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Phylogeography of the Rough Greensnake, Opheodrys aestivus (Squamata: Colubridae), Using Multilocus Sanger Sequence and Genomic ddRADseq Data. J HERPETOL 2021. [DOI: 10.1670/20-040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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2
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Richardson DJ, Hammond CI, Moser WE, Phillips AJ, Lazo-Wasem EA, Barger MA. Molecular Variation and Biogeography of the Common North American Turtle Leech, Placobdella parasitica. BULLETIN OF THE PEABODY MUSEUM OF NATURAL HISTORY 2020. [DOI: 10.3374/014.061.0201] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | | | - William E. Moser
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Suitland, MD 20746 USA
| | - Anna J. Phillips
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560-0163 USA
| | - Eric A. Lazo-Wasem
- Division of Invertebrate Zoology, Peabody Museum of Natural History, Yale University, New Haven, CT 06520 USA
| | - Michael A. Barger
- Department of Biology and Environmental Science, Westminster College, Fulton, MO 68251 USA
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3
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Mack J, de Carle D, Kvist S. Prey, populations, and the pleistocene: evidence for low COI variation in a widespread North American leech. Mitochondrial DNA A DNA Mapp Seq Anal 2019; 30:749-763. [DOI: 10.1080/24701394.2019.1634698] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Joseph Mack
- Department of Natural History, Royal Ontario Museum, Toronto, ON, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Danielle de Carle
- Department of Natural History, Royal Ontario Museum, Toronto, ON, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Sebastian Kvist
- Department of Natural History, Royal Ontario Museum, Toronto, ON, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
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4
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Voss RS, Jansa SA. Minimal genetic divergence among South American samples of the water opossum Chironectes minimus: evidence for transcontinental gene flow? MAMMALIA 2019. [DOI: 10.1515/mammalia-2018-0073] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Cytochrome b sequences from South American specimens of the water opossum Chironectes minimus exhibit uncorrected pairwise differences of 0.6% or less among samples collected thousands of kilometers apart (in Guyana, Bolivia and southeastern Brazil). Despite published evidence of population divergence from recent analyses of craniodental morphology, our results suggest extensive gene flow or recent range expansion across the South American landscapes currently occupied by this seldom-collected species.
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Reid BN, Mladenoff DJ, Peery MZ. Genetic effects of landscape, habitat preference and demography on three co‐occurring turtle species. Mol Ecol 2017; 26:781-798. [DOI: 10.1111/mec.13962] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Revised: 10/28/2016] [Accepted: 11/14/2016] [Indexed: 01/05/2023]
Affiliation(s)
- Brendan N. Reid
- Department of Forest and Wildlife Ecology University of Wisconsin‐Madison 1630 Linden Drive Madison WI 53706 USA
- Department of Herpetology American Museum of Natural History Central Park West at 79th Street New York NY 10024 USA
| | - David J. Mladenoff
- Department of Forest and Wildlife Ecology University of Wisconsin‐Madison 1630 Linden Drive Madison WI 53706 USA
| | - M. Zachariah Peery
- Department of Forest and Wildlife Ecology University of Wisconsin‐Madison 1630 Linden Drive Madison WI 53706 USA
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6
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Davy CM, Kidd AG, Wilson CC. Development and Validation of Environmental DNA (eDNA) Markers for Detection of Freshwater Turtles. PLoS One 2015. [PMID: 26200348 PMCID: PMC4511736 DOI: 10.1371/journal.pone.0130965] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Environmental DNA (eDNA) is a potentially powerful tool for detection and monitoring of rare species, including threatened native species and recently arrived invasive species. Here, we develop DNA primers for a suite of nine sympatric freshwater turtles, and use it to test whether turtle eDNA can be successfully detected in samples from aquaria and an outdoor pond. We also conduct a cost comparison between eDNA detection and detection through traditional survey methods, using data from field surveys at two sites in our target area. We find that eDNA from turtles can be detected using both conventional polymerase chain reaction (PCR) and quantitative PCR (qPCR), and that the cost of detection through traditional survey methods is 2–10X higher than eDNA detection for the species in our study range. We summarize necessary future steps for application of eDNA surveys to turtle monitoring and conservation and propose specific cases in which the application of eDNA could further the conservation of threatened turtle species.
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Affiliation(s)
- Christina M. Davy
- Wildlife Preservation Canada, Guelph, Ontario, Canada
- Trent University, Peterborough, Ontario, Canada
- * E-mail:
| | - Anne G. Kidd
- Ontario Ministry of Natural Resources and Forestry, Peterborough, Ontario, Canada
| | - Chris C. Wilson
- Ontario Ministry of Natural Resources and Forestry, Peterborough, Ontario, Canada
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Torstrom SM, Pangle KL, Swanson BJ. Shedding subspecies: The influence of genetics on reptile subspecies taxonomy. Mol Phylogenet Evol 2014; 76:134-43. [DOI: 10.1016/j.ympev.2014.03.011] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 03/08/2014] [Accepted: 03/11/2014] [Indexed: 10/25/2022]
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8
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Rödder D, Lawing AM, Flecks M, Ahmadzadeh F, Dambach J, Engler JO, Habel JC, Hartmann T, Hörnes D, Ihlow F, Schidelko K, Stiels D, Polly PD. Evaluating the significance of paleophylogeographic species distribution models in reconstructing quaternary range-shifts of nearctic chelonians. PLoS One 2013; 8:e72855. [PMID: 24130664 PMCID: PMC3794015 DOI: 10.1371/journal.pone.0072855] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 07/14/2013] [Indexed: 12/27/2022] Open
Abstract
The climatic cycles of the Quaternary, during which global mean annual temperatures have regularly changed by 5-10°C, provide a special opportunity for studying the rate, magnitude, and effects of geographic responses to changing climates. During the Quaternary, high- and mid-latitude species were extirpated from regions that were covered by ice or otherwise became unsuitable, persisting in refugial retreats where the environment was compatible with their tolerances. In this study we combine modern geographic range data, phylogeny, Pleistocene paleoclimatic models, and isotopic records of changes in global mean annual temperature, to produce a temporally continuous model of geographic changes in potential habitat for 59 species of North American turtles over the past 320 Ka (three full glacial-interglacial cycles). These paleophylogeographic models indicate the areas where past climates were compatible with the modern ranges of the species and serve as hypotheses for how their geographic ranges would have changed in response to Quaternary climate cycles. We test these hypotheses against physiological, genetic, taxonomic and fossil evidence, and we then use them to measure the effects of Quaternary climate cycles on species distributions. Patterns of range expansion, contraction, and fragmentation in the models are strongly congruent with (i) phylogeographic differentiation; (ii) morphological variation; (iii) physiological tolerances; and (iv) intraspecific genetic variability. Modern species with significant interspecific differentiation have geographic ranges that strongly fluctuated and repeatedly fragmented throughout the Quaternary. Modern species with low genetic diversity have geographic distributions that were highly variable and at times exceedingly small in the past. Our results reveal the potential for paleophylogeographic models to (i) reconstruct past geographic range modifications, (ii) identify geographic processes that result in genetic bottlenecks; and (iii) predict threats due to anthropogenic climate change in the future.
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Affiliation(s)
- Dennis Rödder
- Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | - A. Michelle Lawing
- National Institute for Mathematical and Biological Synthesis (NIMBioS), University of Tennessee, Knoxville, Tennessee, United States of America
| | - Morris Flecks
- Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | | | | | - Jan O. Engler
- Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
- Department of Biogeography, Trier University, Trier, Germany
| | | | - Timo Hartmann
- Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | - David Hörnes
- Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | - Flora Ihlow
- Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | | | - Darius Stiels
- Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | - P. David Polly
- Department of Geological Sciences, Indiana University, Bloomington, Indiana, United States of America
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Vargas-Ramírez M, Michels J, Castaño-Mora OV, Cárdenas-Arevalo G, Gallego-García N, Fritz U. Weak genetic divergence between the two South American toad-headed turtles Mesoclemmys dahli and M. zuliae (Testudines: Pleurodira: Chelidae). AMPHIBIA-REPTILIA 2012. [DOI: 10.1163/15685381-00002840] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Mesoclemmys dahli and M. zuliae are two endangered, little-known toad-headed turtles with small distribution ranges in Colombia and Venezuela, respectively. Using the mitochondrial cytochrome b gene as a marker, we investigate their phylogeographic differentiation. Furthermore, based on 2341 bp of mtDNA and 2109 bp of nDNA of M. dahli, M. zuliae and allied chelid turtles, we infer their divergence time using a fossil-calibrated relaxed molecular clock approach. Mesoclemmys dahli and M. zuliae are closely related species, with an estimated mean divergence time of 10.6 million years. This estimate correlates with the uplift of the Serranía de Perijá, an Andean mountain chain separating their distribution ranges, suggesting that this event could have caused the evolution of the two species. Haplotype and nucleotide diversities of M. dahli are markedly higher than in Podocnemis lewyana, another endemic turtle species of Colombia. This pronounced dissimilarity may reflect differences in the phylogeographies and demographic histories of the two species, but also different habitat preferences.
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Affiliation(s)
- Mario Vargas-Ramírez
- 1Museum of Zoology (Museum für Tierkunde), Senckenberg Dresden, A. B. Meyer Building, D-01109 Dresden, Germany
- 3Instituto de Ciencias Naturales, Universidad Nacional de Colombia, Apartado 7495, Bogotá, Colombia
| | - Jan Michels
- 2Department of Functional Morphology and Biomechanics, Institute of Zoology, Christian-Albrechts-Universität zu Kiel, Am Botanischen Garten 1-9, D-24118 Kiel, Germany
| | | | - Gladys Cárdenas-Arevalo
- 3Instituto de Ciencias Naturales, Universidad Nacional de Colombia, Apartado 7495, Bogotá, Colombia
| | - Natalia Gallego-García
- 3Instituto de Ciencias Naturales, Universidad Nacional de Colombia, Apartado 7495, Bogotá, Colombia
| | - Uwe Fritz
- 1Museum of Zoology (Museum für Tierkunde), Senckenberg Dresden, A. B. Meyer Building, D-01109 Dresden, Germany
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Ureña-Aranda CA, de los Monteros AE. The genetic crisis of the Mexican Bolson Tortoise (Gopherus flavomarginatus: Testudinidae). AMPHIBIA-REPTILIA 2012. [DOI: 10.1163/156853811x621508] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Gopherusflavomarginatus(Testudinidae) is endemic to a series of discontinuous, isolated basins collectively known as the Bolson de Mapimí in the Chihuahuan Desert. Its numbers declined after catastrophic levels of exploitation during the mid-20th century. However currently, the Bolson Tortoise appears to be on a path to recovery owing to intensive, sustained conservation efforts. We sequenced an 842-bp-long fragment of the D-loop from 76 individuals distributed throughout the species’ range. The results revealed only two haplotypes. An AMOVA showed that 95% of the variance occurred among populations, whereas the remaining 5% was explained by genetic differences within populations. Tectonic processes together with ecological transformation during the Pleistocene and Holocene may be responsible for the reduction in this species’ genetic variation. A bottleneck during which a significant percentage of the haplotype diversity was lost would result in genetic homogeneity. Although there is demographic growth, the lack of genetic diversity is indicative of the potential crisis that the Bolson Tortoise is facing, and awareness must be brought to this situation.
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Affiliation(s)
- Cinthya Alejandra Ureña-Aranda
- Laboratorio de Sistemática Filogenética, Departamento de Biología Evolutiva, Instituto de Ecología, A. C., Carretera antigua a Coatepec No. 351, Xalapa, Veracruz 91070, México
| | - Alejandro Espinosa de los Monteros
- Laboratorio de Sistemática Filogenética, Departamento de Biología Evolutiva, Instituto de Ecología, A. C., Carretera antigua a Coatepec No. 351, Xalapa, Veracruz 91070, México
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11
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Balmer O, Ciofi C, Galbraith DA, Swingland IR, Zug GR, Caccone A. Population genetic structure of Aldabra giant tortoises. J Hered 2010; 102:29-37. [PMID: 20805288 DOI: 10.1093/jhered/esq096] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Evolution of population structure on islands is the result of physical processes linked to volcanism, orogenic events, changes in sea level, as well as habitat variation. We assessed patterns of genetic structure in the giant tortoise of the Aldabra atoll, where previous ecological studies suggested population subdivisions as a result of landscape discontinuity due to unsuitable habitat and island separation. Analysis of mitochondrial DNA (mtDNA) control region sequences and allelic variation at 8 microsatellite loci were conducted on tortoises sampled in 3 locations on the 2 major islands of Aldabra. We found no variation in mtDNA sequences. This pattern corroborated earlier work supporting the occurrence of a founding event during the last interglacial period and a further reduction in genetic variability during historical time. On the other hand, significant population structure recorded at nuclear loci suggested allopatric divergence possibly due to geographical barriers among islands and ecological partitions hindering tortoise movements within islands. This is the first attempt to study the population genetics of Aldabra tortoises, which are now at carrying capacity in an isolated terrestrial ecosystem where ecological factors appear to have a strong influence on population dynamics.
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Affiliation(s)
- Oliver Balmer
- Institute of Zoology, University of Basel, Basel, Switzerland
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Makowsky R, Marshall JC, McVay J, Chippindale PT, Rissler LJ. Phylogeographic analysis and environmental niche modeling of the plain-bellied watersnake (Nerodia erythrogaster) reveals low levels of genetic and ecological differentiation. Mol Phylogenet Evol 2010; 55:985-95. [PMID: 20302955 DOI: 10.1016/j.ympev.2010.03.012] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2009] [Revised: 02/22/2010] [Accepted: 03/11/2010] [Indexed: 11/25/2022]
Abstract
Species that exhibit geographically defined phenotypic variation traditionally have been divided into subspecies. Subspecies based on phenotypic features may not comprise monophyletic groups due to selection, gene flow, and/or convergent evolution. In many taxonomic groups the number of species once designated as widespread is dwindling rapidly, and many workers reject the concept of subspecies altogether. We tested whether currently recognized subspecies in the plain-bellied watersnake Nerodia erythrogaster are concordant with relationships based on mitochondrial markers, and whether it represents a single widespread species. The range of this taxon spans multiple potential biogeographic barriers (especially the Mississippi and Apalachicola Rivers) that correspond with lineage breaks in many species, including other snakes. We sequenced three mitochondrial genes (NADH-II, Cyt-b, Cox-I) from 156 geo-referenced specimens and developed ecological niche models using Maxent and spatially explicit climate data to examine historical and ecological factors affecting variation in N. erythrogaster across its range. Overall, we found little support for the recognized subspecies as either independent evolutionary lineages or geographically circumscribed units and conclude that although some genetic and niche differentiation has occurred, most populations assigned to N. erythrogaster appear to represent a single, widespread species. However, additional sampling and application of nuclear markers are necessary to clarify the status of the easternmost populations.
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Affiliation(s)
- Robert Makowsky
- University of Texas at Arlington, Department of Biology, Arlington, TX, USA.
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Calvo JH, Calvete C, Martinez-Royo A, Estrada R, Miranda MA, Borras D, Sarto I Monteys V, Pages N, Delgado JA, Collantes F, Lucientes J. Variations in the mitochondrial cytochrome c oxidase subunit I gene indicate northward expanding populations of Culicoides imicola in Spain. BULLETIN OF ENTOMOLOGICAL RESEARCH 2009; 99:583-591. [PMID: 19889254 DOI: 10.1017/s0007485309006622] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Culicoides imicola is the main vector for bluetongue (BT) and African horse sickness (AHS) viruses in the Mediterranean basin and in southern Europe. In this study, we analysed partial mitochondrial cytochrome c oxidase subunit I (COI) gene to characterize and confirm population expansion of Culicoides imicola across Spain. The data were analysed at two hierarchical levels to test the relationship between C. imicola haplotypes in Spain (n = 215 from 58 different locations) and worldwide (n = 277). We found nineteen different haplotypes within the Spanish population, including 11 new haplotypes. No matrilineal subdivision was found within the Spanish population, while western and eastern Mediterranean C. imicola populations were very structured. These findings were further supported by median networks and mismatch haplotype distributions. Median networks demonstrated that the haplotypes we observed in the western Mediterranean region were closely related with one another, creating a clear star-like phylogeny separated only by a single mutation from eastern haplotypes. The two, genetically distinct, sources of C. imicola in the Mediterranean basin, thus, were confirmed. This type of star-like population structure centred around the most frequent haplotype is best explained by rapid expansion. Furthermore, the proposed northern expansion was also supported by the statistically negative Tajima's D and Fu's Fs values, as well as predicted mismatch distributions of sudden and spatially expanding populations. Our results thus indicated that C. imicola population expansion was a rapid and recent phenomenon.
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Affiliation(s)
- J H Calvo
- Unidad de Tecnología en Producción animal, CITA-ARAID, Zaragoza, Spain.
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Echelle AA, Hackler JC, Lack JB, Ballard SR, Roman J, Fox SF, Leslie DM, Van Den Bussche RA. Conservation genetics of the alligator snapping turtle: cytonuclear evidence of range-wide bottleneck effects and unusually pronounced geographic structure. CONSERV GENET 2009. [DOI: 10.1007/s10592-009-9966-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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15
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Amato ML, Brooks RJ, Fu J. A phylogeographic analysis of populations of the wood turtle (Glyptemys insculpta) throughout its range. Mol Ecol 2007; 17:570-81. [PMID: 17971089 DOI: 10.1111/j.1365-294x.2007.03580.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We investigated the phylogeography of wood turtles, Glyptemys insculpta, in North America using 750 bp of the mitochondrial control region from 117 individuals sampled at 29 localities across the species' range. A total of 21 haplotypes were identified and little genetic variation was found. The highest pairwise difference was 2%. From nested clade analysis (NCA), one main postglacial dispersal route was inferred along the east coast, with subsequent westward dispersal. NCA further revealed some patterns of restricted gene flow/dispersal. We propose that wood turtles experienced a combined effect of bottleneck during the Pleistocene as well as of selective sweep, which produced the low level of variation observed. Following the Pleistocene, wood turtles would have undergone a rapid northward expansion from a common southern refugium as glaciers retreated. These findings shed light on where to direct conservation priorities, on conservation strategies needed, and on the potential effects of interpopulation transfers for this vulnerable species.
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Affiliation(s)
- Marina L Amato
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1
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Rosenbaum PA, Robertson JM, Zamudio KR. Unexpectedly low genetic divergences among populations of the threatened bog turtle (Glyptemys muhlenbergii). CONSERV GENET 2007. [DOI: 10.1007/s10592-006-9172-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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18
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Soltis DE, Morris AB, McLachlan JS, Manos PS, Soltis PS. Comparative phylogeography of unglaciated eastern North America. Mol Ecol 2006; 15:4261-93. [PMID: 17107465 DOI: 10.1111/j.1365-294x.2006.03061.x] [Citation(s) in RCA: 510] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Regional phylogeographical studies involving co-distributed animal and plant species have been conducted for several areas, most notably for Europe and the Pacific Northwest of North America. Until recently, phylogeographical studies in unglaciated eastern North America have been largely limited to animals. As more studies emerge for diverse lineages (including plants), it seems timely to assess the phylogeography across this region: (i) comparing and contrasting the patterns seen in plants and animals; (ii) assessing the extent of pseudocongruence; and (iii) discussing the potential applications of regional phylogeography to issues in ecology, such as response to climatic change. Unglaciated eastern North America is a large, geologically and topographically complex area with the species examined having diverse distributions. Nonetheless, some recurrent patterns emerge: (i) maritime - Atlantic vs. Gulf Coast; (ii) Apalachicola River discontinuity; (iii) Tombigbee River discontinuity; (iv) the Appalachian Mountain discontinuity; (v) the Mississippi River discontinuity; and (vi) the Apalachicola River and Mississippi River discontinuities. Although initially documented in animals, most of these patterns are also apparent in plants, providing support for phylogeographical generalizations. These patterns may generally be attributable to isolation and differentiation during Pleistocene glaciation, but in some cases may be older (Pliocene). Molecular studies sometimes agree with longstanding hypotheses of glacial refugia, but also suggest additional possible refugia, such as the southern Appalachian Mountains and areas close to the Laurentide Ice Sheet. Many species exhibit distinct patterns that reflect the unique, rather than the shared, aspects of species' phylogeographical histories. Furthermore, similar modern phylogeographical patterns can result from different underlying causal factors operating at different times (i.e. pseudocongruence). One underemphasized component of pseudocongruence may result from the efforts of researchers to categorize patterns visually - similar patterns may, in fact, not fully coincide, and inferring agreement may obscure the actual patterns and lead to erroneous conclusions. Our modelling analyses indicate no clear spatial patterning and support the hypothesis that phylogeographical structure in diverse temperate taxa is complex and was not shaped by just a few barriers.
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Affiliation(s)
- Douglas E Soltis
- Department of Botany, University of Florida, Gainesville, FL 32611, USA.
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Cisneros-Heredia DF. Turtles of the Tiputini Biodiversity Station with remarks on the diversity and distribution of the Testudines from Ecuador. BIOTA NEOTROPICA 2006. [DOI: 10.1590/s1676-06032006000100011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ten species of Testudines, from four different families: Chelidae, Kinosternidae, Podocnemididae, and Testudinidae, are reported from the Tiputini Biodiversity Station (Universidad San Francisco de Quito), northeastern Amazonian Ecuador; including the second report from Ecuador of Batrachemys heliostemma. These ten species are sympatric but not completely syntopic, thus I comment on their diversity and habitat preferences patterns. The general distribution of some turtles from Amazonian Ecuador is discussed, providing additional records and distribution maps for Chelus fimbriatus, Platemys platycephala, Batrachemys heliostemma, Batrachemys raniceps, Mesoclemmys gibba, Phrynops geoffroanus, Kinosternon scorpioides, and Geochelone denticulata. The presence of Peltocephalus dumerilianus in Amazonian Ecuador is confirmed; based on re-examination of specimens previously reported by Dr. Gustavo Orcés in 1949. The total Ecuadorian richness of Testudines species includes 31 living taxa, and I provide an annotated list of the turtles and tortoises of mainland and insular Ecuador. Much information is still needed in order to understand the ecological relationships of the Testudines from Ecuador and future research should focus on long-term studies designed to answer several questions about their biology and ecology. Several threats are currently jeopardizing the long-term conservation of turtle populations in Ecuador, and we must increase our knowledge on these amazing animals in order to protect and preserve them.
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Wagner RS, Miller MP, Crisafulli CM, Haig SM. Geographic variation, genetic structure, and conservation unit designation in the Larch Mountain salamander (Plethodon larselli). CAN J ZOOL 2005. [DOI: 10.1139/z05-033] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The Larch Mountain salamander (Plethodon larselli Burns, 1954) is an endemic species in the Pacific northwestern United States facing threats related to habitat destruction. To facilitate development of conservation strategies, we used DNA sequences and RAPDs (random amplified polymorphic DNA) to examine differences among populations of this species. Phylogenetic analyses of cytochrome b revealed a clade of haplotypes from populations north of the Columbia River derived from a clade containing haplotypes from the river's southwestern region. Haplotypes from southeastern populations formed a separate clade. Nucleotide diversity was reduced in northern populations relative to southern populations. These results were corroborated by analyses of RAPD loci, which revealed similar patterns of clustering and diversity. Network analyses suggested that northern populations were colonized following a range expansion mediated by individuals from populations located southwest of the river. Changes in the Columbia River's location during the Pliocene and Pleistocene likely released distributional constraints on this species, permitting their northern range expansion. Based on the barrier presented by the Columbia River's present location and differences in haplotype diversity and population structure observed between northern and southern populations, we suggest that designation of separate management units encompassing each region may assist with mitigating different threats to this species.
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Conflicting patterns of genetic structure produced by nuclear and mitochondrial markers in the Oregon slender salamander (Batrachoseps wrighti): Implications for conservation efforts and species management. CONSERV GENET 2005. [DOI: 10.1007/s10592-004-7850-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Hulva P, Horácek I, Strelkov PP, Benda P. Molecular architecture of Pipistrellus pipistrellus/Pipistrellus pygmaeus complex (Chiroptera: Vespertilionidae): further cryptic species and Mediterranean origin of the divergence. Mol Phylogenet Evol 2004; 32:1023-35. [PMID: 15288073 DOI: 10.1016/j.ympev.2004.04.007] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2003] [Revised: 04/06/2004] [Indexed: 11/26/2022]
Abstract
Previous genetic analyses have demonstrated that two phonic types of one of the most common European bats, the Common pipistrelle, belong to distinct species, although they are almost identical morphologically (45 kHz Pipistrellus pipistrellus and 55 kHz Pipistrellus pygmaeus). To reconstruct the history of the species complex and explain the codistribution of both forms in Europe and the Mediterranean, we performed phylogenetic analysis based on a 402-bp portion of the cytochrome b gene. Particular attention was paid to the eastern and southern parts of the range where no data were available. We found further distinctive allopatric haplotypes from Libya and Morocco. The difference of about 6-7% described in the Libyan population suggests the occurrence of a new species in the southern Mediterranean. The species status of Moroccan population is also discussed. The phylogeographic patterns obtained and analysis of fossil records support the hypothesis of expansion of both species into Europe from the Mediterranean region during the Holocene. The allopatric speciation model fits our data best. The paleobiographic scenario envisaged is corroborated also by molecular clock estimations and correlations with Late Neogene environmental changes in the Mediterranean region which ended with the Messinian salinity crisis.
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Affiliation(s)
- Pavel Hulva
- Department of Zoology, Charles University, Vinicná 7, 128 44 Prague 2, Czech Republic.
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Palkovacs EP, Marschner M, Ciofi C, Gerlach J, Caccone A. Are the native giant tortoises from the Seychelles really extinct? A genetic perspective based on mtDNA and microsatellite data. Mol Ecol 2003; 12:1403-13. [PMID: 12755870 DOI: 10.1046/j.1365-294x.2003.01834.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The extinction of the giant tortoises of the Seychelles Archipelago has long been suspected but is not beyond doubt. A recent morphological study of the giant tortoises of the western Indian Ocean concluded that specimens of two native Seychelles species survive in captivity today alongside giant tortoises of Aldabra, which are numerous in zoos as well as in the wild. This claim has been controversial because some of the morphological characters used to identify these species, several measures of carapace morphology, are reputed to be quite sensitive to captive conditions. Nonetheless, the potential survival of giant tortoise species previously thought extinct presents an exciting scenario for conservation. We used mitochondrial DNA sequences and nuclear microsatellites to examine the validity of the rediscovered species of Seychelles giant tortoises. Our results indicate that the morphotypes suspected to represent Seychelles species do not show levels of variation and genetic structuring consistent with long periods of reproductive isolation. We found no variation in the mitochondrial control region among 55 individuals examined and no genetic structuring in eight microsatellite loci, pointing to the survival of just a single lineage of Indian Ocean tortoises.
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Affiliation(s)
- Eric P Palkovacs
- Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, CT 06520, USA.
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Glenn TC, Staton JL, Vu AT, Davis LM, Bremer JRA, Rhodes WE, Brisbin IL, Sawyer RH. Low mitochondrial DNA variation among American alligators and a novel non-coding region in crocodilians. THE JOURNAL OF EXPERIMENTAL ZOOLOGY 2002; 294:312-24. [PMID: 12461811 DOI: 10.1002/jez.10206] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
We analyzed 1317-1823 base pairs (bp) of mitochondrial DNA sequence beginning in the 5' end of cytochrome b (cyt b) and ending in the central domain of the control region for 25 American alligators (Alligator mississippiensis) and compared these to a homologous sequence from a Chinese alligator (A. sinensis). Both species share a non-coding spacer between cyt b and tRNA(Thr). Chinese alligator cyt b differs from that of the American alligator by 17.5% at the nucleotide level and 13.8% for inferred amino acids, which is consistent with their presumed ancient divergence. Only two cyt b haplotypes were detected among the 25 American alligators (693-1199 bp surveyed), with one haplotype shared among 24 individuals. One alligator from Mississippi differed from all other alligators by a single silent substitution. The control region contained only slightly more variation among the 25 American alligators, with two variable positions (624 bp surveyed), yielding three haplotypes with 22, two, and one individuals in each of these groups. Previous genetic studies examining allozymes and the proportion of variable microsatellite DNA loci also found low levels of genetic diversity in American alligators. However, in contrast with allozymes, microsatellites, and morphology, the mtDNA data shows no evidence of differentiation among populations from the extremes of the species range. These results suggest that American alligators underwent a severe population bottleneck in the late Pleistocene, resulting in nearly homogenous mtDNA among all American alligators today.
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Affiliation(s)
- Travis C Glenn
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina 29208, USA.
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