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Butler BO, Smith LL, Flores-Villela O. Phylogeography and taxonomy of Coleonyx elegans Gray 1845 (Squamata: Eublepharidae) in Mesoamerica: The Isthmus of Tehuantepec as an environmental barrier. Mol Phylogenet Evol 2023; 178:107632. [PMID: 36182052 DOI: 10.1016/j.ympev.2022.107632] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 08/05/2022] [Accepted: 09/23/2022] [Indexed: 12/14/2022]
Abstract
Population divergence leading to speciation is often explained by physical barriers causing allopatric distributions of historically connected populations. Environmental barriers have increasingly been shown to cause population divergence through local adaptation to distinct ecological characteristics. In this study, we evaluate population structuring and phylogeographic history within the Yucatán banded gecko Coleonyx elegans Gray 1845 to assess the role of both physical and environmental barriers in shaping the spatio-genetic distribution of a Mesoamerican tropical forest taxon. We generated RADseq and multi-locus Sanger datasets that included sampling across the entire species' range. Results find support for two distinct evolutionary lineages that diverged during the late Pliocene and show recent population expansions. Furthermore, these genetic lineages largely align with subspecies boundaries defined by morphology. Several mountain ranges identified as phylogeographic barriers in other taxa act as physical barriers to gene flow between the two clades. Despite the absence of a physical barrier between lineages across the lowland Isthmus of Tehuantepec, no introgression was observed. Here, a steep environmental cline associated with seasonality of precipitation corresponds exactly with the distributional limits of the lineages, whose closest samples are only 30 km apart. The combination of molecular and environmental evidence, and in conjunction with previous morphological evidence, allows us to reassess the current taxonomy in an integrative framework. Based on our findings, we elevate the previously recognized subspecies from the Pacific versant, the Colima banded gecko C. nemoralis Klauber 1945, to full species status and comment on conservation implications.
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Affiliation(s)
- Brett O Butler
- Museo de Zoología "Alfonso L. Herrera", Facultad de Ciencias, Universidad Nacional Autónoma de México, Av. Ciudad Universitaria 3000, C. P. 04510 Coyoacán, CDMX, Mexico; Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Av. Ciudad Universitaria 3000, C. P. 04510 Coyoacán, CDMX, Mexico.
| | - Lydia L Smith
- Museum of Vertebrate Zoology, 3101 Valley Life Sciences Building, University of California, Berkeley, CA 94720, USA
| | - Oscar Flores-Villela
- Museo de Zoología "Alfonso L. Herrera", Facultad de Ciencias, Universidad Nacional Autónoma de México, Av. Ciudad Universitaria 3000, C. P. 04510 Coyoacán, CDMX, Mexico
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2
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Arifin U, Smart U, Husemann M, Hertwig ST, Smith EN, Iskandar DT, Haas A. Phylogeographic inference of Sumatran ranids bearing gastromyzophorous tadpoles with regard to the Pleistocene drainage systems of Sundaland. Sci Rep 2022; 12:12013. [PMID: 35853951 PMCID: PMC9296532 DOI: 10.1038/s41598-022-14722-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 06/10/2022] [Indexed: 11/18/2022] Open
Abstract
Rivers are known to act as biogeographic barriers in several strictly terrestrial taxa, while possibly serving as conduits of dispersal for freshwater-tolerant or -dependent species. However, the influence of river systems on genetic diversity depends on taxa-specific life history traits as well as other geographic factors. In amphibians, several studies have demonstrated that river systems have only minor influence on their divergence. Here, we assess the role of the paleodrainage systems of the Sunda region (with a focus on the island of Sumatra) in shaping the evolutionary history of two genera of frogs (Sumaterana and Wijayarana) whose tadpoles are highly dependent on cascading stream habitats. Our phylogenetic results show no clear association between the genetic diversification patterns of both anurans genera and the existence of paleodrainage systems. Time-calibrated phylogenies and biogeographical models suggest that these frogs colonized Sumatra and diversified on the island before the occurrence of the Pleistocene drainage systems. Both genera demonstrate phylogenetic structuring along a north–south geographic axis, the temporal dynamics of which coincide with the geological chronology of proto Sumatran and -Javan volcanic islands. Our results also highlight the chronic underestimation of Sumatran biodiversity and call for more intense sampling efforts on the island.
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Affiliation(s)
- Umilaela Arifin
- Centre for Taxonomy and Morphology, Leibniz Institute for the Analysis of Biodiversity Change, Martin-Luther-King-Platz 3, 20146, Hamburg, Germany. .,Universität Hamburg, Edmund-Siemers-Allee 1, 20148, Hamburg, Germany.
| | - Utpal Smart
- Department of Biology, Texas State University, 601 University Drive, San Marcos, TX, 78666, USA.,Amphibian & Reptile Diversity Research Center Department of Biology, University of Texas at Arlington, Arlington, TX, 76019-0498, USA
| | - Martin Husemann
- Centre for Taxonomy and Morphology, Leibniz Institute for the Analysis of Biodiversity Change, Martin-Luther-King-Platz 3, 20146, Hamburg, Germany.,Universität Hamburg, Edmund-Siemers-Allee 1, 20148, Hamburg, Germany
| | - Stefan T Hertwig
- Naturhistorisches Museum der Burgergemeinde Bern, Bernastrasse 15, 3005, Bern, Switzerland.,Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012, Bern, Switzerland
| | - Eric N Smith
- Amphibian & Reptile Diversity Research Center Department of Biology, University of Texas at Arlington, Arlington, TX, 76019-0498, USA
| | - Djoko T Iskandar
- Basic Science Committee, Indonesian Academy of Sciences, Jalan Medan Merdeka Selatan 11, Jakarta, 10110, Indonesia
| | - Alexander Haas
- Centre for Taxonomy and Morphology, Leibniz Institute for the Analysis of Biodiversity Change, Martin-Luther-King-Platz 3, 20146, Hamburg, Germany.,Universität Hamburg, Edmund-Siemers-Allee 1, 20148, Hamburg, Germany
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Naka LN, Costa BMDS, Lima GR, Claramunt S. Riverine Barriers as Obstacles to Dispersal in Amazonian Birds. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.846975] [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
Amazonian rivers represent known barriers for avian dispersal, reducing gene flow and enhancing differentiation. Despite the importance of rivers in the avian evolutionary process, we have made only minor advances in understanding the limitations imposed by rivers on flying birds. To fill that gap, we conducted dispersal-challenge experiments over water, assessing the flying capabilities of 84 tropical bird species of 22 different avian families. We mist-netted and released 484 birds from a stationary boat on the Rio Branco, northern Amazonia, at increasing distances from the shore, including 249 individuals at 100; 219 at 200; 8 at 300; and 5 at 400 m. A successful trial was represented by a bird reaching the riverbank, whereas a failure would refer to birds not reaching the shore and landing on the water, when they were rescued by our team. Our main goal was to understand if the outcome in the experiments could be predicted by (i) phylogenetic constraints, (ii) morphology (body mass and wing shape), (iii) flight speed, (iv) ecological preferences (stratum, habitat, and river-island specialization), and (v) psychological reluctance to fly. Nearly two thirds of the individuals (332) were successful in reaching the riverbank, whereas 152 failed. We found significant differences among lineages. Whereas seven avian families succeeded in all of the trials, two families (antbirds and wrens) were particularly bad dispersers (<40% success). The hand-wing index (HWI) was the single most powerful predictor of trial success. Flying speed was also a significant predictor of success. Overall, ecological attributes had a low explanatory power. Only forest stratum preference had a significant, although weak, effect on dispersal ability: canopy- and ground-dwellers performed better than understory birds. However, we found no effect of habitat preference or river-island specialization on dispersal ability. Our speed estimates for 64 bird species are among the first produced for the tropics and suggest slower flying speeds than those reported from temperate migratory birds. Although birds showed behavioral differences when presented with the opportunity to fly away from the boat, we found no evidence that their reluctance to fly could predict the outcome in the experiments. This represents the first experimental study evaluating the riverine effect through dispersal ability of Amazonian birds, providing important insights to better understand dispersal limitations provided by riverine barriers.
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Ferrão M, de Souza RA, Colatreli OP, Hanken J, Lima AP. Hidden in the litter: cryptic diversity of the leaf-litter toad Rhinella castaneotica– proboscidea complex revealed through integrative taxonomy, with description of a new species from south-western Amazonia. SYST BIODIVERS 2022. [DOI: 10.1080/14772000.2022.2039317] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Miquéias Ferrão
- Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
- Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas, Brazil
| | - Romildo Augusto de Souza
- Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas, Brazil
| | - Olavo Pinhatti Colatreli
- Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas, Brazil
| | - James Hanken
- Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Albertina Pimentel Lima
- Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas, Brazil
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Delazeri F, Ernetti JR, De Bastiani VIM, Lingnau R, Toledo LF, Lucas EM. Forest cover influences chytrid infections in populations of Boana curupi, a threatened treefrog of south Brazil. DISEASES OF AQUATIC ORGANISMS 2021; 144:133-142. [PMID: 33955851 DOI: 10.3354/dao03585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Complex interactions among hosts, pathogens, and the environment affect the vulnerability of amphibians to the emergence of infectious diseases such as chytridiomycosis, caused by Batrachochytrium dendrobatidis (Bd). Boana curupi is a forest-dwelling amphibian endemic to the southern Atlantic Forest of South America, a severely fragmented region. Here, we evaluated whether abiotic factors (including air and water temperature, relative air humidity, and landscape) are correlated with chytrid infection intensity and prevalence in B. curupi. We found individuals infected with Bd in all populations sampled. Prevalence ranged from 25-86%, and the infection burden ranged from 1 to over 130000 zoospore genomic equivalents (g.e.) (mean ± SD: 4913 ± 18081 g.e.). The infection load differed among populations and was influenced by forest cover at scales of 100, 500, and 1000 m, with the highest infection rates recorded in areas with a higher proportion of forest cover. Our results suggest that the fungus is widely distributed in the populations of B. curupi in southern Brazil. Population and disease monitoring are necessary to better understand the relationships between host, pathogen, and environment, especially when, as in the case of B. curupi, threatened species are involved.
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Affiliation(s)
- Francieli Delazeri
- Programa de Pós-graduação em Ciências Ambientais, Universidade Comunitária da Região de Chapecó, Chapecó, Santa Catarina 89809-900, Brazil
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Figueiredo-Vázquez C, Lourenço A, Velo-Antón G. Riverine barriers to gene flow in a salamander with both aquatic and terrestrial reproduction. Evol Ecol 2021. [DOI: 10.1007/s10682-021-10114-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Wollenberg Valero KC, Marshall JC, Bastiaans E, Caccone A, Camargo A, Morando M, Niemiller ML, Pabijan M, Russello MA, Sinervo B, Werneck FP, Sites JW, Wiens JJ, Steinfartz S. Patterns, Mechanisms and Genetics of Speciation in Reptiles and Amphibians. Genes (Basel) 2019; 10:genes10090646. [PMID: 31455040 PMCID: PMC6769790 DOI: 10.3390/genes10090646] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/21/2019] [Accepted: 08/05/2019] [Indexed: 12/22/2022] Open
Abstract
In this contribution, the aspects of reptile and amphibian speciation that emerged from research performed over the past decade are reviewed. First, this study assesses how patterns and processes of speciation depend on knowing the taxonomy of the group in question, and discuss how integrative taxonomy has contributed to speciation research in these groups. This study then reviews the research on different aspects of speciation in reptiles and amphibians, including biogeography and climatic niches, ecological speciation, the relationship between speciation rates and phenotypic traits, and genetics and genomics. Further, several case studies of speciation in reptiles and amphibians that exemplify many of these themes are discussed. These include studies of integrative taxonomy and biogeography in South American lizards, ecological speciation in European salamanders, speciation and phenotypic evolution in frogs and lizards. The final case study combines genomics and biogeography in tortoises. The field of amphibian and reptile speciation research has steadily moved forward from the assessment of geographic and ecological aspects, to incorporating other dimensions of speciation, such as genetic mechanisms and evolutionary forces. A higher degree of integration among all these dimensions emerges as a goal for future research.
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Affiliation(s)
| | - Jonathon C Marshall
- Department of Zoology, Weber State University, 1415 Edvalson Street, Dept. 2505, Ogden, UT 84401, USA
| | - Elizabeth Bastiaans
- Department of Biology, State University of New York, College at Oneonta, Oneonta, NY 13820, USA
| | - Adalgisa Caccone
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
| | - Arley Camargo
- Centro Universitario de Rivera, Universidad de la República, Ituzaingó 667, Rivera 40000, Uruguay
| | - Mariana Morando
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales (IPEEC, CENPAT-CONICET) Bv. Brown 2915, Puerto Madryn U9120ACD, Argentina
| | - Matthew L Niemiller
- Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, AL 35899, USA
| | - Maciej Pabijan
- Department of Comparative Anatomy, Institute of Zoology and Biomedical Research, Jagiellonian University, ul. Gronostajowa 9, 30-387 Kraków, Poland
| | - Michael A Russello
- Department of Biology, University of British Columbia, Okanagan Campus, 3247 University Way, Kelowna, BC V1V 1V7, Canada
| | - Barry Sinervo
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Coastal Biology Building, 130 McAllister Way, Santa Cruz, CA 95060, USA
| | - Fernanda P Werneck
- Programa de Coleções Científicas Biológicas, Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus 69060-000, Brazil
| | - Jack W Sites
- Department of Biological and Marine Sciences, University of Hull, Cottingham Road, Hull HU6 7RX, UK
| | - John J Wiens
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Sebastian Steinfartz
- Molecular Evolution and Systematics of Animals, Institute of Biology, University of Leipzig, Talstrasse 33, 04103 Leipzig, Germany
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Yu Y, Zhou S, Zhu X, Xu X, Wang W, Zha L, Wang P, Wang J, Lai K, Wang S, Hao L, Zhou B. Genetic Differentiation of Eastern Honey Bee ( Apis cerana) Populations Across Qinghai-Tibet Plateau-Valley Landforms. Front Genet 2019; 10:483. [PMID: 31178896 PMCID: PMC6538771 DOI: 10.3389/fgene.2019.00483] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 05/06/2019] [Indexed: 11/13/2022] Open
Abstract
Many species of high-altitude plateaus tend to be narrowly distributed along river valleys at lower elevations due to a limitation of suitable habitats. The eastern honeybee (Apis cerana) is such a species and this study explored the effects of long and narrow geographic distributions on honeybee populations. Genetic differentiation and diversity were assessed across populations of the southeastern Qinghai-Tibet Plateau. A total of 492 honeybee samples from eight sampling sites in four valleys were analyzed for the genetic differentiation and diversity of 31 microsatellite loci and mitochondrial tRNAleu-COII fragments. The following results were obtained: (1) Microsatellite genetic differentiation coefficients (F ST) ranged from 0.06 to 0.16, and mitochondrial F ST estimates ranged from 0.18 to 0.70 for different sampling sites in the same valley, indicating genetic differentiation. (2) Honeybees in adjacent valleys were also genetically differentiated. The F ST of microsatellites and mitochondria were 0.04-0.29 and 0.06-0.76, respectively. (3) Likely a result of small population sizes, the observed genetic diversity was low. The observed impedance of honeybee gene flow among valleys increased both genetic differentiation and population numbers in the Qinghai-Tibet Plateau. This study contributes significantly to the current understanding of the mechanism underlying population genetic differentiation and highlights the potential effects of utilizing genetic resources that are subject to the ecological conditions of the long and narrow geographic distributions of plateau-valley landforms.
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Affiliation(s)
- Yinglong Yu
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.,College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shujing Zhou
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiangjie Zhu
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xinjian Xu
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wenfeng Wang
- Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Luo Zha
- Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Ping Wang
- Ganzi Tibetan Autonomous Prefecture Apiculture Management Station, Ganzi, China
| | - Jianwen Wang
- Sichuan Province Apiculture Management Station, Chengdu, China
| | - Kang Lai
- Sichuan Province Apiculture Management Station, Chengdu, China
| | - Shunhai Wang
- Sichuan Province Apiculture Management Station, Chengdu, China
| | - Lunan Hao
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Bingfeng Zhou
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou, China
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Waraniak JM, Fisher JDL, Purcell K, Mushet DM, Stockwell CA. Landscape genetics reveal broad and fine-scale population structure due to landscape features and climate history in the northern leopard frog ( Rana pipiens) in North Dakota. Ecol Evol 2019; 9:1041-1060. [PMID: 30805139 PMCID: PMC6374656 DOI: 10.1002/ece3.4745] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 10/10/2018] [Accepted: 10/30/2018] [Indexed: 01/06/2023] Open
Abstract
Prehistoric climate and landscape features play large roles structuring wildlife populations. The amphibians of the northern Great Plains of North America present an opportunity to investigate how these factors affect colonization, migration, and current population genetic structure. This study used 11 microsatellite loci to genotype 1,230 northern leopard frogs (Rana pipiens) from 41 wetlands (30 samples/wetland) across North Dakota. Genetic structure of the sampled frogs was evaluated using Bayesian and multivariate clustering methods. All analyses produced concordant results, identifying a major east-west split between two R. pipiens population clusters separated by the Missouri River. Substructuring within the two major identified population clusters was also found. Spatial principal component analysis (sPCA) and variance partitioning analysis identified distance, river basins, and the Missouri River as the most important landscape factors differentiating R. pipiens populations across the state. Bayesian reconstruction of coalescence times suggested the major east-west split occurred ~13-18 kya during a period of glacial retreat in the northern Great Plains and substructuring largely occurred ~5-11 kya during a period of extreme drought cycles. A range-wide species distribution model (SDM) for R. pipiens was developed and applied to prehistoric climate conditions during the Last Glacial Maximum (21 kya) and the mid-Holocene (6 kya) from the CCSM4 climate model to identify potential refugia. The SDM indicated potential refugia existed in South Dakota or further south in Nebraska. The ancestral populations of R. pipiens in North Dakota may have inhabited these refugia, but more sampling outside the state is needed to reconstruct the route of colonization. Using microsatellite genotype data, this study determined that colonization from glacial refugia, drought dynamics in the northern Great Plains, and major rivers acting as barriers to gene flow were the defining forces shaping the regional population structure of R. pipiens in North Dakota.
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Affiliation(s)
- Justin M. Waraniak
- Department of Biological Sciences, Environmental and Conservation Sciences Graduate ProgramNorth Dakota State UniversityFargoNorth Dakota
| | - Justin D. L. Fisher
- Department of Biological Sciences, Environmental and Conservation Sciences Graduate ProgramNorth Dakota State UniversityFargoNorth Dakota
- Present address:
Natural Resource Conservation ServiceFergus FallsMinnesota
| | - Kevin Purcell
- Department of Biological Sciences, Environmental and Conservation Sciences Graduate ProgramNorth Dakota State UniversityFargoNorth Dakota
- Present address:
Data Science and Analytics ProgramHarrisburg UniversityHarrisburgPennsylvania
| | - David M. Mushet
- U.S. Geological SurveyNorthern Prairie Wildlife Research CenterJamestownNorth Dakota
| | - Craig A. Stockwell
- Department of Biological Sciences, Environmental and Conservation Sciences Graduate ProgramNorth Dakota State UniversityFargoNorth Dakota
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10
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Low population genetic differentiation in two Tamarix species (Tamarix austromongolica and Tamarix chinensis) along the Yellow River. Genetica 2018; 147:13-22. [DOI: 10.1007/s10709-018-0047-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 11/16/2018] [Indexed: 10/27/2022]
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Advertisement calls and DNA sequences reveal a new species of Scinax (Anura: Hylidae) on the Pacific lowlands of Ecuador. PLoS One 2018; 13:e0203169. [PMID: 30256795 PMCID: PMC6157856 DOI: 10.1371/journal.pone.0203169] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 08/06/2018] [Indexed: 11/24/2022] Open
Abstract
Scinax is a speciose genus of Neotropical hylid frogs. We describe a new species from western Ecuador (elevations between 0 and 1207 m) using morphology, vocalizations, and DNA sequences. We also present a new phylogeny for Scinax based on mitochondrial DNA genes 12S rRNA, Cytochrome Oxidase sub-unit I, Cytochrome B, 16S rRNA, NADH dehydrogenase subunit 1, and adjacent tRNAs. The new species, Scinax tsachila sp. nov. was previously confused with S. quinquefasciatus, a morphologically similar sympatric species. They differ by having markedly different advisement calls, distinct skin texture in the dorsum, and different bone coloration. The new species is sister to S. elaeochroa, a species that differs in advertisement call and color pattern. We provide an updated species account for Scinax quinquefasciatus and a redescription of its holotype.
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12
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Sultana N, Igawa T, Islam MM, Hasan M, Alam MS, Komaki S, Kawamura K, Khan MMR, Sumida M. Inter- and intra-specific genetic divergence of Asian tiger frogs (genus Hoplobatrachus), with special reference to the population structure of H. tigerinus in Bangladesh. Genes Genet Syst 2017; 91:217-227. [PMID: 27452042 DOI: 10.1266/ggs.16-00006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The five frog species of the genus Hoplobatrachus are widely distributed in Asia and Africa, with Asia being considered the genus' origin. However, the evolutionary relationships of Asian Hoplobatrachus species remain ambiguous. Additionally, genetic diversity and fundamental differentiation processes within species have not been studied. We conducted molecular phylogenetic analysis on Asian Hoplobatrachus frogs and population genetic analysis on H. tigerinus in Bangladesh using the mitochondrial CYTB gene and 21 microsatellite markers. The resultant phylogenetic tree revealed monophyly in each species, notwithstanding the involvement of cryptic species in H. chinensis and H. tigerinus, which are evident from the higher genetic divergence between populations. Bayesian inference of population structure revealed genetic divergence between western and eastern H. tigerinus populations in Bangladesh, suggesting restricted gene flow caused by barriers posed by major rivers. However, genetic distances among populations were generally low. A discrete population is located in the low riverine delta region, which likely reflects long-distance dispersal. These results strongly suggest that the environment specific to this river system has maintained the population structure of H. tigerinus in this region.
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Affiliation(s)
- Nasrin Sultana
- Institute for amphibian Biology, Graduate School of Science, Hiroshima University
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13
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Menezes L, Canedo C, Batalha-Filho H, Garda AA, Gehara M, Napoli MF. Multilocus Phylogeography of the Treefrog Scinax eurydice (Anura, Hylidae) Reveals a Plio-Pleistocene Diversification in the Atlantic Forest. PLoS One 2016; 11:e0154626. [PMID: 27248688 PMCID: PMC4889069 DOI: 10.1371/journal.pone.0154626] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 04/16/2016] [Indexed: 11/21/2022] Open
Abstract
We aim to evaluate the genetic structure of an Atlantic Forest amphibian species, Scinax eurydice, testing the congruence among patterns identified and proposed by the literature for Pleistocene refugia, microrefugia, and geographic barriers to gene flow such as major rivers. Furthermore, we aim to evaluate predictions of such barriers and refugia on the genetic structure of the species, such as presence/absence of dispersal, timing since separation, and population expansions/contractions. We sequenced mitochondrial and nuclear genetic markers on 94 tissue samples from 41 localities. We inferred a gene tree and estimated genetic distances using mtDNA sequences. We then ran population clustering and assignment methods, AMOVA, and estimated migration rates among populations identified through mtDNA and nDNA analyses. We used a dated species tree, skyline plots, and summary statistics to evaluate concordance between population's distributions and geographic barriers and Pleistocene refugia. Scinax eurydice showed high mtDNA divergences and four clearly distinct mtDNA lineages. Species tree and population assignment tests supported the existence of two major clades corresponding to northeastern and southeastern Atlantic Forest in Brazil, each one composed of two other clades. Lineage splitting events occurred from late Pliocene to Pleistocene. We identified demographic expansions in two clades, and inexistent to low levels of migrations among different populations. Genetic patterns and demographic data support the existence of two northern Refuge and corroborate microrefugia south of the Doce/Jequitinhonha Rivers biogeographic divide. The results agree with a scenario of recent demographic expansion of lowland taxa. Scinax eurydice comprises a species complex, harboring undescribed taxa consistent with Pleistocene refugia. Two rivers lie at the boundaries among populations and endorse their role as secondary barriers to gene flow.
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Affiliation(s)
- Lucas Menezes
- Programa de Pós-Graduação em Diversidade Animal, Instituto de Biologia, Universidade Federal da Bahia, Campus Universitário de Ondina, Rua Barão de Jeremoabo, 40170–115, Salvador, Bahia, Brasil
| | - Clarissa Canedo
- Universidade Federal do Rio de Janeiro, Museu Nacional, Departamento de Vertebrados, Quinta da Boa Vista, s/n, 20940–040, Rio de Janeiro, Rio de Janeiro, Brasil
| | - Henrique Batalha-Filho
- Programa de Pós-Graduação em Diversidade Animal, Instituto de Biologia, Universidade Federal da Bahia, Campus Universitário de Ondina, Rua Barão de Jeremoabo, 40170–115, Salvador, Bahia, Brasil
- Museu de Zoologia, Departamento de Zoologia, Instituto de Biologia, Universidade Federal da Bahia, Campus Universitário de Ondina, Rua Barão de Jeremoabo, 40170–115, Salvador, Bahia, Brasil
| | - Adrian Antonio Garda
- Universidade Federal do Rio Grande do Norte, Centro de Biociências, Departamento de Botânica, Ecologia e Zoologia, Laboratório de Anfíbios e Répteis-LAR, Campus Universitário, Lagoa Nova, 59078–900, Natal, Rio Grande do Norte, Brasil
| | - Marcelo Gehara
- Programa de Pós-Graduação em Sistemática e Evolução, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Campus Universitário Lagoa Nova, 59078–900, Natal, Rio Grande do Norte, Brasil
| | - Marcelo Felgueiras Napoli
- Programa de Pós-Graduação em Diversidade Animal, Instituto de Biologia, Universidade Federal da Bahia, Campus Universitário de Ondina, Rua Barão de Jeremoabo, 40170–115, Salvador, Bahia, Brasil
- Universidade Federal do Rio de Janeiro, Museu Nacional, Departamento de Vertebrados, Quinta da Boa Vista, s/n, 20940–040, Rio de Janeiro, Rio de Janeiro, Brasil
- Museu de Zoologia, Departamento de Zoologia, Instituto de Biologia, Universidade Federal da Bahia, Campus Universitário de Ondina, Rua Barão de Jeremoabo, 40170–115, Salvador, Bahia, Brasil
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Hoyos M, Bloor P, Defler T, Vermeer J, Röhe F, Farias I. Phylogenetic relationships within the Callicebus cupreus species group (Pitheciidae: Primates): Biogeographic and taxonomic implications. Mol Phylogenet Evol 2016; 102:208-19. [PMID: 27235549 DOI: 10.1016/j.ympev.2016.05.031] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2015] [Revised: 05/10/2016] [Accepted: 05/24/2016] [Indexed: 10/21/2022]
Abstract
The genus Callicebus (Thomas, 1903) is one of the most diverse of Neotropical primate genera and the only extant member of the Callicebinae subfamily. It has a widespread distribution from Colombia to Brazil, Bolivia, Peru and northern Paraguay. Coat colouring and colour pattern vary substantially within the genus, and this has led to the description of numerous species and subspecies, as well as numerous species groups. However, a lack of molecular phylogenetic analyses on the genus means that phylogenetic relationships and biogeographic history of species are poorly understood. Here, we examined phylogenetic relationships and patterns of diversification within the Callicebus cupreus species Group (sensu Kobayashi, 1995) using complete mitochondrial DNA cytochrome b gene sequence. Analyses indicate that the Callicebus cupreus Group underwent recent and extensive diversification. The common ancestor appears to have emerged some 2.3 million years ago (Ma) from a centre of origin in the western Amazon region, followed by diversification of the group between about 1.5 and 1.2Ma. Phylogenetic analyses were able to recover most previously described species (including the recently described Colombian endemic Callicebus caquetensis). However, there are some notable inconsistences between the obtained phylogeny and current taxonomy. Some previously recognized taxa were not separated by our data (e.g., Callicebus caligatus and Callicebus dubius), while currently unrecognized species diversity was uncovered within C. cupreus in the form of two divergent lineages: one of which exhibited greater phylogenetic similarity to species from the C. moloch Group. Based on the present study, we challenge current taxonomic arrangements for the C. cupreus species Group and call for a thorough taxonomic revision within the genus Callicebus.
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Affiliation(s)
- Manuel Hoyos
- Instituto de Genética, Universidad Nacional de Colombia, Edificio 426, Bogotá D.C., Colombia.
| | - Paul Bloor
- Instituto de Genética, Universidad Nacional de Colombia, Edificio 426, Bogotá D.C., Colombia
| | - Thomas Defler
- Departamento de Biología, Universidad Nacional de Colombia, Edificio 421, Bogotá D.C., Colombia
| | - Jan Vermeer
- Le Conservatoire pour la Protection des Primates. La Vallée des Singes, 86700 Romagne, France
| | - Fabio Röhe
- Wildlife Conservation Society, Manaus, Brazil
| | - Izeni Farias
- Universidade Federal do Amazonas UFAM, Manaus, AM, Brazil
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15
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Rojas RR, Chaparro JC, Carvalho VTD, Ávila RW, Farias IP, Hrbek T, Gordo M. Uncovering the diversity in the Amazophrynella minuta complex: integrative taxonomy reveals a new species of Amazophrynella (Anura, Bufonidae) from southern Peru. Zookeys 2016; 563:43-71. [PMID: 27047239 PMCID: PMC4797212 DOI: 10.3897/zookeys.563.6084] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 11/02/2015] [Indexed: 11/12/2022] Open
Abstract
A new species of the genus Amazophrynella (Anura, Bufonidae) is described from the departments of Madre de Dios, Cusco and Junin in Peru. An integrative taxonomy approach is used. A morphological diagnosis, morphometrics comparisons, description of the advertisement call, and the phylogenetic relationships of the new species are provided. Amazophrynella javierbustamantei sp. n. differs from other species of Amazophrynella by: intermediate body-size (snout-vent length 14.9 mm in males, n = 26 and 19.6 mm in females, n = 20), tuberculate skin texture of body, greatest hand length of the Amazophrynella spp. (3.6 mm in males, n = 26 and 4.6 mm in females, n = 20), venter coloration yellowish, tiny rounded black points covering the venter, and thirteen molecular autapomorphies in the 16S RNA gene. Its distribution varies from 215 to 708 m a.s.l. This discovery highlights the importance of the remnant forest in preserving the biodiversity in Peru, and increase in seven the species formally described in the genus Amazophrynella.
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Affiliation(s)
- Rommel R. Rojas
- Programa de Pós-graduação em Genética Conservação e Biologia Evolutiva- Instituto Nacional de Pesquisas da Amazônia-INPA, Av. André Araújo, 2936, Manaus, Brazil
- Laboratório de Genética e Evolução Animal, Departamento de Genética, ICB, Universidade Federal do Amazonas, Av. Gen. Rodrigo Octávio Jordão Ramos, 3000, Manaus, Brazil
| | - Juan C. Chaparro
- Museo de Historia Natural, Universidad Nacional de San Antonio Abad del Cusco, Peru
| | - Vinícius Tadeu De Carvalho
- Laboratório de Genética e Evolução Animal, Departamento de Genética, ICB, Universidade Federal do Amazonas, Av. Gen. Rodrigo Octávio Jordão Ramos, 3000, Manaus, Brazil
- Programa de Pós-Graduação em Biodiversidade e Biotecnologia, Av. Gen. Rodrigo Octávio Jordão Ramos, 3000, Manaus, Brazil
| | - Robson W. Ávila
- Universidade Regional do Cariri, Centro de Ciências Biológicas e da Saúde, Departamento de Ciências Biológicas, Campus do Pimenta, Rua Cel. Antônio Luiz, 1161, Bairro do Pimenta, Crato, Brazil
| | - Izeni Pires Farias
- Laboratório de Genética e Evolução Animal, Departamento de Genética, ICB, Universidade Federal do Amazonas, Av. Gen. Rodrigo Octávio Jordão Ramos, 3000, Manaus, Brazil
| | - Tomas Hrbek
- Laboratório de Genética e Evolução Animal, Departamento de Genética, ICB, Universidade Federal do Amazonas, Av. Gen. Rodrigo Octávio Jordão Ramos, 3000, Manaus, Brazil
| | - Marcelo Gordo
- Departamento de Biologia, ICB, Universidade Federal do Amazonas, Av. Gen. Rodrigo Octávio Jordão Ramos, 3000, Manaus, Brazil
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16
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Paz A, Ibáñez R, Lips KR, Crawford AJ. Testing the role of ecology and life history in structuring genetic variation across a landscape: a trait-based phylogeographic approach. Mol Ecol 2015; 24:3723-37. [DOI: 10.1111/mec.13275] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 06/09/2015] [Accepted: 06/12/2015] [Indexed: 11/30/2022]
Affiliation(s)
- Andrea Paz
- Department of Biological Sciences; Universidad de los Andes; A.A. 4976 Bogotá Colombia
| | - Roberto Ibáñez
- Smithsonian Tropical Research Institute; Apartado 0843-03092 Panama City Republic of Panama
- Círculo Herpetológico de Panamá; Apartado 0824-00122 Panama City Republic of Panama
| | - Karen R. Lips
- Smithsonian Tropical Research Institute; Apartado 0843-03092 Panama City Republic of Panama
- Department of Biology; University of Maryland; College Park MD 20742-4415 USA
| | - Andrew J. Crawford
- Department of Biological Sciences; Universidad de los Andes; A.A. 4976 Bogotá Colombia
- Smithsonian Tropical Research Institute; Apartado 0843-03092 Panama City Republic of Panama
- Círculo Herpetológico de Panamá; Apartado 0824-00122 Panama City Republic of Panama
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17
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The trans-riverine genetic structure of 28 Amazonian frog species is dependent on life history. JOURNAL OF TROPICAL ECOLOGY 2015. [DOI: 10.1017/s0266467415000206] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Abstract:Among the hypotheses formulated to explain the origin of Amazonian biodiversity, two (the riverine-barrier and the river-refuge hypotheses) focus on the role that rivers play as biotic barriers promoting speciation. However, empirical results have both supported and refuted these hypotheses. This is likely due, at least in part, to river-specific hydrologic characteristics and the biology of the focal species. The rivers of the Guiana Shield represent a model system because they have had more stable courses over time than those of the western Amazon Basin, where most tests of riverine barrier effects have taken place. We tested whether life-history traits (body size, habitat and larval development), expected to be important in determining dispersal ability, of 28 frog species are associated with genetic structure and genetic distances of individuals sampled from both banks of the Oyapock River. Thirteen of these species displayed genetic structure consistent with the river acting as a barrier to dispersal. Surprisingly, body size was not correlated with trans-riverine population structure. However, leaf-litter dwellers and species lacking free-living tadpoles were found to exhibit higher river-associated structure than open habitat/arboreal species and those with exotrophic tadpoles. These results demonstrate that rivers play an important role in structuring the genetic diversity of many frog species though the permeability of such riverine barriers is highly dependent on species-specific traits.
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Wollenberg Valero KC. Evidence for an intrinsic factor promoting landscape genetic divergence in Madagascan leaf-litter frogs. Front Genet 2015; 6:155. [PMID: 26136766 PMCID: PMC4470402 DOI: 10.3389/fgene.2015.00155] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 04/05/2015] [Indexed: 11/16/2022] Open
Abstract
The endemic Malagasy frog radiations are an ideal model system to study patterns and processes of speciation in amphibians. Large-scale diversity patterns of these frogs, together with other endemic animal radiations, led to the postulation of new and the application of known hypotheses of species diversification causing diversity patterns in this biodiversity hotspot. Both extrinsic and intrinsic factors have been studied in a comparative framework, with extrinsic factors usually being related to the physical environment (landscape, climate, river catchments, mountain chains), and intrinsic factors being clade-specific traits or constraints (reproduction, ecology, morphology, physiology). Despite some general patterns emerging from such large-scale comparative analyses, it became clear that the mechanism of diversification in Madagascar may vary among clades, and may be a multifactorial process. In this contribution, I test for intrinsic factors promoting population-level divergence within a clade of terrestrial, diurnal leaf-litter frogs (genus Gephyromantis) that has previously been shown to diversify according to extrinsic factors. Landscape genetic analyses of the microendemic species Gephyromantis enki and its widely distributed, larger sister species Gephyromantis boulengeri over a rugged landscape in the Ranomafana area shows that genetic variance of the smaller species cannot be explained by landscape resistance alone. Both topographic and riverine barriers are found to be important in generating this divergence. This case study yields additional evidence for the probable importance of body size in lineage diversification.
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Affiliation(s)
- Katharina C Wollenberg Valero
- Department of Natural Sciences, College of Science, Engineering and Mathematics, Bethune-Cookman University Daytona Beach, FL, USA
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The Sepik River (Papua New Guinea) is not a dispersal barrier for lowland rain-forest frogs. JOURNAL OF TROPICAL ECOLOGY 2013. [DOI: 10.1017/s0266467413000527] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Abstract:Major tropical rivers have been suggested to be important dispersal barriers that increase the beta diversity of animal communities in lowland rain forests. We tested this hypothesis using assemblages of frogs in the floodplains of the Sepik River, a major river system in Papua New Guinea. We surveyed frogs at five sites within a continuous 150 × 500-km area of lowland rain forest bisected by the Sepik, using standardized visual and auditory survey techniques. We documented 769 frogs from 44 species. The similarity in species composition decreased with logarithm of geographical distance between the sites, which ranged from 82 to 465 km. The similarity decay did not depend on whether or not the compared sites were separated by the Sepik River or whether the species were aquatic or terrestrial breeders. Likewise, a DCA ordination of frog assemblages did not show separation of sites by the river as a significant factor explaining their composition. Our results suggest that even major rivers, such as the Sepik, may not act as dispersal barriers. Rivers may not limit the distribution of frogs and therefore have a limited effect on determining frog species abundance and assemblage structure in rain forests.
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Jackson ND, Austin CC. Testing the role of meander cutoff in promoting gene flow across a riverine barrier in ground skinks (Scincella lateralis). PLoS One 2013; 8:e62812. [PMID: 23658778 PMCID: PMC3642178 DOI: 10.1371/journal.pone.0062812] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Accepted: 03/26/2013] [Indexed: 11/18/2022] Open
Abstract
Despite considerable attention, the long-term impact of rivers on species diversification remains uncertain. Meander loop cutoff (MLC) is one river phenomenon that may compromise a river's diversifying effects by passively transferring organisms from one side of the river to the other. However, the ability of MLC to promote gene flow across rivers has not been demonstrated empirically. Here, we test several predictions of MLC-mediated gene flow in populations of North American ground skinks (Scincella lateralis) separated by a well-established riverine barrier, the Mississippi River: 1) individuals collected from within meander cutoffs should be more closely related to individuals across the river than on the same side, 2) individuals within meander cutoffs should contain more immigrants than individuals away from meander cutoffs, 3) immigration rates estimated across the river should be highest in the direction of the cutoff event, and 4) the distribution of alleles native to one side of the river should be better predicted by the historical rather than current path of the river. To test these predictions we sampled 13 microsatellite loci and mitochondrial DNA from ground skinks collected near three ancient meander loops. These predictions were generally supported by genetic data, although support was stronger for mtDNA than for microsatellite data. Partial support for genetic divergence of samples within ancient meander loops also provides evidence for the MLC hypothesis. Although a role for MLC-mediated gene flow was supported here for ground skinks, the transient nature of river channels and morphologies may limit the long-term importance of MLC in stemming population divergence across major rivers.
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Affiliation(s)
- Nathan D Jackson
- Department of Biological Sciences, Museum of Natural Science, Louisiana State University, Baton Rouge, Louisiana, United States of America.
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Tonini JFR, Costa LP, Carnaval AC. Phylogeographic structure is strong in the Atlantic Forest; predictive power of correlative paleodistribution models, not always. J ZOOL SYST EVOL RES 2013. [DOI: 10.1111/jzs.12014] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- João Filipe Riva Tonini
- Laboratório de Mastozoologia e Biogeografia; Departamento de Ciências Biológicas; Universidade Federal do Espírito Santo; Vitória ES Brazil
- Department of Biology; City College of New York; City University of New York; New York NY USA
- Department of Biology; University of Richmond; Richmond VA USA
| | - Leonora Pires Costa
- Laboratório de Mastozoologia e Biogeografia; Departamento de Ciências Biológicas; Universidade Federal do Espírito Santo; Vitória ES Brazil
| | - Ana Carolina Carnaval
- Department of Biology; City College of New York; City University of New York; New York NY USA
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