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Milá B, Van Tassell JL, Calderón JA, Rüber L, Zardoya R. Cryptic lineage divergence in marine environments: genetic differentiation at multiple spatial and temporal scales in the widespread intertidal goby Gobiosoma bosc. Ecol Evol 2017; 7:5514-5523. [PMID: 28770087 PMCID: PMC5528222 DOI: 10.1002/ece3.3161] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 05/22/2017] [Accepted: 05/23/2017] [Indexed: 01/01/2023] Open
Abstract
The adaptive radiation of the seven-spined gobies (Gobiidae: Gobiosomatini) represents a classic example of how ecological specialization and larval retention can drive speciation through local adaptation. However, geographically widespread and phenotypically uniform species also do occur within Gobiosomatini. This lack of phenotypic variation across large geographic areas could be due to recent colonization, widespread gene flow, or stabilizing selection acting across environmental gradients. We use a phylogeographic approach to test these alternative hypotheses in the naked goby Gobiosoma bosc, a widespread and phenotypically invariable intertidal fish found along the Atlantic Coast of North America. Using DNA sequence from 218 individuals sampled at 15 localities, we document marked intraspecific genetic structure in mitochondrial and nuclear genes at three main geographic scales: (i) between Gulf of Mexico and Atlantic Coast, (ii) between the west coast of the Florida peninsula and adjacent Gulf of Mexico across the Apalachicola Bay, and (iii) at local scales of a few hundred kilometers. Clades on either side of Florida diverged about 8 million years ago, whereas some populations along the East Cost show divergent phylogroups that have differentiated within the last 200,000 years. The absence of noticeable phenotypic or ecological differentiation among lineages suggests the role of stabilizing selection on ancestral phenotypes, together with isolation in allopatry due to reduced dispersal and restricted gene flow, as the most likely explanation for their divergence. Haplotype phylogenies and spatial patterns of genetic diversity reveal frequent population bottlenecks followed by rapid population growth, particularly along the Gulf of Mexico. The magnitude of the genetic divergence among intraspecific lineages suggests the existence of cryptic species within Gobiosoma and indicates that modes of speciation can vary among lineages within Gobiidae.
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Affiliation(s)
- Borja Milá
- National Museum of Natural SciencesSpanish National Research Council (CSIC)MadridSpain
| | - James L. Van Tassell
- Department of IchthyologyAmerican Museum of Natural HistoryNew York, NY 10024USA
| | - Jatziri A. Calderón
- National Museum of Natural SciencesSpanish National Research Council (CSIC)MadridSpain
| | - Lukas Rüber
- Naturhistorisches Museum der BurgergemeindeBernBernastrasse 15, 3005 BernSwitzerland
- Institute of Ecology and EvolutionUniversity of BernBaltzerstrasse 6, 3012 BernSwitzerland
| | - Rafael Zardoya
- National Museum of Natural SciencesSpanish National Research Council (CSIC)MadridSpain
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202
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Ney G, Schul J. Population structure within the one-dimensional range of a coastal plain katydid. PLoS One 2017; 12:e0179361. [PMID: 28599010 PMCID: PMC5466309 DOI: 10.1371/journal.pone.0179361] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 05/30/2017] [Indexed: 11/19/2022] Open
Abstract
Biogeography plays a significant role in species’ dispersal, and in turn population structure, across the landscape. The North American katydid Neoconocephalus melanorhinus belongs to a genus with high mobility. Unlike other members of the genus, N. melanorhinus is a salt marsh specialist restricted to a narrow corridor along the Atlantic and Gulf coasts. In addition, their range crosses at least one known biogeographic barrier and possesses biogeographic characteristics of the stepping-stone as well as the hierarchical island model of dispersal. Using AFLP markers we searched for areas that conform to the predictions of isolation by distance and for areas of non-uniform increases in genetic variance, indicative of isolation by barrier. We found significant genetic differentiation between all twelve sampled sites. Isolation by distance was the predominant pattern of variation across their range. In addition, we saw possible evidence of two biogeographic barriers to gene flow, one at the Atlantic-Gulf divide and the other along the Gulf coast. We also observed a change in body size across the range. Body size, as measured by male hind femur length, correlated closely with latitude, a possible indication of differential selection across the species range.
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Affiliation(s)
- Gideon Ney
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, United States of America
- * E-mail:
| | - Johannes Schul
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, United States of America
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203
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Spatial mixing of mitochondrial lineages and greater genetic diversity in some invasive populations of the American mink (Neovison vison) compared to native populations. Biol Invasions 2017. [DOI: 10.1007/s10530-017-1475-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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204
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Fan D, Sun Z, Li B, Kou Y, Hodel RGJ, Jin Z, Zhang Z. Dispersal corridors for plant species in the Poyang Lake Basin of southeast China identified by integration of phylogeographic and geospatial data. Ecol Evol 2017; 7:5140-5148. [PMID: 28770054 PMCID: PMC5528243 DOI: 10.1002/ece3.2999] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Revised: 03/15/2017] [Accepted: 03/21/2017] [Indexed: 11/24/2022] Open
Abstract
Measuring the dispersal of wildlife through landscapes is notoriously difficult. Recently, the categorical least cost path algorithm that integrates population genetic data with species distribution models has been applied to reveal population connectivity. In this study, we use this method to identify the possible dispersal corridors of five plant species (Castanopsis tibetana, Schima superba, Cyclocarya paliurus, Sargentodoxa cuneata, Eomecon chionantha) in the Poyang Lake Basin (PLB, largely coinciding with Jiangxi Province), China, in the late Quaternary. The results showed that the strongest population connectivity for the five species occurred in the Wuyi Mountains and the Yu Mountains of the eastern PLB (East Corridor) during the late Quaternary. In the western PLB, populations of the five species were connected by the Luoxiao Mountains and the Jiuling Mountains (West Corridor) but with a lower degree of connectivity. There were some minor connections between the eastern and the western populations across the Gannan Hills. When the corridors of five species were overlaid, the East Corridor and the West Corridor were mostly shared by multiple species. These results indicate that plant species in the PLB could have responded to the Quaternary climate changes by moving along the East Corridor and the West Corridor. Given that dispersal corridors have seldom been considered in the governmental strategies of biodiversity conservation in the PLB, preserving and restoring natural vegetation along these corridors should be prioritized to mitigate the effects of anthropogenic climate change by facilitating migration of plant species and other biota.
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Affiliation(s)
- Dengmei Fan
- Laboratory of Subtropical Biodiversity Jiangxi Agricultural University Nanchang Jiangxi China
| | - Zhixia Sun
- Laboratory of Subtropical Biodiversity Jiangxi Agricultural University Nanchang Jiangxi China
| | - Bo Li
- Laboratory of Subtropical Biodiversity Jiangxi Agricultural University Nanchang Jiangxi China
| | - Yixuan Kou
- Laboratory of Subtropical Biodiversity Jiangxi Agricultural University Nanchang Jiangxi China
| | | | - Zhinong Jin
- Nanchang Institute of Technology Nanchang Jiangxi China
| | - Zhiyong Zhang
- Laboratory of Subtropical Biodiversity Jiangxi Agricultural University Nanchang Jiangxi China
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205
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Satler JD, Carstens BC. Do ecological communities disperse across biogeographic barriers as a unit? Mol Ecol 2017; 26:3533-3545. [DOI: 10.1111/mec.14137] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 03/13/2017] [Accepted: 03/29/2017] [Indexed: 01/15/2023]
Affiliation(s)
- Jordan D. Satler
- Department of Evolution, Ecology and Organismal BiologyThe Ohio State University Columbus OH USA
- Department of Ecology, Evolution, and Organismal Biology Iowa State University Ames IA USA
| | - Bryan C. Carstens
- Department of Evolution, Ecology and Organismal BiologyThe Ohio State University Columbus OH USA
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206
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Yu H, Zhang Y, Wang Z, Liu L, Chen Z, Qi W. Diverse range dynamics and dispersal routes of plants on the Tibetan Plateau during the late Quaternary. PLoS One 2017; 12:e0177101. [PMID: 28475607 PMCID: PMC5419580 DOI: 10.1371/journal.pone.0177101] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Accepted: 04/22/2017] [Indexed: 11/19/2022] Open
Abstract
Phylogeographical studies have suggested that several plant species on the Tibetan Plateau (TP) underwent recolonization during the Quaternary and may have had distinct range dynamics in response to the last glacial. To further test this hypothesis and locate the possible historical dispersal routes, we selected 20 plant species from different parts of the TP and modeled their geographical distributions over four time periods using species distribution models (SDMs). Furthermore, we applied the least-cost path method together with SDMs and shared haplotypes to estimate their historical dispersal corridors. We identified three general scenarios of species distribution change during the late Quaternary: the 'contraction-expansion' scenario for species in the northeastern TP, the 'expansion-contraction' scenario for species in the southeast and the 'stable' scenario for widespread species. During the Quaternary, we identified that these species were likely to recolonize along the low-elevation valleys, huge mountain ranges and flat plateau platform (e.g. the Yarlung Zangbo Valley and the Himalaya). We inferred that Quaternary cyclic glaciations along with the various topographic and climatic conditions of the TP could have resulted in the diverse patterns of range shift and dispersal of Tibetan plant species. Finally, we believe that this study would provide valuable insights for the conservation of alpine species under future climate change.
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Affiliation(s)
- Haibin Yu
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resource Research, Chinese Academy of Sciences, Beijing, P. R. China
- School of Life Sciences, Sun Yat-sen University, Guangzhou, P. R. China
| | - Yili Zhang
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resource Research, Chinese Academy of Sciences, Beijing, P. R. China
- University of Chinese Academy of Sciences, Beijing, P. R. China
- * E-mail:
| | - Zhaofeng Wang
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resource Research, Chinese Academy of Sciences, Beijing, P. R. China
| | - Linshan Liu
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resource Research, Chinese Academy of Sciences, Beijing, P. R. China
| | - Zhao Chen
- Guangdong Institute of Eco-environmental Science & Technology, Guangzhou, P. R. China
| | - Wei Qi
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resource Research, Chinese Academy of Sciences, Beijing, P. R. China
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207
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Cornejo-Romero A, Vargas-Mendoza CF, Aguilar-Martínez GF, Medina-Sánchez J, Rendón-Aguilar B, Valverde PL, Zavala-Hurtado JA, Serrato A, Rivas-Arancibia S, Pérez-Hernández MA, López-Ortega G, Jiménez-Sierra C. Alternative glacial-interglacial refugia demographic hypotheses tested on Cephalocereus columna-trajani (Cactaceae) in the intertropical Mexican drylands. PLoS One 2017; 12:e0175905. [PMID: 28426818 PMCID: PMC5398652 DOI: 10.1371/journal.pone.0175905] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 04/02/2017] [Indexed: 12/27/2022] Open
Abstract
Historic demography changes of plant species adapted to New World arid environments could be consistent with either the Glacial Refugium Hypothesis (GRH), which posits that populations contracted to refuges during the cold-dry glacial and expanded in warm-humid interglacial periods, or with the Interglacial Refugium Hypothesis (IRH), which suggests that populations contracted during interglacials and expanded in glacial times. These contrasting hypotheses are developed in the present study for the giant columnar cactus Cephalocereus columna-trajani in the intertropical Mexican drylands where the effects of Late Quaternary climatic changes on phylogeography of cacti remain largely unknown. In order to determine if the historic demography and phylogeographic structure of the species are consistent with either hypothesis, sequences of the chloroplast regions psbA-trnH and trnT-trnL from 110 individuals from 10 populations comprising the full distribution range of this species were analysed. Standard estimators of genetic diversity and structure were calculated. The historic demography was analysed using a Bayesian approach and the palaeodistribution was derived from ecological niche modelling to determine if, in the arid environments of south-central Mexico, glacial-interglacial cycles drove the genetic divergence and diversification of this species. Results reveal low but statistically significant population differentiation (FST = 0.124, P < 0.001), although very clear geographic clusters are not formed. Genetic diversity, haplotype network and Approximate Bayesian Computation (ABC) demographic analyses suggest a population expansion estimated to have taken place in the Last Interglacial (123.04 kya, 95% CI 115.3–130.03). The species palaeodistribution is consistent with the ABC analyses and indicates that the potential area of palaedistribution and climatic suitability were larger during the Last Interglacial and Holocene than in the Last Glacial Maximum. Overall, these results suggest that C. columna-trajani experienced an expansion following the warm conditions of interglacials, in accordance with the GRH.
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Affiliation(s)
- Amelia Cornejo-Romero
- Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, CD México, México
| | - Carlos Fabián Vargas-Mendoza
- Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, CD México, México
- * E-mail:
| | - Gustavo F. Aguilar-Martínez
- Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, CD México, México
| | | | - Beatriz Rendón-Aguilar
- Departamento de Biología, Universidad Autónoma Metropolitana-Iztapalapa, CD México, México
| | - Pedro Luis Valverde
- Departamento de Biología, Universidad Autónoma Metropolitana-Iztapalapa, CD México, México
| | | | - Alejandra Serrato
- Departamento de Hidrobiología, Universidad Autónoma Metropolitana-Iztapalapa, CD México, México
| | | | | | - Gerardo López-Ortega
- Departamento de Biología, Universidad Autónoma Metropolitana-Iztapalapa, CD México, México
| | - Cecilia Jiménez-Sierra
- Departamento de Biología, Universidad Autónoma Metropolitana-Iztapalapa, CD México, México
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208
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Wallis GP, Cameron-Christie SR, Kennedy HL, Palmer G, Sanders TR, Winter DJ. Interspecific hybridization causes long-term phylogenetic discordance between nuclear and mitochondrial genomes in freshwater fishes. Mol Ecol 2017; 26:3116-3127. [DOI: 10.1111/mec.14096] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 02/22/2017] [Accepted: 03/01/2017] [Indexed: 12/22/2022]
Affiliation(s)
- Graham P. Wallis
- Department of Zoology; University of Otago; PO Box 56 Dunedin 9054 New Zealand
| | - Sophia R. Cameron-Christie
- Women's and Children's Health; Paediatrics & Child Health; Dunedin School of Medicine; University of Otago; PO Box 56 Dunedin 9054 New Zealand
| | - Hannah L. Kennedy
- Molecular Pathology Laboratory; Canterbury Health Laboratories; PO Box 151 Christchurch 8140 New Zealand
- Department of Pathology; University of Otago; Riccarton Avenue PO Box 4345 Christchurch 8140 New Zealand
| | - Gemma Palmer
- Melbourne IVF; Suite 10 320 Victoria Parade East Melbourne Vic. 3002 Australia
| | - Tessa R. Sanders
- National Institutes of Health; 9000 Rockville Pike Bethesda MD 20892 USA
| | - David J. Winter
- Institute of Fundamental Sciences; Massey University; Private Bag 11 222 Palmerston North 4442 New Zealand
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209
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Vickruck JL, Richards MH. Nesting habits influence population genetic structure of a bee living in anthropogenic disturbance. Mol Ecol 2017; 26:2674-2686. [DOI: 10.1111/mec.14064] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 01/30/2017] [Accepted: 02/09/2017] [Indexed: 01/22/2023]
Affiliation(s)
- J. L. Vickruck
- Department of Biological Sciences; Brock University; 1812 Sir Isaac Brock Way St. Catharines ON Canada L2S 3A1
| | - M. H. Richards
- Department of Biological Sciences; Brock University; 1812 Sir Isaac Brock Way St. Catharines ON Canada L2S 3A1
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210
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211
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Nalepa CA, Shimada K, Maekawa K, Luykx P. Distribution of Karyotypes of the Cryptocercus punctulatus Species Complex (Blattodea: Cryptocercidae) in Great Smoky Mountains National Park. JOURNAL OF INSECT SCIENCE (ONLINE) 2017; 17:3793261. [PMID: 28475683 PMCID: PMC5416888 DOI: 10.1093/jisesa/iex045] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Indexed: 06/07/2023]
Abstract
During the period between 1999 and 2006, wood-feeding cockroaches in the Cryptocercus punctulatus Scudder species complex were collected throughout Great Smoky Mountains National Park, USA. The chromosome numbers of insects from 59 sites were determined, and phylogenetic analyses were performed based on mitochondrial COII and nuclear ITS2 DNA. The distribution of the three male karyotypes found in the park (2n = 37, 39, and 45) is mapped and discussed in relation to recent disturbances and glacial history. Clades of the three karyotype groups meet near the ridgeline separating North Carolina from Tennessee in the center of the park, suggesting that these may have originated from separate lower elevation refugia after the last glacial maximum. The timing of divergence and a significant correlation between elevation difference and genetic distance in two of the clades supports this hypothesis. The ecological role of the cockroaches in the park is discussed.
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Affiliation(s)
- Christine A Nalepa
- Department of Entomology, North Carolina State University, Campus Box 7613, Raleigh, NC 27695-7613, USA
| | - Keisuke Shimada
- Graduate School of Science and Engineering, University of Toyama, 3190 Gofuku, Toyama, Toyama 930-8555, Japan ( ; )
- Current address: Ishikawa Museum of Natural History, Ri-441 Choshi-machi, Kanazawa, Ishikawa 920-1147, Japan
| | - Kiyoto Maekawa
- Graduate School of Science and Engineering, University of Toyama, 3190 Gofuku, Toyama, Toyama 930-8555, Japan (; )
| | - Peter Luykx
- Department of Biology, University of Miami, Coral Gables, FL 33124, USA
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212
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Bagley RK, Sousa VC, Niemiller ML, Linnen CR. History, geography and host use shape genomewide patterns of genetic variation in the redheaded pine sawfly (
Neodiprion lecontei
). Mol Ecol 2017; 26:1022-1044. [DOI: 10.1111/mec.13972] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 11/10/2016] [Accepted: 12/01/2016] [Indexed: 01/03/2023]
Affiliation(s)
- Robin K. Bagley
- Department of Biology University of Kentucky Lexington KY 40506 USA
| | - Vitor C. Sousa
- cE3c ‐ Centre for Ecology, Evolution and Environmental Changes Faculdade de Ciências Universidade de Lisboa 1749‐016 Lisboa Portugal
| | - Matthew L. Niemiller
- Illinois Natural History Survey Prairie Research Institute University of Illinois Urbana‐Champaign Champaign IL 61820 USA
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213
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Landscape Genomics of Angiosperm Trees: From Historic Roots to Discovering New Branches of Adaptive Evolution. COMPARATIVE AND EVOLUTIONARY GENOMICS OF ANGIOSPERM TREES 2017. [DOI: 10.1007/7397_2016_19] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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214
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Ecological divergence in the yellow-bellied kingsnake (Lampropeltis calligaster) at two North American biodiversity hotspots. Mol Phylogenet Evol 2017; 106:61-72. [DOI: 10.1016/j.ympev.2016.09.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 08/25/2016] [Accepted: 09/12/2016] [Indexed: 11/22/2022]
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215
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Pennings SC, Zengel S, Oehrig J, Alber M, Bishop TD, Deis DR, Devlin D, Hughes AR, Hutchens JJ, Kiehn WM, McFarlin CR, Montague CL, Powers S, Proffitt CE, Rutherford N, Stagg CL, Walters K. Marine ecoregion and
D
eepwater
H
orizon
oil spill affect recruitment and population structure of a salt marsh snail. Ecosphere 2016. [DOI: 10.1002/ecs2.1588] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Affiliation(s)
- Steven C. Pennings
- Department of Biology and Biochemistry University of Houston Houston Texas 77204 USA
| | - Scott Zengel
- Research Planning, Inc. (RPI) Tallahassee Florida 32303 USA
| | | | - Merryl Alber
- Department of Marine Sciences University of Georgia Athens Georgia 30602 USA
| | - T. Dale Bishop
- No Bones Coastal Biological Consultants, LLC 1114 Hyatt Avenue Murrells Inlet South Carolina 29576 USA
| | | | - Donna Devlin
- Department of Biological Sciences Harbor Branch Oceanographic Institution Florida Atlantic University 5600 U.S. 1 N Fort Pierce Florida 34946 USA
| | - A. Randall Hughes
- Marine and Environmental Science Northeastern University Nahant Massachusetts 01908 USA
| | - John J. Hutchens
- Department of Biology Coastal Carolina University PO Box 261954 Conway South Carolina 29528 USA
| | | | | | - Clay L. Montague
- Howard T. Odum Center For Wetlands Department of Environmental Engineering Sciences University of Florida Gainesville Florida 32611 USA
| | - Sean Powers
- Department of Marine Sciences University of South Alabama Mobile Alabama 36688 USA
| | - C. Edward Proffitt
- Department of Biological Sciences Harbor Branch Oceanographic Institution Florida Atlantic University 5600 U.S. 1 N Fort Pierce Florida 34946 USA
| | - Nicolle Rutherford
- Emergency Response Division National Oceanic and Atmospheric Administration Seattle Washington 98115 USA
| | - Camille L. Stagg
- U.S. Geological Survey Wetland and Aquatic Research Center Lafayette Louisiana 70506 USA
| | - Keith Walters
- Department of Marine Science Coastal Carolina University PO Box 261954 Conway South Carolina 29528 USA
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216
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Françoso E, Zuntini AR, Carnaval AC, Arias MC. Comparative phylogeography in the Atlantic forest and Brazilian savannas: pleistocene fluctuations and dispersal shape spatial patterns in two bumblebees. BMC Evol Biol 2016; 16:267. [PMID: 27927169 PMCID: PMC5142330 DOI: 10.1186/s12862-016-0803-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Accepted: 10/14/2016] [Indexed: 01/23/2023] Open
Abstract
Background Bombus morio and B. pauloensis are sympatric widespread bumblebee species that occupy two major Brazilian biomes, the Atlantic forest and the savannas of the Cerrado. Differences in dispersion capacity, which is greater in B. morio, likely influence their phylogeographic patterns. This study asks which processes best explain the patterns of genetic variation observed in B. morio and B. pauloensis, shedding light on the phenomena that shaped the range of local populations and the spatial distribution of intra-specific lineages. Results Results suggest that Pleistocene climatic oscillations directly influenced the population structure of both species. Correlative species distribution models predict that the warmer conditions of the Last Interglacial contributed to population contraction, while demographic expansion happened during the Last Glacial Maximum. These results are consistent with physiological data suggesting that bumblebees are well adapted to colder conditions. Intra-specific mitochondrial genealogies are not congruent between the two species, which may be explained by their documented differences in dispersal ability. Conclusions While populations of the high-dispersal B. morio are morphologically and genetically homogeneous across the species range, B. pauloensis encompasses multiple (three) mitochondrial lineages, and show clear genetic, geographic, and morphological differences. Because the lineages of B. pauloensis are currently exposed to distinct climatic conditions (and elevations), parapatric diversification may occur within this taxon. The eastern portion of the state of São Paulo, the most urbanized area in Brazil, represents the center of genetic diversity for B. pauloensis. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0803-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elaine Françoso
- Instituto de Biociências, Universidade de São Paulo, Rua do Matão, 277, sala 320, 05508-090, São Paulo, SP, Brazil.
| | - Alexandre Rizzo Zuntini
- Instituto de Biologia, Universidade Estadual de Campinas, Rua Monteiro Lobato, 255, 13083-970, Campinas, SP, Brazil
| | - Ana Carolina Carnaval
- Department of Biology, City College of New York, New York, USA.,The Graduate Center, City University of New York, New York, NY, USA
| | - Maria Cristina Arias
- Instituto de Biociências, Universidade de São Paulo, Rua do Matão, 277, sala 320, 05508-090, São Paulo, SP, Brazil
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217
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Casazza G, Grassi F, Zecca G, Minuto L. Phylogeographic Insights into a Peripheral Refugium: The Importance of Cumulative Effect of Glaciation on the Genetic Structure of Two Endemic Plants. PLoS One 2016; 11:e0166983. [PMID: 27870888 PMCID: PMC5117763 DOI: 10.1371/journal.pone.0166983] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 11/07/2016] [Indexed: 11/18/2022] Open
Abstract
Quaternary glaciations and mostly last glacial maximum have shaped the contemporary distribution of many species in the Alps. However, in the Maritime and Ligurian Alps a more complex picture is suggested by the presence of many Tertiary paleoendemisms and by the divergence time between lineages in one endemic species predating the Late Pleistocene glaciation. The low number of endemic species studied limits the understanding of the processes that took place within this region. We used species distribution models and phylogeographical methods to infer glacial refugia and to reconstruct the phylogeographical pattern of Silene cordifolia All. and Viola argenteria Moraldo & Forneris. The predicted suitable area for last glacial maximum roughly fitted current known distribution. Our results suggest that separation of the major clades predates the last glacial maximum and the following repeated glacial and interglacial periods probably drove differentiations. The complex phylogeographical pattern observed in the study species suggests that both populations and genotypes extinction was minimal during the last glacial maximum, probably due to the low impact of glaciations and to topographic complexity in this area. This study underlines the importance of cumulative effect of previous glacial cycles in shaping the genetic structure of plant species in Maritime and Ligurian Alps, as expected for a Mediterranean mountain region more than for an Alpine region.
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Affiliation(s)
- Gabriele Casazza
- DISTAV, Università degli studi di Genova, Genova, Italy
- * E-mail:
| | - Fabrizio Grassi
- Dipartimento di Biologia, Università degli studi di Bari, Bari, Italy
| | - Giovanni Zecca
- Dipartimento di Bioscienze, Università degli studi di Milano, Milano, Italy
| | - Luigi Minuto
- DISTAV, Università degli studi di Genova, Genova, Italy
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Ikezaki Y, Suyama Y, Middleton BA, Tsumura Y, Teshima K, Tachida H, Kusumi J. Inferences of population structure and demographic history for Taxodium distichum, a coniferous tree in North America, based on amplicon sequencing analysis. AMERICAN JOURNAL OF BOTANY 2016; 103:1937-1949. [PMID: 27849160 DOI: 10.3732/ajb.1600046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 10/03/2016] [Indexed: 06/06/2023]
Abstract
PREMISE OF THE STUDY Studies of natural genetic variation can elucidate the genetic basis of phenotypic variation and the past population structure of species. Our study species, Taxodium distichum, is a unique conifer that inhabits the flood plains and swamps of North America. Morphological and ecological differences in two varieties, T. distichum var. distichum (bald cypress) and T. distichum var. imbricarium (pond cypress), are well known, but little is known about the level of genetic differentiation between the varieties and the demographic history of local populations. METHODS We analyzed nucleotide polymorphisms at 47 nuclear loci from 96 individuals collected from the Mississippi River Alluvial Valley (MRAV), and Gulf Coastal populations in Texas, Louisiana, and Florida using high-throughput DNA sequencing. Standard population genetic statistics were calculated, and demographic parameters were estimated using a composite-likelihood approach. KEY RESULTS Taxodium distichum in North America can be divided into at least three genetic groups, bald cypress in the MRAV and Texas, bald cypress in Florida, and pond cypress in Florida. The levels of genetic differentiation among the groups were low but significant. Several loci showed the signatures of positive selection, which might be responsible for local adaptation or varietal differentiation. CONCLUSIONS Bald cypress was genetically differentiated into two geographical groups, and the boundary was located between the MRAV and Florida. This differentiation could be explained by population expansion from east to west. Despite the overlap of the two varieties' ranges, they were genetically differentiated in Florida. The estimated demographic parameters suggested that pond cypress split from bald cypress during the late Miocene.
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Affiliation(s)
- Yuka Ikezaki
- Graduate School of Systems Life Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Yoshihisa Suyama
- Graduate School of Agricultural Science, Tohoku University, 232-3 Yomogida, Naruko-onsen, Osaki, Miyagi 989-6711, Japan
| | - Beth A Middleton
- Wetland and Aquatic Research Center, U.S. Geological Survey, Lafayette, Louisiana 70506 USA
| | - Yoshihiko Tsumura
- Faculty of Life & Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Kousuke Teshima
- Department of Biology, Faculty of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Hidenori Tachida
- Department of Biology, Faculty of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Junko Kusumi
- Department of Environmental Changes, Faculty of Social and Cultural Studies, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
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219
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Dolman G, Joseph L. Multi-locus sequence data illuminate demographic drivers of Pleistocene speciation in semi-arid southern Australian birds (Cinclosoma spp.). BMC Evol Biol 2016; 16:226. [PMID: 27770777 PMCID: PMC5075194 DOI: 10.1186/s12862-016-0798-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 10/12/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND During the Pleistocene, shifts of species distributions and their isolation in disjunct refugia led to varied outcomes in how taxa diversified. Some species diverged, others did not. Here, we begin to address another facet of the role of the Pleistocene in generating today's diversity. We ask which processes contributed to divergence in semi-arid southern Australian birds. We isolated 11 autosomal nuclear loci and one mitochondrial locus from a total of 29 specimens of the sister species pair, Chestnut Quail-thrush Cinclosoma castanotum and Copperback Quail-thrush C. clarum. RESULTS A population clustering analysis confirmed the location of the current species boundary as a well-known biogeographical barrier in southern Australia, the Eyrean Barrier. Coalescent-based analyses placed the time of species divergence to the Middle Pleistocene. Gene flow between the species since divergence has been low. The analyses suggest the effective population size of the ancestor was 54 to 178 times smaller than populations since divergence. This contrasts with recent multi-locus studies in some other Australian birds (butcherbirds, ducks) where a lack of phenotypic divergence was accompanied by larger historical population sizes. Post-divergence population size histories of C. clarum and C. castanotum were inferred using the extended Bayesian skyline model. The population size of C. clarum increased substantially during the late Pleistocene and continued to increase through the Last Glacial Maximum and Holocene. The timing of this expansion across its vast range is broadly concordant with that documented in several other Australian birds. In contrast, effective population size of C. castanotum was much more constrained and may reflect its smaller range and more restricted habitat east of the Eyrean Barrier compared with that available to C. clarum to the west. CONCLUSIONS Our results contribute to awareness of increased population sizes, following significant contractions, as having been important in shaping diversity in Australian arid and semi-arid zones. Further, we improve knowledge of the role of Pleistocene climatic shifts in areas of the planet that were not glaciated at that time but which still experienced that period's cyclical climatic fluctuations.
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Affiliation(s)
- Gaynor Dolman
- Molecular Systematics Unit, Western Australian Museum, Locked Bag 49, Welshpool DC, WA, 6986, Australia. .,Australian National Wildlife Collection, CSIRO National Research Collections Australia, GPO Box 1700, Canberra, ACT, 2601, Australia. .,Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, University of Adelaide, Adelaide, SA, 5005, Australia.
| | - Leo Joseph
- Australian National Wildlife Collection, CSIRO National Research Collections Australia, GPO Box 1700, Canberra, ACT, 2601, Australia
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220
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Manthey JD, Tollis M, Lemmon AR, Moriarty Lemmon E, Boissinot S. Diversification in wild populations of the model organism Anolis carolinensis: A genome-wide phylogeographic investigation. Ecol Evol 2016; 6:8115-8125. [PMID: 27891220 PMCID: PMC5108263 DOI: 10.1002/ece3.2547] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 09/14/2016] [Accepted: 09/19/2016] [Indexed: 01/14/2023] Open
Abstract
The green anole (Anolis carolinensis) is a lizard widespread throughout the southeastern United States and is a model organism for the study of reproductive behavior, physiology, neural biology, and genomics. Previous phylogeographic studies of A. carolinensis using mitochondrial DNA and small numbers of nuclear loci identified conflicting and poorly supported relationships among geographically structured clades; these inconsistencies preclude confident use of A. carolinensis evolutionary history in association with morphological, physiological, or reproductive biology studies among sampling localities and necessitate increased effort to resolve evolutionary relationships among natural populations. Here, we used anchored hybrid enrichment of hundreds of genetic markers across the genome of A. carolinensis and identified five strongly supported phylogeographic groups. Using multiple analyses, we produced a fully resolved species tree, investigated relative support for each lineage across all gene trees, and identified mito‐nuclear discordance when comparing our results to previous studies. We found fixed differences in only one clade—southern Florida restricted to the Everglades region—while most polymorphisms were shared between lineages. The southern Florida group likely diverged from other populations during the Pliocene, with all other diversification during the Pleistocene. Multiple lines of support, including phylogenetic relationships, a latitudinal gradient in genetic diversity, and relatively more stable long‐term population sizes in southern phylogeographic groups, indicate that diversification in A. carolinensis occurred northward from southern Florida.
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Affiliation(s)
| | - Marc Tollis
- Biodesign Institute Arizona State University Tempe AZ USA
| | - Alan R Lemmon
- Department of Scientific Computing Florida State University Tallahassee FL USA
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Désamoré A, Patiño J, Mardulyn P, Mcdaniel SF, Zanatta F, Laenen B, Vanderpoorten A. High migration rates shape the postglacial history of amphi-Atlantic bryophytes. Mol Ecol 2016; 25:5568-5584. [PMID: 27661065 DOI: 10.1111/mec.13839] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Revised: 08/29/2016] [Accepted: 08/31/2016] [Indexed: 11/28/2022]
Abstract
Paleontological evidence and current patterns of angiosperm species richness suggest that European biota experienced more severe bottlenecks than North American ones during the last glacial maximum. How well this pattern fits other plant species is less clear. Bryophytes offer a unique opportunity to contrast the impact of the last glacial maximum in North America and Europe because about 60% of the European bryoflora is shared with North America. Here, we use population genetic analyses based on approximate Bayesian computation on eight amphi-Atlantic species to test the hypothesis that North American populations were less impacted by the last glacial maximum, exhibiting higher levels of genetic diversity than European ones and ultimately serving as a refugium for the postglacial recolonization of Europe. In contrast with this hypothesis, the best-fit demographic model involved similar patterns of population size contractions, comparable levels of genetic diversity and balanced migration rates between European and North American populations. Our results thus suggest that bryophytes have experienced comparable demographic glacial histories on both sides of the Atlantic. Although a weak, but significant genetic structure was systematically recovered between European and North American populations, evidence for migration from and towards both continents suggests that amphi-Atlantic bryophyte population may function as a metapopulation network. Reconstructing the biogeographic history of either North American or European bryophyte populations therefore requires a large, trans-Atlantic geographic framework.
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Affiliation(s)
- Aurélie Désamoré
- Institute of Botany, University of Liège, B22 Sart Tilman, Liège, Belgium. .,Department of Zoology, Swedish Museum of Natural History, Box 50007, SE-104 05, Stockholm, Sweden.
| | - Jairo Patiño
- Institute of Botany, University of Liège, B22 Sart Tilman, Liège, Belgium.,Island Ecology and Evolution Research Group, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), Tenerife, Canary Islands, 38206, Spain.,Centre for Ecology, Evolution and Environmental Changes and Platform for Enhancing Ecological Research & Sustainability, Universidade dos Açores, 9700-042, Angra do Heroísmo, Terceira, Açores, Portugal
| | - Patrick Mardulyn
- Department of Evolutionary Biology and Ecology, Université libre de Bruxelles, Campus du Solbosch, Avenue F.D. Roosevelt 50, 1050, Bruxelles, Belgium
| | - Stuart F Mcdaniel
- Department of Biology, University of Florida, Box 118525, Gainesville, FL, 32611-8525, USA
| | - Florian Zanatta
- Institute of Botany, University of Liège, B22 Sart Tilman, Liège, Belgium
| | - Benjamin Laenen
- Institute of Botany, University of Liège, B22 Sart Tilman, Liège, Belgium.,SciLifeLab Stockholm, Department of Ecology, Environment and Plant Sciences, Stockholm University, Tomtebodav. 23a, 171 21, Solna, Stockholm, Sweden
| | - Alain Vanderpoorten
- Institute of Botany, University of Liège, B22 Sart Tilman, Liège, Belgium.,Island Ecology and Evolution Research Group, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), Tenerife, Canary Islands, 38206, Spain
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Bemmels JB, Title PO, Ortego J, Knowles LL. Tests of species‐specific models reveal the importance of drought in postglacial range shifts of a Mediterranean‐climate tree: insights from integrative distributional, demographic and coalescent modelling and
ABC
model selection. Mol Ecol 2016; 25:4889-906. [DOI: 10.1111/mec.13804] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Revised: 08/02/2016] [Accepted: 08/04/2016] [Indexed: 01/15/2023]
Affiliation(s)
- Jordan B. Bemmels
- Department of Ecology and Evolutionary Biology University of Michigan 830 N. University Ave. Ann Arbor MI 48109 USA
| | - Pascal O. Title
- Department of Ecology and Evolutionary Biology University of Michigan 830 N. University Ave. Ann Arbor MI 48109 USA
| | - Joaquín Ortego
- Department of Integrative Ecology Estación Biológica de Doñana EBD‐CSIC Avda. Américo Vespucio s/n E‐41092 Seville Spain
| | - L. Lacey Knowles
- Department of Ecology and Evolutionary Biology University of Michigan 830 N. University Ave. Ann Arbor MI 48109 USA
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223
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Idiosyncratic responses of evergreen broad-leaved forest constituents in China to the late Quaternary climate changes. Sci Rep 2016; 6:31044. [PMID: 27534981 PMCID: PMC4989166 DOI: 10.1038/srep31044] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 07/06/2016] [Indexed: 11/24/2022] Open
Abstract
Subtropical evergreen broad-leaved forest (EBLF) is one of the most important vegetation types in China. Inferences from palaeo-biome reconstruction (PBR) and phylogeography regarding range shift history of EBLF during the late Quaternary are controversial and should be reconciled. We compared phylogeographic patterns of three EBLF constituents in China, Castanopsis tibetana, Machilus thunbergii and Schima superba. Contrary to a chorus of previous phylogeographic studies and the results of species distribution modelling (SDM) of this study (in situ survival during the LGM), the three species displayed three different phylogeographic patterns that conform to either an in situ survival model or an expansion-contraction model. These results are partially congruent with the inference of PBR that EBLF was absent to the north of 24° N at the LGM. This study suggests that the constituents of EBLF could have responded idiosyncratically to climate changes during the Late Quaternary. The community assemblages of EBLF could have been changing over time, resulting in no palaeo-analogs to modern-day EBLF, which may be the main reason responsible for the failure of PBR to detect the occurrence of EBLF north of 24° N at the LGM.
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Roy T, Catlin NS, Garner DMG, Cantino PD, Scheen AC, Lindqvist C. Evolutionary relationships within the lamioid tribe Synandreae (Lamiaceae) based on multiple low-copy nuclear loci. PeerJ 2016; 4:e2220. [PMID: 27547537 PMCID: PMC4958014 DOI: 10.7717/peerj.2220] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Accepted: 06/15/2016] [Indexed: 11/20/2022] Open
Abstract
The subfamily Lamioideae (Lamiaceae) comprises ten tribes, of which only Stachydeae and Synandreae include New World members. Previous studies have investigated the phylogenetic relationships among the members of Synandreae based on plastid and nuclear ribosomal DNA loci. In an effort to re-examine the phylogenetic relationships within Synandreae, the current study incorporates data from four low-copy nuclear loci, PHOT1, PHOT2, COR, and PPR. Our results confirm previous studies based on chloroplast and nuclear ribosomal markers in supporting the monophyly of tribe Synandreae, as well as sister relationships between Brazoria and Warnockia, and between that pair of genera and a monophyletic Physostegia. However, we observe incongruence in the relationships of Macbridea and Synandra. The placement of Synandreae within Lamioideae is poorly resolved and incongruent among different analyses, and the sister group of Synandreae remains enigmatic. Comparison of the colonization and migration patterns corroborates a single colonization of the New World by Synandreae during the Late Miocene/Tortonian age. This is in contrast to the only other lamioid tribe that includes New World members, Stachydeae, which colonized the New World at least twice—during the mid-Miocene and Pliocene. Edaphic conditions and intolerance of soil acidity may be factors that restricted the distribution of most genera of Synandreae to southeastern and south–central North America, whereas polyploidy could have increased the colonizing capability of the more wide-ranging genus, Physostegia.
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Affiliation(s)
- Tilottama Roy
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, United States; Current affiliation: Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, United States
| | - Nathan S Catlin
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, United States; Current affiliation: Department of Biology, University of Florida, Gainesville, FL, United States
| | - Drake M G Garner
- Department of Biological Sciences, University at Buffalo , Buffalo , NY , United States
| | - Philip D Cantino
- Department of Environmental and Plant Biology, Ohio University , Athens , OH , United States
| | | | - Charlotte Lindqvist
- Department of Biological Sciences, University at Buffalo , Buffalo , NY , United States
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225
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Papadopoulou A, Knowles LL. Toward a paradigm shift in comparative phylogeography driven by trait-based hypotheses. Proc Natl Acad Sci U S A 2016; 113:8018-24. [PMID: 27432974 PMCID: PMC4961141 DOI: 10.1073/pnas.1601069113] [Citation(s) in RCA: 138] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
For three decades, comparative phylogeography has conceptually and methodologically relied on the concordance criterion for providing insights into the historical/biogeographic processes driving population genetic structure and divergence. Here we discuss how this emphasis, and the corresponding lack of methods for extracting information about biotic/intrinsic contributions to patterns of genetic variation, may bias our general understanding of the factors driving genetic structure. Specifically, this emphasis has promoted a tendency to attribute discordant phylogeographic patterns to the idiosyncracies of history, as well as an adherence to generic null expectations of concordance with reduced predictive power. We advocate that it is time for a paradigm shift in comparative phylogeography, especially given the limited utility of the concordance criterion as genomic data provide ever-increasing levels of resolution. Instead of adhering to the concordance-discordance dichotomy, comparative phylogeography needs to emphasize the contribution of taxon-specific traits that will determine whether concordance is a meaningful criterion for evaluating hypotheses or may predict discordant phylogeographic structure. Through reference to some case studies we illustrate how refined hypotheses based on taxon-specific traits can provide improved predictive frameworks to forecast species responses to climatic change or biogeographic barriers while gaining unique insights about the taxa themselves and their interactions with their environment. We outline a potential avenue toward a synthetic comparative phylogeographic paradigm that includes addressing some important conceptual and methodological challenges related to study design and application of model-based approaches for evaluating support of trait-based hypotheses under the proposed paradigm.
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Affiliation(s)
- Anna Papadopoulou
- Department of Ecology and Evolutionary Biology, Museum of Zoology, University of Michigan, Ann Arbor, MI 48109; Department of Integrative Ecology, Estación Biológica de Doñana, Consejo Superior de Investigaciones Cientificas, 41092 Seville, Spain
| | - L Lacey Knowles
- Department of Ecology and Evolutionary Biology, Museum of Zoology, University of Michigan, Ann Arbor, MI 48109;
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226
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Craft JD, Harrelson D, Setzer WN. Chemotypic Variation of Conocephalum salebrosum in the Southeastern Appalachian Range: A Search for Cryptic Plant Biodiversity Around the Tennessee River Valley. Nat Prod Commun 2016. [DOI: 10.1177/1934578x1601100735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The chemotaxonomy of the Conocephalum spp. complex, based on GC-MS analysis of the volatile compositions, has helped to reveal cryptic biodiversity and delineate actual distribution patterns of chemotypes. In the Appalachian Mountains, two samples from eastern central part of the range were previously shown to be C. salebrosum. Additionally, it has recently come to light that stress can alter the volatile composition of C. conicum. This study address a previously unsampled region of the southeastern Appalachians, a region that is a biodiversity epicenter, to determine if more chemotypic diversity remains to be seen for the Conocephalum spp. complex. A common garden experiment was performed, but yielded more of a common stress experiment, and significantly altered the volatile compositions. Wild-collected controls and a meta-analysis of these data and those from previous works suggest that the common garden experiment caused stress and that the liverworts sampled belong to the C. salebrosum clade of of the Conocephalum spp. complex.
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Affiliation(s)
- Jonathan D. Craft
- Department of Chemistry, University of Alabama in Huntsville, Huntsville, AL 35899, USA
| | - Daniel Harrelson
- Department of Chemistry, University of Alabama in Huntsville, Huntsville, AL 35899, USA
| | - William N. Setzer
- Department of Chemistry, University of Alabama in Huntsville, Huntsville, AL 35899, USA
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227
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Su ZH, Zhang ML. Evolutionary History of a Desert Shrub Ephedra przewalskii (Ephedraceae): Allopatric Divergence and Range Shifts in Northwestern China. PLoS One 2016; 11:e0158284. [PMID: 27351630 PMCID: PMC4924853 DOI: 10.1371/journal.pone.0158284] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2015] [Accepted: 06/13/2016] [Indexed: 11/30/2022] Open
Abstract
Based on two chloroplast DNA sequences, psbA-trnH and trnT-trnF, phylogeographical patterns of a desert shrub, Ephedra przewalskii, were examined across most of its geographic range in northwestern China. A total of sixteen haplotypes were detected. There was a common haplotype in each basin, that was haplotype A in Tarim Basin, haplotype G in Junggar Basin, and haplotype M in Qaidam Basin. Genetic variance mainly occurred among populations, geographic regions, and eleven geographic groups subdivided by SAMOVA analysis. E. przewalskii likely had a smaller and more fragmented geographic range during the Last Glacial Maximum, which was determined based on ecological niche modelling. Three groups of E. przewalskii populations were detected to have experience range expansion, and this was based on significant values of Fu’s FS, Tajima’s D, and unimodel mismatch distributions. The cold and dry climate during the glacial period of the Quaternary is postulated to have been a driver for significant genetic isolation and divergence among populations or groups in E. przewalskii, whereas the warmer and wetter climate during the interglacial period is speculated to have provided favourable conditions for range expansion of the species.
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Affiliation(s)
- Zhi-Hao Su
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
| | - Ming-Li Zhang
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
- Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- * E-mail:
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228
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Martin MD, Olsen MT, Samaniego JA, Zimmer EA, Gilbert MTP. The population genomic basis of geographic differentiation in North American common ragweed ( Ambrosia artemisiifolia L.). Ecol Evol 2016; 6:3760-3771. [PMID: 28725355 PMCID: PMC5513308 DOI: 10.1002/ece3.2143] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Revised: 03/25/2016] [Accepted: 03/27/2016] [Indexed: 12/30/2022] Open
Abstract
Common ragweed (Ambrosia artemisiifolia L.) is an invasive, wind-pollinated plant nearly ubiquitous in disturbed sites in its eastern North American native range and present across growing portions of Europe, Africa, Asia, and Australia. Phenotypic divergence between European and native-range populations has been described as rapid evolution. However, a recent study demonstrated major human-mediated shifts in ragweed genetic structure before introduction to Europe and suggested that native-range genetic structure and local adaptation might fully explain accelerated growth and other invasive characteristics of introduced populations. Genomic differentiation that potentially influenced this structure has not yet been investigated, and it remains unclear whether substantial admixture during historical disturbance of the native range contributed to the development of invasiveness in introduced European ragweed populations. To investigate fine-scale population genetic structure across the species' native range, we characterized diallelic SNP loci via a reduced-representation genotyping-by-sequencing (GBS) approach. We corroborate phylogeographic domains previously discovered using traditional sequencing methods, while demonstrating increased power to resolve weak genetic structure in this highly admixed plant species. By identifying exome polymorphisms underlying genetic differentiation, we suggest that geographic differentiation of this important invasive species has occurred more often within pathways that regulate growth and response to defense and stress, which may be associated with survival in North America's diverse climatic regions.
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Affiliation(s)
- Michael D. Martin
- Centre for GeoGeneticsNatural History Museum of DenmarkFaculty of ScienceUniversity of CopenhagenØster Voldgade 5‐71350Copenhagen KDenmark
- Center for Theoretical Evolutionary GenomicsUniversity of CaliforniaValley Life Sciences BuildingBerkeleyCalifornia
- Department of Natural HistoryUniversity MuseumNorwegian University of Science and Technology (NTNU)NO‐7491TrondheimNorway
| | - Morten Tange Olsen
- Centre for GeoGeneticsNatural History Museum of DenmarkFaculty of ScienceUniversity of CopenhagenØster Voldgade 5‐71350Copenhagen KDenmark
| | - Jose A. Samaniego
- Centre for GeoGeneticsNatural History Museum of DenmarkFaculty of ScienceUniversity of CopenhagenØster Voldgade 5‐71350Copenhagen KDenmark
| | - Elizabeth A. Zimmer
- Department of Botany and Laboratories of Analytical BiologyNational Museum of Natural HistorySmithsonian InstitutionMuseum Support CenterMRC 534, 4210 Silver Hill RoadSuitlandMaryland20746
| | - M. Thomas P. Gilbert
- Centre for GeoGeneticsNatural History Museum of DenmarkFaculty of ScienceUniversity of CopenhagenØster Voldgade 5‐71350Copenhagen KDenmark
- Department of Natural HistoryUniversity MuseumNorwegian University of Science and Technology (NTNU)NO‐7491TrondheimNorway
- Trace and Environmental DNA LaboratoryDepartment of Environment and AgricultureCurtin UniversityPerthWestern Australia6102Australia
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229
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Colin R, Eguiarte LE. Phylogeographic analyses and genetic structure illustrate the complex evolutionary history of Phragmites australis in Mexico. AMERICAN JOURNAL OF BOTANY 2016; 103:876-887. [PMID: 27208356 DOI: 10.3732/ajb.1500399] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 03/06/2016] [Indexed: 06/05/2023]
Abstract
PREMISE OF THE STUDY Genetic data suggest that three lineages of Phragmites australis are found in North America: the Native North American lineage, the Gulf Coast lineage, and the Invasive lineage. In Mexico, P. australis is a common species, but nothing is known about the distribution or ecology of these lineages. We examined the phylogeography of P. australis to analyze the current geographic distribution of genetic variation, demographic history, and dispersal patterns to better understand its evolutionary history in Mexico. METHODS We sampled 427 individuals from 28 populations. We used two noncoding regions of chloroplast DNA to estimate the levels of genetic variation and identified the genetic groups across the species' geographical range in Mexico. We compared the genealogical relationships among haplotypes with those previously reported. A hypothesis of demographic expansion was also tested for the Mexican P. australis lineages. KEY RESULTS We found 13 new haplotypes native to Mexico that might be undergoing an active process of expansion and diversification. Genealogical analyses provided evidence that two independent lineages of P. australis are present in Mexico. The invasive lineage was not detected with our sampling. Our estimates of population expansions in Mexico ranged from 0.202 to 0.726 mya. CONCLUSIONS Phragmites australis is a native species that has been in Mexico for thousands of years. Genetic data suggest that climatic changes during the Pleistocene played an important role in the demographic expansion of the populations that constitute the different genetic groups of P. australis in Mexico.
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Affiliation(s)
- Ricardo Colin
- Laboratorio de Evolución Molecular y Experimental, Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Circuito exterior s/n anexo al Jardín Botánico, Ciudad Universitaria 04510 México D.F., México
| | - Luis E Eguiarte
- Laboratorio de Evolución Molecular y Experimental, Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Circuito exterior s/n anexo al Jardín Botánico, Ciudad Universitaria 04510 México D.F., México
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Satler JD, Carstens BC. Phylogeographic concordance factors quantify phylogeographic congruence among co-distributed species in the Sarracenia alata pitcher plant system. Evolution 2016; 70:1105-19. [PMID: 27076412 DOI: 10.1111/evo.12924] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 03/28/2016] [Accepted: 04/01/2016] [Indexed: 12/18/2022]
Abstract
Comparative phylogeographic investigations have identified congruent phylogeographic breaks in co-distributed species in nearly every region of the world. The qualitative assessments of phylogeographic patterns traditionally used to identify such breaks, however, are limited because they rely on identifying monophyletic groups across species and do not account for coalescent stochasticity. Only long-standing phylogeographic breaks are likely to be obvious; many species could have had a concerted response to more recent landscape events, yet possess subtle signs of phylogeographic congruence because ancestral polymorphism has not completely sorted. Here, we introduce Phylogeographic Concordance Factors (PCFs), a novel method for quantifying phylogeographic congruence across species. We apply this method to the Sarracenia alata pitcher plant system, a carnivorous plant with a diverse array of commensal organisms. We explore whether a group of ecologically associated arthropods have co-diversified with the host pitcher plant, and identify if there is a positive correlation between ecological interaction and PCFs. Results demonstrate that multiple arthropods share congruent phylogeographic breaks with S. alata, and provide evidence that the level of ecological association can be used to predict the degree of similarity in the phylogeographic pattern. This study outlines an approach for quantifying phylogeographic congruence, a central concept in biogeographic research.
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Affiliation(s)
- Jordan D Satler
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, Ohio, 43210.
| | - Bryan C Carstens
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, Ohio, 43210
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231
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Schmitt T, Louy D, Zimmermann E, Habel JC. Species radiation in the Alps: multiple range shifts caused diversification in Ringlet butterflies in the European high mountains. ORG DIVERS EVOL 2016. [DOI: 10.1007/s13127-016-0282-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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232
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Perez MF, Bonatelli IAS, Moraes EM, Carstens BC. Model-based analysis supports interglacial refugia over long-dispersal events in the diversification of two South American cactus species. Heredity (Edinb) 2016; 116:550-7. [PMID: 27071846 DOI: 10.1038/hdy.2016.17] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2015] [Revised: 01/26/2016] [Accepted: 02/02/2016] [Indexed: 02/06/2023] Open
Abstract
Pilosocereus machrisii and P. aurisetus are cactus species within the P. aurisetus complex, a group of eight cacti that are restricted to rocky habitats within the Neotropical savannas of eastern South America. Previous studies have suggested that diversification within this complex was driven by distributional fragmentation, isolation leading to allopatric differentiation, and secondary contact among divergent lineages. These events have been associated with Quaternary climatic cycles, leading to the hypothesis that the xerophytic vegetation patches which presently harbor these populations operate as refugia during the current interglacial. However, owing to limitations of the standard phylogeographic approaches used in these studies, this hypothesis was not explicitly tested. Here we use Approximate Bayesian Computation to refine the previous inferences and test the role of different events in the diversification of two species within P. aurisetus group. We used molecular data from chloroplast DNA and simple sequence repeats loci of P. machrisii and P. aurisetus, the two species with broadest distribution in the complex, in order to test if the diversification in each species was driven mostly by vicariance or by long-dispersal events. We found that both species were affected primarily by vicariance, with a refuge model as the most likely scenario for P. aurisetus and a soft vicariance scenario most probable for P. machrisii. These results emphasize the importance of distributional fragmentation in these species, and add support to the hypothesis of long-term isolation in interglacial refugia previously proposed for the P. aurisetus species complex diversification.
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Affiliation(s)
- M F Perez
- Departamento de Biologia, Universidade Federal de São Carlos, Sorocaba, São Paulo, Brazil
| | - I A S Bonatelli
- Departamento de Biologia, Universidade Federal de São Carlos, Sorocaba, São Paulo, Brazil
| | - E M Moraes
- Departamento de Biologia, Universidade Federal de São Carlos, Sorocaba, São Paulo, Brazil
| | - B C Carstens
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
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Galván-Quesada S, Doadrio I, Alda F, Perdices A, Reina RG, García Varela M, Hernández N, Campos Mendoza A, Bermingham E, Domínguez-Domínguez O. Molecular Phylogeny and Biogeography of the Amphidromous Fish Genus Dormitator Gill 1861 (Teleostei: Eleotridae). PLoS One 2016; 11:e0153538. [PMID: 27074006 PMCID: PMC4830628 DOI: 10.1371/journal.pone.0153538] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Accepted: 03/28/2016] [Indexed: 11/23/2022] Open
Abstract
Species of the genus Dormitator, also known as sleepers, are representatives of the amphidromous freshwater fish fauna that inhabit the tropical and subtropical coastal environments of the Americas and Western Africa. Because of the distribution of this genus, it could be hypothesized that the evolutionary patterns in this genus, including a pair of geminate species across the Central American Isthmus, could be explained by vicariance following the break-up of Gondwana. However, the evolutionary history of this group has not been evaluated. We constructed a time-scaled molecular phylogeny of Dormitator using mitochondrial (Cytochrome b) and nuclear (Rhodopsin and β-actin) DNA sequence data to infer and date the cladogenetic events that drove the diversification of the genus and to relate them to the biogeographical history of Central America. Two divergent lineages of Dormitator were recovered: one that included all of the Pacific samples and another that included all of the eastern and western Atlantic samples. In contrast to the Pacific lineage, which showed no phylogeographic structure, the Atlantic lineage was geographically structured into four clades: Cameroon, Gulf of Mexico, West Cuba and Caribbean, showing evidence of potential cryptic species. The separation of the Pacific and Atlantic lineages was estimated to have occurred ~1 million years ago (Mya), whereas the four Atlantic clades showed mean times of divergence between 0.2 and 0.4 Mya. The splitting times of Dormitator between ocean basins are similar to those estimated for other geminate species pairs with shoreline estuarine preferences, which may indicate that the common evolutionary histories of the different clades are the result of isolation events associated with the closure of the Central American Isthmus and the subsequent climatic and oceanographic changes.
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Affiliation(s)
- Sesángari Galván-Quesada
- Programa Institucional de Doctorado en Ciencias Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, México
- Laboratorio de Biología Acuática, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, México
- * E-mail: (SGQ); (ODD)
| | - Ignacio Doadrio
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain
| | - Fernando Alda
- Smithsonian Tropical Research Institute, Apartado 2072, Balboa, Republic of Panama
| | - Anabel Perdices
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain
- Smithsonian Tropical Research Institute, Apartado 2072, Balboa, Republic of Panama
| | - Ruth Gisela Reina
- Smithsonian Tropical Research Institute, Apartado 2072, Balboa, Republic of Panama
| | - Martín García Varela
- Instituto de Biología, Universidad Nacional Autónoma de México, Distrito Federal, México
| | | | - Antonio Campos Mendoza
- Laboratorio de Biología Acuática, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, México
| | - Eldredge Bermingham
- Smithsonian Tropical Research Institute, Apartado 2072, Balboa, Republic of Panama
| | - Omar Domínguez-Domínguez
- Laboratorio de Biología Acuática, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, México
- * E-mail: (SGQ); (ODD)
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234
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Wang SH, Bao L, Wang TM, Wang HF, Ge JP. Contrasting genetic patterns between two coexisting Eleutherococcus species in northern China. Ecol Evol 2016; 6:3311-24. [PMID: 27103988 PMCID: PMC4833501 DOI: 10.1002/ece3.2118] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2016] [Revised: 03/11/2016] [Accepted: 03/21/2016] [Indexed: 11/07/2022] Open
Abstract
Climate oscillations are the key factors to understand the patterns in modern biodiversity. East Asia harbors the most diverse temperate flora, largely because an extensive terrestrial ice cap was absent during repeated Pleistocene glaciation-interglacial cycles. Comparing the demographic histories of species that are codistributed and are close relatives may provide insight into how the process of climate change influences species ranges. In this study, we compared the spatial genetic structure and demographic histories of two coexisting Eleutherococcus species, Eleutherococcus senticosus and E. sessiliflorus. Both species are distributed in northern China, regions that are generally considered to be sensitive to climatic fluctuations. These regions once hosted temperate forest, but this temperate forest was replaced by tundra and taiga forest during the Last Glacial Maximum (LGM), according to pollen records. Using three chloroplast DNA fragments, we assessed the genetic structure of 20 and 9 natural populations of E. senticosus and E. sessiliflorus, respectively. Extremely contrasting genetic patterns were found between the two species; E. sessiliflorus had little genetic variation, whereas E. senticosus had considerably higher levels of genetic variation (15 haplotypes). We speculated that a recent severe bottleneck may have resulted in the extremely low genetic diversity in E. sessiliflorus. In E. senticosus, populations in Northeast China (NEC) harbored all of the haplotypes found in this species and included private haplotypes. The populations in NEC had higher levels of genetic diversity than did those from North China (NC). Therefore, we suggest that both the NC and NEC regions can sustain LGM refugia and that lineage admixture from multiple refugia took place after the LGM elevated the local genetic diversity in NEC. In NEC, multiple genetic hot spots were found in the Changbai Mountains and the Xiaoxing'an Range, which implied that multiple locations in NEC may sustain LGM refugia, even in the Xiaoxing'an Range.
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Affiliation(s)
- Sheng-Hong Wang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and MOE Key Laboratory for Biodiversity Science and Ecological Engineering College of Life Sciences Beijing Normal University Beijing 100875 China
| | - Lei Bao
- State Key Laboratory of Earth Surface Processes and Resource Ecology and MOE Key Laboratory for Biodiversity Science and Ecological Engineering College of Life Sciences Beijing Normal University Beijing 100875 China
| | - Tian-Ming Wang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and MOE Key Laboratory for Biodiversity Science and Ecological Engineering College of Life Sciences Beijing Normal University Beijing 100875 China
| | - Hong-Fang Wang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and MOE Key Laboratory for Biodiversity Science and Ecological Engineering College of Life Sciences Beijing Normal University Beijing 100875 China
| | - Jian-Ping Ge
- State Key Laboratory of Earth Surface Processes and Resource Ecology and MOE Key Laboratory for Biodiversity Science and Ecological Engineering College of Life Sciences Beijing Normal University Beijing 100875 China
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235
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Hope AG, Malaney JL, Bell KC, Salazar-Miralles F, Chavez AS, Barber BR, Cook JA. Revision of widespread red squirrels (genus: Tamiasciurus) highlights the complexity of speciation within North American forests. Mol Phylogenet Evol 2016; 100:170-182. [PMID: 27083861 DOI: 10.1016/j.ympev.2016.04.014] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 04/07/2016] [Accepted: 04/11/2016] [Indexed: 11/27/2022]
Abstract
Integration of molecular methods, ecological modeling, and statistical hypothesis testing are increasing our understanding of differentiation within species and phylogenetic relationships among species by revealing environmental connections to evolutionary processes. Within mammals, novel diversity is being discovered and characterized as more complete geographic sampling is coupled with newer multi-disciplinary approaches. North American red squirrels exemplify a forest obligate genus whose species are monitored as indicators of forest ecosystem condition, yet phylogenetic relationships reflecting evolutionary history within this genus remain tentative. Through testing of competing systematic and niche-based divergence hypotheses, we recognize three species, Tamiasciurus douglasii, T. hudsonicus, and T. fremonti. Our data provide evidence of regional differences in evolutionary dynamics and continental gradients of complexity that are important both for future management and for investigating multiple pathways that can lead to the formation of new species.
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Affiliation(s)
- Andrew G Hope
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA.
| | - Jason L Malaney
- Department of Biology, Austin Peay State University, Clarksville, TN 37044, USA.
| | - Kayce C Bell
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131, USA.
| | - Fernando Salazar-Miralles
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131, USA.
| | - Andreas S Chavez
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California-Berkeley, Berkeley, CA 94720, USA.
| | - Brian R Barber
- Biodiversity Institute, University of Wyoming, Laramie, WY 82071, USA.
| | - Joseph A Cook
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131, USA.
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236
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Hodel RGJ, Cortez MBDS, Soltis PS, Soltis DE. Comparative phylogeography of black mangroves (Avicennia germinans) and red mangroves (Rhizophora mangle) in Florida: Testing the maritime discontinuity in coastal plants. AMERICAN JOURNAL OF BOTANY 2016; 103:730-739. [PMID: 27056925 DOI: 10.3732/ajb.1500260] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 02/22/2016] [Indexed: 06/05/2023]
Abstract
PREMISE OF THE STUDY Previous studies of the comparative phylogeography of coastal and marine species in the southeastern United States revealed that phylogenetically diverse taxa share a phylogeographic break at the southern tip of Florida (the maritime discontinuity). These studies have focused nearly exclusively on animals; few coastal plant species in Florida have been analyzed phylogeographically. We investigated phylogeographic patterns of black mangroves (Avicennia germinans) and red mangroves (Rhizophora mangle), two coastal trees that occur on both coasts of the peninsula of Florida. METHODS We sampled and genotyped 150 individuals each of A. germinans and R. mangle, using eight microsatellite loci per species. We used observed and expected heterozygosity to quantify genetic diversity in each sampling location and allele frequencies to identify putative phylogeographic breaks and measure gene flow using BayesAss and Migrate-n. We tested the hypothesis that both species would exhibit a phylogeographic break at the southern tip of Florida. KEY RESULTS We did not find any significant phylogeographic breaks in either species. Rhizophora mangle exhibits greater genetic structure than A. germinans, contrary to expectations based on propagule dispersal capability. However, directional gene flow from the Gulf to the Atlantic was more pronounced in R. mangle, indicating that the Gulf Stream may affect genetic patterns in R. mangle more than in A. germinans. CONCLUSIONS The high dispersal capability of these species may lead to high genetic connectivity between sampling locations and little geographic structure. We also identified several locations that, based on genetic data, should be the focus of conservation efforts.
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Affiliation(s)
- Richard G J Hodel
- Department of Biology, University of Florida, Gainesville, Florida 32611, USA Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611, USA
| | - Maria B de Souza Cortez
- Department of Plant Biology, University of Campinas-UNICAMP, 13083-970 Campinas, São Paulo, Brazil
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611, USA The Genetics Institute, University of Florida, Gainesville, Florida 32610, USA
| | - Douglas E Soltis
- Department of Biology, University of Florida, Gainesville, Florida 32611, USA Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611, USA The Genetics Institute, University of Florida, Gainesville, Florida 32610, USA
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237
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Zinck JWR, Rajora OP. Post-glacial phylogeography and evolution of a wide-ranging highly-exploited keystone forest tree, eastern white pine (Pinus strobus) in North America: single refugium, multiple routes. BMC Evol Biol 2016; 16:56. [PMID: 26936598 PMCID: PMC4774161 DOI: 10.1186/s12862-016-0624-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 02/16/2016] [Indexed: 01/28/2023] Open
Abstract
Background Knowledge of the historical distribution and postglacial phylogeography and evolution of a species is important to better understand its current distribution and population structure and potential fate in the future, especially under climate change conditions, and conservation of its genetic resources. We have addressed this issue in a wide-ranging and heavily exploited keystone forest tree species of eastern North America, eastern white pine (Pinus strobus). We examined the range-wide population genetic structure, tested various hypothetical population history and evolutionary scenarios and inferred the location of glacial refugium and post-glacial recolonization routes. Our hypothesis was that eastern white pine survived in a single glacial refugium and expanded through multiple post-glacial recolonization routes. Results We studied the range-wide genetic diversity and population structure of 33 eastern white pine populations using 12 nuclear and 3 chloroplast microsatellite DNA markers. We used Approximate Bayesian Computation approach to test various evolutionary scenarios. We observed high levels of genetic diversity, and significant genetic differentiation (FST = 0.104) and population structure among eastern white pine populations across its range. A south to north trend of declining genetic diversity existed, consistent with repeated founder effects during post-glaciation migration northwards. We observed broad consensus from nuclear and chloroplast genetic markers supporting the presence of two main post-glacial recolonization routes that originated from a single southern refugium in the mid-Atlantic plain. One route gave rise to populations at the western margin of the species’ range in Minnesota and western Ontario. The second route gave rise to central-eastern populations, which branched into two subgroups: central and eastern. We observed minimal sharing of chloroplast haplotypes between recolonization routes but there was evidence of admixture between the western and west-central populations. Conclusions Our study reveals a single southern refugium, two recolonization routes and three genetically distinguishable lineages in eastern white pine that we suggest to be treated as separate Evolutionarily Significant Units. Like many wide-ranging North American species, eastern white pine retains the genetic signatures of post-glacial recolonization and evolution, and its contemporary population genetic structure reflects not just the modern distribution and effects of heavy exploitation but also routes northward from its glacial refugium. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0624-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- John W R Zinck
- Faculty of Forestry and Environmental Management, University of New Brunswick, 28 Dineen Drive, Fredericton, NB, E3B 5A3, Canada. .,Present address: Athletigen Technologies Inc., 535 Legget Drive, Kanata, ON, K2K 3B8, Canada.
| | - Om P Rajora
- Faculty of Forestry and Environmental Management, University of New Brunswick, 28 Dineen Drive, Fredericton, NB, E3B 5A3, Canada.
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238
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Pyron RA, Hsieh FW, Lemmon AR, Lemmon EM, Hendry CR. Integrating phylogenomic and morphological data to assess candidate species-delimitation models in brown and red-bellied snakes (Storeria). Zool J Linn Soc 2016. [DOI: 10.1111/zoj.12392] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- R. Alexander Pyron
- Department of Biological Sciences; The George Washington University; 2023 G St. NW Washington DC 20052 USA
| | - Felisa W. Hsieh
- Department of Biological Sciences; The George Washington University; 2023 G St. NW Washington DC 20052 USA
| | - Alan R. Lemmon
- Department of Scientific Computing; Florida State University; Tallahassee FL 32306-4120 USA
| | - Emily M. Lemmon
- Department of Biological Science; Florida State University; Tallahassee FL 32306-4295 USA
| | - Catriona R. Hendry
- Department of Biological Sciences; The George Washington University; 2023 G St. NW Washington DC 20052 USA
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239
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Glotzbecker GJ, Alda F, Broughton RE, Neely DA, Mayden RL, Blum MJ. Geographic independence and phylogenetic diversity of red shiner introductions. CONSERV GENET 2016. [DOI: 10.1007/s10592-016-0822-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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240
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Folt B, Garrison N, Guyer C, Rodriguez J, Bond JE. Phylogeography and evolution of the Red Salamander (Pseudotriton ruber). Mol Phylogenet Evol 2016; 98:97-110. [PMID: 26872531 DOI: 10.1016/j.ympev.2016.01.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 01/04/2016] [Accepted: 01/28/2016] [Indexed: 11/27/2022]
Abstract
Phylogeographic studies frequently result in the elevation of subspecific taxa to species given monophyly, or the synonymy of subspecies that are not monophyletic. However, given limited or incongruent datasets, retention of subspecies can be useful to describe hypothesized incipient species or to illustrate interesting biological phenomena driving morphological diversity. Four subspecific taxa have been used to describe largely allopatric geographic variation within the species Pseudotriton ruber, a plethodontid salamander occupying stream and spring habitats across eastern North America: P. r. vioscai occurs in lowland Coastal Plain habitats, while P. r. ruber, P. r. nitidus, and P. r. schencki occupy upland regions in and around the Appalachian Mountains. Pseudotriton ruber co-occurs through its distribution with the aposematic newt Notophthalmus viridescens, and both species are hypothesized to be part of a Müllerian mimicry complex. In this study, we sequenced regions of two mitochondrial (cytochrome b, NADH dehydrogenase subunit 2) and one single copy nuclear protein-coding gene (pro-opiomelanocortin) from individuals sampled across much of the distribution of P. ruber and then used maximum-likelihood and Bayesian phylogenetic inference to test the monophyly of subspecies, reconstruct biogeographic history, and make inferences about morphological evolution. Phylogeographic hypotheses from mitochondrial and nuclear datasets described structure among populations of P. ruber which separated Coastal Plain and upland Appalachian populations, but subspecies were not monophyletic. Biogeographic reconstruction estimated the ancestor of all populations to have occupied and initially diverged in the Coastal Plain during the Pliocene (∼3.6mya), before one lineage subsequently invaded upland areas of Appalachia. Bold bright coloration of high elevation subspecies P. r. nitidus and P. r. schencki appears to have evolved twice. We hypothesize that the Müllerian mimicry complex with N. viridescens and P. ruber may provide a selective mechanism driving the co-evolution of striking bright and dull morphological variation among populations of both species. While P. ruber subspecies were not consistent with our criteria for diagnosing species (monophyly) and therefore could not be elevated to species, we advocate for the retention of subspecies because they describe hypotheses about an incipient species (P. r. vioscai) and how Müllerian mimicry may shape morphological diversity of species.
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Affiliation(s)
- Brian Folt
- Department of Biological Sciences and Museum of Natural History, 331 Funchess Hall, Auburn University, AL 36849, USA.
| | - Nicole Garrison
- Department of Biological Sciences and Museum of Natural History, 331 Funchess Hall, Auburn University, AL 36849, USA
| | - Craig Guyer
- Department of Biological Sciences and Museum of Natural History, 331 Funchess Hall, Auburn University, AL 36849, USA
| | - Juanita Rodriguez
- Department of Biological Sciences and Museum of Natural History, 331 Funchess Hall, Auburn University, AL 36849, USA
| | - Jason E Bond
- Department of Biological Sciences and Museum of Natural History, 331 Funchess Hall, Auburn University, AL 36849, USA
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241
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Satler JD, Zellmer AJ, Carstens BC. Biogeographic barriers drive co-diversification within associated eukaryotes of the Sarracenia alata pitcher plant system. PeerJ 2016; 4:e1576. [PMID: 26788436 PMCID: PMC4715430 DOI: 10.7717/peerj.1576] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 12/16/2015] [Indexed: 12/29/2022] Open
Abstract
Understanding if the members of an ecological community have co-diversified is a central concern of evolutionary biology, as co-diversification suggests prolonged association and possible coevolution. By sampling associated species from an ecosystem, researchers can better understand how abiotic and biotic factors influence diversification in a region. In particular, studies of co-distributed species that interact ecologically can allow us to disentangle the effect of how historical processes have helped shape community level structure and interactions. Here we investigate the Sarracenia alata pitcher plant system, an ecological community where many species from disparate taxonomic groups live inside the fluid-filled pitcher leaves. Direct sequencing of the eukaryotes present in the pitcher plant fluid enables us to better understand how a host plant can shape and contribute to the genetic structure of its associated inquilines, and to ask whether genetic variation in the taxa are structured in a similar manner to the host plant. We used 454 amplicon-based metagenomics to demonstrate that the pattern of genetic diversity in many, but not all, of the eukaryotic community is similar to that of S. alata, providing evidence that associated eukaryotes share an evolutionary history with the host pitcher plant. Our work provides further evidence that a host plant can influence the evolution of its associated commensals.
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Affiliation(s)
- Jordan D Satler
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University , Columbus, OH , United States
| | - Amanda J Zellmer
- Department of Biology, Occidental College , Los Angeles, CA , United States
| | - Bryan C Carstens
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University , Columbus, OH , United States
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Krysko KL, Nuñez LP, Lippi CA, Smith DJ, Granatosky MC. Pliocene-Pleistocene lineage diversifications in the Eastern Indigo Snake (Drymarchon couperi) in the Southeastern United States. Mol Phylogenet Evol 2016; 98:111-22. [PMID: 26778258 DOI: 10.1016/j.ympev.2015.12.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 12/04/2015] [Accepted: 12/30/2015] [Indexed: 11/18/2022]
Abstract
Indigo Snakes (Drymarchon; with five currently recognized species) occur from northern Argentina, northward to the United States in southern Texas and eastward in disjunct populations in Florida and Georgia. Based on this known allopatry and a difference in supralabial morphology the two United States taxa previously considered as subspecies within D. corais (Boie 1827), the Western Indigo Snake, D. melanurus erebennus (Cope 1860), and Eastern Indigo Snake, D. couperi (Holbrook 1842), are currently recognized as separate species. Drymarchon couperi is a Federally-designated Threatened species by the United States Fish and Wildlife Service under the Endangered Species Act, and currently being incorporated into a translocation program. This, combined with its disjunct distribution makes it a prime candidate for studying speciation and genetic divergence. In this study, we (1) test the hypothesis that D. m. erebennus and D. couperi are distinct lineages by analyzing 2411 base pairs (bp) of two mitochondrial (mtDNA) loci and one single copy nuclear (scnDNA) locus; (2) estimate the timing of speciation using a relaxed phylogenetics method to determine if Milankovitch cycles during the Pleistocene might have had an influence on lineage diversifications; (3) examine historical population demography to determine if identified lineages have undergone population declines, expansions, or remained stable during the most recent Milankovitch cycles; and (4) use this information to assist in an effective and scientifically sound translocation program. Our molecular data support the initial hypothesis that D. melanurus and D. couperi should be recognized as distinct species, but further illustrate that D. couperi is split into two distinct genetic lineages that correspond to historical biogeography and sea level changes in peninsular Florida. These two well-supported genetic lineages (herein termed Atlantic and Gulf lineages) illustrate a common biogeographic distributional break previously identified for other plants and animals, suggesting that these organisms might have shared a common evolutionary history related to historic sea level changes caused by Milankovitch cycles. Our estimated divergence times suggest that the most recent common ancestor (MRCA) between D. melanurus and southeastern United States Drymarchon occurred ca. 5.9Ma (95% HPD=2.5-9.8Ma; during the late Blancan of the Pleistocene through the Hemphillian of the Miocene), whereas the MRCA between the Atlantic and Gulf lineages in the southeastern United States occurred ca. 2.0Ma (95% HPD=0.7-3.7Ma; during the Irvingtonian of the Pleistocene through the Blancan of the Pliocene). During one or more glacial intervals within these times, these two lineages must have become separated and evolved independently. Despite numerous Milankovitch cycles along with associated forming of physical barriers (i.e., sea level fluctuations, high elevation sand ridges, clayey soils, and/or insufficient habitats) since their initial lineage diversification, these two lineages have likely come in and out of contact with each other many times, yet today they still illustrate near discrete geographic distributions. Although the Atlantic and Gulf lineages appear to be cryptic, a thorough study examining morphological characters should be conducted. We believe that our molecular data is crucial and should be incorporated in making conscious decisions in the management of a translocation program. We suggest that source populations for translocations include maintaining the integrity of the known genetic lineages found herein, as well as those coming from the closest areas that currently support sizable Drymarchon populations.
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Affiliation(s)
- Kenneth L Krysko
- Florida Museum of Natural History, Museum Road, Dickinson Hall, University of Florida, Gainesville, FL 32611, USA.
| | - Leroy P Nuñez
- Florida Museum of Natural History, Museum Road, Dickinson Hall, University of Florida, Gainesville, FL 32611, USA; School of Natural Resources and Environment, 103 Black Hall, University of Florida, Gainesville, FL 32611, USA.
| | - Catherine A Lippi
- Department of Epidemiology and Biostatistics, College of Public Health, University of South Florida, 13201 Bruce B Downs, MDC56, Tampa, FL 33612, USA.
| | - Daniel J Smith
- Department of Biology, University of Central Florida, 4000 Central Florida Blvd, Orlando, FL 32816, USA.
| | - Michael C Granatosky
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA.
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243
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Roberts DG, Forrest CN, Denham AJ, Ayre DJ. Varying levels of clonality and ploidy create barriers to gene flow and challenges for conservation of an Australian arid-zone ecosystem engineer,Acacia loderi. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12728] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- David G. Roberts
- School of Biological Sciences; University of Wollongong; Northfields Avenue Wollongong NSW 2522 Australia
- Centre of Excellence in Natural Resource Management; The University of Western Australia; The Albany Centre; 35 Stirling Terrace Albany WA 6332 Australia
| | - Cairo N. Forrest
- School of Biological Sciences; University of Wollongong; Northfields Avenue Wollongong NSW 2522 Australia
| | - Andrew J. Denham
- School of Biological Sciences; University of Wollongong; Northfields Avenue Wollongong NSW 2522 Australia
- New South Wales Office of Environment and Heritage; PO Box 1967 Hurstville NSW 2220 Australia
| | - David J. Ayre
- School of Biological Sciences; University of Wollongong; Northfields Avenue Wollongong NSW 2522 Australia
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244
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Williford D, Deyoung RW, Honeycutt RL, Brennan LA, Hernández F. Phylogeography of the bobwhite (Colinus) quails. WILDLIFE MONOGRAPHS 2015. [DOI: 10.1002/wmon.1017] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Damon Williford
- Caesar Kleberg Wildlife Research Institute; Texas A&M University-Kingsville; 700 University Boulevard MSC 218; Kingsville TX 78363 USA
| | - Randy W. Deyoung
- Caesar Kleberg Wildlife Research Institute; Texas A&M University-Kingsville; 700 University Boulevard MSC 218; Kingsville TX 78363 USA
| | - Rodney L. Honeycutt
- Natural Science Division; Pepperdine University, 24255 Pacific Coast Highway; Malibu CA 90263 USA
| | - Leonard A. Brennan
- Caesar Kleberg Wildlife Research Institute; Texas A&M University-Kingsville; 700 University Boulevard MSC 218; Kingsville TX 78363 USA
| | - Fidel Hernández
- Caesar Kleberg Wildlife Research Institute; Texas A&M University-Kingsville; 700 University Boulevard MSC 218; Kingsville TX 78363 USA
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245
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Stewart KA, Austin JD, Zamudio KR, Lougheed SC. Contact zone dynamics during early stages of speciation in a chorus frog (Pseudacris crucifer). Heredity (Edinb) 2015; 116:239-47. [PMID: 26626576 DOI: 10.1038/hdy.2015.96] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Revised: 08/08/2015] [Accepted: 09/01/2015] [Indexed: 01/29/2023] Open
Abstract
Characterizing the genetic and behavioural consequences of contact between previously geographically isolated lineages provides insights into the mechanisms underlying diversification and ultimately speciation. The spring peeper (Pseudacris crucifer) is a widespread Nearctic chorus frog with six divergent mitochondrial DNA (mtDNA) lineages, many of which came into secondary contact during the Holocene. We examined genetics, morphology, advertisement calls and female preference for two lineages that began diverging in allopatry in the Pliocene and now overlap in southwestern Ontario, Canada. We found non-coincident clines in mtDNA and nuclear DNA, mirroring directionality of premating isolation barriers. We also found divergence in a range of traits between these two lineages, displacement in male call attributes and female preference for calls of their natal lineage in sympatry. Hybrids were morphologically distinct from both parental lineages, but hybrid male calls were acoustically intermediate. Female hybrids showed asymmetrical preference for Eastern male calls. These results considered together provide evidence of either unidirectional hybridization or selection against hybrids, potentially implying reproductive character displacement. Our work demonstrates the utility of integrated, multi-character approaches to understanding the processes of divergence and the nature of speciation.
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Affiliation(s)
- K A Stewart
- Department of Biology, Queen's University, Kingston, Ontario, Canada.,College of Environmental Science and Engineering, Sino-Canada Centre for Environmental and Sustainable Development, Tongji University, Shanghai, People's Republic of China
| | - J D Austin
- Department of Wildlife Ecology and Conservation, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA
| | - K R Zamudio
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - S C Lougheed
- Department of Biology, Queen's University, Kingston, Ontario, Canada
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246
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Xue AT, Hickerson MJ. The aggregate site frequency spectrum for comparative population genomic inference. Mol Ecol 2015; 24:6223-40. [PMID: 26769405 PMCID: PMC4717917 DOI: 10.1111/mec.13447] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 10/26/2015] [Accepted: 10/28/2015] [Indexed: 12/11/2022]
Abstract
Understanding how assemblages of species responded to past climate change is a central goal of comparative phylogeography and comparative population genomics, an endeavour that has increasing potential to integrate with community ecology. New sequencing technology now provides the potential to perform complex demographic inference at unprecedented resolution across assemblages of nonmodel species. To this end, we introduce the aggregate site frequency spectrum (aSFS), an expansion of the site frequency spectrum to use single nucleotide polymorphism (SNP) data sets collected from multiple, co-distributed species for assemblage-level demographic inference. We describe how the aSFS is constructed over an arbitrary number of independent population samples and then demonstrate how the aSFS can differentiate various multispecies demographic histories under a wide range of sampling configurations while allowing effective population sizes and expansion magnitudes to vary independently. We subsequently couple the aSFS with a hierarchical approximate Bayesian computation (hABC) framework to estimate degree of temporal synchronicity in expansion times across taxa, including an empirical demonstration with a data set consisting of five populations of the threespine stickleback (Gasterosteus aculeatus). Corroborating what is generally understood about the recent postglacial origins of these populations, the joint aSFS/hABC analysis strongly suggests that the stickleback data are most consistent with synchronous expansion after the Last Glacial Maximum (posterior probability = 0.99). The aSFS will have general application for multilevel statistical frameworks to test models involving assemblages and/or communities, and as large-scale SNP data from nonmodel species become routine, the aSFS expands the potential for powerful next-generation comparative population genomic inference.
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Affiliation(s)
- Alexander T. Xue
- Department of Biology: Subprogram in Ecology, Evolutionary Biology, and Behavior, City College and Graduate Center of City University of New York, 160 Convent Avenue, Marshak Science Building, Room 526, New York, NY 10031
| | - Michael J. Hickerson
- Department of Biology: Subprogram in Ecology, Evolutionary Biology, and Behavior, City College and Graduate Center of City University of New York, 160 Convent Avenue, Marshak Science Building, Room 526, New York, NY 10031
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247
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Yu H, Zhang Y, Liu L, Qi W, Li S, Hu Z. Combining the least cost path method with population genetic data and species distribution models to identify landscape connectivity during the late Quaternary in Himalayan hemlock. Ecol Evol 2015; 5:5781-91. [PMID: 26811753 PMCID: PMC4717335 DOI: 10.1002/ece3.1840] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 10/13/2015] [Accepted: 10/14/2015] [Indexed: 11/18/2022] Open
Abstract
Himalayan hemlock (Tsuga dumosa) experienced a recolonization event during the Quaternary period; however, the specific dispersal routes are remain unknown. Recently, the least cost path (LCP) calculation coupled with population genetic data and species distribution models has been applied to reveal the landscape connectivity. In this study, we utilized the categorical LCP method, combining species distribution of three periods (the last interglacial, the last glacial maximum, and the current period) and locality with shared chloroplast, mitochondrial, and nuclear haplotypes, to identify the possible dispersal routes of T. dumosa in the late Quaternary. Then, both a coalescent estimate of migration rates among regional groups and establishment of genetic divergence pattern were conducted. After those analyses, we found that the species generally migrated along the southern slope of Himalaya across time periods and genomic makers, and higher degree of dispersal was in the present and mtDNA haplotype. Furthermore, the direction of range shifts and strong level of gene flow also imply the existence of Himalayan dispersal path, and low area of genetic divergence pattern suggests that there are not any obvious barriers against the dispersal pathway. Above all, we inferred that a dispersal route along the Himalaya Mountains could exist, which is an important supplement for the evolutionary history of T. dumosa. Finally, we believed that this integrative genetic and geospatial method would bring new implications for the evolutionary process and conservation priority of species in the Tibetan Plateau.
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Affiliation(s)
- Haibin Yu
- Key Laboratory of Land Surface Pattern and Simulation Institute of Geographic Sciences and Natural Resource Research Chinese Academy of Sciences (CAS) Beijing 100101 China; School of Life Sciences Sun Yat-sen University Guangzhou 510275 China
| | - Yili Zhang
- Key Laboratory of Land Surface Pattern and Simulation Institute of Geographic Sciences and Natural Resource Research Chinese Academy of Sciences (CAS) Beijing 100101 China; CAS Center for Excellence in Tibetan Plateau Earth Sciences Beijing 100101 China
| | - Linshan Liu
- Key Laboratory of Land Surface Pattern and Simulation Institute of Geographic Sciences and Natural Resource Research Chinese Academy of Sciences (CAS) Beijing 100101 China
| | - Wei Qi
- Key Laboratory of Land Surface Pattern and Simulation Institute of Geographic Sciences and Natural Resource Research Chinese Academy of Sciences (CAS) Beijing 100101 China
| | - Shicheng Li
- Key Laboratory of Land Surface Pattern and Simulation Institute of Geographic Sciences and Natural Resource Research Chinese Academy of Sciences (CAS) Beijing 100101 China; University of Chinese Academy of Sciences Beijing 100049 China
| | - Zhongjun Hu
- Key Laboratory of Land Surface Pattern and Simulation Institute of Geographic Sciences and Natural Resource Research Chinese Academy of Sciences (CAS) Beijing 100101 China
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248
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Sánchez-Ramírez S, Tulloss RE, Guzmán-Dávalos L, Cifuentes-Blanco J, Valenzuela R, Estrada-Torres A, Ruán-Soto F, Díaz-Moreno R, Hernández-Rico N, Torres-Gómez M, León H, Moncalvo JM. In and out of refugia: historical patterns of diversity and demography in the North American Caesar's mushroom species complex. Mol Ecol 2015; 24:5938-56. [PMID: 26465233 DOI: 10.1111/mec.13413] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 10/05/2015] [Accepted: 10/06/2015] [Indexed: 11/30/2022]
Abstract
Some of the effects of past climate dynamics on plant and animal diversity make-up have been relatively well studied, but to less extent in fungi. Pleistocene refugia are thought to harbour high biological diversity (i.e. phylogenetic lineages and genetic diversity), mainly as a product of increased reproductive isolation and allele conservation. In addition, high extinction rates and genetic erosion are expected in previously glaciated regions. Some of the consequences of past climate dynamics might involve changes in range and population size that can result in divergence and incipient or cryptic speciation. Many of these dynamic processes and patterns can be inferred through phylogenetic and coalescent methods. In this study, we first delimit species within a group of closely related edible ectomycorrhizal Amanita from North America (the American Caesar's mushrooms species complex) using multilocus coalescent-based approaches; and then address questions related to effects of Pleistocene climate change on the diversity and genetics of the group. Our study includes extensive geographical sampling throughout the distribution range, and DNA sequences from three nuclear protein-coding genes. Results reveal cryptic diversity and high speciation rates in refugia. Population sizes and expansions seem to be larger at midrange latitudes (Mexican highlands and SE USA). Range shifts are proportional to population size expansions, which were overall more common during the Pleistocene. This study documents responses to past climate change in fungi and also highlights the applicability of the multispecies coalescent in comparative phylogeographical analyses and diversity assessments that include ancestral species.
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Affiliation(s)
- Santiago Sánchez-Ramírez
- Department of Natural History, Royal Ontario Museum, 100 Queen's Park, Toronto, ON, M5S 2C6, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks, Toronto, ON, M5S 3B2, Canada
| | | | - Laura Guzmán-Dávalos
- Departamento de Botánica y Zoología, Universidad de Guadalajara, Zapopan, 45101, México
| | - Joaquín Cifuentes-Blanco
- Facultad de Ciencias, Departamento de Biología Comparada, UNAM, Ciudad Universitaria, México City, 04510, México
| | - Ricardo Valenzuela
- Escuela Nacional de Ciencias Biólogicas, Instituto Politécnico Nacional, México City, 11340, México
| | - Arturo Estrada-Torres
- Centro de Investigación en Ciencias Biológicas, Universidad Autónoma de Tlaxcala, Tlaxcala, 90122, México
| | - Felipe Ruán-Soto
- Facultad de Ciencias Biológicas, Universidad de Ciencias y Artes de Chiapas, Tuxtla Gutiérrez, 29039, Mexico
| | - Raúl Díaz-Moreno
- Instituto de Silvicultura e Industria de la Madera, Universidad Juárez del Estado de Durango, Durango, 34120, México
| | - Nallely Hernández-Rico
- Laboratorio de Etnobiología, Centro de Investigaciones Biológicas, Universidad Autónoma del Estado de Hidalgo, Pachuca, México
| | - Mariano Torres-Gómez
- Centro de Investigaciones en Ecosistemas CIEco, Antigua carretera a Pátzcuaro # 8701, Col. Ex-Hacienda de San José de La Huerta, Morelia, 58190, México
| | - Hugo León
- Coleccion Etnomicológica "Dr. Teófilo Herrera Suárez", Instituto Tecnológico del Valle de Oaxaca, Xoxocotlán, 71230, México
| | - Jean-Marc Moncalvo
- Department of Natural History, Royal Ontario Museum, 100 Queen's Park, Toronto, ON, M5S 2C6, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks, Toronto, ON, M5S 3B2, Canada
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249
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Vargas-Rodriguez YL, Platt WJ, Urbatsch LE, Foltz DW. Large scale patterns of genetic variation and differentiation in sugar maple from tropical Central America to temperate North America. BMC Evol Biol 2015; 15:257. [PMID: 26586372 PMCID: PMC4653954 DOI: 10.1186/s12862-015-0518-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 10/22/2015] [Indexed: 12/02/2022] Open
Abstract
Background Geological events in the latter Cenozoic have influenced the distribution, abundance and genetic structure of tree populations in temperate and tropical North America. The biogeographical history of temperate vegetation that spans large ranges of latitude is complex, involving multiple latitudinal shifts that might have occurred via different migration routes. We determined the regional structuring of genetic variation of sugar maple (Acer saccharum subsp. saccharum) and its only subspecies in tropical America (Acer saccharum subsp. skutchii) using nuclear and chloroplast data. The studied populations span a geographic range from Maine, USA (46°N), to El Progreso, Guatemala (15°N). We examined genetic subdivisions, explored the locations of ancestral haplotypes, analyzed genetic data to explore the presence of a single or multiple glacial refugia, and tested whether genetic lineages are temporally consistent with a Pleistocene or older divergence. Results Nuclear and chloroplast data indicated that populations in midwestern USA and western Mexico were highly differentiated from populations in the rest of the sites. The time of the most recent common ancestor of the western Mexico haplotype lineage was dated to the Pliocene (5.9 Ma, 95 % HPD: 4.3–7.3 Ma). Splits during the Pleistocene separated the rest of the phylogroups. The most frequent and widespread haplotype occurred in half of the sites (Guatemala, eastern Mexico, southeastern USA, and Ohio). Our data also suggested that multiple Pleistocene refugia (tropics-southeastern USA, midwestern, and northeastern USA), but not western Mexico (Jalisco), contributed to post-glacial northward expansion of ranges. Current southern Mexican and Guatemalan populations have reduced population sizes, genetic bottlenecks and tend toward homozygosity, as indicated using nuclear and chloroplast markers. Conclusions The divergence of western Mexican populations from the rest of the sugar maples likely resulted from orographic and volcanic barriers to gene flow. Past connectivity among populations in the southeastern USA and eastern Mexico and Guatemala possible occurred through gene flow during the Pleistocene. The time to the most common ancestor values revealed that populations from the Midwest and Northeast USA represented different haplotype lineages, indicating major divergence of haplotypes lineages before the Last Glacial Maximum and suggesting the existence of multiple glacial refugia. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0518-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yalma L Vargas-Rodriguez
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, 70803, USA.
| | - William J Platt
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, 70803, USA.
| | - Lowell E Urbatsch
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, 70803, USA.
| | - David W Foltz
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, 70803, USA.
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250
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Hayden JE, Dickel TS. A new Antaeotricha species from Florida sandhills and scrub (Lepidoptera, Depressariidae, Stenomatinae). Zookeys 2015; 533:133-50. [PMID: 26668543 PMCID: PMC4669926 DOI: 10.3897/zookeys.533.6004] [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: 04/04/2015] [Accepted: 10/08/2015] [Indexed: 11/23/2022] Open
Abstract
Antaeotricha floridella sp. n. is described and diagnosed from the closely similar Antaeotricha albulella (Walker). The species is distributed in xeric sandhill and scrub habitats in peninsular Florida, USA, and larvae feed on Quercus species. Keys are given for pale-winged Stenomatinae and similar Gelechioidea based on external characters and genitalia.
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Affiliation(s)
- James E. Hayden
- Florida Department of Agriculture and Consumer Services, Division of Plant Industry, 1911 SW 34th Street, Gainesville, FL 32608 USA
| | - Terhune S. Dickel
- P.O. Box 567, Anthony, FL 32617 USA; Research Associate, Florida State Collection of Arthropods, Gainesville, FL, USA
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