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PVA-based assessment of resiliency, redundancy, and representation in an imperiled freshwater turtle. Glob Ecol Conserv 2023. [DOI: 10.1016/j.gecco.2023.e02419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023] Open
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Antonio Baeza J, Rajapakse D, Pearson L, Kreiser BR. Low coverage sequencing provides insights into the key features of the nuclear and mitochondrial genomes of the Alligator Snapping Turtle Macrochelys temminckii. Gene 2023; 873:147478. [PMID: 37182558 DOI: 10.1016/j.gene.2023.147478] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 04/24/2023] [Accepted: 05/08/2023] [Indexed: 05/16/2023]
Abstract
The alligator snapping turtle Macrochelys temminckii is a culturally, ecologically, and evolutionary relevant species of conservation concern. In this study, we conducted a genome survey of M. temminckii. Using a low-coverage short read sequencing strategy, this study estimated the genome size, repetitive genome content, annotated and quantified repetitive elements, assembled the 45S rRNA DNA operon, and characterized in detail the mitochondrial genome of M. temminckii. Using a k-mer strategy, the estimated haploid genome size varied between 3.77 and 3.19 Gbp, which is within the range previously reported for other representatives of the family Chelydridae. Repetitive genome content estimates using different k-mers (21 to 51) indicated that more than 75% of the genome of M. temminckii comprised repetitive elements. Taking into account only annotated repetitive elements, the most common repetitive elements were classified as Class I - Long Interspersed Nuclear Element (LINE) which were more abundant than Class I - Penelope and Class I - Long Terminal Repeat (LTR) Ty3-gypsy mobile elements. Less abundant repeat element families in the nuclear genome of M. temminckii included Class I - DIRS mobile elements and Satellite DNA. The nuclear ribosomal operon was partially assembled into two contigs, one encoding the complete ssrDNA and a second comprising the full lsrDNA. The AT-rich complete mitochondrial genome was 16,570 bp long. These new genomic resources are of utmost importance to aid in the development of conservation plans for this freshwater turtle.
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Affiliation(s)
- J Antonio Baeza
- Department of Biological Sciences, Clemson University, Clemson, SC, USA; Departamento de Biología Marina, Universidad Catolica del Norte, Coquimbo, Chile; Smithsonian Marine Station at Fort Pierce, Smithsonian Institution, Fort Pierce, FL, USA.
| | - Dilani Rajapakse
- Department of Biological Sciences, Clemson University, Clemson, SC, USA
| | - Luke Pearson
- U.S. Fish and Wildlife Service, Mississippi Ecological Services Field Office, 6578 Dogwood View Parkway, Jackson, MS 39213
| | - Brian R Kreiser
- School of Biological, Environmental and Earth Sciences, University of Southern Mississippi, Hattiesburg, Mississippi 39406 USA
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Pearson L, Kreiser BR, Qualls CP. Characterization of Microsatellite Loci for the Alligator Snapping Turtle and Cross-Amplification in Two Chelydrid Species†. CHELONIAN CONSERVATION AND BIOLOGY 2022. [DOI: 10.2744/ccb-1538.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Luke Pearson
- US Fish and Wildlife Service, Mississippi Ecological Services Field Office, Jackson, Mississippi 39213-7856 USA []
| | - Brian R. Kreiser
- School of Biological, Environmental and Earth Sciences, University of Southern Mississippi, Hattiesburg, Mississippi 39406 USA [; ]
| | - Carl P. Qualls
- School of Biological, Environmental and Earth Sciences, University of Southern Mississippi, Hattiesburg, Mississippi 39406 USA [; ]
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Dutton HR, Du Preez LH, Verneau O, Whelan NV, Bullard SA. First Record of a Polystome from Alligator Snapping Turtle, Macrochelys temminckii (Cryptodira: Chelydridae) or Mississippi; with Comments on "Neopolystoma orbiculare (Stunkard, 1916)" and Its Junior Subjective Synonyms. J Parasitol 2021; 107:74-88. [PMID: 33556183 DOI: 10.1645/20-96] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Herein, we describe several newly-collected specimens of Neopolystoma cf. orbiculare from the urinary bladder of 2 alligator snapping turtles, Macrochelys temminckii (Troost in Harland, 1835) (Cryptodira: Chelydridae Gray, 1831) from Comet Lake (30°35'46.94″N, 88°36'3.12″W), Pascagoula River, Mississippi. Our specimens differed from all previous descriptions of N. orbiculare and its junior subjective synonyms by the combination of having intestinal ceca adorned with triangular pockets and that terminate dorsal to the haptor, distinctive hooklets each having a handle and guard of approximately equal length and having a much longer and curved blade, 16 genital coronet spines that each possess 1-2 flanges per spine, pre-testicular vaginal pores, and vaginal ducts that are anterior to the junction of the oviduct and genito-intestinal canal. Some of our specimens were enantiomorphic (4 and 3 had a dextral and sinistral ovary, respectively). Nucleotide sequences (large subunit ribosomal DNA [28S], small subunit ribosomal DNA [18S], and cytochrome oxidase subunit 1 mitochondrial gene [COI]) for our specimens were most similar to GenBank sequences ascribed to N. orbiculare. Single-gene and concatenated phylogenetic analyses confirmed that NeopolystomaPrice, 1939 is polyphyletic and that our isolates share a recent common ancestor with those ascribed to N. orbiculare. This is the first record of a polystomatid from Mississippi, from the Pascagoula River, and from the alligator snapping turtle (and only the second species of Neopolystoma reported from any snapping turtle).
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Affiliation(s)
- Haley R Dutton
- Auburn University, Aquatic Parasitology Laboratory and Southeastern Cooperative Fish Parasite and Disease Laboratory, School of Fisheries, Aquaculture, & Aquatic Sciences, College of Agriculture, Auburn University, 203 Swingle Hall, Auburn, Alabama 36849
| | - Louis H Du Preez
- African Amphibian Conservation Research Group, Unit for Environmental Sciences and Management, North-West University, Private Bag X6001, Potchefstroom, 2520, South Africa.,South African Institute for Aquatic Biodiversity, Somerset Street, Grahamstown 6139, South Africa
| | - Olivier Verneau
- South African Institute for Aquatic Biodiversity, Somerset Street, Grahamstown 6139, South Africa.,University of Perpignan Via Domitia, Centre de Formation et de Recherche sur les Environnements Méditerranéens, UMR 5110, F-66860, Perpignan, France.,CNRS, Centre de Formation et de Recherche sur les Environnements Méditerranéens, UMR5110, F-66860, Perpignan, France
| | - Nathan V Whelan
- Warm Springs Fish Technology Center, U.S. Fish and Wildlife Service, Auburn, Alabama 36849
| | - Stephen A Bullard
- Auburn University, Aquatic Parasitology Laboratory and Southeastern Cooperative Fish Parasite and Disease Laboratory, School of Fisheries, Aquaculture, & Aquatic Sciences, College of Agriculture, Auburn University, 203 Swingle Hall, Auburn, Alabama 36849
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Folt B, Bauder J, Spear S, Stevenson D, Hoffman M, Oaks JR, Wood PL, Jenkins C, Steen DA, Guyer C. Taxonomic and conservation implications of population genetic admixture, mito-nuclear discordance, and male-biased dispersal of a large endangered snake, Drymarchon couperi. PLoS One 2019; 14:e0214439. [PMID: 30913266 PMCID: PMC6435180 DOI: 10.1371/journal.pone.0214439] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 03/11/2019] [Indexed: 01/08/2023] Open
Abstract
Accurate species delimitation and description are necessary to guide effective conservation of imperiled species, and this synergy is maximized when multiple data sources are used to delimit species. We illustrate this point by examining Drymarchon couperi (Eastern Indigo Snake), a large, federally-protected species in North America that was recently divided into two species based on gene sequence data from three loci and heuristic morphological assessment. Here, we re-evaluate the two-species hypothesis for D. couperi by evaluating both population genetic and gene sequence data. Our analyses of 14 microsatellite markers revealed 6–8 genetic population clusters with significant admixture, particularly across the contact zone between the two hypothesized species. Phylogenetic analyses of gene sequence data with maximum-likelihood methods suggested discordance between mitochondrial and nuclear markers and provided phylogenetic support for one species rather than two. For these reasons, we place Drymarchon kolpobasileus into synonymy with D. couperi. We suggest inconsistent patterns between mitochondrial and nuclear DNA are driven by high dispersal of males relative to females. We advocate for species delimitation exercises that evaluate admixture and gene flow in addition to phylogenetic analyses, particularly when the latter reveal monophyletic lineages. This is particularly important for taxa, such as squamates, that exhibit strong sex-biased dispersal. Problems associated with over-delimitation of species richness can become particularly acute for threatened and endangered species, because of high costs to conservation when taxonomy demands protection of more individual species than are supported by accumulating data.
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Affiliation(s)
- Brian Folt
- Department of Biological Sciences and Auburn University Museum of Natural History, Auburn University, Auburn, Alabama, United States of America
- * E-mail:
| | - Javan Bauder
- The Orianne Society, 11 Fruitstand Lane, Tiger, Georgia, United States of America
- Department of Environmental Conservation, University of Massachusetts, Amherst, Massachusetts, United States of America
- Illinois Natural History Survey, University of Illinois, Champaign, Illinois, United States of America
| | - Stephen Spear
- The Orianne Society, 11 Fruitstand Lane, Tiger, Georgia, United States of America
- The Wilds, Cumberland, Ohio United States of America
| | - Dirk Stevenson
- The Orianne Society, 11 Fruitstand Lane, Tiger, Georgia, United States of America
- Altamaha Environmental Consulting, Hinesville, Georgia, United States of America
| | - Michelle Hoffman
- The Orianne Center for Indigo Conservation, Central Florida Zoo and Botanical Gardens, Sanford, Florida, United States of America
| | - Jamie R. Oaks
- Department of Biological Sciences and Auburn University Museum of Natural History, Auburn University, Auburn, Alabama, United States of America
| | - Perry L. Wood
- Department of Biological Sciences and Auburn University Museum of Natural History, Auburn University, Auburn, Alabama, United States of America
| | - Christopher Jenkins
- The Orianne Society, 11 Fruitstand Lane, Tiger, Georgia, United States of America
| | - David A. Steen
- Georgia Sea Turtle Center, Jekyll Island Authority, Jekyll Island, Georgia, United States of America
| | - Craig Guyer
- Department of Biological Sciences and Auburn University Museum of Natural History, Auburn University, Auburn, Alabama, United States of America
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Feist SM, Jones RL, Copley JL, Pearson LS, Berry GA, Qualls CP. Development and Validation of an Environmental DNA Method for Detection of the Alligator Snapping Turtle (Macrochelys temminckii). CHELONIAN CONSERVATION AND BIOLOGY 2018. [DOI: 10.2744/ccb-1315.1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Sheena M. Feist
- Mississippi Department of Wildlife, Fisheries, and Parks, Museum of Natural Science, 2148 Riverside
| | - Robert L. Jones
- Mississippi Department of Wildlife, Fisheries, and Parks, Museum of Natural Science, 2148 Riverside
| | - Jeremy L. Copley
- Mississippi Department of Wildlife, Fisheries, and Parks, Museum of Natural Science, 2148 Riverside
| | - Luke S. Pearson
- University of Southern Mississippi, Department of Biological Sciences, 118 College Drive #5018, Hatt
| | - Gabrielle A. Berry
- University of Southern Mississippi, Department of Biological Sciences, 118 College Drive #5018, Hatt
| | - Carl P. Qualls
- University of Southern Mississippi, Department of Biological Sciences, 118 College Drive #5018, Hatt
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Hayes MM, Piller KR. Patterns of diversification in a North American endemic fish, the Blackbanded Darter (Perciformes, Percidae). ZOOL SCR 2018. [DOI: 10.1111/zsc.12288] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Malorie M. Hayes
- Department of Biological Sciences; Southeastern Louisiana University; Hammond Louisiana
- Auburn University; Auburn Alabama
| | - Kyle R. Piller
- Department of Biological Sciences; Southeastern Louisiana University; Hammond Louisiana
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The First Record of an Alligator Snapping Turtle (Macrochelys temminckii) in Illinois in 30 Years. SOUTHEAST NAT 2017. [DOI: 10.1656/058.016.0316] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Mali I, Villamizar-Gomez A, Guerra TM, Vandewege MW, Forstner MR. Population Genetics of Texas Spiny Softshell Turtles (Apalone spinifera emoryi) Under Various Anthropogenic Pressures in Two Distinct Regions of Their Range in Texas. CHELONIAN CONSERVATION AND BIOLOGY 2015. [DOI: 10.2744/ccb-1149.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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11
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Andrews KR, Norton EL, Fernandez-Silva I, Portner E, Goetze E. Multilocus evidence for globally distributed cryptic species and distinct populations across ocean gyres in a mesopelagic copepod. Mol Ecol 2015; 23:5462-79. [PMID: 25283587 DOI: 10.1111/mec.12950] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Revised: 09/17/2014] [Accepted: 09/23/2014] [Indexed: 11/29/2022]
Abstract
Zooplanktonic taxa have a greater number of distinct populations and species than might be predicted based on their large population sizes and open-ocean habitat, which lacks obvious physical barriers to dispersal and gene flow. To gain insight into the evolutionary mechanisms driving genetic diversification in zooplankton, we developed eight microsatellite markers to examine the population structure of an abundant, globally distributed mesopelagic copepod, Haloptilus longicornis, at 18 sample sites across the Atlantic and Pacific Oceans (n = 761). When comparing our microsatellite results with those of a prior study that used a mtDNA marker (mtCOII, n = 1059, 43 sample sites), we unexpectedly found evidence for the presence of a cryptic species pair. These species were globally distributed and apparently sympatric, and were separated by relatively weak genetic divergence (reciprocally monophyletic mtCOII lineages 1.6% divergent; microsatellite FST ranging from 0.28 to 0.88 across loci, P < 0.00001). Using both mtDNA and microsatellite data for the most common of the two species (n = 669 for microsatellites, n = 572 for mtDNA), we also found evidence for allopatric barriers to gene flow within species, with distinct populations separated by continental landmasses and equatorial waters in both the Atlantic and Pacific Ocean basins. Our study shows that oceanic barriers to gene flow can act as a mechanism promoting allopatric diversification in holoplanktonic taxa, despite the high potential dispersal abilities and pelagic habitat for these species.
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Affiliation(s)
- Kimberly R Andrews
- Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA; School of Biological and Biomedical Sciences, Durham University, South Road, Durham, DH1 3LE, UK
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Johnston GR, Thomas TM, Suarez E, Lau A, Mitchell JC. Population Structure and Body Size of the Suwannee Alligator Snapping Turtle (Macrochelys suwanniensis) in Northern Florida. CHELONIAN CONSERVATION AND BIOLOGY 2015. [DOI: 10.2744/ccab-14-01-73-81.1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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13
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Anthony T, Riedle JD, East MB, Fillmore B, Ligon DB. Monitoring of a Reintroduced Population of Juvenile Alligator Snapping Turtles. CHELONIAN CONSERVATION AND BIOLOGY 2015. [DOI: 10.2744/1071-8443-14.1.43] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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14
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Murray CM, McMahan CD, Dobie JL, Guyer C. Cranial variation amongst independent lineages of the alligator snapping turtle ( Macrochelys temminckii
). J ZOOL SYST EVOL RES 2014. [DOI: 10.1111/jzs.12072] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Caleb D. McMahan
- LSU Museum of Natural Science (Ichthyology); Department of Biological Sciences; Louisiana State University; Baton Rouge LA USA
| | - James L. Dobie
- Department of Biological Sciences; Auburn University; Auburn AL USA
| | - Craig Guyer
- Department of Biological Sciences; Auburn University; Auburn AL USA
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15
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Moore DB, Ligon DB, Fillmore BM, Fox SF. Spatial use and selection of habitat in a reintroduced population of alligator snapping turtles ( Macrochelys temminckii). SOUTHWEST NAT 2014. [DOI: 10.1894/f05-nbf-05.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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16
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Davy CM, Murphy RW. Conservation genetics of the endangered Spotted Turtle (Clemmys guttata) illustrate the risks of “bottleneck tests”. CAN J ZOOL 2014. [DOI: 10.1139/cjz-2013-0188] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Studies of population genetics in turtles have suggested that turtles do not experience genetic impacts of bottlenecks as strongly as expected. However, recent studies cast doubt on two commonly used tests implemented in the program BOTTLENECK, suggesting that these findings should be re-evaluated. The Spotted Turtle (Clemmys guttata (Schneider, 1792)) is endangered both globally and within Canada, but genetic data required to develop effective recovery strategies are unavailable. Here, we conducted the first study of population genetic structure in C. guttata. We then used multiple small populations of C. guttata as replicates to test whether the commonly used program BOTTLENECK could detect the genetic signature of bottlenecks in our study populations, which are all thought to have experienced significant declines in the past 2–3 generations (75 years). Turtles (n = 256) were genotyped at 11 microsatellite loci. A suite of Bayesian population genetics analyses and a principal coordinates analysis identified a minimum of 6 distinct genetic populations and a maximum of 10 differentiated subpopulations across the sampled Canadian range of C. guttata, which corresponded to demographically independent units. BOTTLENECK failed to detect population declines. A literature review found that bottleneck tests in 17 of 18 previous genetic studies of tortoises and freshwater turtles were based on suboptimal sampling, potentially confounding their results. High retention of genetic diversity (allelic richness and heterozygosity) in isolated populations of C. guttata and other turtle species is encouraging for species recovery, but conclusions about the prevalence of genetic bottlenecks in such populations should be re-examined.
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Affiliation(s)
- Christina M. Davy
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2, Canada; Department of Natural History, Royal Ontario Museum, 100 Queen’s Park, Toronto, ON M5S 2C6, Canada
| | - Robert W. Murphy
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2, Canada; Department of Natural History, Royal Ontario Museum, 100 Queen’s Park, Toronto, ON M5S 2C6, Canada
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Selman W, Kreiser B, Qualls C. Conservation genetics of the yellow-blotched sawback Graptemys flavimaculata (Testudines: Emydidae). CONSERV GENET 2013. [DOI: 10.1007/s10592-013-0507-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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18
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Unger SD, Rhodes OE, Sutton TM, Williams RN. Population genetics of the Eastern Hellbender (Cryptobranchus alleganiensis alleganiensis) across multiple spatial scales. PLoS One 2013; 8:e74180. [PMID: 24204565 PMCID: PMC3800131 DOI: 10.1371/journal.pone.0074180] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 07/28/2013] [Indexed: 02/07/2023] Open
Abstract
Conservation genetics is a powerful tool to assess the population structure of species and provides a framework for informing management of freshwater ecosystems. As lotic habitats become fragmented, the need to assess gene flow for species of conservation management becomes a priority. The eastern hellbender (Cryptobranchus alleganiensis alleganiensis) is a large, fully aquatic paedamorphic salamander. Many populations are experiencing declines throughout their geographic range, yet the genetic ramifications of these declines are currently unknown. To this end, we examined levels of genetic variation and genetic structure at both range-wide and drainage (hierarchical) scales. We collected 1,203 individuals from 77 rivers throughout nine states from June 2007 to August 2011. Levels of genetic diversity were relatively high among all sampling locations. We detected significant genetic structure across populations (Fst values ranged from 0.001 between rivers within a single watershed to 0.218 between states). We identified two genetically differentiated groups at the range-wide scale: 1) the Ohio River drainage and 2) the Tennessee River drainage. An analysis of molecular variance (AMOVA) based on landscape-scale sampling of basins within the Tennessee River drainage revealed the majority of genetic variation (∼94-98%) occurs within rivers. Eastern hellbenders show a strong pattern of isolation by stream distance (IBSD) at the drainage level. Understanding levels of genetic variation and differentiation at multiple spatial and biological scales will enable natural resource managers to make more informed decisions and plan effective conservation strategies for cryptic, lotic species.
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Affiliation(s)
- Shem D. Unger
- Savannah River Ecology Laboratory, University of Georgia, Aiken, South Carolina, United States of America
- * E-mail:
| | - Olin E. Rhodes
- Savannah River Ecology Laboratory, University of Georgia, Aiken, South Carolina, United States of America
| | - Trent M. Sutton
- School of Fisheries and Ocean Sciences, University of Alaska Fairbanks, Fairbanks, Alaska, United States of America
| | - Rod N. Williams
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, Indiana, United States of America
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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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Cryptic population structuring and the role of the Isthmus of Tehuantepec as a gene flow barrier in the critically endangered Central American River Turtle. PLoS One 2013; 8:e71668. [PMID: 24086253 PMCID: PMC3783458 DOI: 10.1371/journal.pone.0071668] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Accepted: 07/05/2013] [Indexed: 11/25/2022] Open
Abstract
The critically endangered Central American River Turtle (Dermatemys mawii) is the only remaining member of the Dermatemydidae family, yet little is known about its population structuring. In a previous study of mitochondrial (mt) DNA in the species, three main lineages were described. One lineage (Central) was dominant across most of the range, while two other lineages were restricted to Papaloapan (PAP; isolated by the Isthmus of Tehuantepec and the Sierra de Santa Marta) or the south-eastern part of the range (1D). Here we provide data from seven polymorphic microsatellite loci and the R35 intron to re-evaluate these findings using DNA from the nuclear genome. Based on a slightly expanded data set of a total of 253 samples from the same localities, we find that mtDNA and nuclear DNA markers yield a highly congruent picture of the evolutionary history and population structuring of D. mawii. While resolution provided by the R35 intron (sequenced for a subset of the samples) was very limited, the microsatellite data revealed pronounced population structuring. Within the Grijalva-Usumacinta drainage basin, however, many populations separated by more than 300 kilometers showed signals of high gene flow. Across the entire range, neither mitochondrial nor nuclear DNA show a significant isolation-by-distance pattern, but both genomes highlight that the D. mawii population in the Papaloapan basin is genetically distinctive. Further, both marker systems detect unique genomic signals in four individuals with mtDNA clade 1D sampled on the southeast edge of the Grijalva-Usumacinta basin. These individuals may represent a separate cryptic taxon that is likely impacted by recent admixture.
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Hoehn M, Dimond W, Osborne W, Sarre SD. Genetic analysis reveals the costs of peri-urban development for the endangered grassland earless dragon. CONSERV GENET 2013. [DOI: 10.1007/s10592-013-0515-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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References. Mol Ecol 2012. [DOI: 10.1002/9780470979365.refs] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Karl SA, Toonen RJ, Grant WS, Bowen BW. Common misconceptions in molecular ecology: echoes of the modern synthesis. Mol Ecol 2012; 21:4171-89. [PMID: 22574714 DOI: 10.1111/j.1365-294x.2012.05576.x] [Citation(s) in RCA: 112] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The field of molecular ecology has burgeoned into a large discipline spurred on by technical innovations that facilitate the rapid acquisition of large amounts of genotypic data, by the continuing development of theory to interpret results, and by the availability of computer programs to analyse data sets. As the discipline grows, however, misconceptions have become enshrined in the literature and are perpetuated by routine citations to other articles in molecular ecology. These misconceptions hamper a better understanding of the processes that influence genetic variation in natural populations and sometimes lead to erroneous conclusions. Here, we consider eight misconceptions commonly appearing in the literature: (i) some molecular markers are inherently better than other markers; (ii) mtDNA produces higher F(ST) values than nDNA; (iii) estimated population coalescences are real; (iv) more data are always better; (v) one needs to do a Bayesian analysis; (vi) selective sweeps influence mtDNA data; (vii) equilibrium conditions are critical for estimating population parameters; and (viii) having better technology makes us smarter than our predecessors. This is clearly not an exhaustive list and many others can be added. It is, however, sufficient to illustrate why we all need to be more critical of our own understanding of molecular ecology and to be suspicious of self-evident truths.
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Affiliation(s)
- Stephen A Karl
- Hawai'i Institute of Marine Biology, University of Hawai'i, Mānoa, Kāne'ohe, HI 96744, USA.
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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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Extremely low genetic diversity and weak population differentiation in the endangered Colombian river turtle Podocnemis lewyana (Testudines: Podocnemididae). CONSERV GENET 2011. [DOI: 10.1007/s10592-011-0263-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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