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Hu P, Lu L, Hu S, Da W, Huang CL, Zhang H, Wang D, Zhang Y, Xu Y, Wang R. Differentiation of the Chestnut Tiger Butterfly Parantica sita (Lepidoptera: Nymphalidae: Danainae) in China. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.846499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The chestnut tiger butterfly, Parantica sita (Kollar) (Lepidoptera: Nymphalidae: Danainae), occurs in Asia, along the Himalayas, and into the Malayan region. Previous studies found three types of mitogenomes with substantial genetic divergence in samples from China. To clarify the level of differentiation within P. sita, we investigated both molecular data and morphological features in 429 individuals from China. Upon examination, mitochondrial cytochrome oxidase subunit I (COI) sequences showed three substantially diverged haplotype groups. Based on microsatellite genotypes, the samples divided into three clusters that were consistent with the COI haplotype groups. With that genetic data, we named three distinguishable P. sita lineages: PS-A, PS-B, and PS-C. We also found obvious morphological differences in wing color, male sex brand, and genitalia structures among the three lineages. According to the published structure of male genitalia, that of PS-A is identical to that of P. s. sita, and that of PS-B is identical to that of P. pedonga. Based on all the results, we tentatively propose dividing P. sita into three species: PS-A (the former P. s. sita) is the typical Parantica sita [Kollar, (1844)], mainly distributed in southwestern China; PS-C (the former P. s. niphonica) is elevated to full species as Parantica niphonica (Moore, 1883), distributed in Taiwan Island and Japan; and PS-B will be Parantica pedongaFujioka, 1970, mainly distributed in Tibet and western Sichuan. Divergence time estimates showed that PS-A separated from the PS-B + PS-C clade about 8.79 million years ago (Ma), when the Hengduan Mountains underwent an appreciable elevation increase, isolating the Tibet population from the others. PS-B and PS-C diverged about 4.87 Ma, in accord with the formation of Taiwan Island mountains. The founder effect may explain why PS-C’s genetic diversity is lower than that of the other clades.
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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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Rankin AM, Anderson FE, Clutts SA, Espíndola A, Carstens BC, Lucid M, Sullivan J. Comparative phylogeography of two Northern Rocky Mountain endemics: the widespread Anguispira kochi occidentalis and the narrow-range Anguispira nimapuna (Gastropoda: Discidae). Biol J Linn Soc Lond 2021; 133:817-834. [PMID: 34220190 DOI: 10.1093/biolinnean/blab030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 02/08/2021] [Accepted: 02/12/2021] [Indexed: 11/14/2022]
Abstract
The Northern Rocky Mountain ecosystem supports rich biological diversity with many endemic and rare species. Extant endemics display two biogeographic patterns: widespread species with fragmented populations, and narrow-range endemics. These distributions are shown by the congeneric snails Anguispira kochi occidentalis and Anguispira nimapuna. These two taxa are disjunct from the remaining species of the genus, which achieves its greatest diversity in eastern North America. Given the disjunct nature of A. k. occidentalis and A. nimapuna, we here present a mtDNA phylogeny of the genus that includes both eastern and western species to assess the phylogenetic position of A. k. occidentalis and A. nimapuna. We then reconstruct the demographic history of A. k. occidentalis and A. nimapuna by analysing current patterns of genetic variation and interpreting the results considering the historical biogeography of the region. Both A. k. occidentalis and A. nimapuna represent unique taxa that are genetically and geographically distinct from their congeners. The current distribution and genetic structure of A. k. occidentalis has been shaped by both historical isolation in refugia and more recent northward shifts, whereas A. nimapuna is represented by two populations with shallow divergence in an area of long-term habitat stability.
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Affiliation(s)
- Andrew M Rankin
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA.,Institute for Bioinformatics and Evolutionary Studies (IBEST), Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA
| | - Frank E Anderson
- School of Biological Sciences, Southern Illinois University, Carbondale, IL 62901, USA
| | - Stephanie A Clutts
- School of Biological Sciences, Southern Illinois University, Carbondale, IL 62901, USA
| | - Anahí Espíndola
- Department of Entomology, University of Maryland, College Park, 4291 Fieldhouse Drive, 3138 Plant Sciences Building, College Park, MD 20742-4454, USA
| | - Bryan C Carstens
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH 43210, USA
| | | | - Jack Sullivan
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA.,Institute for Bioinformatics and Evolutionary Studies (IBEST), Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA
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Rankin AM, Wilke T, Lucid M, Leonard W, Espíndola A, Smith ML, Carstens BC, Sullivan J. Complex interplay of ancient vicariance and recent patterns of geographical speciation in north-western North American temperate rainforests explains the phylogeny of jumping slugs (Hemphillia spp.). Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz040] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
AbstractThe history of the currently disjunct temperate rainforests of the Pacific Northwest of North America has shaped the evolution and diversity of endemics. This study focuses on how geological and climatic perturbations have driven speciation in the area by isolating lineages. We investigated the phylogenetic relationships and historical biogeography of the endemic jumping slugs (genus Hemphillia) using a multi-locus phylogeny. We evaluated the spatial distribution and divergence times of major lineages, generated ancestral area probabilities and inferred the biogeographical history of the genus. Our study revealed eight genetic lineages that formed three clades: one clade consisting of two Coast/Cascade lineages, and two reciprocally monophyletic clades that each contain a Coast/Cascade and two Rocky Mountains taxa. The results of the biogeographical analysis suggest that the ancestral range of the genus occupied Coast/Cascade habitats and then spread across into Northern Rocky Mountain interior habitats with subsequent fragmentations isolating coastal and inland lineages. Finally, there have been more recent speciation events among three lineage pairs that have shaped shallow structures of all clades. We add to our knowledge of the biogeographical history of the region in that we discovered diversification and speciation events that have occurred in ways more complex than previously thought.
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Affiliation(s)
- Andrew M Rankin
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA
- Institute for Bioinformatics and Evolutionary Studies (IBEST), Biological Sciences, University of Idaho, Moscow, ID, USA
| | - Thomas Wilke
- Animal Ecology and Systematics, Justus Liebig University, Heinrich-Buff-Ring (IFZ), Giessen, Germany
| | - Michael Lucid
- Idaho Department of Fish and Game, Coeur d’Alene, ID, USA
| | | | - Anahí Espíndola
- Department of Entomology, University of Maryland, College Park, MD, USA
| | - Megan L Smith
- Department of Evolution, Ecology, & Organismal Biology, The Ohio State University, Columbus, OH, USA
| | - Bryan C Carstens
- Department of Evolution, Ecology, & Organismal Biology, The Ohio State University, Columbus, OH, USA
| | - Jack Sullivan
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA
- Institute for Bioinformatics and Evolutionary Studies (IBEST), Biological Sciences, University of Idaho, Moscow, ID, USA
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5
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Phylogeography of Atlantic Forest glassfrogs (Vitreorana): when geography, climate dynamics and rivers matter. Heredity (Edinb) 2018; 122:545-557. [PMID: 30356224 DOI: 10.1038/s41437-018-0155-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 09/10/2018] [Accepted: 09/25/2018] [Indexed: 11/08/2022] Open
Abstract
Recent advances in the field of landscape genetics provide ways to jointly analyze the role of present-day climate and landscape configuration in current biodiversity patterns. Expanding this framework into a phylogeographic study, we incorporate information on historical climatic shifts, tied to descriptions of the local topography and river configuration, to explore the processes that underlie genetic diversity patterns in the Atlantic Forest hotspot. We study two montane, stream-associated species of glassfrogs: Vitreorana eurygnatha and V. uranoscopa. By integrating species distribution modeling with geographic information systems and molecular data, we find that regional patterns of molecular diversity are jointly explained by geographic distance, historical (last 120 ky) climatic stability, and (in one species) river configuration. Mitochondrial DNA genealogies recover significant regional structure in both species, matching previous classifications of the northern and southern forests in the Atlantic Forest, and are consistent with patterns reported in other taxa. Yet, these spatial patterns of genetic diversity are only partially supported by nuclear data. Contrary to data from lowland taxa, historical climate projections suggest that these montane species were able to persist in the southern Atlantic Forest during glacial periods, particularly during the Last Glacial Maximum. These results support generally differential responses to climatic cycling by northern (lowland) and southern (montane) Atlantic Forest species, triggered by the joint impact of regional landscape configuration and climate change.
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Smith ML, Ruffley M, Rankin AM, Espíndola A, Tank DC, Sullivan J, Carstens BC. Testing for the presence of cryptic diversity in tail-dropper slugs (Prophysaon) using molecular data. Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/bly067] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Megan L Smith
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Aronoff Labs, Columbus, OH, USA
| | - Megan Ruffley
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA
- Institute for Bioinformatics and Evolutionary Studies (IBEST), Biological Sciences, University of Idaho, Moscow, ID, USA
| | - Andrew M Rankin
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA
- Institute for Bioinformatics and Evolutionary Studies (IBEST), Biological Sciences, University of Idaho, Moscow, ID, USA
| | - Anahí Espíndola
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA
- Institute for Bioinformatics and Evolutionary Studies (IBEST), Biological Sciences, University of Idaho, Moscow, ID, USA
| | - David C Tank
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA
- Institute for Bioinformatics and Evolutionary Studies (IBEST), Biological Sciences, University of Idaho, Moscow, ID, USA
| | - Jack Sullivan
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA
- Institute for Bioinformatics and Evolutionary Studies (IBEST), Biological Sciences, University of Idaho, Moscow, ID, USA
| | - Bryan C Carstens
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Aronoff Labs, Columbus, OH, USA
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Lait LA, Hebert PDN. Phylogeographic structure in three North American tent caterpillar species (Lepidoptera: Lasiocampidae): Malacosoma americana, M. californica, and M. disstria. PeerJ 2018; 6:e4479. [PMID: 29576956 PMCID: PMC5863710 DOI: 10.7717/peerj.4479] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Accepted: 02/19/2018] [Indexed: 11/23/2022] Open
Abstract
While phylogeographic structure has been examined in many North American vertebrate species, insects have received much less attention despite their central ecological roles. The moth genus Malacosoma (Hübner, 1820), is an important group of forestry pests responsible for large-scale defoliation across much of the Nearctic and Palearctic. The present study uses sequence variation in the mitochondrial cytochrome c oxidase 1 (COI) gene to examine the population genetic structure of the three widespread Malacosoma species (M. americana, M. californica, and M. disstria). Populations of all three species showed highest diversity in the south, suggesting that modern populations derived from southern refugia with loss of variation as these lineages dispersed northwards. However, despite similar life histories and dispersal abilities, the extent of regional variation varied among the taxa. M. americana, a species restricted to eastern North America, showed much less genetic structure than the western M. californica or the widespread M. disstria. The regional differentiation in the latter reflects the likely derivation of modern lineages from several refugia, as well as taxonomic uncertainty in M. californica. In these respects, the three species of Malacosoma share phylogeographic patterns similar to those detected in vertebrates which are characterised by greater phylogeographic breaks in the western half of the continent and limited structure in the east.
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Affiliation(s)
- Linda A Lait
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Paul D N Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
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Ruffley M, Smith ML, Espíndola A, Carstens BC, Sullivan J, Tank DC. Combining allele frequency and tree-based approaches improves phylogeographic inference from natural history collections. Mol Ecol 2018; 27:1012-1024. [PMID: 29334417 PMCID: PMC5878120 DOI: 10.1111/mec.14491] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 12/07/2017] [Accepted: 12/08/2017] [Indexed: 01/25/2023]
Abstract
Model selection approaches in phylogeography have allowed researchers to evaluate the support for competing demographic histories, which provides a mode of inference and a measure of uncertainty in understanding climatic and spatial influences on intraspecific diversity. Here, to rank all models in the comparison set and determine what proportion of the total support the top-ranked model garners, we conduct model selection using two analytical approaches-allele frequency-based, implemented in fastsimcoal2, and gene tree-based, implemented in phrapl. We then expand this model selection framework by including an assessment of absolute fit of the models to the data. For this, we utilize DNA isolated from existing natural history collections that span the distribution of red alder (Alnus rubra) in the Pacific Northwest of North America to generate genomic data for the evaluation of 13 demographic scenarios. The quality of DNA recovered from herbarium specimen leaf tissue was assessed for its utility and effectiveness in demographic model selection, specifically in the two approaches mentioned. We present strong support for the use of herbarium tissue in the generation of genomic DNA, albeit with the inclusion of additional quality control checks prior to library preparation and analyses with multiple approaches that incorporate various data. Analyses with allele frequency spectra and gene trees predominantly support A. rubra having experienced an ancient vicariance event with intermittent and frequent gene flow between the disjunct populations. Additionally, the data consistently fit the most frequently selected model, corroborating the model selection techniques. Finally, these results suggest that the A. rubra disjunct populations do not represent separate species.
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Affiliation(s)
- Megan Ruffley
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA
- Institute for Bioinformatics and Evolutionary Studies (IBEST), Biological Sciences, Moscow, ID, USA
- Stillinger Herbarium, University of Idaho, Moscow, ID, USA
| | - Megan L Smith
- Department of Evolution, Ecology, & Organismal Biology, The Ohio State University, Columbus, OH, USA
| | - Anahí Espíndola
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA
- Institute for Bioinformatics and Evolutionary Studies (IBEST), Biological Sciences, Moscow, ID, USA
| | - Bryan C Carstens
- Department of Evolution, Ecology, & Organismal Biology, The Ohio State University, Columbus, OH, USA
| | - Jack Sullivan
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA
- Institute for Bioinformatics and Evolutionary Studies (IBEST), Biological Sciences, Moscow, ID, USA
| | - David C Tank
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA
- Institute for Bioinformatics and Evolutionary Studies (IBEST), Biological Sciences, Moscow, ID, USA
- Stillinger Herbarium, University of Idaho, Moscow, ID, USA
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Espíndola A, Ruffley M, Smith ML, Carstens BC, Tank DC, Sullivan J. Identifying cryptic diversity with predictive phylogeography. Proc Biol Sci 2017; 283:rspb.2016.1529. [PMID: 27798300 DOI: 10.1098/rspb.2016.1529] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 09/27/2016] [Indexed: 01/14/2023] Open
Abstract
Identifying units of biological diversity is a major goal of organismal biology. An increasing literature has focused on the importance of cryptic diversity, defined as the presence of deeply diverged lineages within a single species. While most discoveries of cryptic lineages proceed on a taxon-by-taxon basis, rapid assessments of biodiversity are needed to inform conservation policy and decision-making. Here, we introduce a predictive framework for phylogeography that allows rapidly identifying cryptic diversity. Our approach proceeds by collecting environmental, taxonomic and genetic data from codistributed taxa with known phylogeographic histories. We define these taxa as a reference set, and categorize them as either harbouring or lacking cryptic diversity. We then build a random forest classifier that allows us to predict which other taxa endemic to the same biome are likely to contain cryptic diversity. We apply this framework to data from two sets of disjunct ecosystems known to harbour taxa with cryptic diversity: the mesic temperate forests of the Pacific Northwest of North America and the arid lands of Southwestern North America. The predictive approach presented here is accurate, with prediction accuracies placed between 65% and 98.79% depending of the ecosystem. This seems to indicate that our method can be successfully used to address ecosystem-level questions about cryptic diversity. Further, our application for the prediction of the cryptic/non-cryptic nature of unknown species is easily applicable and provides results that agree with recent discoveries from those systems. Our results demonstrate that the transition of phylogeography from a descriptive to a predictive discipline is possible and effective.
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Affiliation(s)
- Anahí Espíndola
- Department of Biological Sciences, University of Idaho, 875 Perimeter Drive MS 3051, Moscow, ID 83844-3051, USA .,Biological Sciences, Institute for Bioinformatics and Evolutionary Studies (IBEST), 875 Perimeter Drive MS 3051, Moscow, ID 83844-3051, USA
| | - Megan Ruffley
- Department of Biological Sciences, University of Idaho, 875 Perimeter Drive MS 3051, Moscow, ID 83844-3051, USA.,Biological Sciences, Institute for Bioinformatics and Evolutionary Studies (IBEST), 875 Perimeter Drive MS 3051, Moscow, ID 83844-3051, USA
| | - Megan L Smith
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, 318 W. 12th Avenue, 300 Aronoff Labs, Columbus, OH 43210-1293, USA
| | - Bryan C Carstens
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, 318 W. 12th Avenue, 300 Aronoff Labs, Columbus, OH 43210-1293, USA
| | - David C Tank
- Department of Biological Sciences, University of Idaho, 875 Perimeter Drive MS 3051, Moscow, ID 83844-3051, USA.,Biological Sciences, Institute for Bioinformatics and Evolutionary Studies (IBEST), 875 Perimeter Drive MS 3051, Moscow, ID 83844-3051, USA
| | - Jack Sullivan
- Department of Biological Sciences, University of Idaho, 875 Perimeter Drive MS 3051, Moscow, ID 83844-3051, USA.,Biological Sciences, Institute for Bioinformatics and Evolutionary Studies (IBEST), 875 Perimeter Drive MS 3051, Moscow, ID 83844-3051, USA
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Smith ML, Noonan BP, Colston TJ. The role of climatic and geological events in generating diversity in Ethiopian grass frogs (genus Ptychadena). ROYAL SOCIETY OPEN SCIENCE 2017; 4:170021. [PMID: 28878964 PMCID: PMC5579079 DOI: 10.1098/rsos.170021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Accepted: 07/24/2017] [Indexed: 06/07/2023]
Abstract
Ethiopia is a world biodiversity hotspot and harbours levels of biotic endemism unmatched in the Horn of Africa, largely due to topographic-and thus habitat-complexity, which results from a very active geological and climatic history. Among Ethiopian vertebrate fauna, amphibians harbour the highest levels of endemism, making amphibians a compelling system for the exploration of the impacts of Ethiopia's complex abiotic history on biotic diversification. Grass frogs of the genus Ptychadena are notably diverse in Ethiopia, where they have undergone an evolutionary radiation. We used molecular data and expanded taxon sampling to test for cryptic diversity and to explore diversification patterns in both the highland radiation and two widespread lowland Ptychadena. Species delimitation results support the presence of nine highland species and four lowland species in our dataset, and divergence dating suggests that both geologic events and climatic fluctuations played a complex and confounded role in the diversification of Ptychadena in Ethiopia. We rectify the taxonomy of the endemic P. neumanni species complex, elevating one formally synonymized name and describing three novel taxa. Finally, we describe two novel lowland Ptychadena species that occur in Ethiopia and may be more broadly distributed.
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Affiliation(s)
- Megan L. Smith
- Department of Biology, University of Mississippi, 108 Shoemaker Hall, University, MS 38677, USA
| | - Brice P. Noonan
- Department of Biology, University of Mississippi, 108 Shoemaker Hall, University, MS 38677, USA
| | - Timothy J. Colston
- Department of Biology, University of Mississippi, 108 Shoemaker Hall, University, MS 38677, USA
- Zoological Natural History Museum, Addis Ababa University, Arat Kilo, Addis Ababa, Ethiopia
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Do dams also stop frogs? Assessing population connectivity of coastal tailed frogs (Ascaphus truei) in the North Cascades National Park Service Complex. CONSERV GENET 2017. [DOI: 10.1007/s10592-016-0919-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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12
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Bryson RW, Savary WE, Zellmer AJ, Bury RB, McCormack JE. Genomic data reveal ancient microendemism in forest scorpions across the California Floristic Province. Mol Ecol 2016; 25:3731-51. [DOI: 10.1111/mec.13707] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 05/03/2016] [Indexed: 01/16/2023]
Affiliation(s)
- Robert W. Bryson
- Department of Biology and Burke Museum of Natural History and Culture; University of Washington; Box 351800 Seattle WA 98195-1800 USA
| | - Warren E. Savary
- Department of Entomology; California Academy of Sciences; 55 Music Concourse Drive, Golden Gate Park San Francisco CA 94118 USA
| | - Amanda J. Zellmer
- Department of Biology; Occidental College; 1600 Campus Road Los Angeles CA 90041 USA
| | | | - John E. McCormack
- Department of Biology; Occidental College; 1600 Campus Road Los Angeles CA 90041 USA
- Moore Laboratory of Zoology; Occidental College; 1600 Campus Road Los Angeles CA 90041 USA
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13
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Metzger G, Espindola A, Waits LP, Sullivan J. Genetic Structure across Broad Spatial and Temporal Scales: Rocky Mountain Tailed Frogs (Ascaphus montanus; Anura: Ascaphidae) in the Inland Temperate Rainforest. J Hered 2015; 106:700-10. [PMID: 26285914 DOI: 10.1093/jhered/esv061] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 07/24/2015] [Indexed: 11/13/2022] Open
Abstract
Contemporary and historical processes interact to structure genetic variation, however discerning between these can be difficult. Here, we analyze range-wide variation at 13 microsatellite loci in 2098 Rocky Mountain tailed frogs, Ascaphus montanus, collected from 117 streams across the species distribution in the Inland Northwest (INW) and interpret that variation in light of historical phylogeography, contemporary landscape genetics, and the reconstructed paleodistribution of the species. Further, we project species distribution models (SDMs) to predict future changes in the range as a function of changing climate. Genetic structure has a strong spatial signature that is precisely congruent with a deep (~1.8 MY) phylogeographic split in mtDNA when we partition populations into 2 clusters (K = 2), and is congruent with refugia areas inferred from our paleorange reconstructions. There is a hierarchical pattern of geographic structure as we permit additional clusters, with populations clustering following mountain ranges. Nevertheless, genetic diversity is the highest in populations at the center of the range and is attenuated in populations closer to the range edges. Similarly, geographic distance is the single best predictor of pairwise genetic differentiation, but connectivity also is an important predictor. At intermediate and local geographic scales, deviations from isolation-by-distance are more apparent, at least in the northern portion of the distribution. These results indicate that both historical and landscape factors are contributing to the genetic structure and diversity of tailed frogs in the Inland Northwest.
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Affiliation(s)
- Genevieve Metzger
- From the Department of Biological Sciences, University of Idaho, Moscow, ID 84844-3051 (Metzger, Espindola, and Sullivan); Center for Research on Invasive Species and Small Populations, University of Idaho, Moscow, ID (Waits and Sullivan); Program in Bioinformatics and Computational Biology, University of Idaho, Moscow, ID (Metzger and Sullivan); and Department of Fish and Wildlife Sciences, University of Idaho, Moscow ID 83844-1136 (Waits)
| | - Anahi Espindola
- From the Department of Biological Sciences, University of Idaho, Moscow, ID 84844-3051 (Metzger, Espindola, and Sullivan); Center for Research on Invasive Species and Small Populations, University of Idaho, Moscow, ID (Waits and Sullivan); Program in Bioinformatics and Computational Biology, University of Idaho, Moscow, ID (Metzger and Sullivan); and Department of Fish and Wildlife Sciences, University of Idaho, Moscow ID 83844-1136 (Waits)
| | - Lisette P Waits
- From the Department of Biological Sciences, University of Idaho, Moscow, ID 84844-3051 (Metzger, Espindola, and Sullivan); Center for Research on Invasive Species and Small Populations, University of Idaho, Moscow, ID (Waits and Sullivan); Program in Bioinformatics and Computational Biology, University of Idaho, Moscow, ID (Metzger and Sullivan); and Department of Fish and Wildlife Sciences, University of Idaho, Moscow ID 83844-1136 (Waits)
| | - Jack Sullivan
- From the Department of Biological Sciences, University of Idaho, Moscow, ID 84844-3051 (Metzger, Espindola, and Sullivan); Center for Research on Invasive Species and Small Populations, University of Idaho, Moscow, ID (Waits and Sullivan); Program in Bioinformatics and Computational Biology, University of Idaho, Moscow, ID (Metzger and Sullivan); and Department of Fish and Wildlife Sciences, University of Idaho, Moscow ID 83844-1136 (Waits).
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Gavin DG, Fitzpatrick MC, Gugger PF, Heath KD, Rodríguez-Sánchez F, Dobrowski SZ, Hampe A, Hu FS, Ashcroft MB, Bartlein PJ, Blois JL, Carstens BC, Davis EB, de Lafontaine G, Edwards ME, Fernandez M, Henne PD, Herring EM, Holden ZA, Kong WS, Liu J, Magri D, Matzke NJ, McGlone MS, Saltré F, Stigall AL, Tsai YHE, Williams JW. Climate refugia: joint inference from fossil records, species distribution models and phylogeography. THE NEW PHYTOLOGIST 2014; 204:37-54. [PMID: 25039238 DOI: 10.1111/nph.12929] [Citation(s) in RCA: 166] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 06/06/2014] [Indexed: 05/16/2023]
Abstract
Climate refugia, locations where taxa survive periods of regionally adverse climate, are thought to be critical for maintaining biodiversity through the glacial-interglacial climate changes of the Quaternary. A critical research need is to better integrate and reconcile the three major lines of evidence used to infer the existence of past refugia - fossil records, species distribution models and phylogeographic surveys - in order to characterize the complex spatiotemporal trajectories of species and populations in and out of refugia. Here we review the complementary strengths, limitations and new advances for these three approaches. We provide case studies to illustrate their combined application, and point the way towards new opportunities for synthesizing these disparate lines of evidence. Case studies with European beech, Qinghai spruce and Douglas-fir illustrate how the combination of these three approaches successfully resolves complex species histories not attainable from any one approach. Promising new statistical techniques can capitalize on the strengths of each method and provide a robust quantitative reconstruction of species history. Studying past refugia can help identify contemporary refugia and clarify their conservation significance, in particular by elucidating the fine-scale processes and the particular geographic locations that buffer species against rapidly changing climate.
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Affiliation(s)
- Daniel G Gavin
- Department of Geography, University of Oregon, Eugene, OR, 97403, USA
| | - Matthew C Fitzpatrick
- Appalachian Laboratory, University of Maryland Center for Environmental Science, Frostburg, MD, 21532, USA
| | - Paul F Gugger
- Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095, USA
| | - Katy D Heath
- Department of Plant Biology, University of Illinois, Urbana, IL, 61801, USA
| | | | - Solomon Z Dobrowski
- Department of Forest Management, College of Forestry and Conservation, University of Montana, Missoula, MT, 59812, USA
| | - Arndt Hampe
- INRA, BIOGECO, UMR 1202, 33610, Cestas, France
- BIOGECO, UMR 1202, University of Bordeaux, 33400, Talence, France
| | - Feng Sheng Hu
- Department of Plant Biology, University of Illinois, Urbana, IL, 61801, USA
| | | | | | - Jessica L Blois
- School of Natural Sciences, University of California, Merced, CA, 95343, USA
| | - Bryan C Carstens
- Department of Evolution, Ecology & Organismal Biology, The Ohio State University, Columbus, OH, 43210, USA
| | - Edward B Davis
- Department of Geological Sciences, University of Oregon, Eugene, OR, 97403, USA
| | - Guillaume de Lafontaine
- Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research, Institute for Systems and Integrative Biology, Université Laval, Québec City, QC, G1V 0A6, Canada
| | - Mary E Edwards
- Geography and Environment, University of Southampton, Southampton, SO17 1BJ, UK
| | - Matias Fernandez
- Department of Plant Biology, University of Illinois, Urbana, IL, 61801, USA
| | - Paul D Henne
- Oeschger Centre for Climate Change Research, Institute of Plant Sciences, University of Bern, 3013, Bern, Switzerland
| | - Erin M Herring
- Department of Geography, University of Oregon, Eugene, OR, 97403, USA
| | | | - Woo-Seok Kong
- Department of Geography, Kyung Hee University, Seoul, 130-701, Korea
| | - Jianquan Liu
- College of Life Science, Lanzhou University, Lanzhou, 730000, China
| | - Donatella Magri
- Dipartimento di Biologia Ambientale, Sapienza University, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Nicholas J Matzke
- Department of Ecology and Evolutionary Biology, National Institute for Mathematical and Biological Synthesis, University of Tennessee, Knoxville, TN, 37996, USA
| | | | - Frédérik Saltré
- Environment Institute, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Alycia L Stigall
- Department of Geological Sciences, OHIO Center for Ecology and Evolutionary Studies, Ohio University, Athens, OH, 45701, USA
| | - Yi-Hsin Erica Tsai
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - John W Williams
- Department of Geography, Nelson Center for Climatic Research, University of Wisconsin, Madison, WI, 53706, USA
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15
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Influence of ecological and geological features on rangewide patterns of genetic structure in a widespread passerine. Heredity (Edinb) 2014; 114:143-54. [PMID: 25074576 DOI: 10.1038/hdy.2014.64] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Revised: 05/29/2014] [Accepted: 06/03/2014] [Indexed: 01/22/2023] Open
Abstract
Geological and ecological features restrict dispersal and gene flow, leading to isolated populations. Dispersal barriers can be obvious physical structures in the landscape; however microgeographic differences can also lead to genetic isolation. Our study examined dispersal barriers at both macro- and micro-geographical scales in the black-capped chickadee, a resident North American songbird. Although birds have high dispersal potential, evidence suggests dispersal is restricted by barriers. The chickadee's range encompasses a number of physiological features which may impede movement and lead to divergence. Analyses of 913 individuals from 34 sampling sites across the entire range using 11 microsatellite loci revealed as many as 13 genetic clusters. Populations in the east were largely panmictic whereas populations in the western portion of the range showed significant genetic structure, which often coincided with large mountain ranges, such as the Cascade and Rocky Mountains, as well as areas of unsuitable habitat. Unlike populations in the central and southern Rockies, populations on either side of the northern Rockies were not genetically distinct. Furthermore, Northeast Oregon represents a forested island within the Great Basin; genetically isolated from all other populations. Substructuring at the microgeographical scale was also evident within the Fraser Plateau of central British Columbia, and in the southeast Rockies where no obvious physical barriers are present, suggesting additional factors may be impeding dispersal and gene flow. Dispersal barriers are therefore not restricted to large physical structures, although mountain ranges and large water bodies do play a large role in structuring populations in this study.
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16
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Sork VL, Werth S. Phylogeography of Ramalina menziesii, a widely distributed lichen-forming fungus in western North America. Mol Ecol 2014; 23:2326-39. [PMID: 24673777 DOI: 10.1111/mec.12735] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Accepted: 03/13/2014] [Indexed: 11/28/2022]
Abstract
The complex topography and climate history of western North America offer a setting where lineage formation, accumulation and migration have led to elevated inter- and intraspecific biodiversity in many taxa. Here, we study Ramalina menziesii, an epiphytic lichenized fungus with a range encompassing major ecosystems from Baja California to Alaska to explore the predictions of two hypotheses: (i) that the widespread distribution of R. menziesii is due to a single migration episode from a single lineage and (ii) that the widespread distribution is due to the formation and persistence of multiple lineages structured throughout the species' range. To obtain evidence for these predictions, we first construct a phylogenetic tree and identify multiple lineages structured throughout the species' range--some ancient ones that are localized and other more recent lineages that are widely distributed. Second, we use an isolation with migration model to show that sets of ecoregion populations diverged from each other at different times, demonstrating the importance of historical and current barriers to gene flow. Third, we estimated migration rates among ecoregions and find that Baja California populations are relatively isolated, that inland California ecoregion populations do not send out emigrants and that migration out of California coastal and Pacific Northwest populations into inland California ecoregions is high. Such intraspecific geographical patterns of population persistence and dispersal both contribute to the wide range of this genetically diverse lichen fungus and provide insight into the evolutionary processes that enhance species diversity of the California Floristic Province.
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Affiliation(s)
- Victoria L Sork
- Department of Ecology and Evolutionary Biology, University of California at Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA, 90095-7239, USA; Institute of the Environment and Sustainability, University of California, Los Angeles, CA, 90095-1496, USA
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17
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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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18
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van Els P, Spellman GM, Smith BT, Klicka J. Extensive gene flow characterizes the phylogeography of a North American migrant bird: Black-headed Grosbeak (Pheucticus melanocephalus). Mol Phylogenet Evol 2014; 78:148-59. [PMID: 24841539 DOI: 10.1016/j.ympev.2014.04.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Revised: 04/17/2014] [Accepted: 04/23/2014] [Indexed: 11/26/2022]
Abstract
We describe range-wide phylogeographic variation in the Black-headed Grosbeak (Pheucticus melanocephalus), a songbird that is widely distributed across North American scrublands and forests. Phylogenetic analysis of mitochondrial DNA (mtDNA, n=424) revealed three geographically structured clades. One widespread clade occurs throughout the Rocky Mountains, Great Basin, and Mexican Plateau, a second clade is found on the Pacific coast and in coastal ranges; and, a third in the Sierra Madre del Sur of Oaxaca and Guerrero. Some geographical structuring occurs in Mexican Plateau and Sierra Madre Oriental mtDNA clade, presumably because these populations have been more stable over time than northern populations. Multiple mitochondrial groups are found sympatrically in the Okanogan River Valley in Washington, the eastern Sierra Nevada, and the Transvolcanic Belt across central Mexico, indicating that there is a potential for introgression. Analyses of 12 nuclear loci did not recover the same geographically structured clades. Population analyses show high levels of gene flow in nucDNA from the Interior into the Sierra Madre del Sur and Pacific population groups, possibly indicating expansion of the Interior population at the expense of peripheral populations.
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Affiliation(s)
- Paul van Els
- University of Nevada Las Vegas, Marjorie Barrick Museum of Natural History, 4505 S. Maryland Parkway, Las Vegas, NV 89154, USA.
| | - Garth M Spellman
- Center for the Conservation of Biological Resources, School of Natural Sciences, Black Hills State University, Spearfish, SD 57799, USA
| | - Brian Tilston Smith
- University of Nevada Las Vegas, Marjorie Barrick Museum of Natural History, 4505 S. Maryland Parkway, Las Vegas, NV 89154, USA
| | - John Klicka
- University of Nevada Las Vegas, Marjorie Barrick Museum of Natural History, 4505 S. Maryland Parkway, Las Vegas, NV 89154, USA
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19
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Dufresnes C, Wassef J, Ghali K, Brelsford A, Stöck M, Lymberakis P, Crnobrnja-Isailovic J, Perrin N. Conservation phylogeography: does historical diversity contribute to regional vulnerability in European tree frogs (Hyla arborea)? Mol Ecol 2013; 22:5669-84. [PMID: 24102652 DOI: 10.1111/mec.12513] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Revised: 08/24/2013] [Accepted: 08/28/2013] [Indexed: 11/28/2022]
Abstract
Documenting and preserving the genetic diversity of populations, which conditions their long-term survival, have become a major issue in conservation biology. The loss of diversity often documented in declining populations is usually assumed to result from human disturbances; however, historical biogeographic events, otherwise known to strongly impact diversity, are rarely considered in this context. We apply a multilocus phylogeographic study to investigate the late-Quaternary history of a tree frog (Hyla arborea) with declining populations in the northern and western part of its distribution range. Mitochondrial and nuclear polymorphisms reveal high genetic diversity in the Balkan Peninsula, with a spatial structure moulded by the last glaciations. While two of the main refugial lineages remained limited to the Balkans (Adriatic coast, southern Balkans), a third one expanded to recolonize Northern and Western Europe, loosing much of its diversity in the process. Our findings show that mobile and a priori homogeneous taxa may also display substructure within glacial refugia ('refugia within refugia') and emphasize the importance of the Balkans as a major European biodiversity centre. Moreover, the distribution of diversity roughly coincides with regional conservation situations, consistent with the idea that historically impoverished genetic diversity may interact with anthropogenic disturbances, and increase the vulnerability of populations. Phylogeographic models seem important to fully appreciate the risks of local declines and inform conservation strategies.
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Affiliation(s)
- Christophe Dufresnes
- Department of Ecology & Evolution, University of Lausanne, Biophore Building, 1015, Lausanne, Switzerland
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20
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Malaney JL, Conroy CJ, Moffitt LA, Spoonhunter HD, Patton JL, Cook JA. Phylogeography of the western jumping mouse (Zapus princeps) detects deep and persistent allopatry with expansion. J Mammal 2013. [DOI: 10.1644/12-mamm-a-006.1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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21
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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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22
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Carstens BC, Brennan RS, Chua V, Duffie CV, Harvey MG, Koch RA, McMahan CD, Nelson BJ, Newman CE, Satler JD, Seeholzer G, Posbic K, Tank DC, Sullivan J. Model selection as a tool for phylogeographic inference: an example from the willow Salix melanopsis. Mol Ecol 2013; 22:4014-28. [PMID: 23848064 DOI: 10.1111/mec.12347] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Revised: 04/09/2013] [Accepted: 04/09/2013] [Indexed: 12/29/2022]
Abstract
Phylogeographic inference has typically relied on analyses of data from one or a few genes to provide estimates of demography and population histories. While much has been learned from these studies, all phylogeographic analysis is conditioned on the data, and thus, inferences derived from data that represent a small sample of the genome are unavoidably tenuous. Here, we demonstrate one approach for moving beyond classic phylogeographic research. We use sequence capture probes and Illumina sequencing to generate data from >400 loci in order to infer the phylogeographic history of Salix melanopsis, a riparian willow with a disjunct distribution in coastal and the inland Pacific Northwest. We evaluate a priori phylogeographic hypotheses using coalescent models for parameter estimation, and the results support earlier findings that identified post-Pleistocene dispersal as the cause of the disjunction in S. melanopsis. We also conduct a series of model selection exercises using IMa2, Migrate-n and ∂a∂i. The resulting ranking of models indicates that refugial dynamics were complex, with multiple regions in the inland regions serving as the source for postglacial colonization. Our results demonstrate that new sources of data and new approaches to data analysis can rejuvenate phylogeographic research by allowing for the identification of complex models that enable researchers to both identify and estimate the most relevant parameters for a given system.
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Affiliation(s)
- Bryan C Carstens
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH 43210, USA.
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23
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Richart CH, Hedin M. Three new species in the harvestmen genus Acuclavella (Opiliones, Dyspnoi, Ischyropsalidoidea), including description of male Acuclavella quattuor Shear, 1986. Zookeys 2013; 311:19-68. [PMID: 23825441 PMCID: PMC3698555 DOI: 10.3897/zookeys.311.2920] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Accepted: 06/06/2013] [Indexed: 11/12/2022] Open
Abstract
In Shear's (1986) cladistic analysis of the Ischyropsalidoidea, he described the new genus Acuclavella including four new species from the Pacific Northwest states of Washington and Idaho. Several of these species descriptions were based on very limited sample sizes. Our recent field work has increased by more than an order of magnitude both the number of specimens and known localities for Acuclavella. We use this new material to interpret species limits in Acuclavella using morphometric analyses and DNA sequence data from four gene regions. We sequence for the first time the protein-coding homolog of the Wnt2 gene for phylogenetic reconstruction in Opiliones. Our multi-locus phylogeny corroborates a sister relationship between Acuclavella and Ceratolasma, as hypothesized using morphology by Shear (1986). Within Acuclavella, morphometric clusters and reciprocal allelic monophyly allows recognition of three additional species: Acuclavella leonardi sp. n., Acuclavella sheari sp. n., and Acuclavella makah sp. n. This work also describes the previously unknown male of Acuclavella quattuor, from specimens collected at the type locality. Our research identifies a number of novel morphologies for Acuclavella, including females with four pairs of spines, individuals with three pairs of spines on scute areas I-III, and a population with two pairs of spines disjunct from Acuclavella quattuor, which was diagnosed with this spination character. We were unable to assign these populations to existing species, and conservatively do not yet recognize them as new. Intrageneric morphometrics and phylogenetic inference in Acuclavella were often concordant. However, we demonstrate that species delimitation signal would not be detected if only a single line of evidence were utilized.
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Affiliation(s)
- Casey H. Richart
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, California, 92182, USA
| | - Marshal Hedin
- Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, California, 92182, USA
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24
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Klymus KE, Carl Gerhardt H. AFLP markers resolve intra-specific relationships and infer genetic structure among lineages of the canyon treefrog, Hyla arenicolor. Mol Phylogenet Evol 2012; 65:654-67. [DOI: 10.1016/j.ympev.2012.07.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Revised: 07/22/2012] [Accepted: 07/23/2012] [Indexed: 10/28/2022]
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25
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Griswold CE, Audisio T, Ledford JM. An extraordinary new family of spiders from caves in the Pacific Northwest (Araneae, Trogloraptoridae, new family). Zookeys 2012; 215:77-102. [PMID: 22936872 PMCID: PMC3428790 DOI: 10.3897/zookeys.215.3547] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Accepted: 07/19/2012] [Indexed: 11/12/2022] Open
Abstract
The new spider genus and species Trogloraptor marchingtoni Griswold, Audisio & Ledford is described as the type of the new family Trogloraptoridae. The oblique membranous division of the basal segment of the anterior lateral spinnerets of Trogloraptor suggests that this haplogyne family is the sister group of the other Dysderoidea (Dysderidae, Oonopidae, Orsolobidae and Segestriidae). Trogloraptor is known only from caves and old growth forest understory in the Klamath-Siskiyou region of Oregon and California.
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Affiliation(s)
- Charles E. Griswold
- Arachnology Lab, California Academy of Sciences
- Department of Biological Sciences, San Francisco State University
- Environmental Science, Policy and Management, University of California, Berkeley
| | - Tracy Audisio
- Arachnology Lab, California Academy of Sciences
- Department of Biological Sciences, San Francisco State University
- Summer Systematics Institute, California Academy of Sciences
| | - Joel M. Ledford
- Arachnology Lab, California Academy of Sciences
- Environmental Science, Policy and Management, University of California, Berkeley
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26
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Cossel JO, Gaige MG, Sauder JD. Electroshocking as a survey technique for stream-dwelling amphibians. WILDLIFE SOC B 2012. [DOI: 10.1002/wsb.145] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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27
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Huang Z, Yu X, Liang W. Population genetic structure of golden pheasant Chrysolophus pictus in the Qinling Mountains, China. ANIM BIOL 2012. [DOI: 10.1163/157075611x618183] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The golden pheasant (Chrysolophus pictus) is an endemic pheasant of central China and is protected under national legislation. The Qinling Mountains form a natural barrier between northern and southern China. We investigated the population genetic structure using 1123 nucleotides of mitochondrial DNA (mtDNA) control-region from 55 individuals sampled from five populations of gold pheasant in the Qinling Mountains. We found sixteen haplotypes defined by fourteen polymorphic sites. Phylogenetic analyses showed that the haplotypes sampled from the five putative populations did not cluster into separate geographic branches. There was an insignificant genetic differentiation among the putative populations (except GSTS population), probably due to high levels of gene flow. Results from the mismatch distribution and neutrality test analyses indicated the populations did not experience a range expansion over the course of their histories. They also suggested there was no geographical isolation shaped by the Qingling Mountains for Chrysolophus pictus.
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Affiliation(s)
- Zuhao Huang
- School of Life Sciences, Jinggangshan University, Ji’an, Jiangxi Province 343009, China
| | - Xiaoping Yu
- School of Life Sciences, Shaanxi Normal University, Xi’an, Shaanxi Province 710062, China
| | - Wei Liang
- College of Life Sciences, Hainan Normal University, Haikou, Hainan Province 571158, China
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28
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Benzekri NA, Reiss JO. Olfactory metamorphosis in the coastal tailed frog Ascaphus truei (Amphibia, Anura, Leiopelmatidae). J Morphol 2011; 273:68-87. [PMID: 21935974 DOI: 10.1002/jmor.11008] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2011] [Revised: 06/09/2011] [Accepted: 06/28/2011] [Indexed: 11/10/2022]
Abstract
The structure of the olfactory organ in larvae and adults of the basal anuran Ascaphus truei was examined using light micrography, electron micrography, and resin casts of the nasal cavity. The larval olfactory organ consists of nonsensory anterior and posterior nasal tubes connected to a large, main olfactory cavity containing olfactory epithelium; the vomeronasal organ is a ventrolateral diverticulum of this cavity. A small patch of olfactory epithelium (the "epithelial band") also is present in the preoral buccal cavity, anterolateral to the choana. The main olfactory epithelium and epithelial band have both microvillar and ciliated receptor cells, and both microvillar and ciliated supporting cells. The epithelial band also contains secretory ciliated supporting cells. The vomeronasal epithelium contains only microvillar receptor cells. After metamorphosis, the adult olfactory organ is divided into the three typical anuran olfactory chambers: the principal, middle, and inferior cavities. The anterior part of the principal cavity contains a "larval type" epithelium that has both microvillar and ciliated receptor cells and both microvillar and ciliated supporting cells, whereas the posterior part is lined with an "adult-type" epithelium that has only ciliated receptor cells and microvillar supporting cells. The middle cavity is nonsensory. The vomeronasal epithelium of the inferior cavity resembles that of larvae but is distinguished by a novel type of microvillar cell. The presence of two distinct types of olfactory epithelium in the principal cavity of adult A. truei is unique among previously described anuran olfactory organs. A comparative review suggests that the anterior olfactory epithelium is homologous with the "recessus olfactorius" of other anurans and with the accessory nasal cavity of pipids and functions to detect water-borne odorants.
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Affiliation(s)
- Noëlle A Benzekri
- Department of Biological Sciences, Humboldt State University, Arcata, California 95521, USA
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29
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Frogs, Fish and Forestry: An Integrated Watershed Network Paradigm Conserves Biodiversity and Ecological Services. DIVERSITY 2011. [DOI: 10.3390/d3030503] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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30
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Goldberg CS, Pilliod DS, Arkle RS, Waits LP. Molecular detection of vertebrates in stream water: a demonstration using Rocky Mountain tailed frogs and Idaho giant salamanders. PLoS One 2011; 6:e22746. [PMID: 21818382 PMCID: PMC3144250 DOI: 10.1371/journal.pone.0022746] [Citation(s) in RCA: 223] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2011] [Accepted: 07/04/2011] [Indexed: 11/24/2022] Open
Abstract
Stream ecosystems harbor many secretive and imperiled species, and studies of vertebrates in these systems face the challenges of relatively low detection rates and high costs. Environmental DNA (eDNA) has recently been confirmed as a sensitive and efficient tool for documenting aquatic vertebrates in wetlands and in a large river and canal system. However, it was unclear whether this tool could be used to detect low-density vertebrates in fast-moving streams where shed cells may travel rapidly away from their source. To evaluate the potential utility of eDNA techniques in stream systems, we designed targeted primers to amplify a short, species-specific DNA fragment for two secretive stream amphibian species in the northwestern region of the United States (Rocky Mountain tailed frogs, Ascaphus montanus, and Idaho giant salamanders, Dicamptodon aterrimus). We tested three DNA extraction and five PCR protocols to determine whether we could detect eDNA of these species in filtered water samples from five streams with varying densities of these species in central Idaho, USA. We successfully amplified and sequenced the targeted DNA regions for both species from stream water filter samples. We detected Idaho giant salamanders in all samples and Rocky Mountain tailed frogs in four of five streams and found some indication that these species are more difficult to detect using eDNA in early spring than in early fall. While the sensitivity of this method across taxa remains to be determined, the use of eDNA could revolutionize surveys for rare and invasive stream species. With this study, the utility of eDNA techniques for detecting aquatic vertebrates has been demonstrated across the majority of freshwater systems, setting the stage for an innovative transformation in approaches for aquatic research.
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Affiliation(s)
- Caren S Goldberg
- Fish and Wildlife Resources, University of Idaho, Moscow, Idaho, United States of America.
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Conlon JM. Structural diversity and species distribution of host-defense peptides in frog skin secretions. Cell Mol Life Sci 2011; 68:2303-15. [PMID: 21560068 PMCID: PMC11114843 DOI: 10.1007/s00018-011-0720-8] [Citation(s) in RCA: 134] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2011] [Revised: 04/26/2011] [Accepted: 04/26/2011] [Indexed: 01/24/2023]
Abstract
Cationic peptides that adopt an amphipathic α-helical conformation in a membrane-mimetic environment are synthesized in the skins of many frog species. These peptides often display cytolytic activities against bacteria and fungi consistent with the idea that they play a role in the host's system of defense against pathogenic microorganisms, but their importance in the survival strategy of the animal is not clearly understood. Despite the common misconception that antimicrobial peptides are synthesized in the skins of all anurans, the species distribution is sporadic, suggesting that their production may confer some evolutionary advantage to the organism but is not necessary for survival. The low potency of many frog skin antimicrobial peptides is consistent with the hypothesis that cutaneous symbiotic bacteria may provide the major system of defense against pathogenic microorganisms in the environment with antimicrobial peptides assuming a supplementary role in some species.
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Affiliation(s)
- J Michael Conlon
- Department of Biochemistry, Faculty of Medicine and Health Sciences, United Arab Emirates University, 17666, Al-Ain, United Arab Emirates.
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Miller MP, Haig SM. Identifying shared genetic structure patterns among Pacific Northwest forest taxa: insights from use of visualization tools and computer simulations. PLoS One 2010; 5:e13683. [PMID: 21060824 PMCID: PMC2966394 DOI: 10.1371/journal.pone.0013683] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Accepted: 10/05/2010] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Identifying causal relationships in phylogeographic and landscape genetic investigations is notoriously difficult, but can be facilitated by use of multispecies comparisons. METHODOLOGY/PRINCIPAL FINDINGS We used data visualizations to identify common spatial patterns within single lineages of four taxa inhabiting Pacific Northwest forests (northern spotted owl: Strix occidentalis caurina; red tree vole: Arborimus longicaudus; southern torrent salamander: Rhyacotriton variegatus; and western white pine: Pinus monticola). Visualizations suggested that, despite occupying the same geographical region and habitats, species responded differently to prevailing historical processes. S. o. caurina and P. monticola demonstrated directional patterns of spatial genetic structure where genetic distances and diversity were greater in southern versus northern locales. A. longicaudus and R. variegatus displayed opposite patterns where genetic distances were greater in northern versus southern regions. Statistical analyses of directional patterns subsequently confirmed observations from visualizations. Based upon regional climatological history, we hypothesized that observed latitudinal patterns may have been produced by range expansions. Subsequent computer simulations confirmed that directional patterns can be produced by expansion events. CONCLUSIONS/SIGNIFICANCE We discuss phylogeographic hypotheses regarding historical processes that may have produced observed patterns. Inferential methods used here may become increasingly powerful as detailed simulations of organisms and historical scenarios become plausible. We further suggest that inter-specific comparisons of historical patterns take place prior to drawing conclusions regarding effects of current anthropogenic change within landscapes.
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Affiliation(s)
- Mark P Miller
- Department of Biology and Center for High Performance Computing, Utah State University, Logan, Utah, United States of America.
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Yan J, Wang Q, Chang Q, Ji X, Zhou K. The divergence of two independent lineages of an endemic Chinese gecko, Gekko swinhonis, launched by the Qinling orogenic belt. Mol Ecol 2010; 19:2490-500. [PMID: 20636892 DOI: 10.1111/j.1365-294x.2010.04660.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The genetic structure and demographic history of an endemic Chinese gecko, Gekko swinhonis, were investigated by analysing the mitochondrial cytochrome b gene and 10 microsatellite loci for samples collected from 27 localities. Mitochondrial DNA data provided a detailed distribution of two highly divergent evolutionary lineages, between which the average pairwise distance achieved was 0.14. The geographic division of the two lineages coincided with a plate boundary consisting of the Qinling and Taihang Mts, suggesting a historical vicariant pattern. The orogeny of the Qinling Mts, a dispersal and major climatic barrier of the region, may have launched the independent lineage divergence. Both lineages have experienced recent expansion, and the current sympatric localities comprised the region of contact between the lineages. Individual-based phylogenetic analyses of nucDNA and Bayesian-clustering approaches revealed a deep genetic structure analogous to mtDNA. Incongruence between nucDNA and mtDNA at the individual level at localities outside of the contact region can be explained by the different inheritance patterns and male-biased dispersal in this species. High genetic divergence, long-term isolation and ecological adaptation, as well as the morphological differences, suggest the presence of a cryptic species.
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Affiliation(s)
- Jie Yan
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210046, China
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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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GUGGER PAULF, SUGITA SHINYA, CAVENDER-BARES JEANNINE. Phylogeography of Douglas-fir based on mitochondrial and chloroplast DNA sequences: testing hypotheses from the fossil record. Mol Ecol 2010; 19:1877-97. [DOI: 10.1111/j.1365-294x.2010.04622.x] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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BELL BEND, PLEDGER SHIRLEYA. How has the remnant population of the threatened frogLeiopelma pakeka(Anura: Leiopelmatidae) fared on Maud Island, New Zealand, over the past 25 years? AUSTRAL ECOL 2010. [DOI: 10.1111/j.1442-9993.2009.02024.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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MARKO PETERB, HOFFMAN JESSICAM, EMME SANDRAA, MCGOVERN TAMARAM, KEEVER CARSONC, NICOLE COX L. The ‘Expansion-Contraction’ model of Pleistocene biogeography: rocky shores suffer a sea change? Mol Ecol 2010; 19:146-69. [DOI: 10.1111/j.1365-294x.2009.04417.x] [Citation(s) in RCA: 166] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Gavin DG. The coastal-disjunct mesic flora in the inland Pacific Northwest of USA and Canada: refugia, dispersal and disequilibrium. DIVERS DISTRIB 2009. [DOI: 10.1111/j.1472-4642.2009.00597.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Houston DD, Shiozawa DK, Riddle BR. Phylogenetic relationships of the western North American cyprinid genus Richardsonius, with an overview of phylogeographic structure. Mol Phylogenet Evol 2009; 55:259-273. [PMID: 19874904 DOI: 10.1016/j.ympev.2009.10.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2009] [Revised: 10/09/2009] [Accepted: 10/13/2009] [Indexed: 10/20/2022]
Abstract
Diversification of many North American taxa, including freshwater fishes, has been heavily influenced by the effects of complex geological and climatic events throughout the Cenozoic that have significantly altered the landscape. Here, we employ an array of phylogenetic analyses using a multiple gene tree approach to address several questions regarding the phylogenetic relationships of the North American cyprinid genus Richardsonius and two other closely related genera, Clinostomus and Iotichthys. We also use divergence time estimates generated using fossil calibrations to qualitatively assess the phylogeographic implications of evolution within the group. Mitochondrial and nuclear DNA sequences show a sister relationship between Iotichthys and Richardsonius, with Clinostomus being sister to an Iotichthys-Richardsonius clade, hence the currently recognized sister relationship between Clinostomus and Richardsonius is not supported. These genera appear to be monophyletic lineages, and sister species within genera appear to be reciprocally monophyletic. The two species within the genus Richardsonius both exhibit phylogeographic structure that is worthy of further investigation. Divergence time estimates between genera and species are Miocene or Pliocene in age, and divergence between phylogroups within species occurred in the late Pliocene to Pleistocene. These splits coincide with documented geological and climatic events.
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Affiliation(s)
- Derek D Houston
- University of Nevada Las Vegas, School of Life Sciences, 4505 Maryland Parkway, Las Vegas, NV 89154-4004, USA.
| | - Dennis K Shiozawa
- Brigham Young University, Department of Biology, 147-A WIDB, Provo, UT 84602, USA.
| | - Brett R Riddle
- University of Nevada Las Vegas, School of Life Sciences, 4505 Maryland Parkway, Las Vegas, NV 89154-4004, USA.
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King MG, Horning ME, Roalson EH. Range persistence during the last glacial maximum: Carex macrocephala was not restricted to glacial refugia. Mol Ecol 2009; 18:4256-69. [PMID: 19754517 DOI: 10.1111/j.1365-294x.2009.04280.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The distribution of many species inhabiting northwestern North America has been heavily influenced by the climatic changes during the late Pleistocene. Several studies have suggested that species were restricted to glacial refugia north and/or south of the continental ice sheet front. It is also hypothesized that the coast of northwestern North America could have been a prime location for glacial refugia because of the lowering of the eustatic sea level and the concomitant rise of the continental shelf because of tectonic rebound. Alternatively, some coastal species distributions and demographics may have been unaffected in the long-term by the last glacial maximum (LGM). We tested the glacial refugium hypothesis on an obligate coastal plant species, Carex macrocephala by sampling 600 individuals from 41 populations with 11 nuclear microsatellite loci and the rpL16 plastid intragenic spacer region. The microsatellite data sets suggest a low level of population differentiation with a standardized G'(ST) = 0.032 and inbreeding was high with an F = 0.969. The homogenization of the populations along the coast was supported by a principal coordinate analysis, amovas and samova analyses. Analyses using the rpL16 data set support the results of the microsatellite analyses, with a low F(ST) of 0.042. Coalescent and mismatch analyses using rpL16 suggest that C. macrocephala has not gone through a significant bottleneck within the past 100,000 years, although a much earlier population expansion was indicated by the mismatch analysis. Carex macrocephala exhibits the characteristics of metapopulation dynamics and on the basis of these results, we concluded that it was not restricted to glacial refugia during the LGM, but that it existed as a large metapopulation.
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Affiliation(s)
- Matthew G King
- Department of Botany, University of British Columbia, Vancouver, BC, Canada.
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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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KING MATTHEWG, ROALSON ERICH. Discordance between phylogenetics and coalescent-based divergence modelling: exploring phylogeographic patterns of speciation in theCarex macrocephalaspecies complex. Mol Ecol 2009; 18:468-82. [DOI: 10.1111/j.1365-294x.2008.04033.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Beauclerc KB, Johnson B, White BN. Genetic rescue of an inbred captive population of the critically endangered Puerto Rican crested toad (Peltophryne lemur) by mixing lineages. CONSERV GENET 2009. [DOI: 10.1007/s10592-008-9782-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Conlon JM, Kolodziejek J, Nowotny N. Antimicrobial peptides from the skins of North American frogs. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2008; 1788:1556-63. [PMID: 18983817 DOI: 10.1016/j.bbamem.2008.09.018] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2008] [Revised: 09/22/2008] [Accepted: 09/26/2008] [Indexed: 11/19/2022]
Abstract
North America is home to anuran species belonging to the families Bufonidae, Eleutherodactylidae, Hylidae, Leiopelmatidae, Ranidae, and Scaphiopodidae but antimicrobial peptides have been identified only in skin secretions and/or skin extracts of frogs belonging to the Leiopelmatidae ("tailed frogs") and Ranidae ("true frogs"). Eight structurally-related cationic alpha-helical peptides with broad-spectrum antibacterial activity, termed ascaphins, have been isolated from specimens of Ascaphus truei (Leiopelmatidae) occupying a coastal range. Characterization of orthologous antimicrobial peptides from Ascaphus specimens occupying an inland range supports the proposal that this population should be regarded as a separate species A. montanus. Ascaphin-8 shows potential for development into a therapeutically valuable anti-infective agent. Peptides belonging to the brevinin-1, esculentin-1, esculentin-2, palustrin-1, palustrin-2, ranacyclin, ranatuerin-1, ranatuerin-2, and temporin families have been isolated from North American ranids. It is proposed that "ranalexins" represent brevinin-1 peptides that have undergone a four amino acid residue internal deletion. Current taxonomic recommendations divide North American frogs from the family Ranidae into two genera: Lithobates and Rana. Cladistic analysis based upon the amino acid sequences of the brevinin-1 peptides provides strong support for this assignment.
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Affiliation(s)
- J Michael Conlon
- Department of Biochemistry, Faculty of Medicine and Health Sciences, United Arab Emirates University, 17666 Al-Ain, United Arab Emirates.
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45
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Amphibian phylogeography: a model for understanding historical aspects of species distributions. Heredity (Edinb) 2008; 101:109-19. [DOI: 10.1038/hdy.2008.30] [Citation(s) in RCA: 118] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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GODBOUT JULIE, FAZEKAS ARON, NEWTON CRAIGH, YEH FRANCISC, BOUSQUET JEAN. Glacial vicariance in the Pacific Northwest: evidence from a lodgepole pine mitochondrial DNA minisatellite for multiple genetically distinct and widely separated refugia. Mol Ecol 2008; 17:2463-75. [DOI: 10.1111/j.1365-294x.2008.03761.x] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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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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48
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A striking lack of genetic diversity across the wide-ranging amphibian Gastrophryne carolinensis (Anura: Microhylidae). Genetica 2008; 135:169-83. [DOI: 10.1007/s10709-008-9267-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2007] [Accepted: 02/20/2008] [Indexed: 11/27/2022]
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Marlowe K, Hufford L. Evolution of Synthyris sect. Dissecta (Plantaginaceae) on sky islands in the Northern Rocky Mountains. AMERICAN JOURNAL OF BOTANY 2008; 95:381-392. [PMID: 21632362 DOI: 10.3732/ajb.95.3.381] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
We examined the phylogeography of Synthyris sect. Dissecta (Plantaginaceae), which is restricted to the Olympic (S. lanuginosa) and Northern Rocky Mountains (S. dissecta and S. canbyi), to infer effects of sky islands and modes of speciation. Sequences of cpDNA trnT-trnL and psbA-trnH intergenic spacers resolved 22 haplotypes among 185 individuals sampled from 16 populations of the three species. Gene flow in the ancestral lineage and random capture of haplotypes in species lineages of sect. Dissecta have resulted in haplotype clades that are not exclusive to species. Nested clade analysis (NCA) indicates that allopatric fragmentation separated Olympic and Northern Rocky Mountain populations, giving rise to the Olympic endemic S. lanuginosa, which is characterized by unique haplotypes consistent with long temporal isolation. Low haplotype and nucleotide diversity in S. canbyi are consistent with newly founded populations experiencing a bottleneck. Furthermore, we infer S. canbyi evolved as a peripheral isolate of S. dissecta. NCA indicated limited migration in S. dissecta with possible isolation by distance. Both isolation on interglacial sky islands and valley glaciers during at least the last glaciation limited gene flow among populations of S. dissecta in different ranges of the Northern Rocky Mountains.
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Affiliation(s)
- K Marlowe
- School of Biological Sciences, Washington State University, Pullman, Washington 99164-4236 USA
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Zhang H, Yan J, Zhang G, Zhou K. Phylogeography and demographic history of Chinese black-spotted frog populations (Pelophylax nigromaculata): evidence for independent refugia expansion and secondary contact. BMC Evol Biol 2008; 8:21. [PMID: 18215328 PMCID: PMC2262875 DOI: 10.1186/1471-2148-8-21] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2007] [Accepted: 01/24/2008] [Indexed: 11/17/2022] Open
Abstract
Background Pleistocene glaciations had considerable impact on phylogeographic patterns within and among closely related species of many vertebrates. Compared to Europe and North America, research on the phylogeography of vertebrates in East Asia, particularly in China, remains limited. The black-spotted frog (Pelophylax nigromaculata) is a widespread species in East Asia. The wide distribution of this species in China makes it an ideal model for the study of palaeoclimatic effects on vertebrates in East Asia. Our previous studies of P. nigromaculata revealed significant subdivisions between the northeast China populations and populations in other regions of the mainland. In the present study, we aim to see whether the deepest splits among lineages and perhaps subsequent genealogical divisions are temporally consistent with a Pleistocene origin and whether clade geographic distributions, with insight into expansion patterns, are similarly spatially consistent with this model. Results Using 1143 nucleotides of the mitochondrial cytochrome b gene from 262 individuals sampled from 28 localities, two main clades (clade A and clade B) differing by c. 7.72% sequence divergence were defined from parsimony analyses. The corresponding timing of lineage divergence, 0.92 Mya, indicates a most likely Pleistocene split. The A clade is further subdivided into two sub-clades, A1 and A2 with 1.22% sequence divergence. Nested clade phylogeographical and population demographic analyses suggested that the current distribution of this frog species was the result of range expansion from two independent refugia during the last interglacial period. We discovered a population within which haplotype lineages A and B of P. nigromaculata coexist in the Dongliao area of China by nucleotide sequences, PCR-RFLP and ISSR (inter simple sequence repeat) patterns. The ISSR result in particular supported divergence between the mitochondrial clades A and B and implied introgressive gene flow between the two divergent lineages. Conclusion Nested clade phylogeographical and population demographic analyses indicate that the current distribution of P. nigromaculata is the result of range expansion from two independent refugia during the last interglacial period in late Pleistocene. One refugium was in east China and the lower elevations of south-western plateau. The distribution of the other mitochondrial clade is consistent with the presence of a refugium in the Korean Peninsula. The gene flow as detected by ISSR markers suggests a range expansion of the two refugia and a secondary contact between the two highly divergent lineages in the Dongliao (DL) area of northeast China.
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Affiliation(s)
- Hua Zhang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210046, China.
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