and variability in Engelmann oak (Quercus engelmannii), a wind-pollinated species with high potential for gene flow. We first test whether genetic diversity is associated with climatic niche suitability and stability since the Last Glacial Maximum (LGM). Second, we use causal modelling to analyse the potential influence of climatic factors (current and LGM niche suitability) and altitude in the observed patterns of genetic structure. We found that genetic diversity is negatively associated with local climatic stability since the LGM, which may be due to higher immigration rates in unstable patches during favourable climatic periods and/or temporally varying selection. Analyses of spatial genetic structure revealed the presence of three main genetic clusters, a pattern that is mainly driven by two highly differentiated populations located in the northern edge of the species distribution range. After controlling for geographic distance, causal modelling analyses showed that genetic relatedness decreases with the environmental divergence among sampling sites estimated as altitude and current and LGM niche suitability. Natural selection against nonlocal genotypes and/or asynchrony in reproductive phenology may explain this pattern. Overall, this study suggests that local environmental conditions can shape patterns of genetic structure and variability even in species with high potential for gene flow and relatively small distribution ranges.
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Affiliation(s)
- Joaquín Ortego
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Box 957239, Los Angeles, CA 90095-7239, USA.
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Synergy between Allopatry and Ecology in Population Differentiation and Speciation. INTERNATIONAL JOURNAL OF ECOLOGY 2012. [DOI: 10.1155/2012/273413] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The general diversity pattern of the Caribbean anole radiation has been described in detail; however, the actual mechanisms at the origin of their diversification remain controversial. In particular, the role of ecological speciation, and the relative importance of divergence in allopatry and in parapatry, is debated. We describe the genetic structure of anole populations across lineage contact zones and ecotones to investigate the effect of allopatric divergence, natural selection, and the combination of both factors on population differentiation. Allopatric divergence had no significant impact on differentiation across the lineage boundary, while a clear bimodality in genetic and morphological characters was observed across an ecotone within a single lineage. Critically, the strongest differentiation was observed when allopatry and ecology act together, leading to a sharp reduction in gene flow between two lineages inhabiting different habitats. We suggest that, for Caribbean anoles to reach full speciation, a synergistic combination of several historical and ecological factors may be requisite.
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ANGETTER LEASU, LÖTTERS STEFAN, RÖDDER DENNIS. Climate niche shift in invasive species: the case of the brown anole. Biol J Linn Soc Lond 2011. [DOI: 10.1111/j.1095-8312.2011.01780.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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NG JULIENNE, GLOR RICHARDE. Genetic differentiation among populations of a Hispaniolan trunk anole that exhibit geographical variation in dewlap colour. Mol Ecol 2011; 20:4302-17. [DOI: 10.1111/j.1365-294x.2011.05267.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Chan LM, Brown JL, Yoder AD. Integrating statistical genetic and geospatial methods brings new power to phylogeography. Mol Phylogenet Evol 2011; 59:523-37. [DOI: 10.1016/j.ympev.2011.01.020] [Citation(s) in RCA: 156] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2010] [Revised: 01/31/2011] [Accepted: 01/31/2011] [Indexed: 01/29/2023]
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