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Atencio GWG, Zanini R, Deprá M, Romanowski HP. Preliminary population studies of the grassland swallowtail butterfly Euryades corethrus (Lepidoptera, Papilionidae). AN ACAD BRAS CIENC 2023; 95:e20210503. [PMID: 37341269 DOI: 10.1590/0001-3765202320210503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 06/10/2021] [Indexed: 06/22/2023] Open
Abstract
Euryades corethrus is a Troidini butterfly (Papilionidae, Papilioninae), endemic to grasslands in southern Brazil, Uruguay, Argentina and Paraguay. Formerly abundant, nowadays it is in the Red list of endangered species for those areas. During its larval stage, it feeds on Aristolochia spp, commonly found in southern grasslands. These native grassland areas are diminishing, being converted to crops and pastures, causing habitat loss for Aristolochia and E. corethrus. This study aimed to assess the genetic diversity, population structure and demographic history of E. corethrus. We sampled eight populations from Rio Grande do Sul, Brazil and based on Cytochrome Oxidase subunit I (COI) molecular marker, our results suggest a low genetic variability between populations, presence of gene flow and, consequently, lack of population structure. A single maternally inherited-genetic marker is insufficient for population-level decisions, but barcoding is a useful tool during early stages of population investigation, bringing out genomic diversity patterns within the target species. Those populations likely faced a bottleneck followed by a rapid expansion during the last glaciation and subsequent stabilization in effective population size. Habitat loss is a threat, which might cause isolation, loss of genetic variability and, ultimately, extinction of E. corethrus if no habitat conservation policy is adopted.
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Affiliation(s)
- Guilherme Wagner G Atencio
- Programa de Pós-Graduação em Biologia Animal, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves, 9500, Bloco IV, Prédio 43433, Sala 214, Agronomia, 91501-970 Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Departamento de Zoologia, Laboratório de Ecologia de Insetos, Av. Bento Gonçalves, 9500, Bloco IV, Prédio 43435, Sala 218, Agronomia, 91501-970 Porto Alegre, RS, Brazil
- Universidade de Lisboa, Faculdade de Ciências, Centro de Ecologia, Evolução e Alterações Ambientais, Edifício C2, 5.º piso, Sala 2.5.46, Código Postal 1749-016, Campo Grande, Lisboa, Portugal
| | - Rebeca Zanini
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Laboratório de Drosophila, Av. Bento Gonçalves, 9500, Prédio 43323, Sala 210, Agronomia, 90650-001 Porto Alegre, RS, Brazil
- Universidade Nova de Lisboa, Faculdade de Ciências Médicas, Laboratório de Biomedicina Integrativa, Rua do Instituto Bacteriológico 5, Código Postal 1169-056, Lisboa, Portugal
| | - Maríndia Deprá
- Programa de Pós-Graduação em Biologia Animal, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves, 9500, Bloco IV, Prédio 43433, Sala 214, Agronomia, 91501-970 Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Laboratório de Drosophila, Av. Bento Gonçalves, 9500, Prédio 43323, Sala 210, Agronomia, 90650-001 Porto Alegre, RS, Brazil
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves, 9500, Prédio 43312 M, Caixa Postal 15053, Agronomia, 90650-001 Porto Alegre, RS, Brazil
| | - Helena P Romanowski
- Programa de Pós-Graduação em Biologia Animal, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves, 9500, Bloco IV, Prédio 43433, Sala 214, Agronomia, 91501-970 Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Departamento de Zoologia, Laboratório de Ecologia de Insetos, Av. Bento Gonçalves, 9500, Bloco IV, Prédio 43435, Sala 218, Agronomia, 91501-970 Porto Alegre, RS, Brazil
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2
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The genetic structure and connectivity in two sympatric rodent species with different life histories are similarly affected by land use disturbances. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01485-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
AbstractThe negative impact of habitat fragmentation due to human activities may be different in different species that co-exist in the same area, with consequences on the development of environmental protection plans. Here we aim at understanding the effects produced by different natural and anthropic landscape features on gene flow patterns in two sympatric species with different specializations, one generalist and one specialist, sampled in the same locations. We collected and genotyped 194 wood mice (generalist species) and 199 bank voles (specialist species) from 15 woodlands in a fragmented landscape characterized by different potential barriers to dispersal. Genetic variation and structure were analyzed in the two species, respectively. Effective migration surfaces, isolation-by-resistance (IBR) analysis, and regression with randomization were used to investigate isolation-by-distance (IBD) and the relative importance of land cover elements on gene flow. We observed similar patterns of heterozygosity and IBD for both species, but the bank vole showed higher genetic differences among geographic areas. The IBR analysis suggests that (i) connectivity is reduced in both species by urban areas but more strongly in the specialist bank vole; (ii) cultivated areas act as dispersal corridors in both species; (iii) woodlands appear to be an important factor in increasing connectivity in the bank vole, and less so in the wood mouse. The difference in dispersal abilities between a generalist and specialist species was reflected in the difference in genetic structure, despite extensive habitat changes due to human activities. The negative effects of fragmentation due to the process of urbanization were, at least partially, mitigated by another human product, i.e., cultivated terrains subdivided by hedgerows, and this was true for both species.
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3
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Hemstrom WB, Freedman MG, Zalucki MP, Ramírez SR, Miller MR. Population genetics of a recent range expansion and subsequent loss of migration in monarch butterflies. Mol Ecol 2022; 31:4544-4557. [PMID: 35779004 PMCID: PMC9546011 DOI: 10.1111/mec.16592] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 06/15/2022] [Accepted: 06/22/2022] [Indexed: 11/29/2022]
Abstract
Range expansions-whether permanent or transient-strongly influence the distribution of genetic variation in space. Monarch butterflies are best known for long-distance seasonal migration within North America but are also established as nonmigratory populations around the world, including on Pacific Islands. Previous research has highlighted stepwise expansion across the Pacific, though questions remain about expansion timing and the population genetic consequences of migration loss. Here, we present reduced-representation sequencing data for 275 monarchs from North America (n = 85), 12 Pacific Islands (n = 136) and three locations in Australia (n = 54), with the goal of understanding (i) how the monarch's Pacific expansion has shaped patterns of population genetic variation and (ii) how loss of migration has influenced spatial patterns of differentiation. We find support for previously described stepwise dispersal across the Pacific and document an additional expansion from Hawaii into the Mariana Islands. Nonmigratory monarchs within the Mariana Islands show strong patterns of differentiation, despite their proximity; by contrast, migratory North American samples form a single genetically panmictic population across the continent. Estimates of Pacific establishment timing are highly uncertain (~100-1,000,000 years ago) but overlap with historical records that indicate a recent expansion. Our data support (i) a recent expansion across the Pacific whose timing overlaps with available historical records of establishment and (ii) a strong role for seasonal migration in determining patterns of spatial genetic variation. Our results are noteworthy because they demonstrate how the evolution of partial migration can drive population differentiation over contemporary timescales.
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Affiliation(s)
| | - Micah G. Freedman
- Department of Evolution and EcologyUniversity of CaliforniaDavisCaliforniaUSA
- Center for Population BiologyUniversity of CaliforniaDavisCaliforniaUSA
| | - Myron P. Zalucki
- School of Biological SciencesThe University of QueenslandBrisbaneAustralia
| | - Santiago R. Ramírez
- Department of Evolution and EcologyUniversity of CaliforniaDavisCaliforniaUSA
- Center for Population BiologyUniversity of CaliforniaDavisCaliforniaUSA
| | - Michael R. Miller
- Department of Animal ScienceUniversity of CaliforniaDavisCaliforniaUSA
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4
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Mosher CM, Johnson CJ, Murray BW. Reduced genetic diversity associated with the northern expansion of an amphibian species with high habitat specialization, Ascaphus truei, resolved using two types of genetic markers. Ecol Evol 2022; 12:e8716. [PMID: 35342604 PMCID: PMC8931771 DOI: 10.1002/ece3.8716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 01/18/2022] [Accepted: 01/24/2022] [Indexed: 11/13/2022] Open
Abstract
Reconstruction of historical relationships between geographic regions within a species' range can indicate dispersal patterns and help predict future responses to shifts in climate. Ascaphus truei (coastal tailed frog) is an indicator species of the health of forests and perennial streams in the Coastal and Cascade Mountains of the Pacific Northwest of North America. We used two genetic techniques-microsatellite and genotype-by-sequencing (GBS)-to compare the within-region genetic diversity of populations near the northern extent of the species' range (British Columbia, Canada) to two geographic regions in British Columbia and two in Washington, USA, moving toward the core of the range. Allelic richness and heterozygosity declined substantially as latitude increased. The northernmost region had the lowest mean expected heterozygosities for both techniques (microsatellite, M = 0.20, SE = 0.080; GBS, M = 0.025, SE = 0.0010) and the southernmost region had the highest (microsatellite, M = 0.88, SE = 0.054; GBS, M = 0.20, SE = 0.0029). The northernmost regions (NC and MC) clustered together in population structure models for both genetic techniques. Our discovery of reduced diversity may have important conservation and management implications for population connectivity and the response of A. truei to climate change.
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Affiliation(s)
- Cherie M Mosher
- University of Northern British Columbia Prince George British Columbia Canada
| | - Chris J Johnson
- University of Northern British Columbia Prince George British Columbia Canada
| | - Brent W Murray
- University of Northern British Columbia Prince George British Columbia Canada
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Shakya SB, Wang-Claypool CY, Cicero C, Bowie RCK, Mason NA. Neo-sex chromosome evolution and phenotypic differentiation across an elevational gradient in horned larks (Eremophila Alpestris). Mol Ecol 2022; 31:1783-1799. [PMID: 35048444 DOI: 10.1111/mec.16357] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 12/16/2021] [Accepted: 01/07/2022] [Indexed: 11/29/2022]
Abstract
Genetic structure and phenotypic variation among populations is affected by both geographic distance and environmental variation across species' distributions. Understanding the relative contributions of isolation by distance (IBD) and isolation by environment (IBE) is important for elucidating population dynamics across habitats and ecological gradients. In this study, we compared phenotypic and genetic variation among Horned Lark (Eremophila alpestris) populations from 10 sites encompassing an elevational gradient from low-elevation desert scrub in Death Valley (285 a.s.l.) to high-elevation meadows in the White Mountains of the Sierra Nevada of California (greater than 3000 m a.s.l.). Using a ddRAD dataset of 28,474 SNPs aligned to a high-quality reference genome, we compared genetic structure with elevational, environmental, and spatial distance to quantify how different aspects of the landscape drive genomic and phenotypic differentiation in Horned Larks. We found larger-bodied birds were associated with sites that had less seasonality and higher annual precipitation, and longer spurs occurred in soils with more clay and silt content, less sand, and finer fragments. Larks have large neo-sex chromosomes, and we found that associations with elevation and environmental variation were much stronger among neo-sex chromosomes compared to autosomes. Furthermore, we found that putative chromosomal translocations, fusions, and inversions were associated with elevation and may underlie local adaptation across an elevational gradient in Horned Larks. Our results suggest that genetic variation in Horned Larks is affected more by IBD than IBE, but specific phenotypes and genomic regions-particually on neo-sex chromosomes-bear stronger associations with the environment.
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Affiliation(s)
- Subir B Shakya
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Cynthia Y Wang-Claypool
- Museum of Vertebrate Zoology, University of California, Berkeley, California, USA.,Department of Integrative Biology, University of California, Berkeley, California, USA
| | - Carla Cicero
- Museum of Vertebrate Zoology, University of California, Berkeley, California, USA
| | - Rauri C K Bowie
- Museum of Vertebrate Zoology, University of California, Berkeley, California, USA.,Department of Integrative Biology, University of California, Berkeley, California, USA
| | - Nicholas A Mason
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA.,Museum of Vertebrate Zoology, University of California, Berkeley, California, USA
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6
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Mebs D, Schneider JV, Schröder O, Yotsu-Yamashita M, Harley JR, Mogk L, Köhler G. A study on the genetic population structure and the tetrodotoxin content of rough-skinned newts, Taricha granulosa (Salamandridae), from their northern range of distribution. Toxicon 2021; 206:38-41. [PMID: 34919907 DOI: 10.1016/j.toxicon.2021.12.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 12/05/2021] [Accepted: 12/13/2021] [Indexed: 11/30/2022]
Abstract
Rough-skinned newts, Taricha granulosa, which contain tetrodotoxin (TTX), a potent neurotoxin, are widely distributed along the west-coast of North America up to British Columbia (BC), Canada, and Southeast Alaska. Their genetic population structure using DNA-microsatellites and the TTX-content of specimens from British Columbia (Prince Rupert area) and Alaska (Revillagigedo Island, Shelter Island, and Juneau) were analysed. TTX-concentrations were low in newts from BC and Revillagigedo Island, but high in specimens from mainland Juneau, which had been deliberately introduced from Shelter Island, where TTX was not detectable in the individuals sampled. No significant genetic differences were detected between these populations, which may correlate with the high intraspecies variability of TTX. It is still an open question, which factors favour or induce the toxin production in the newts.
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Affiliation(s)
- Dietrich Mebs
- Institute of Legal Medicine, Goethe University Frankfurt, Kennedyallee 104, 60596, Frankfurt, Germany.
| | - Julio V Schneider
- Terrestrial Zoology, Senckenberg Forschungsinstitut und Museum, Senckenberganlage 25, 60325, Frankfurt, Germany
| | - Oskar Schröder
- Terrestrial Zoology, Senckenberg Forschungsinstitut und Museum, Senckenberganlage 25, 60325, Frankfurt, Germany
| | - Mari Yotsu-Yamashita
- Graduate School of Agricultural Science, Tohoku University, 468-1 Aramaki-Aza-Aoba, Aoba-ku, Sendai, 980-8572, Japan
| | - John R Harley
- Alaska Coastal Rainforest Center, University of Alaska Southeast, Juneau, AK, 99801, USA
| | - Linda Mogk
- Terrestrial Zoology, Senckenberg Forschungsinstitut und Museum, Senckenberganlage 25, 60325, Frankfurt, Germany
| | - Gunther Köhler
- Terrestrial Zoology, Senckenberg Forschungsinstitut und Museum, Senckenberganlage 25, 60325, Frankfurt, Germany
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7
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Phylogeography of an endemic California silkmoth genus suggests the importance of an unheralded central California province in generating regional endemic biodiversity. Mol Phylogenet Evol 2021; 164:107256. [PMID: 34256128 DOI: 10.1016/j.ympev.2021.107256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 07/02/2021] [Accepted: 07/07/2021] [Indexed: 11/21/2022]
Abstract
The California Floristic province is a biodiversity hotspot. Understanding the phylogeographic patterns that exist in this diverse region is essential to understanding its evolution and for guiding conservation efforts. Calosaturnia is a charismatic silkmoth genus endemic to large portions of the region with three described species, C. mendocino, C. walterorum, and C. albofasciata. We sampled all three species from across their ranges, sequenced 1463 bp of mitochondrial COI and 1941 bp of nuclear DNA from three genes, and reconstructed phylogenetic relationships and estimated divergence times within the lineages. All three species show pronounced evidence of isolation and, in two cases, secondary reconnection. An unexpected monophyletic mtDNA lineage was found in the Central Coast region, in a region thought to represent an intergrade between C. mendocino and C. walterorum. Our genetic data also significantly revise previous hypotheses as to which species occur in which regions, suggesting that historical ecological changes around four Ma ago isolated some lineages, and a secondary isolation event two Ma ago led to isolation of populations both in the Central Coast region and the southern Sierra Nevada. Our results add to a currently under-appreciated pattern suggesting that coastal Central California is not a transition zone between Northern and Southern California Floristic Province faunas but rather its own unique, periodically isolated, biogeographic region. They also suggest cryptic diversity may be present in many other currently unrecognized groups. Additional research should focus on this central California region because many species may be highly restricted in range and in need of conservation attention.
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Nottingham S, Pelletier TA. The impact of climate change on western Plethodon salamanders' distribution. Ecol Evol 2021; 11:9370-9384. [PMID: 34306628 PMCID: PMC8293714 DOI: 10.1002/ece3.7735] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 04/07/2021] [Accepted: 05/14/2021] [Indexed: 02/06/2023] Open
Abstract
AIM Given that salamanders have experienced large shifts in their distributions over time, we determined how each species of Plethodon in the Pacific Northwest would respond to climate change. We incorporated several greenhouse scenarios both on a species-by-species basis, and also using phylogenetic groups, with the aim to determine the best course of action in managing land area to conserve diversity in this group. LOCATION Pacific Northwest of the United States (northern CA, OR, WA, ID, and MT). MAJOR TAXA STUDIED Western Plethodon salamanders. METHODS Species distribution models were estimated using MaxEnt for the current time period and for several future climate scenarios using bioclimatic data layers. We used several methods to quantify the change in habitat suitability over time from the models. We explored aspects of the climate layers to determine whether we can expect a concerted response to climate change due to similarity in ecological niche or independent responses that could be harder to manage. RESULTS The distribution of western Plethodon salamander species is strongly influenced by precipitation and less so by temperature. Species responses to climate change resulted in both increases and decreases in predicted suitable habitat, though most species ranges do not contract, especially when taken as a phylogenetic group. MAIN CONCLUSIONS While some established habitats may become more or less climatically suitable, the overall distribution of species in this group is unlikely to be significantly affected. Clades of Plethodon species are unlikely to be in danger of extirpation despite the possibility that individual species may be threatened as a result of limited distributions. Grouping species into lineages with similar geographic ranges can be a viable method of determining conservation needs. More biotic and dispersal information is needed to determine the true impact that changes in climate will have on the distribution of Plethodon species.
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Stone BW, Wolfe AD. Phylogeographic analysis of shrubby beardtongues reveals range expansions during the Last Glacial Maximum and implicates the Klamath Mountains as a hotspot for hybridization. Mol Ecol 2021; 30:3826-3839. [PMID: 34013537 DOI: 10.1111/mec.15992] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 05/12/2021] [Accepted: 05/14/2021] [Indexed: 12/26/2022]
Abstract
Quaternary glacial cycles often altered species' geographic distributions, which in turn altered the geographic structure of species' genetic diversity. In many cases, glacial expansion forced species in temperate climates to contract their ranges and reside in small pockets of suitable habitat (refugia), where they were likely to interact closely with other species, setting the stage for potential gene exchange. These introgression events, in turn, would have degraded species boundaries, making the inference of phylogenetic relationships challenging. Using high-throughput sequence data, we employed a combination of species distribution models and hybridization tests to assess the effect of glaciation on the geographic distributions, phylogenetic relationships, and patterns of gene flow of five species of Penstemon subgenus Dasanthera, long-lived shrubby angiosperms distributed throughout the Pacific Northwest of North America. Surprisingly, we found that rather than reducing their ranges to small refugia, most Penstemon subgenus Dasanthera species experienced increased suitable habitat during the Last Glacial Maximum relative to the present day. We also found substantial evidence for gene exchange between species, with the bulk of introgression events occurring in or near the Klamath Mountains of southwestern Oregon and northwestern California. Subsequently, our phylogenetic inference reveals blurred taxonomic boundaries in the Klamath Mountains, where introgression is most prevalent. Our results question the classical paradigm of temperate species' responses to glaciation and highlight the importance of contextualizing phylogenetic inference with species' histories of introgression.
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Affiliation(s)
- Benjamin W Stone
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
| | - Andrea D Wolfe
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
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Sukumaran J, Holder MT, Knowles LL. Incorporating the speciation process into species delimitation. PLoS Comput Biol 2021; 17:e1008924. [PMID: 33983918 PMCID: PMC8118268 DOI: 10.1371/journal.pcbi.1008924] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 03/29/2021] [Indexed: 11/22/2022] Open
Abstract
The "multispecies" coalescent (MSC) model that underlies many genomic species-delimitation approaches is problematic because it does not distinguish between genetic structure associated with species versus that of populations within species. Consequently, as both the genomic and spatial resolution of data increases, a proliferation of artifactual species results as within-species population lineages, detected due to restrictions in gene flow, are identified as distinct species. The toll of this extends beyond systematic studies, getting magnified across the many disciplines that rely upon an accurate framework of identified species. Here we present the first of a new class of approaches that addresses this issue by incorporating an extended speciation process for species delimitation. We model the formation of population lineages and their subsequent development into independent species as separate processes and provide for a way to incorporate current understanding of the species boundaries in the system through specification of species identities of a subset of population lineages. As a result, species boundaries and within-species lineages boundaries can be discriminated across the entire system, and species identities can be assigned to the remaining lineages of unknown affinities with quantified probabilities. In addition to the identification of species units in nature, the primary goal of species delimitation, the incorporation of a speciation model also allows us insights into the links between population and species-level processes. By explicitly accounting for restrictions in gene flow not only between, but also within, species, we also address the limits of genetic data for delimiting species. Specifically, while genetic data alone is not sufficient for accurate delimitation, when considered in conjunction with other information we are able to not only learn about species boundaries, but also about the tempo of the speciation process itself.
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Affiliation(s)
- Jeet Sukumaran
- Department of Biology, San Diego State University, San Diego, California, United States of America
| | - Mark T. Holder
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, United States of America
| | - L. Lacey Knowles
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America
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Radomski T, Hantak MM, Brown AD, Kuchta SR. Multilocus Phylogeography of Eastern Red-Backed Salamanders (Plethodon cinereus): Cryptic Appalachian Diversity and Postglacial Range Expansion. HERPETOLOGICA 2020. [DOI: 10.1655/herpetologica-d-19-00045] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Tom Radomski
- Ohio Center for Ecological and Evolutionary Studies, Department of Biological Sciences, Ohio University, Athens, OH 45701, USA
| | - Maggie M. Hantak
- Ohio Center for Ecological and Evolutionary Studies, Department of Biological Sciences, Ohio University, Athens, OH 45701, USA
| | - Ashley D. Brown
- Ohio Center for Ecological and Evolutionary Studies, Department of Biological Sciences, Ohio University, Athens, OH 45701, USA
| | - Shawn R. Kuchta
- Ohio Center for Ecological and Evolutionary Studies, Department of Biological Sciences, Ohio University, Athens, OH 45701, USA
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An integrative study of island diversification: Insights from the endemic Haemodracon geckos of the Socotra Archipelago. Mol Phylogenet Evol 2019; 133:166-175. [DOI: 10.1016/j.ympev.2019.01.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 01/07/2019] [Accepted: 01/07/2019] [Indexed: 11/22/2022]
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Pelletier TA, Carstens BC. Geographical range size and latitude predict population genetic structure in a global survey. Biol Lett 2018; 14:rsbl.2017.0566. [PMID: 29343561 DOI: 10.1098/rsbl.2017.0566] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 12/11/2017] [Indexed: 12/31/2022] Open
Abstract
While genetic diversity within species is influenced by both geographical distance and environmental gradients, it is unclear what other factors are likely to promote population genetic structure. Using a machine learning framework and georeferenced DNA sequences from more than 8000 species, we demonstrate that geographical attributes of the species range, including total size, latitude and elevation, are the most important predictors of which species are likely to contain structured genetic variation. While latitude is well known as an important predictor of biodiversity, our work suggests that it also plays a key role in shaping diversity within species.
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Affiliation(s)
- Tara A Pelletier
- Department of Evolution, Ecology, and Organismal Biology, Ohio State University, 318 W. 12th Avenue, Columbus, OH 43210-1293, USA
| | - Bryan C Carstens
- Department of Evolution, Ecology, and Organismal Biology, Ohio State University, 318 W. 12th Avenue, Columbus, OH 43210-1293, USA
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Sim Z, Davis CS, Jex B, Hegel T, Coltman DW. Management implications of highly resolved hierarchical population genetic structure in thinhorn sheep. CONSERV GENET 2018. [DOI: 10.1007/s10592-018-1123-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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15
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Cox CL, Stringer JF, Moseley MA, Chippindale PT, Streicher JW. Testing the geographical dimensions of genetic diversity following range expansion in a North American snake. Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/bly137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Christian L Cox
- Department of Biology, Georgia Southern University, Statesboro, GA, USA
- Department of Biology, University of Texas at Arlington, South Nedderman Drive, Arlington, USA
| | - Joel F Stringer
- Department of Biology, University of Texas at Arlington, South Nedderman Drive, Arlington, USA
| | - Matthew A Moseley
- Department of Biology, University of Texas at Arlington, South Nedderman Drive, Arlington, USA
| | - Paul T Chippindale
- Department of Biology, University of Texas at Arlington, South Nedderman Drive, Arlington, USA
| | - Jeffrey W Streicher
- Department of Biology, University of Texas at Arlington, South Nedderman Drive, Arlington, USA
- Department of Life Sciences, The Natural History Museum, London, UK
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Teske PR, Golla TR, Sandoval-Castillo J, Emami-Khoyi A, van der Lingen CD, von der Heyden S, Chiazzari B, Jansen van Vuuren B, Beheregaray LB. Mitochondrial DNA is unsuitable to test for isolation by distance. Sci Rep 2018; 8:8448. [PMID: 29855482 PMCID: PMC5981212 DOI: 10.1038/s41598-018-25138-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 04/16/2018] [Indexed: 12/04/2022] Open
Abstract
Tests for isolation by distance (IBD) are the most commonly used method of assessing spatial genetic structure. Many studies have exclusively used mitochondrial DNA (mtDNA) sequences to test for IBD, but this marker is often in conflict with multilocus markers. Here, we report a review of the literature on IBD, with the aims of determining (a) whether significant IBD is primarily a result of lumping spatially discrete populations, and (b) whether microsatellite datasets are more likely to detect IBD when mtDNA does not. We also provide empirical data from four species in which mtDNA failed to detect IBD by comparing these with microsatellite and SNP data. Our results confirm that IBD is mostly found when distinct regional populations are pooled, and this trend disappears when each is analysed separately. Discrepancies between markers were found in almost half of the studies reviewed, and microsatellites were more likely to detect IBD when mtDNA did not. Our empirical data rejected the lack of IBD in the four species studied, and support for IBD was particularly strong for the SNP data. We conclude that mtDNA sequence data are often not suitable to test for IBD, and can be misleading about species' true dispersal potential. The observed failure of mtDNA to reliably detect IBD, in addition to being a single-locus marker, is likely a result of a selection-driven reduction in genetic diversity obscuring spatial genetic differentiation.
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Affiliation(s)
- Peter R Teske
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park, 2006, South Africa.
| | - Tirupathi Rao Golla
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park, 2006, South Africa
| | - Jonathan Sandoval-Castillo
- Molecular Ecology Lab, College of Science and Engineering, Flinders University, Adelaide, SA, 5001, Australia
| | - Arsalan Emami-Khoyi
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park, 2006, South Africa
| | - Carl D van der Lingen
- Branch: Fisheries Management, Department of Agriculture, Forestry and Fisheries, Private Bag X2, Vlaeberg, 8012, South Africa
- Department of Biological Sciences and Marine Research Institute, University of Cape Town, Private Bag X3, Rondebosch, 7700, South Africa
| | - Sophie von der Heyden
- Evolutionary Genomics Group, Department of Botany and Zoology, University of Stellenbosch, Private Bag X1, 7602, Matieland, South Africa
| | - Brent Chiazzari
- School of Life Sciences, University of KwaZulu-Natal, Westville, Durban, 4001, South Africa
| | - Bettine Jansen van Vuuren
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park, 2006, South Africa
| | - Luciano B Beheregaray
- Molecular Ecology Lab, College of Science and Engineering, Flinders University, Adelaide, SA, 5001, Australia
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Cao YN, Wang IJ, Chen LY, Ding YQ, Liu LX, Qiu YX. Inferring spatial patterns and drivers of population divergence of Neolitsea sericea (Lauraceae), based on molecular phylogeography and landscape genomics. Mol Phylogenet Evol 2018; 126:162-172. [PMID: 29678646 DOI: 10.1016/j.ympev.2018.04.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Revised: 03/02/2018] [Accepted: 04/09/2018] [Indexed: 11/24/2022]
Abstract
The relative roles of geography, climate and ecology in driving population divergence and (incipient) speciation has so far been largely neglected in studies addressing the evolution of East Asia's island flora. Here, we employed chloroplast and ribosomal DNA sequences and restriction site-associated DNA sequencing (RADseq) loci to investigate the phylogeography and drivers of population divergence of Neolitsea sericea. These data sets support the subdivision of N. sericea populations into the Southern and Northern lineages across the 'Tokara gap'. Two distinct sublineages were further identified for the Northern lineage of N. sericea from the RADseq data. RADseq was also used along with approximate Bayesian computation to show that the current distribution and differentiation of N. sericea populations resulted from a combination of relatively ancient migration and successive vicariant events that likely occurred during the mid to late Pleistocene. Landscape genomic analyses showed that, apart from geographic barriers, barrier, potentially local adaptation to different climatic conditions appears to be one of the major drivers for lineage diversification of N. sericea.
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Affiliation(s)
- Ya-Nan Cao
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Ian J Wang
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720, USA
| | - Lu-Yao Chen
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yan-Qian Ding
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Lu-Xian Liu
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Ying-Xiong Qiu
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, and College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China.
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Kuchta SR, Brown AD, Highton R. Disintegrating over space and time: Paraphyly and species delimitation in the Wehrle's Salamander complex. ZOOL SCR 2018. [DOI: 10.1111/zsc.12281] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Shawn R. Kuchta
- Department of Biological Sciences; Ohio Center for Ecology and Evolutionary Studies; Ohio University; Athens OH USA
| | - Ashley D. Brown
- Department of Biological Sciences; Ohio Center for Ecology and Evolutionary Studies; Ohio University; Athens OH USA
| | - Richard Highton
- Department of Biology; University of Maryland; College Park MD USA
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Hague MT, Feldman CR, Brodie ED, Brodie ED. Convergent adaptation to dangerous prey proceeds through the same first‐step mutation in the garter snake
Thamnophis sirtalis. Evolution 2017; 71:1504-1518. [DOI: 10.1111/evo.13244] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 03/24/2017] [Indexed: 12/28/2022]
Affiliation(s)
- Michael T.J. Hague
- Department of Biology University of Virginia Charlottesville Virginia 22904
| | | | | | - Edmund D. Brodie
- Department of Biology University of Virginia Charlottesville Virginia 22904
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20
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Lecocq T, Gérard M, Michez D, Dellicour S. Conservation genetics of European bees: new insights from the continental scale. CONSERV GENET 2016. [DOI: 10.1007/s10592-016-0917-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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21
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Hague MTJ, Avila LA, Hanifin CT, Snedden WA, Stokes AN, Brodie ED, Brodie ED. Toxicity and population structure of the Rough-Skinned Newt (Taricha granulosa) outside the range of an arms race with resistant predators. Ecol Evol 2016; 6:2714-24. [PMID: 27066249 PMCID: PMC4798830 DOI: 10.1002/ece3.2068] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 02/11/2016] [Accepted: 02/22/2016] [Indexed: 01/07/2023] Open
Abstract
Species interactions, and their fitness consequences, vary across the geographic range of a coevolutionary relationship. This spatial heterogeneity in reciprocal selection is predicted to generate a geographic mosaic of local adaptation, wherein coevolutionary traits are phenotypically variable from one location to the next. Under this framework, allopatric populations should lack variation in coevolutionary traits due to the absence of reciprocal selection. We examine phenotypic variation in tetrodotoxin (TTX) toxicity of the Rough-Skinned Newt (Taricha granulosa) in regions of allopatry with its TTX-resistant predator, the Common Garter Snake (Thamnophis sirtalis). In sympatry, geographic patterns of phenotypic exaggeration in toxicity and toxin-resistance are closely correlated in prey and predator, implying that reciprocal selection drives phenotypic variation in coevolutionary traits. Therefore, in allopatry with TTX-resistant predators, we expect to find uniformly low levels of newt toxicity. We characterized TTX toxicity in northwestern North America, including the Alaskan panhandle where Ta. granulosa occur in allopatry with Th. sirtalis. First, we used microsatellite markers to estimate population genetic structure and determine if any phenotypic variation in toxicity might be explained by historical divergence. We found northern populations of Ta. granulosa generally lacked population structure in a pattern consistent with northern range expansion after the Pleistocene. Next, we chose a cluster of sites in Alaska, which uniformly lacked genetic divergence, to test for phenotypic divergence in toxicity. As predicted, overall levels of newt toxicity were low; however, we also detected unexpected among- and within-population variation in toxicity. Most notably, a small number of individuals contained large doses of TTX that rival means of toxic populations in sympatry with Th. sirtalis. Phenotypic variation in toxicity, despite limited neutral genetic divergence, suggests that factors other than reciprocal selection with Th. sirtalis likely contribute to geographic patterns of toxicity in Ta. granulosa.
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Affiliation(s)
- Michael T J Hague
- Department of Biology University of Virginia Charlottesville Virginia
| | - Leleña A Avila
- Museum of Vertebrate Zoology University of California Berkeley California
| | - Charles T Hanifin
- Department of Biology Utah State University, Uintah Basin Campus Vernal Utah
| | | | - Amber N Stokes
- Department of Biology California State University Bakersfield California
| | | | - Edmund D Brodie
- Department of Biology University of Virginia Charlottesville Virginia
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Kuchta SR, Brown AD, Converse PE, Highton R. Multilocus Phylogeography and Species Delimitation in the Cumberland Plateau Salamander, Plethodon kentucki: Incongruence among Data Sets and Methods. PLoS One 2016; 11:e0150022. [PMID: 26974148 PMCID: PMC4790894 DOI: 10.1371/journal.pone.0150022] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2015] [Accepted: 02/08/2016] [Indexed: 11/29/2022] Open
Abstract
Species are a fundamental unit of biodiversity, yet can be challenging to delimit objectively. This is particularly true of species complexes characterized by high levels of population genetic structure, hybridization between genetic groups, isolation by distance, and limited phenotypic variation. Previous work on the Cumberland Plateau Salamander, Plethodon kentucki, suggested that it might constitute a species complex despite occupying a relatively small geographic range. To examine this hypothesis, we sampled 135 individuals from 43 populations, and used four mitochondrial loci and five nuclear loci (5693 base pairs) to quantify phylogeographic structure and probe for cryptic species diversity. Rates of evolution for each locus were inferred using the multidistribute package, and time calibrated gene trees and species trees were inferred using BEAST 2 and *BEAST 2, respectively. Because the parameter space relevant for species delimitation is large and complex, and all methods make simplifying assumptions that may lead them to fail, we conducted an array of analyses. Our assumption was that strongly supported species would be congruent across methods. Putative species were first delimited using a Bayesian implementation of the GMYC model (bGMYC), Geneland, and Brownie. We then validated these species using the genealogical sorting index and BPP. We found substantial phylogeographic diversity using mtDNA, including four divergent clades and an inferred common ancestor at 14.9 myr (95% HPD: 10.8-19.7 myr). By contrast, this diversity was not corroborated by nuclear sequence data, which exhibited low levels of variation and weak phylogeographic structure. Species trees estimated a far younger root than did the mtDNA data, closer to 1.0 myr old. Mutually exclusive putative species were identified by the different approaches. Possible causes of data set discordance, and the problem of species delimitation in complexes with high levels of population structure and introgressive hybridization, are discussed.
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Affiliation(s)
- Shawn R. Kuchta
- Department of Biological Sciences, Ohio Center for Ecology and Evolutionary Studies, Ohio University, Athens, Ohio, United States of America
| | - Ashley D. Brown
- Department of Biological Sciences, Ohio Center for Ecology and Evolutionary Studies, Ohio University, Athens, Ohio, United States of America
| | - Paul E. Converse
- Department of Biological Sciences, Ohio Center for Ecology and Evolutionary Studies, Ohio University, Athens, Ohio, United States of America
| | - Richard Highton
- Department of Biology, University of Maryland, College Park, Maryland, United States of America
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Reilly SB, Corl A, Wake DB. An integrative approach to phylogeography: investigating the effects of ancient seaways, climate, and historical geology on multi-locus phylogeographic boundaries of the Arboreal Salamander (Aneides lugubris). BMC Evol Biol 2015; 15:241. [PMID: 26537350 PMCID: PMC4632495 DOI: 10.1186/s12862-015-0524-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 10/28/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Phylogeography is an important tool that can be used to reveal cryptic biodiversity and to better understand the processes that promote lineage diversification. We studied the phylogeographic history of the Arboreal Salamander (Aneides lugubris), a wide-ranging species endemic to the California floristic province. We used multi-locus data to reconstruct the evolutionary history of A. lugubris and to discover the geographic location of major genetic breaks within the species. We also used species distribution modeling and comparative phylogeography to better understand the environmental factors that have shaped the genetic history of A. lugubris. RESULTS We found six major mitochondrial clades in A. lugubris. Nuclear loci supported the existence of at least three genetically distinct groups, corresponding to populations north of the San Francisco Bay and in the Sierra Nevada, in the Santa Cruz Mountains, and in the central coast and southern California. All of the genetic breaks in mitochondrial and nuclear loci corresponded to regions where historical barriers to dispersal have been observed in other species. Geologic or water barriers likely were the most important factors restricting gene flow among clades. Climatic unsuitability during glacial maximum may have contributed to the isolation of the mitochondrial clades in the central coast and southern California. A projection of our species distribution model to a future scenario with a moderate amount of climate change suggests that most of the range of A. lugubris will remain climatically suitable, but climatic conditions in the Sierra Nevada and low elevation areas in Southern California are likely to deteriorate. CONCLUSIONS Aneides lugubris contains substantial cryptic genetic diversity as a result of historical isolation of populations. At least two (and perhaps three) evolutionarily significant units in A. lugubris merit protection; all six mitochondrial clades should be considered as management units within the species.
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Affiliation(s)
- Sean B Reilly
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, 3101 Valley Life Sciences Building, Berkeley, CA, 94720-3160, USA.
| | - Ammon Corl
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, 3101 Valley Life Sciences Building, Berkeley, CA, 94720-3160, USA.
| | - David B Wake
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, 3101 Valley Life Sciences Building, Berkeley, CA, 94720-3160, USA.
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24
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Jirapatrasilp P, Prasankok P, Chanabun R, Panha S. Allozyme data reveal genetic diversity and isolation by distance in sympatric Glyphidrilus Horst, 1889 (Oligochaeta: Almidae) of the Lower Mekong River Basin. BIOCHEM SYST ECOL 2015. [DOI: 10.1016/j.bse.2015.05.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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25
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Manthey JD, Moyle RG. Isolation by environment in White-breasted Nuthatches (Sitta carolinensis) of the Madrean Archipelago sky islands: a landscape genomics approach. Mol Ecol 2015; 24:3628-38. [DOI: 10.1111/mec.13258] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 05/29/2015] [Indexed: 12/31/2022]
Affiliation(s)
- Joseph D. Manthey
- Biodiversity Institute and Department of Ecology and Evolutionary Biology; University of Kansas; Lawrence KS 66045 USA
| | - Robert G. Moyle
- Biodiversity Institute and Department of Ecology and Evolutionary Biology; University of Kansas; Lawrence KS 66045 USA
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26
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Rodríguez A, Börner M, Pabijan M, Gehara M, Haddad CFB, Vences M. Genetic divergence in tropical anurans: deeper phylogeographic structure in forest specialists and in topographically complex regions. Evol Ecol 2015. [DOI: 10.1007/s10682-015-9774-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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27
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Discovery of a New, Disjunct Population of a Narrowly Distributed Salamander (Taricha rivularis) in California Presents Conservation Challenges. J HERPETOL 2014. [DOI: 10.1670/13-066] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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28
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Houston DD, Shiozawa DK, Smith BT, Riddle BR. Investigating the effects of Pleistocene events on genetic divergence within Richardsonius balteatus, a widely distributed western North American minnow. BMC Evol Biol 2014; 14:111. [PMID: 24885371 PMCID: PMC4038058 DOI: 10.1186/1471-2148-14-111] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 05/12/2014] [Indexed: 11/29/2022] Open
Abstract
Background Biogeographers seek to understand the influences of global climate shifts and geologic changes to the landscape on the ecology and evolution of organisms. Across both longer and shorter timeframes, the western North American landscape has experienced dynamic transformations related to various geologic processes and climatic oscillations, including events as recently as the Last Glacial Maximum (LGM; ~20 Ka) that have impacted the evolution of the North American biota. Redside shiner is a cyprinid species that is widely distributed throughout western North America. The species’ native range includes several well-documented Pleistocene refugia. Here we use mitochondrial DNA sequence data to assess phylogeography, and to test two biogeographic hypotheses regarding post-glacial colonization by redside shiner: 1) Redside shiner entered the Bonneville Basin at the time of the Bonneville Flood (Late Pleistocene; 14.5 Ka), and 2) redside shiner colonized British Columbia post-glacially from a single refugium in the Upper Columbia River drainage. Results Genetic diversification in redside shiner began in the mid to late Pleistocene, but was not associated with LGM. Different clades of redside shiner were distributed in multiple glacial age refugia, and each clade retains a signature of population expansion, with clades having secondary contact in some areas. Conclusions Divergence times between redside shiner populations in the Bonneville Basin and the Upper Snake/Columbia River drainage precedes the Bonneville Flood, thus it is unlikely that redside shiner invaded the Bonneville Basin during this flooding event. All but one British Columbia population of redside shiner are associated with the Upper Columbia River drainage with the lone exception being a population near the coast, suggesting that the province as a whole was colonized from multiple refugia, but the inland British Columbia redside shiner populations are affiliated with a refugium in the Upper Columbia River drainage.
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Affiliation(s)
- Derek D Houston
- School of Life Sciences, University of Nevada-Las Vegas, Las Vegas, NV 89154-4004, USA.
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de Lafontaine G, Ducousso A, Lefèvre S, Magnanou E, Petit RJ. Stronger spatial genetic structure in recolonized areas than in refugia in the European beech. Mol Ecol 2014; 22:4397-412. [PMID: 23980761 DOI: 10.1111/mec.12403] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Revised: 05/17/2013] [Accepted: 05/21/2013] [Indexed: 11/29/2022]
Abstract
Extant rear-edge populations located in former glacial refugia remain understudied despite their high conservation value. These populations should have experienced strong genetic drift due to their small size and long isolation. Moreover, the prolonged action of isolation by distance in refugial areas should result in stronger regional spatial genetic structure (SGS) than in recolonized areas, but empirical tests of this prediction are scarce. To fill this gap, we first used a set of 16 microsatellite markers to investigate the genetic structure of European beech in France in 65 populations from three refugial areas and one control recolonized (nonrefugial) area. Then, using the same approach, we reanalysed published isozyme data from 375 populations distributed across the entire species range. We found stronger genetic differentiation among populations in refugia than in recolonized areas. However, contrary to expectations, regional SGS was lower within refugia than within recolonized areas. Published studies presenting similar analyses suggest that our results could have generality across different biogeographical settings and types of organisms. Strong and prolonged genetic drift in refugial areas could have erased the signature of range expansions that is still visible in recolonized areas. Our results therefore suggest that Pleistocene population isolation has played a key role in increasing the genetic complexity of extant rear-edge populations.
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Orozco-terWengel P, Andreone F, Louis E, Vences M. Mitochondrial introgressive hybridization following a demographic expansion in the tomato frogs of Madagascar, genusDyscophus. Mol Ecol 2013; 22:6074-90. [DOI: 10.1111/mec.12558] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Revised: 10/06/2013] [Accepted: 10/07/2013] [Indexed: 01/01/2023]
Affiliation(s)
| | - Franco Andreone
- Museo Regionale di Scienze Naturali; Via Giolitti 36 10123 Torino Italy
| | - Edward Louis
- Omaha's Henry Doorly Zoo; 3701 S 10th Street Omaha NE 68107 USA
| | - Miguel Vences
- Division of Evolutionary Biology, Zoological Institute; Technical University of Braunschweig; Mendelssohnstr. 4 38106 Braunschweig Germany
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Genetic Diversity of Black Salamanders (Aneides flavipunctatus) across Watersheds in the Klamath Mountains. DIVERSITY-BASEL 2013. [DOI: 10.3390/d5030657] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Vences M, Hauswaldt JS, Steinfartz S, Rupp O, Goesmann A, Künzel S, Orozco-terWengel P, Vieites DR, Nieto-Roman S, Haas S, Laugsch C, Gehara M, Bruchmann S, Pabijan M, Ludewig AK, Rudert D, Angelini C, Borkin LJ, Crochet PA, Crottini A, Dubois A, Ficetola GF, Galán P, Geniez P, Hachtel M, Jovanovic O, Litvinchuk SN, Lymberakis P, Ohler A, Smirnov NA. Radically different phylogeographies and patterns of genetic variation in two European brown frogs, genus Rana. Mol Phylogenet Evol 2013; 68:657-70. [PMID: 23632031 DOI: 10.1016/j.ympev.2013.04.014] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Revised: 04/10/2013] [Accepted: 04/16/2013] [Indexed: 11/26/2022]
Abstract
We reconstruct range-wide phylogeographies of two widespread and largely co-occurring Western Palearctic frogs, Rana temporaria and R. dalmatina. Based on tissue or saliva samples of over 1000 individuals, we compare a variety of genetic marker systems, including mitochondrial DNA, single-copy protein-coding nuclear genes, microsatellite loci, and single nucleotide polymorphisms (SNPs) of transcriptomes of both species. The two focal species differ radically in their phylogeographic structure, with R. temporaria being strongly variable among and within populations, and R. dalmatina homogeneous across Europe with a single strongly differentiated population in southern Italy. These differences were observed across the various markers studied, including microsatellites and SNP density, but especially in protein-coding nuclear genes where R. dalmatina had extremely low heterozygosity values across its range, including potential refugial areas. On the contrary, R. temporaria had comparably high range-wide values, including many areas of probable postglacial colonization. A phylogeny of R. temporaria based on various concatenated mtDNA genes revealed that two haplotype clades endemic to Iberia form a paraphyletic group at the base of the cladogram, and all other haplotypes form a monophyletic group, in agreement with an Iberian origin of the species. Demographic analysis suggests that R. temporaria and R. dalmatina have genealogies of roughly the same time to coalescence (TMRCA ~3.5 mya for both species), but R. temporaria might have been characterized by larger ancestral and current effective population sizes than R. dalmatina. The high genetic variation in R. temporaria can therefore be explained by its early range expansion out of Iberia, with subsequent cycles of differentiation in cryptic glacial refugial areas followed by admixture, while the range expansion of R. dalmatina into central Europe is a probably more recent event.
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Affiliation(s)
- Miguel Vences
- Zoological Institute, Technische Universität Braunschweig, Mendelssohnstr. 4, 38106 Braunschweig, Germany.
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Lee-Yaw JA, Irwin DE. Large geographic range size reflects a patchwork of divergent lineages in the long-toed salamander (Ambystoma macrodactylum). J Evol Biol 2012; 25:2276-87. [DOI: 10.1111/j.1420-9101.2012.02604.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Revised: 07/24/2012] [Accepted: 07/27/2012] [Indexed: 11/28/2022]
Affiliation(s)
- J. A. Lee-Yaw
- Department of Zoology; University of British Columbia; Vancouver; BC; Canada
| | - D. E. Irwin
- Department of Zoology; University of British Columbia; Vancouver; BC; Canada
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Testing Hypotheses of Pleistocene Population History Using Coalescent Simulations: Refugial Isolation and Secondary Contact in Pseudepidalea raddei (Amphibia: Bufonidae). ASIAN HERPETOL RES 2012. [DOI: 10.3724/sp.j.1245.2012.00103] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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35
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Brown AD, Temple-Miller K, Roosenburg WM, White MM. Mitochondrial DNA Variation in the Ouachita Map Turtle. COPEIA 2012. [DOI: 10.1643/ch-11-009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Abstract
The genetic population structure of many species is characterised by a pattern of isolation by distance (IBD): due to limited dispersal, individuals that are geographically close tend to be genetically more similar than individuals that are far apart. Despite the ubiquity of IBD in nature, many commonly used statistical tests are based on a null model that is completely non-spatial, the Island model. Here, I argue that patterns of spatial autocorrelation deriving from IBD present a problem for such tests as it can severely bias their outcome. I use simulated data to illustrate this problem for two widely used types of tests: tests of hierarchical population structure and the detection of loci under selection. My results show that for both types of tests the presence of IBD can indeed lead to a large number of false positives. I therefore argue that all analyses in a study should take the spatial dependence in the data into account, unless it can be shown that there is no spatial autocorrelation in the allele frequency distribution that is under investigation. Thus, it is urgent to develop additional statistical approaches that are based on a spatially explicit null model instead of the non-spatial Island model.
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Affiliation(s)
- Patrick G Meirmans
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, P.O. Box 94248, 1090GE Amsterdam, The Netherlands.
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37
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Genetic diversity and differentiation of Sinocalycanthus chinensis populations revealed by chloroplast microsatellite (cpSSRs) markers. BIOCHEM SYST ECOL 2012. [DOI: 10.1016/j.bse.2011.12.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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38
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Pelletier TA, Duffield DA, DeGrauw EA. Rangewide Phylogeography of the Western Red-Backed Salamander (Plethodon vehiculum). ACTA ACUST UNITED AC 2011. [DOI: 10.1898/10-23.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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39
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Li T, Zhang M, Qu Y, Ren Z, Zhang J, Guo Y, Heong KL, Villareal B, Zhong Y, Ma E. Population genetic structure and phylogeographical pattern of rice grasshopper, Oxya hyla intricata, across Southeast Asia. Genetica 2011; 139:511-24. [PMID: 21505761 DOI: 10.1007/s10709-011-9573-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2010] [Accepted: 04/02/2011] [Indexed: 11/28/2022]
Abstract
The rice grasshopper, Oxya hyla intricata, is a rice pest in Southeast Asia. In this study, population genetic diversity and structure of this Oxya species was examined using both DNA sequences and AFLP technology. The samples of 12 populations were collected from four Southeast Asian countries, among which 175 individuals were analysed using mitochondrial DNA cytochrome c oxidase subunit I (COI) sequences, and 232 individuals were examined using amplified fragment length polymorphisms (AFLP) to test whether the phylogeographical pattern and population genetics of this species are related to past geological events and/or climatic oscillations. No obvious trend of genetic diversity was found along a latitude/longitude gradient among different geographical groups. Phylogenetic analysis indicated three deep monophyletic clades that approximately correspond to three geographical regions separated by high mountains and a deep strait, and TCS analysis also revealed three disconnected networks, suggesting that spatial and temporal separations by vicariance, which were also supported by AMOVA as a source of the molecular variance presented among groups. Gene flow analysis showed that there had been frequent historical gene flow among local populations in different regions, but the networks exhibited no shared haplotype among populations. In conclusion, the past geological events and climatic fluctuations are the most important factor on the phylogeographical structure and genetic patterns of O. hyla intricata in Southeast Asia. Habitat, vegetation, and anthropogenic effect may also contribute to gene flow and introgression of this species. Moreover, temperature, abundant rainfall and a diversity of graminaceous species are beneficial for the migration of O. hyla intricata. High haplotype diversity, deep phylogenetic division, negative Fu's F (s) values and unimodal and multimodal distribution shapes all suggest a complicated demographic expansion pattern of these O. hyla intricata populations, which might have been caused by climatic oscillations during glacial periods in the Quaternary.
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Affiliation(s)
- Tao Li
- Institute of Applied Biology, Shanxi University, 030006 Taiyuan, Shanxi, China
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40
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RISSLER LESLIEJ, SMITH WALTERH. Mapping amphibian contact zones and phylogeographical break hotspots across the United States. Mol Ecol 2010; 19:5404-16. [DOI: 10.1111/j.1365-294x.2010.04879.x] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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41
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SHAFER AARONBA, CULLINGHAM CATHERINEI, CÔTÉ STEEVED, COLTMAN DAVIDW. Of glaciers and refugia: a decade of study sheds new light on the phylogeography of northwestern North America. Mol Ecol 2010; 19:4589-621. [PMID: 20849561 DOI: 10.1111/j.1365-294x.2010.04828.x] [Citation(s) in RCA: 261] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- AARON B. A. SHAFER
- Department of Biological Sciences, CW 405 Biological Sciences Building, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - CATHERINE I. CULLINGHAM
- Department of Biological Sciences, CW 405 Biological Sciences Building, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - STEEVE D. CÔTÉ
- Département de Biologie and Centre for Northern Studies, Université Laval, Québec, Québec G1V 0A6, Canada
| | - DAVID W. COLTMAN
- Department of Biological Sciences, CW 405 Biological Sciences Building, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
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42
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Reconstruction of the climate envelopes of salamanders and their evolution through time. Proc Natl Acad Sci U S A 2009; 106 Suppl 2:19715-22. [PMID: 19887643 DOI: 10.1073/pnas.0902956106] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ecological niches evolve through time, but at different rates and to different degrees. An integrated approach using diverse databases, methods, and analytical tools is used to estimate climate envelopes for species of salamanders (family Salamandridae). These species, which range widely across the Holarctic and have a rich and long fossil record, are used to probe the evolutionary dynamics of niches studied in a phylogenetic context through time and across space. Climate data and statistical methods are used to estimate niche dimensions related to precipitation and temperature, in both a phylogenetic and ecogeographic context. Using phylogenetic methods, climate envelopes are estimated for segments of a time-calibrated phylogenetic tree of salamandrids, to explore how far back in time it is reasonable to make such estimates. Our research strategy illuminates some of the challenges and limitations of the available data and methods and identifies potential solutions, such as the need for physiological and behavioral data that may help to better define species' niches or the development of novel evolutionary models that account for paleoclimatic data. We explore and analyze limits to the application of currently available methodologies. Organisms known to have evolved slowly and conservatively, and which are ectotherms and likely to be profoundly affected by climatic variables, may be the most useful for studies of this kind.
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Goebel AM, Ranker TA, Corn PS, Olmstead RG. Mitochondrial DNA evolution in the Anaxyrus boreas species group. Mol Phylogenet Evol 2009; 50:209-25. [DOI: 10.1016/j.ympev.2008.06.019] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2007] [Revised: 06/10/2008] [Accepted: 06/24/2008] [Indexed: 11/27/2022]
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44
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Kuchta SR, Parks DS, Wake DB. Pronounced phylogeographic structure on a small spatial scale: Geomorphological evolution and lineage history in the salamander ring species Ensatina eschscholtzii in central coastal California. Mol Phylogenet Evol 2009; 50:240-55. [DOI: 10.1016/j.ympev.2008.10.019] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2008] [Revised: 10/05/2008] [Accepted: 10/27/2008] [Indexed: 10/21/2022]
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Hanifin CT, Brodie ED, Brodie ED. Phenotypic mismatches reveal escape from arms-race coevolution. PLoS Biol 2008; 6:e60. [PMID: 18336073 PMCID: PMC2265764 DOI: 10.1371/journal.pbio.0060060] [Citation(s) in RCA: 144] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2007] [Accepted: 01/24/2008] [Indexed: 11/18/2022] Open
Abstract
Because coevolution takes place across a broad scale of time and space, it is virtually impossible to understand its dynamics and trajectories by studying a single pair of interacting populations at one time. Comparing populations across a range of an interaction, especially for long-lived species, can provide insight into these features of coevolution by sampling across a diverse set of conditions and histories. We used measures of prey traits (tetrodotoxin toxicity in newts) and predator traits (tetrodotoxin resistance of snakes) to assess the degree of phenotypic mismatch across the range of their coevolutionary interaction. Geographic patterns of phenotypic exaggeration were similar in prey and predators, with most phenotypically elevated localities occurring along the central Oregon coast and central California. Contrary to expectations, however, these areas of elevated traits did not coincide with the most intense coevolutionary selection. Measures of functional trait mismatch revealed that over one-third of sampled localities were so mismatched that reciprocal selection could not occur given current trait distributions. Estimates of current locality-specific interaction selection gradients confirmed this interpretation. In every case of mismatch, predators were “ahead” of prey in the arms race; the converse escape of prey was never observed. The emergent pattern suggests a dynamic in which interacting species experience reciprocal selection that drives arms-race escalation of both prey and predator phenotypes at a subset of localities across the interaction. This coadaptation proceeds until the evolution of extreme phenotypes by predators, through genes of large effect, allows snakes to, at least temporarily, escape the arms race. Arms races between natural enemies can lead to the rapid evolution of extreme traits, high degrees of specialization, and the formation of new species. They also serve as the ecological model for the evolution of drug resistance by diseases and for host–pathogen interactions in general. Revealing who wins these arms races and how they do so is critical to our understanding of these processes. Capitalizing on the geographic mosaic of species interactions, we examined the dynamics of the arms race between snakes and their toxic newt prey. Garter snakes in some populations have evolved dramatic resistance to the tetrodotoxin defense of the their local prey. By evaluating the pattern of mismatches between toxicity and resistance, we discovered that predators sometimes escape the arms race through the evolution of extreme resistance, but that prey never come out ahead. The reason for this one-sided outcome appears to depend on the molecular genetic basis of resistance in snakes, wherein changes to a single amino acid residue can confer huge differences in resistance. Who wins in the arms race between predators and prey? In the interaction between snakes and toxic newts, predators sometimes escape the arms race through the evolution of extreme resistance, but prey never come out ahead.
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Affiliation(s)
- Charles T Hanifin
- Department of Biology, Utah State University, Logan, Utah, United States of America.
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46
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RICH KATHERINEA, THOMPSON JOHNN, FERNANDEZ CATHERINEC. Diverse historical processes shape deep phylogeographical divergence in the pollinating seed parasite Greya politella. Mol Ecol 2008; 17:2430-48. [DOI: 10.1111/j.1365-294x.2008.03754.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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47
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Hubert N, Duponchelle F, Nuñez J, Rivera R, Bonhomme F, Renno JF. Isolation by distance and Pleistocene expansion of the lowland populations of the white piranha Serrasalmus rhombeus. Mol Ecol 2008; 16:2488-503. [PMID: 17561908 DOI: 10.1111/j.1365-294x.2007.03338.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The genetic variability and distribution of Amazonian fish species have likely been influenced by major disturbance events in recent geological times. Alternatively, the great diversity of aquatic habitat in the Amazon is likely to shape ongoing gene flow and genetic diversity. In this context, complex patterns of genetic structure originating from a joint influence of historical and contemporary gene flow are to be expected. We explored the relative influence of Pleistocene climatic fluctuations and current water chemistry on the genetic structure of a piranha, Serrasalmus rhombeus, in the Upper Amazon by the simultaneous analysis of intron length polymorphism and mitochondrial DNA sequences. The Madeira river is well suited for that purpose as it is characterized by a great diversity of water types, the presence of one of the largest floodplain of the Amazon and the potential occurrence of two Pleistocene refuges. We found evidence of genetic structure even at a small geographical scale (less than 10 km), indicating that the floodplain is not a homogenizing factor promoting interdrainage dispersal in S. rhombeus. Likewise, the hierarchical genetic structure inferred was correlated to geographical distance instead of habitat characteristic. Our results also support the hypothesis that the area underwent population expansion during the last 800,000 years. In addition, a higher level of genetic diversity was found in the samples from the putative Aripuanã refuge. The present findings suggest that Pleistocene refuges contributed significantly to the colonization of the lowlands in the Upper Amazon valley during the Pleistocene.
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Affiliation(s)
- Nicolas Hubert
- U.R. 175 Institut de Recherche pour le Développement (IRD), GAMET, BP 5095, 361 rue JF Breton, 34196 Montpellier Cedex 05, France. myloplus.excite.com
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48
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Martínez-Solano I, Jockusch EL, Wake DB. Extreme population subdivision throughout a continuous range: phylogeography of Batrachoseps attenuatus (Caudata: Plethodontidae) in western North America. Mol Ecol 2007; 16:4335-55. [PMID: 17868287 DOI: 10.1111/j.1365-294x.2007.03527.x] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Low-vagility species with deep evolutionary histories are key to our understanding of the biogeographical history of geologically complex areas, such as the west coast of North America. We present a detailed study of the phylogeography of the salamander Batrachoseps attenuatus (Caudata: Plethodontidae) using sequences of the mitochondrial gene cob from 178 individuals sampled from throughout the species' range. Sequences of three other mitochondrial genes (16S, cox1, nad4) and a nuclear gene (RAG-1) were used to investigate the deeper evolutionary history of the species. We found high levels of genetic diversity and deep divergences within a mostly continuous distribution, with five genetically well-differentiated and geographically structured mitochondrial DNA clades. Significant association between geographical and genetic distances within these clades suggests demographic stability, whereas Fu's FS tests suggest demographic expansions in three of them. Mantel tests identify two biogeographical barriers, the San Andreas Fault and the Sacramento-San Joaquin Delta, as important in the diversification of lineages. The timing of the main splitting events between intraspecific lineages was estimated by applying relaxed molecular clock methods combining several mutation rates and a fossil calibration. The earliest splitting events are old (Pliocene/Miocene), with more recent (Pleistocene) subdivisions in some clades. Disjunct populations distributed along the western foothills of the Sierra Nevada colonized this area relatively recently from a single refugium east of San Francisco Bay. The combination of fine-scale, comprehensive sampling with phylogenetic, historical demographic and hypothesis-based tests allowed delineation of a complex biogeographical scenario with general implications for the study of codistributed taxa.
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Affiliation(s)
- Iñigo Martínez-Solano
- Museum of Vertebrate Zoology, University of California, Berkeley, 3101 VLSB, Berkeley, California 94720, USA.
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49
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Kuchta SR. CONTACT ZONES AND SPECIES LIMITS: HYBRIDIZATION BETWEEN LINEAGES OF THE CALIFORNIA NEWT, TARICHA TOROSA, IN THE SOUTHERN SIERRA NEVADA. HERPETOLOGICA 2007. [DOI: 10.1655/0018-0831(2007)63[332:czaslh]2.0.co;2] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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50
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Vredenburg VT, Bingham R, Knapp R, Morgan JAT, Moritz C, Wake D. Concordant molecular and phenotypic data delineate new taxonomy and conservation priorities for the endangered mountain yellow-legged frog. J Zool (1987) 2007. [DOI: 10.1111/j.1469-7998.2006.00258.x] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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