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Hague MTJ, Miller LE, Stokes AN, Feldman CR, Brodie ED, Brodie ED. Conspicuous coloration of toxin-resistant predators implicates additional trophic interactions in a predator-prey arms race. Mol Ecol 2023; 32:4482-4496. [PMID: 36336815 DOI: 10.1111/mec.16772] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 10/21/2022] [Accepted: 11/03/2022] [Indexed: 08/08/2023]
Abstract
Antagonistic coevolution between natural enemies can produce highly exaggerated traits, such as prey toxins and predator resistance. This reciprocal process of adaptation and counter-adaptation may also open doors to other evolutionary novelties not directly involved in the phenotypic interface of coevolution. We tested the hypothesis that predator-prey coevolution coincided with the evolution of conspicuous coloration on resistant predators that retain prey toxins. In western North America, common garter snakes (Thamnophis sirtalis) have evolved extreme resistance to tetrodotoxin (TTX) in the coevolutionary arms race with their deadly prey, Pacific newts (Taricha spp.). TTX-resistant snakes can retain large amounts of ingested TTX, which could serve as a deterrent against the snakes' own predators if TTX toxicity and resistance are coupled with a conspicuous warning signal. We evaluated whether arms race escalation covaries with bright red coloration in snake populations across the geographic mosaic of coevolution. Snake colour variation departs from the neutral expectations of population genetic structure and covaries with escalating clines of newt TTX and snake resistance at two coevolutionary hotspots. In the Pacific Northwest, bright red coloration fits an expected pattern of an aposematic warning to avian predators: TTX-resistant snakes that consume highly toxic newts also have relatively large, reddish-orange dorsal blotches. Snake coloration also seems to have evolved with the arms race in California, but overall patterns are less intuitively consistent with aposematism. These results suggest that interactions with additional trophic levels can generate novel traits as a cascading consequence of arms race coevolution across the geographic mosaic.
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Affiliation(s)
- Michael T J Hague
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
| | - Lauren E Miller
- Department of Biology, University of Virginia, Charlottesville, Virginia, USA
| | - Amber N Stokes
- Department of Biology, California State University, Bakersfield, California, USA
| | - Chris R Feldman
- Department of Biology, University of Nevada, Reno, Nevada, USA
| | - Edmund D Brodie
- Department of Biology, Utah State University, Logan, Utah, USA
| | - Edmund D Brodie
- Department of Biology, University of Virginia, Charlottesville, Virginia, USA
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2
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Zink RM, Klicka LB. The taxonomic basis of subspecies listed as threatened and endangered under the endangered species act. FRONTIERS IN CONSERVATION SCIENCE 2022. [DOI: 10.3389/fcosc.2022.971280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
More than 170 subspecies are listed as threatened or endangered under the US Endangered Species Act. Most of these subspecies were described decades ago on the basis of geographical variation in morphology using relatively primitive taxonomic methods. The US Fish and Wildlife Service defaults to subspecies descriptions by taxonomists working with specific groups of organisms, but there is no single definition of subspecies across plants and animals. Valid tests today usually entail molecular analyses of variation within and among populations, although there is no reason that behavioral, ecological or molecular characters could not be used, and include tests for significant differences between samples of the putative endangered subspecies and its nearest geographic relatives. We evaluated data gathered since subspecies listed under the ESA were described finding about one-third are valid (distinct evolutionary taxa), one-third are not, and one-third have not been tested. Therefore, it should not be assumed that because a subspecies occurs in a checklist, it is taxonomically valid. If the US Fish and Wildlife Service intends to continue listing subspecies, we suggest that they convene taxonomic experts representing various groups of organisms to provide a minimal set of criteria for a subspecies to be listed under the ESA.
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3
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Lattanzio MS, Buontempo MJ. Ecogeographic Divergence Linked to Dorsal Coloration in Eastern Hog-Nosed Snakes (Heterodon platirhinos). HERPETOLOGICA 2021. [DOI: 10.1655/herpetologica-d-19-00031.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Matthew S. Lattanzio
- Department of Organismal and Environmental Biology, Christopher Newport University, Newport News, VA 23606, USA
| | - Michael J. Buontempo
- Department of Organismal and Environmental Biology, Christopher Newport University, Newport News, VA 23606, USA
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4
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Hardy BM, Pope KL, Latch EK. Genomic signatures of demographic declines in an imperiled amphibian inform conservation action. Anim Conserv 2021. [DOI: 10.1111/acv.12695] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- B. M. Hardy
- Behavioral and Molecular Ecology Research Group Department of Biological Sciences University of Wisconsin‐Milwaukee Milwaukee WI USA
- Graduate Degree Program in Ecology Colorado State University Fort Collins CO USA
| | - K. L. Pope
- United States Forest Service Pacific Southwest Research Station Arcata CA USA
| | - E. K. Latch
- Behavioral and Molecular Ecology Research Group Department of Biological Sciences University of Wisconsin‐Milwaukee Milwaukee WI USA
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Hague MTJ, Stokes AN, Feldman CR, Brodie ED, Brodie ED. The geographic mosaic of arms race coevolution is closely matched to prey population structure. Evol Lett 2020; 4:317-332. [PMID: 32774881 PMCID: PMC7403720 DOI: 10.1002/evl3.184] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 05/11/2020] [Accepted: 05/22/2020] [Indexed: 01/09/2023] Open
Abstract
Reciprocal adaptation is the hallmark of arms race coevolution. Local coadaptation between natural enemies should generate a geographic mosaic pattern where both species have roughly matched abilities across their shared range. However, mosaic variation in ecologically relevant traits can also arise from processes unrelated to reciprocal selection, such as population structure or local environmental conditions. We tested whether these alternative processes can account for trait variation in the geographic mosaic of arms race coevolution between resistant garter snakes (Thamnophis sirtalis) and toxic newts (Taricha granulosa). We found that predator resistance and prey toxin levels are functionally matched in co-occurring populations, suggesting that mosaic variation in the armaments of both species results from the local pressures of reciprocal selection. By the same token, phenotypic and genetic variation in snake resistance deviates from neutral expectations of population genetic differentiation, showing a clear signature of adaptation to local toxin levels in newts. Contrastingly, newt toxin levels are best predicted by genetic differentiation among newt populations, and to a lesser extent, by the local environment and snake resistance. Exaggerated armaments suggest that coevolution occurs in certain hotspots, but prey population structure seems to be of particular influence on local phenotypic variation in both species throughout the geographic mosaic. Our results imply that processes other than reciprocal selection, like historical biogeography and environmental pressures, represent an important source of variation in the geographic mosaic of coevolution. Such a pattern supports the role of "trait remixing" in the geographic mosaic theory, the process by which non-adaptive forces dictate spatial variation in the interactions among species.
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Affiliation(s)
- Michael T J Hague
- Division of Biological Sciences University of Montana Missoula Montana 59812.,Department of Biology University of Virginia Charlottesville Virginia 22904
| | - Amber N Stokes
- Department of Biology California State University Bakersfield California 93311
| | - Chris R Feldman
- Department of Biology University of Nevada Reno Nevada 89557
| | - Edmund D Brodie
- Department of Biology Utah State University Logan Utah 84322
| | - Edmund D Brodie
- Department of Biology University of Virginia Charlottesville Virginia 22904
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Wood DA, Rose JP, Halstead BJ, Stoelting RE, Swaim KE, Vandergast AG. Combining genetic and demographic monitoring better informs conservation of an endangered urban snake. PLoS One 2020; 15:e0231744. [PMID: 32369486 PMCID: PMC7200000 DOI: 10.1371/journal.pone.0231744] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 04/05/2020] [Indexed: 11/24/2022] Open
Abstract
Conversion and fragmentation of wildlife habitat often leads to smaller and isolated populations and can reduce a species' ability to disperse across the landscape. As a consequence, genetic drift can quickly lower genetic variation and increase vulnerability to extirpation. For species of conservation concern, quantification of population size and connectivity can clarify the influence of genetic drift in local populations and provides important information for conservation management and recovery strategies. Here, we used genome-wide single nucleotide polymorphism (SNP) data and capture-mark-recapture methods to evaluate the genetic diversity and demography within seven focal sites of the endangered San Francisco gartersnake (Thamnophis sirtalis tetrataenia), a species affected by alteration and isolation of wetland habitats throughout its distribution. The primary goals were to determine the population structure and degree of genetic isolation among T. s. tetrataenia populations and estimate effective size and population abundance within sites to better understand the present and future importance of genetic drift. We also used temporally sampled datasets to examine the magnitude of genetic change over time. We found moderate population genetic structure throughout the San Francisco Peninsula that partitions sites into northern and southern regional clusters. Point estimates of both effective size and population abundance were generally small (≤ 100) for a majority of the sites, and estimates were particularly low in the northern populations. Genetic analyses of temporal datasets indicated an increase in genetic differentiation, especially for the most geographically isolated sites, and decreased genetic diversity over time in at least one site (Pacifica). Our results suggest that drift-mediated processes as a function of small population size and reduced connectivity from neighboring populations may decrease diversity and increase differentiation. Improving genetic diversity and connectivity among T. s. tetrataenia populations could promote persistence of this endangered snake.
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Affiliation(s)
- Dustin A. Wood
- U.S. Geological Survey, Western Ecological Research Center, San Diego Field Station, San Diego, California, United States of America
| | - Jonathan P. Rose
- U.S. Geological Survey, Western Ecological Research Center, Santa Cruz Field Station, Santa Cruz, California, United States of America
| | - Brian J. Halstead
- U.S. Geological Survey, Western Ecological Research Center, Dixon Field Station, Dixon, California, United States of America
| | - Ricka E. Stoelting
- Swaim Biological Incorporated, Livermore, California, United States of America
| | - Karen E. Swaim
- Swaim Biological Incorporated, Livermore, California, United States of America
| | - Amy G. Vandergast
- U.S. Geological Survey, Western Ecological Research Center, San Diego Field Station, San Diego, California, United States of America
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Key KN, Banta JA, Gluesenkamp AG, Hertweck KL, Placyk JS. CONSERVATION BIOLOGY OF A SOUTHWESTERN ENDEMIC, THE TEXAS GARTER SNAKE, THAMNOPHIS SIRTALIS ANNECTENS: AN INTEGRATIVE PERSPECTIVE. SOUTHWEST NAT 2019. [DOI: 10.1894/0038-4909-64-1-8] [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]
Affiliation(s)
- Kayla N. Key
- Department of Biology, University of Texas at Tyler, Tyler, TX 75799 (KNK, JAB, KLH, JSP)
| | - Joshua A. Banta
- Department of Biology, University of Texas at Tyler, Tyler, TX 75799 (KNK, JAB, KLH, JSP)
| | | | - Kate L. Hertweck
- Department of Biology, University of Texas at Tyler, Tyler, TX 75799 (KNK, JAB, KLH, JSP)
| | - John S. Placyk
- Department of Biology, University of Texas at Tyler, Tyler, TX 75799 (KNK, JAB, KLH, JSP)
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8
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Hague MTJ, Toledo G, Geffeney SL, Hanifin CT, Brodie ED, Brodie ED. Large-effect mutations generate trade-off between predatory and locomotor ability during arms race coevolution with deadly prey. Evol Lett 2018; 2:406-416. [PMID: 30283691 PMCID: PMC6121790 DOI: 10.1002/evl3.76] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 07/10/2018] [Accepted: 07/13/2018] [Indexed: 01/06/2023] Open
Abstract
Adaptive evolution in response to one selective challenge may disrupt other important aspects of performance. Such evolutionary trade‐offs are predicted to arise in the process of local adaptation, but it is unclear if these phenotypic compromises result from the antagonistic effects of simple amino acid substitutions. We tested for trade‐offs associated with beneficial mutations that confer tetrodotoxin (TTX) resistance in the voltage‐gated sodium channel (NaV1.4) in skeletal muscle of the common garter snake (Thamnophis sirtalis). Separate lineages in California and the Pacific Northwest independently evolved TTX‐resistant changes to the pore of NaV1.4 as a result of arms race coevolution with toxic prey, newts of the genus Taricha. Snakes from the California lineage that were homozygous for an allele known to confer large increases in toxin resistance (NaV1.4LVNV) had significantly reduced crawl speed compared to individuals with the ancestral TTX‐sensitive channel. Heterologous expression of native snake NaV1.4 proteins demonstrated that the same NaV1.4LVNV allele confers a dramatic increase in TTX resistance and a correlated decrease in overall channel excitability. Our results suggest the same mutations that accumulate during arms race coevolution and beneficially interfere with toxin‐binding also cause changes in electrophysiological function of the channel that may affect organismal performance. This trade‐off was only evident in the predator lineage where coevolution has led to the most extreme resistance phenotype, determined by four critical amino acid substitutions. If these biophysical changes also translate to a fitness cost—for example, through the inability of T. sirtalis to quickly escape predators—then pleiotropy at this single locus could contribute to observed variation in levels of TTX resistance across the mosaic landscape of coevolution.
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Affiliation(s)
- Michael T J Hague
- Department of Biology University of Virginia Charlottesville Virginia 22903
| | - Gabriela Toledo
- Department of Biology University of Virginia Charlottesville Virginia 22903
| | - Shana L Geffeney
- Department of Biology Utah State University Uintah Basin Vernal Utah 84322
| | - Charles T Hanifin
- Department of Biology Utah State University Uintah Basin Vernal Utah 84322
| | - Edmund D Brodie
- Department of Biology Utah State University Logan Utah 84322
| | - Edmund D Brodie
- Department of Biology University of Virginia Charlottesville Virginia 22903
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9
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Salvador de Jesús-Bonilla V, García-París M, Ibarra-Cerdeña CN, Zaldívar-Riverón A. Geographic patterns of phenotypic diversity in incipient species of North American blister beetles (Coleoptera: Meloidae) are not determined by species niches, but driven by demography along the speciation process. INVERTEBR SYST 2018. [DOI: 10.1071/is17072] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The Epicauta stigmata complex is a group of blister beetles composed of three parapatric or sympatric species that occur in central Mexico to southern USA: E. stigmata, E. uniforma and E. melanochroa. These species are morphologically very similar, and are mainly distinguished by body colour differences. Here we assessed whether phenotypic divergence in coloration patterns define evolutionary units within the complex. We studied the phylogenetic relationships, demographic history and concordances between morphological and ecological traits in the group. The complex apparently had a demographic history of recent population expansion during the last glaciation period 75000 to 9500 years ago. The three species show no reciprocal monophyly, and thus their allospecificity was not confirmed. The current distribution of haplotypes and the genetic divergences in these taxa can be explained by either recent mitochondrial introgression events caused by hybridisation or by incomplete lineage sorting. Colour pattern differences in the complex are not likely a product of local selection acting over a common genetic background. We suggest that phenotypic divergence in colour patterns during an incipient speciation process might be seen as an enhancing factor of cohesion within each of the three evolutionary units.
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10
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Hague MT, Feldman CR, Brodie ED, Brodie ED. Convergent adaptation to dangerous prey proceeds through the same first‐step mutation in the garter snake
Thamnophis sirtalis. Evolution 2017; 71:1504-1518. [DOI: 10.1111/evo.13244] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 03/24/2017] [Indexed: 12/28/2022]
Affiliation(s)
- Michael T.J. Hague
- Department of Biology University of Virginia Charlottesville Virginia 22904
| | | | | | - Edmund D. Brodie
- Department of Biology University of Virginia Charlottesville Virginia 22904
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11
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Bernardi M, Angielczyk KD, Mitchell JS, Ruta M. Phylogenetic Stability, Tree Shape, and Character Compatibility: A Case Study Using Early Tetrapods. Syst Biol 2016; 65:737-58. [PMID: 27288479 DOI: 10.1093/sysbio/syw049] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2014] [Accepted: 05/19/2016] [Indexed: 11/13/2022] Open
Abstract
Phylogenetic tree shape varies as the evolutionary processes affecting a clade change over time. In this study, we examined an empirical phylogeny of fossil tetrapods during several time intervals, and studied how temporal constraints manifested in patterns of tree imbalance and character change. The results indicate that the impact of temporal constraints on tree shape is minimal and highlights the stability through time of the reference tetrapod phylogeny. Unexpected values of imbalance for Mississippian and Pennsylvanian time slices strongly support the hypothesis that the Carboniferous was a period of explosive tetrapod radiation. Several significant diversification shifts take place in the Mississippian and underpin increased terrestrialization among the earliest limbed vertebrates. Character incompatibility is relatively high at the beginning of tetrapod history, but quickly decreases to a relatively stable lower level, relative to a null distribution based on constant rates of character change. This implies that basal tetrapods had high, but declining, rates of homoplasy early in their evolutionary history, although the origin of Lissamphibia is an exception to this trend. The time slice approach is a powerful method of phylogenetic analysis and a useful tool for assessing the impact of combining extinct and extant taxa in phylogenetic analyses of large and speciose clades.
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Affiliation(s)
- Massimo Bernardi
- MUSE-Museo delle Scienze, Corso del Lavoro e della Scienza, 3, 38122 Trento, Italy; School of Earth Sciences, University of Bristol, Wills Memorial Building, Queens Road, Bristol BS8 1RJ, UK;
| | - Kenneth D Angielczyk
- Integrative Research Center, Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, IL 60605-2496, USA
| | - Jonathan S Mitchell
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48103, USA; and
| | - Marcello Ruta
- School of Life Sciences, Joseph Banks Laboratories, University of Lincoln, Green Lane, Lincoln LN6 7DL, UK
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12
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Dowie NJ, Grubisha LC, Trowbridge SM, Klooster MR, Miller SL. Variability of ecological and autotrophic host specificity in a mycoheterotrophic system: Pterospora andromedea and associated fungal and conifer hosts. FUNGAL ECOL 2016. [DOI: 10.1016/j.funeco.2015.11.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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13
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Hague MTJ, Avila LA, Hanifin CT, Snedden WA, Stokes AN, Brodie ED, Brodie ED. Toxicity and population structure of the Rough-Skinned Newt (Taricha granulosa) outside the range of an arms race with resistant predators. Ecol Evol 2016; 6:2714-24. [PMID: 27066249 PMCID: PMC4798830 DOI: 10.1002/ece3.2068] [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: 11/05/2015] [Revised: 02/11/2016] [Accepted: 02/22/2016] [Indexed: 01/07/2023] Open
Abstract
Species interactions, and their fitness consequences, vary across the geographic range of a coevolutionary relationship. This spatial heterogeneity in reciprocal selection is predicted to generate a geographic mosaic of local adaptation, wherein coevolutionary traits are phenotypically variable from one location to the next. Under this framework, allopatric populations should lack variation in coevolutionary traits due to the absence of reciprocal selection. We examine phenotypic variation in tetrodotoxin (TTX) toxicity of the Rough-Skinned Newt (Taricha granulosa) in regions of allopatry with its TTX-resistant predator, the Common Garter Snake (Thamnophis sirtalis). In sympatry, geographic patterns of phenotypic exaggeration in toxicity and toxin-resistance are closely correlated in prey and predator, implying that reciprocal selection drives phenotypic variation in coevolutionary traits. Therefore, in allopatry with TTX-resistant predators, we expect to find uniformly low levels of newt toxicity. We characterized TTX toxicity in northwestern North America, including the Alaskan panhandle where Ta. granulosa occur in allopatry with Th. sirtalis. First, we used microsatellite markers to estimate population genetic structure and determine if any phenotypic variation in toxicity might be explained by historical divergence. We found northern populations of Ta. granulosa generally lacked population structure in a pattern consistent with northern range expansion after the Pleistocene. Next, we chose a cluster of sites in Alaska, which uniformly lacked genetic divergence, to test for phenotypic divergence in toxicity. As predicted, overall levels of newt toxicity were low; however, we also detected unexpected among- and within-population variation in toxicity. Most notably, a small number of individuals contained large doses of TTX that rival means of toxic populations in sympatry with Th. sirtalis. Phenotypic variation in toxicity, despite limited neutral genetic divergence, suggests that factors other than reciprocal selection with Th. sirtalis likely contribute to geographic patterns of toxicity in Ta. granulosa.
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Affiliation(s)
- Michael T J Hague
- Department of Biology University of Virginia Charlottesville Virginia
| | - Leleña A Avila
- Museum of Vertebrate Zoology University of California Berkeley California
| | - Charles T Hanifin
- Department of Biology Utah State University, Uintah Basin Campus Vernal Utah
| | | | - Amber N Stokes
- Department of Biology California State University Bakersfield California
| | | | - Edmund D Brodie
- Department of Biology University of Virginia Charlottesville Virginia
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14
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Vidal MA, Ibáñez S, Moreno PI, Poulin E. Phylogeography of a Patagonian lizard and frog: Congruent signature of southern glacial refuges. AUSTRAL ECOL 2016. [DOI: 10.1111/aec.12325] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Marcela A. Vidal
- Department of Basic Sciences, Faculty of Science; Universidad del Bío-Bío; Chillan
| | - Soledad Ibáñez
- Department of Basic Sciences, Faculty of Science; Universidad del Bío-Bío; Chillan
| | - Patricio I. Moreno
- Institute of Ecology and Biodiversity, Department of Ecological Sciences, Faculty of Science; Universidad de Chile; Santiago Chile
| | - Elie Poulin
- Institute of Ecology and Biodiversity, Department of Ecological Sciences, Faculty of Science; Universidad de Chile; Santiago Chile
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15
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McVay JD, Flores-Villela O, Carstens B. Diversification of North American natricine snakes. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12558] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- John D. McVay
- Department of Biological Sciences; Louisiana State University; Baton Rouge LA 70803 USA
| | - Oscar Flores-Villela
- Facultad de Ciencias; Museo de Zoologia; Universidad Nacional Autonoma de Mexico; Circuito Extrior de CU Mexico DF 04510 Mexico
| | - Bryan Carstens
- Department of Evolution, Ecology and Organismal Biology; The Ohio State University; 318 W. 12th Avenue Columbus OH 43210-1293 USA
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16
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Sullivan BK, Douglas MR, Walker JM, Cordes JE, Davis MA, Anthonysamy WJB, Sullivan KO, Douglas ME. Conservation and Management of Polytypic Species: The Little Striped Whiptail Complex (Aspidoscelis inornata) as a Case Study. COPEIA 2014. [DOI: 10.1643/cg-13-140] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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17
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Stoelting RE, Measey GJ, Drewes RC. Population genetics of the São Tomé caecilian (Gymnophiona: Dermophiidae: Schistometopum thomense) reveals strong geographic structuring. PLoS One 2014; 9:e104628. [PMID: 25171066 PMCID: PMC4149351 DOI: 10.1371/journal.pone.0104628] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Accepted: 07/15/2014] [Indexed: 11/18/2022] Open
Abstract
Islands provide exciting opportunities for exploring ecological and evolutionary mechanisms. The oceanic island of São Tomé in the Gulf of Guinea exhibits high diversity of fauna including the endemic caecilian amphibian, Schistometopum thomense. Variation in pigmentation, morphology and size of this taxon over its c. 45 km island range is extreme, motivating a number of taxonomic, ecological, and evolutionary hypotheses to explain the observed diversity. We conducted a population genetic study of S. thomense using partial sequences of two mitochondrial DNA genes (ND4 and 16S), together with morphological examination, to address competing hypotheses of taxonomic or clinal variation. Using Bayesian phylogenetic analysis and Spatial Analysis of Molecular Variance, we found evidence of four geographic clades, whose range and approximated age (c. 253 Kya – 27 Kya) are consistent with the spread and age of recent volcanic flows. These clades explained 90% of variation in ND4 (φCT = 0.892), and diverged by 4.3% minimum pairwise distance at the deepest node. Most notably, using Mismatch Distributions and Mantel Tests, we identified a zone of population admixture that dissected the island. In the northern clade, we found evidence of recent population expansion (Fu's Fs = −13.08 and Tajima's D = −1.80) and limited dispersal (Mantel correlation coefficient = 0.36, p = 0.01). Color assignment to clades was not absolute. Paired with multinomial regression of chromatic data, our analyses suggested that the genetic groups and a latitudinal gradient together describe variation in color of S. thomense. We propose that volcanism and limited dispersal ability are the likely proximal causes of the observed genetic structure. This is the first population genetic study of any caecilian and demonstrates that these animals have deep genetic divisions over very small areas in accordance with previous speculations of low dispersal abilities.
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Affiliation(s)
- Ricka E. Stoelting
- Department of Herpetology, California Academy of Sciences, San Francisco, California, United States of America
- Department of Forest and Wildlife Ecology, University of Wisconsin, Madison, Wisconsin, United States of America
- * E-mail:
| | - G. John Measey
- Centre for Invasion Biology, Department of Botany and Zoology, University of Stellenbosch, Stellenbosch, South Africa
| | - Robert C. Drewes
- Department of Herpetology, California Academy of Sciences, San Francisco, California, United States of America
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18
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Abstract
Coevolution, reciprocal adaptation between two or more taxa, is commonly invoked as a primary mechanism responsible for generating much of Earth's biodiversity. This conceptually appealing hypothesis is incredibly broad in evolutionary scope, encompassing diverse patterns and processes operating over timescales ranging from microbial generations to geological eras. However, we have surprisingly little evidence that large-scale associations between coevolution and diversity reflect a causal relationship at smaller timescales, in which coevolutionary selection is directly responsible for the formation of new species. In this synthesis, we critically evaluate evidence for the often-invoked hypothesis that coevolution is an important process promoting biological diversification. We conclude that the lack of widespread evidence for coevolutionary diversification may be best explained by the fact that coevolution's importance in diversification varies depending on the type of interaction and the scale of the diversification under consideration.
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Affiliation(s)
- David H Hembry
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, California 94720
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Takeuchi H, Zhu GX, Ding L, Tang Y, Ota H, Mori A, Oh HS, Hikida T. Taxonomic Validity and Phylogeography of the East Eurasian Natricine Snake,Rhabdophis lateralis(Berthold, 1859) (Serpentes: Colubridae), as Inferred from Mitochondrial DNA Sequence Data. CURRENT HERPETOLOGY 2014. [DOI: 10.5358/hsj.33.148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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20
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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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21
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Houston DD, Shiozawa DK, Smith BT, Riddle BR. Investigating the effects of Pleistocene events on genetic divergence within Richardsonius balteatus, a widely distributed western North American minnow. BMC Evol Biol 2014; 14:111. [PMID: 24885371 PMCID: PMC4038058 DOI: 10.1186/1471-2148-14-111] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 05/12/2014] [Indexed: 11/29/2022] Open
Abstract
Background Biogeographers seek to understand the influences of global climate shifts and geologic changes to the landscape on the ecology and evolution of organisms. Across both longer and shorter timeframes, the western North American landscape has experienced dynamic transformations related to various geologic processes and climatic oscillations, including events as recently as the Last Glacial Maximum (LGM; ~20 Ka) that have impacted the evolution of the North American biota. Redside shiner is a cyprinid species that is widely distributed throughout western North America. The species’ native range includes several well-documented Pleistocene refugia. Here we use mitochondrial DNA sequence data to assess phylogeography, and to test two biogeographic hypotheses regarding post-glacial colonization by redside shiner: 1) Redside shiner entered the Bonneville Basin at the time of the Bonneville Flood (Late Pleistocene; 14.5 Ka), and 2) redside shiner colonized British Columbia post-glacially from a single refugium in the Upper Columbia River drainage. Results Genetic diversification in redside shiner began in the mid to late Pleistocene, but was not associated with LGM. Different clades of redside shiner were distributed in multiple glacial age refugia, and each clade retains a signature of population expansion, with clades having secondary contact in some areas. Conclusions Divergence times between redside shiner populations in the Bonneville Basin and the Upper Snake/Columbia River drainage precedes the Bonneville Flood, thus it is unlikely that redside shiner invaded the Bonneville Basin during this flooding event. All but one British Columbia population of redside shiner are associated with the Upper Columbia River drainage with the lone exception being a population near the coast, suggesting that the province as a whole was colonized from multiple refugia, but the inland British Columbia redside shiner populations are affiliated with a refugium in the Upper Columbia River drainage.
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Affiliation(s)
- Derek D Houston
- School of Life Sciences, University of Nevada-Las Vegas, Las Vegas, NV 89154-4004, USA.
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Wood DA, Fisher RN, Vandergast AG. Fuzzy boundaries: color and gene flow patterns among parapatric lineages of the western shovel-nosed snake and taxonomic implication. PLoS One 2014; 9:e97494. [PMID: 24848638 PMCID: PMC4029750 DOI: 10.1371/journal.pone.0097494] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Accepted: 04/16/2014] [Indexed: 11/23/2022] Open
Abstract
Accurate delineation of lineage diversity is increasingly important, as species distributions are becoming more reduced and threatened. During the last century, the subspecies category was often used to denote phenotypic variation within a species range and to provide a framework for understanding lineage differentiation, often considered incipient speciation. While this category has largely fallen into disuse, previously recognized subspecies often serve as important units for conservation policy and management when other information is lacking. In this study, we evaluated phenotypic subspecies hypotheses within shovel-nosed snakes on the basis of genetic data and considered how evolutionary processes such as gene flow influenced possible incongruence between phenotypic and genetic patterns. We used both traditional phylogenetic and Bayesian clustering analyses to infer range-wide genetic structure and spatially explicit analyses to detect possible boundary locations of lineage contact. Multilocus analyses supported three historically isolated groups with low to moderate levels of contemporary gene exchange. Genetic data did not support phenotypic subspecies as exclusive groups, and we detected patterns of discordance in areas where three subspecies are presumed to be in contact. Based on genetic and phenotypic evidence, we suggested that species-level diversity is underestimated in this group and we proposed that two species be recognized, Chionactis occipitalis and C. annulata. In addition, we recommend retention of two subspecific designations within C. annulata (C. a. annulata and C. a. klauberi) that reflect regional shifts in both genetic and phenotypic variation within the species. Our results highlight the difficultly in validating taxonomic boundaries within lineages that are evolving under a time-dependent, continuous process.
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Affiliation(s)
- Dustin A. Wood
- U.S. Geological Survey, Western Ecological Research Center, San Diego Field Station, San Diego, California, United States of America
| | - Robert N. Fisher
- U.S. Geological Survey, Western Ecological Research Center, San Diego Field Station, San Diego, California, United States of America
| | - Amy G. Vandergast
- U.S. Geological Survey, Western Ecological Research Center, San Diego Field Station, San Diego, California, United States of America
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Chavez AS, Maher SP, Arbogast BS, Kenagy GJ. DIVERSIFICATION AND GENE FLOW IN NASCENT LINEAGES OF ISLAND AND MAINLAND NORTH AMERICAN TREE SQUIRRELS (TAMIASCIURUS). Evolution 2014; 68:1094-109. [DOI: 10.1111/evo.12336] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 11/29/2013] [Indexed: 11/30/2022]
Affiliation(s)
- Andreas S. Chavez
- Burke Museum and Department of Biology; University of Washington; Seattle Washington 98195
| | - Sean P. Maher
- Museum of Vertebrate Zoology; University of California; Berkeley California 94720
| | - Brian S. Arbogast
- Department of Biology and Marine Biology; University of North Carolina Wilmington; Wilmington North Carolina 28403
| | - G. J. Kenagy
- Burke Museum and Department of Biology; University of Washington; Seattle Washington 98195
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Evidence of Hybridization between Common Gartersnakes (Thamnophis sirtalis) and Butler's Gartersnakes (Thamnophis butleri) in Wisconsin, USA. J HERPETOL 2013. [DOI: 10.1670/12-057] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Reynolds RG, Niemiller ML, Hedges SB, Dornburg A, Puente-Rolón AR, Revell LJ. Molecular phylogeny and historical biogeography of West Indian boid snakes (Chilabothrus). Mol Phylogenet Evol 2013; 68:461-70. [DOI: 10.1016/j.ympev.2013.04.029] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Revised: 04/05/2013] [Accepted: 04/22/2013] [Indexed: 10/26/2022]
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Population genetics of Blanding’s turtle (Emys blandingii) in the midwestern United States. CONSERV GENET 2013. [DOI: 10.1007/s10592-013-0521-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Genetic Analysis and Captive Breeding Program Design for the Eastern Massasauga Sistrurus catenatus catenatus. JOURNAL OF FISH AND WILDLIFE MANAGEMENT 2013. [DOI: 10.3996/032012-jfwm-026] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Abstract
The eastern massasauga Sistrurus catenatus catenatus is a declining species for which a captive breeding program was established in 2006. To effectively manage wild and captive populations, an understanding of genetic diversity within the species is necessary. We analyzed mitochondrial DNA sequences of 186 individuals: 109 wild snakes from 34 U.S. and Canadian counties and districts, all 52 breeding program members (23 of known and 29 of unknown origin), 18 other captives of unknown origin, and 7 outgroup representatives of desert massasauga S. c. edwardsii, and western massasauga, S. c. tergeminus. Statistical parsimony, maximum likelihood, and maximum parsimony analyses all identified eastern massasaugas as divergent from western and desert massasaugas. We found 18 different haplotypes among eastern massasaugas, comprising three geographically and genetically differentiated NADH dehydrogenase II (ND2) subunits that potentially reflect post-Pleistocene range expansion from unglaciated into formerly glaciated regions. Snakes of unknown origin could all be assigned unambiguously to these ND2 subunits. To maintain natural genetic variation, preserve diversity in captive lineages, and allow future augmentation or reintroduction, the Association of Zoos and Aquariums is managing these three geographic ND2 subunits separately within the Eastern Massasauga Species Survival Plan breeding program.
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Puente-Rolón AR, Reynolds RG, Revell LJ. Preliminary genetic analysis supports cave populations as targets for conservation in the endemic endangered Puerto Rican boa (Boidae: Epicrates inornatus). PLoS One 2013; 8:e63899. [PMID: 23691110 PMCID: PMC3655012 DOI: 10.1371/journal.pone.0063899] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Accepted: 04/09/2013] [Indexed: 11/18/2022] Open
Abstract
The endemic Puerto Rican boa (Epicrates inornatus) has spent 42 years on the Endangered Species List with little evidence for recovery. One significant impediment to effective conservation planning has been a lack of knowledge of the distribution of genetic variability in the species. It has previously been suggested that boas might best be protected around caves that harbor large populations of bats. Prior study has found Puerto Rican boas at relatively high densities in and around bat caves, which they use both to feed and seek shelter. However, it is unknown whether these behaviorally distinctive populations represent a distinct evolutionary lineage, or (conversely) whether caves harbor representative genetic diversity for the species across the island. We provide the first genetic study of the Puerto Rican boa, and we examine and compare genetic diversity and divergence among two cave populations and two surface populations of boas. We find three haplogroups and an apparent lack of phylogeographic structure across the island. In addition, we find that the two cave populations appear no less diverse than the two surface populations, and harbor multiple mtDNA lineages. We discuss the conservation implications of these findings, including a call for the immediate protection of the remaining cave-associated populations of boas.
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Affiliation(s)
- Alberto R. Puente-Rolón
- Departamento de Ciencias y Tecnología, Universidad Interamericana de Puerto Rico, Recinto de Arecibo, Arecibo, Puerto Rico
| | - R. Graham Reynolds
- Department of Biology, University of Massachusetts Boston, Boston, Massachusetts, United States of America
- * E-mail:
| | - Liam J. Revell
- Department of Biology, University of Massachusetts Boston, Boston, Massachusetts, United States of America
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Baumsteiger J, Kinziger AP, Aguilar A. Life history and biogeographic diversification of an endemic western North American freshwater fish clade using a comparative species tree approach. Mol Phylogenet Evol 2012; 65:940-52. [PMID: 22982759 DOI: 10.1016/j.ympev.2012.08.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Revised: 08/18/2012] [Accepted: 08/20/2012] [Indexed: 10/27/2022]
Abstract
The west coast of North America contains a number of biogeographic freshwater provinces which reflect an ever-changing aquatic landscape. Clues to understanding this complex structure are often encapsulated genetically in the ichthyofauna, though frequently as unresolved evolutionary relationships and putative cryptic species. Advances in molecular phylogenetics through species tree analyses now allow for improved exploration of these relationships. Using a comprehensive approach, we analyzed two mitochondrial and nine nuclear loci for a group of endemic freshwater fish (sculpin-Cottus) known for a wide ranging distribution and complex species structure in this region. Species delimitation techniques identified three novel cryptic lineages, all well supported by phylogenetic analyses. Comparative phylogenetic analyses consistently found five distinct clades reflecting a number of unique biogeographic provinces. Some internal node relationships varied by species tree reconstruction method, and were associated with either Bayesian or maximum likelihood statistical approaches or between mitochondrial, nuclear, and combined datasets. Limited cases of mitochondrial capture were also evident, suggestive of putative ancestral hybridization between species. Biogeographic diversification was associated with four major regions and revealed historical faunal exchanges across regions. Mapping of an important life-history character (amphidromy) revealed two separate instances of trait evolution, a transition that has occurred repeatedly in Cottus. This study demonstrates the power of current phylogenetic methods, the need for a comprehensive phylogenetic approach, and the potential for sculpin to serve as an indicator of biogeographic history for native ichthyofauna in the region.
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Affiliation(s)
- Jason Baumsteiger
- School of Natural Sciences & Sierra Nevada Research Institute, University of California Merced, 5200 N. Lake Rd., Merced, CA 95343, USA.
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30
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Vidal MA, Ortiz JC, Marín JC, Poulin E, Moreno PI. Comparative phylogeography of two co-distributed species of lizards of the genus Liolaemus (Squamata: Tropiduridae) from Southern Chile. AMPHIBIA-REPTILIA 2012. [DOI: 10.1163/156853811x622039] [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
Comparative phylogeography describes the patterns of evolutionary divergence and whether or not they are congruent, in co-distributed populations of different taxa. If the populations of these taxa have been co-distributed for a prolonged time, and if the times between processes of perturbation or vicariance have been more or less stable, it is expected that patterns of divergence will be congruent in closely related species, for example because of similar biological and demographic characteristics.Liolaemus pictusandL. cyanogasterare widely co-distributed lizard species in southern Chile, occurring in a region with a complex topology. We analyzed the phylogeographic structure of the two lizard species usingCytochromebDNA sequences to estimate their genetic structure in response to historical events. Our results suggest an evolutionary pattern of genetic diversity for each species that is consistent with the geomorphological history of the region, suggesting a complex phylogeographic history inLiolaemusspecies. Also, the high levels of divergence among haplotypes in several populations suggest the possibility that their origin might predate the middle Pleistocene in both species. Finally, our results are consistent with our hypothesis that two species have responded to historical events in parallel, where historical process have been sufficient to influence their phylogeographical structure (0.80 congruency between topologies).
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Affiliation(s)
- Marcela A. Vidal
- 1Laboratorio de Genómica y Biodiversidad, Departamento de Ciencias Básicas, Facultad de Ciencias, Universidad del Bío-Bío, Casilla 447, Chillán, Chile
| | - Juan Carlos Ortiz
- 2Departamento de Zoología, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Casilla 160-C, Concepción, Chile
| | - Juan Carlos Marín
- 1Laboratorio de Genómica y Biodiversidad, Departamento de Ciencias Básicas, Facultad de Ciencias, Universidad del Bío-Bío, Casilla 447, Chillán, Chile
| | - Elie Poulin
- 3Instituto de Ecología y Biodiversidad, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Casilla 653, Santiago, Chile
| | - Patricio I. Moreno
- 3Instituto de Ecología y Biodiversidad, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Casilla 653, Santiago, Chile
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TAKEUCHI HIROHIKO, OTA HIDETOSHI, OH HONGSHIK, HIKIDA TSUTOMU. Extensive genetic divergence in the East Asian natricine snake, Rhabdophis tigrinus (Serpentes: Colubridae), with special reference to prominent geographical differentiation of the mitochondrial cytochrome b gene in Japanese populations. Biol J Linn Soc Lond 2011. [DOI: 10.1111/j.1095-8312.2011.01792.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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33
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Westphal MF, Massie JL, Bronkema JM, Smith BE, Morgan TJ. Heritable variation in garter snake color patterns in postglacial populations. PLoS One 2011; 6:e24199. [PMID: 21935386 PMCID: PMC3173445 DOI: 10.1371/journal.pone.0024199] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2011] [Accepted: 08/03/2011] [Indexed: 11/19/2022] Open
Abstract
Global climate change is expected to trigger northward shifts in the ranges of natural populations of plants and animals, with subsequent effects on intraspecific genetic diversity. Investigating how genetic diversity is patterned among populations that arose following the last Ice Age is a promising method for understanding the potential future effects of climate change. Theoretical and empirical work has suggested that overall genetic diversity can decrease in colonial populations following rapid expansion into postglacial landscapes, with potential negative effects on the ability of populations to adapt to new environmental regimes. The crucial measure of this genetic variation and a population's overall adaptability is the heritable variation in phenotypic traits, as it is this variation that mediates the rate and direction of a population's multigenerational response to selection. Using two large full-sib quantitative genetic studies (N(Manitoba) = 144; N(South Dakota) = 653) and a smaller phenotypic analysis from Kansas (N(Kansas) = 44), we compared mean levels of pigmentation, genetic variation and heritability in three pigmentation traits among populations of the common garter snake, Thamnophis sirtalis, along a north-south gradient, including a postglacial northern population and a putative southern refuge population. Counter to our expectations, we found that genetic variance and heritability for the three pigmentation traits were the same or higher in the postglacial population than in the southern population.
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Affiliation(s)
- Michael F Westphal
- Division of Biology and The Ecological Genomics Institute, Kansas State University, Manhattan, Kansas, United States of America.
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Castoe TA, Bronikowski AM, Brodie ED, Edwards SV, Pfrender ME, Shapiro MD, Pollock DD, Warren WC. A proposal to sequence the genome of a garter snake (Thamnophis sirtalis). Stand Genomic Sci 2011; 4:257-70. [PMID: 21677863 PMCID: PMC3111982 DOI: 10.4056/sigs.1664145] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Here we develop an argument in support of sequencing a garter snake (Thamnophis sirtalis) genome, and outline a plan to accomplish this. This snake is a common, widespread, nonvenomous North American species that has served as a model for diverse studies in evolutionary biology, physiology, genomics, behavior and coevolution. The anole lizard is currently the only genome sequence available for a non-avian reptile. Thus, the garter snake at this time would be the first available snake genome sequence and as such would provide much needed comparative representation of non-avian reptilian genomes, and would also allow critical new insights for vertebrate comparative genomic studies. We outline the major areas of discovery that the availability of the garter snake genome would enable, and describe a plan for whole-genome sequencing.
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Affiliation(s)
- Todd A. Castoe
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO
- Corresponding Author: Todd A. Castoe,
| | - Anne M. Bronikowski
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA
| | - Edmund D. Brodie
- Department of Biology, University of Virginia, Charlottesville, VA
| | - Scott V. Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA
| | | | | | - David D. Pollock
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO
| | - Wesley C. Warren
- Genome Sequencing Center, Washington University School of Medicine, St. Louis, MO
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35
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Mooi RD, Wiens JP, Casper GS. Extreme Color Variation within Populations of the Common Gartersnake, Thamnophis sirtalis, in Central North America, with Implications for Subspecies Status. COPEIA 2011. [DOI: 10.1643/ch-10-067] [Citation(s) in RCA: 7] [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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VIDAL MARCELAA, MORENO PATRICIOI, POULIN ELIE. Genetic diversity and insular colonization of Liolaemus pictus (Squamata, Liolaeminae) in north-western Patagonia. AUSTRAL ECOL 2011. [DOI: 10.1111/j.1442-9993.2011.02241.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Using Mitochondrial DNA to Determine the Identity and Origin of a Gartersnake Found in Alaska. J HERPETOL 2011. [DOI: 10.1670/09-180.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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38
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Sallaberry-Pincheira N, Garin CF, González-Acuña D, Sallaberry MA, Vianna JA. Genetic divergence of Chilean long-tailed snake (Philodryas chamissonis) across latitudes: conservation threats for different lineages. DIVERS DISTRIB 2010. [DOI: 10.1111/j.1472-4642.2010.00729.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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SHAFER AARONBA, CULLINGHAM CATHERINEI, CÔTÉ STEEVED, COLTMAN DAVIDW. Of glaciers and refugia: a decade of study sheds new light on the phylogeography of northwestern North America. Mol Ecol 2010; 19:4589-621. [PMID: 20849561 DOI: 10.1111/j.1365-294x.2010.04828.x] [Citation(s) in RCA: 261] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- AARON B. A. SHAFER
- Department of Biological Sciences, CW 405 Biological Sciences Building, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - CATHERINE I. CULLINGHAM
- Department of Biological Sciences, CW 405 Biological Sciences Building, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - STEEVE D. CÔTÉ
- Département de Biologie and Centre for Northern Studies, Université Laval, Québec, Québec G1V 0A6, Canada
| | - DAVID W. COLTMAN
- Department of Biological Sciences, CW 405 Biological Sciences Building, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
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Hanifin CT. The chemical and evolutionary ecology of tetrodotoxin (TTX) toxicity in terrestrial vertebrates. Mar Drugs 2010; 8:577-93. [PMID: 20411116 PMCID: PMC2857372 DOI: 10.3390/md8030577] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2010] [Revised: 03/03/2010] [Accepted: 03/08/2010] [Indexed: 01/05/2023] Open
Abstract
Tetrodotoxin (TTX) is widely distributed in marine taxa, however in terrestrial taxa it is limited to a single class of vertebrates (Amphibia). Tetrodotoxin present in the skin and eggs of TTX-bearing amphibians primarily serves as an antipredator defense and these taxa have provided excellent models for the study of the evolution and chemical ecology of TTX toxicity. The origin of TTX present in terrestrial vertebrates is controversial. In marine organisms the accepted hypothesis is that the TTX present in metazoans results from either dietary uptake of bacterially produced TTX or symbiosis with TTX producing bacteria, but this hypothesis may not be applicable to TTX-bearing amphibians. Here I review the taxonomic distribution and evolutionary ecology of TTX in amphibians with some attention to the origin of TTX present in these taxa.
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Affiliation(s)
- Charles T Hanifin
- Hopkins Marine Station of Stanford University, 120 Oceanview Blvd., Pacific Grove, CA 93950, USA.
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The evolutionary origins of beneficial alleles during the repeated adaptation of garter snakes to deadly prey. Proc Natl Acad Sci U S A 2009; 106:13415-20. [PMID: 19666534 DOI: 10.1073/pnas.0901224106] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Where do the genetic variants underlying adaptive change come from? Are currently adaptive alleles recruited by selection from standing genetic variation within populations, moved through introgression from other populations, or do they arise as novel mutations? Here, we examine the molecular basis of repeated adaptation to the toxin of deadly prey in 3 species of garter snakes (Thamnophis) to determine whether adaptation has evolved through novel mutations, sieving of existing variation, or transmission of beneficial alleles across species. Functional amino acid substitutions in the skeletal muscle sodium channel (Na(v)1.4) are largely responsible for the physiological resistance of garter snakes to tetrodotoxin found in their newt (Taricha) prey. Phylogenetic analyses reject the hypotheses that the unique resistance alleles observed in multiple Thamnophis species were present before the split of these lineages, or that alleles were shared among species through occasional hybridization events. Our results demonstrate that adaptive evolution has occurred independently multiple times in garter snakes via the de novo acquisition of beneficial mutations.
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BARRETTE MARIEFRANCE, DAIGLE GAÉTAN, DODSON JULIANJ. Intraspecific vicariant history and the evolution of adaptive morphological diversity in a fish species (Osmerus mordax). Biol J Linn Soc Lond 2009. [DOI: 10.1111/j.1095-8312.2008.01195.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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43
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McGaugh SE, Eckerman CM, Janzen FJ. Molecular phylogeography of Apalone spinifera (Reptilia, Trionychidae). ZOOL SCR 2008. [DOI: 10.1111/j.1463-6409.2008.00329.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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44
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Hanifin CT, Brodie ED, Brodie ED. Phenotypic mismatches reveal escape from arms-race coevolution. PLoS Biol 2008; 6:e60. [PMID: 18336073 PMCID: PMC2265764 DOI: 10.1371/journal.pbio.0060060] [Citation(s) in RCA: 144] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2007] [Accepted: 01/24/2008] [Indexed: 11/18/2022] Open
Abstract
Because coevolution takes place across a broad scale of time and space, it is virtually impossible to understand its dynamics and trajectories by studying a single pair of interacting populations at one time. Comparing populations across a range of an interaction, especially for long-lived species, can provide insight into these features of coevolution by sampling across a diverse set of conditions and histories. We used measures of prey traits (tetrodotoxin toxicity in newts) and predator traits (tetrodotoxin resistance of snakes) to assess the degree of phenotypic mismatch across the range of their coevolutionary interaction. Geographic patterns of phenotypic exaggeration were similar in prey and predators, with most phenotypically elevated localities occurring along the central Oregon coast and central California. Contrary to expectations, however, these areas of elevated traits did not coincide with the most intense coevolutionary selection. Measures of functional trait mismatch revealed that over one-third of sampled localities were so mismatched that reciprocal selection could not occur given current trait distributions. Estimates of current locality-specific interaction selection gradients confirmed this interpretation. In every case of mismatch, predators were “ahead” of prey in the arms race; the converse escape of prey was never observed. The emergent pattern suggests a dynamic in which interacting species experience reciprocal selection that drives arms-race escalation of both prey and predator phenotypes at a subset of localities across the interaction. This coadaptation proceeds until the evolution of extreme phenotypes by predators, through genes of large effect, allows snakes to, at least temporarily, escape the arms race. Arms races between natural enemies can lead to the rapid evolution of extreme traits, high degrees of specialization, and the formation of new species. They also serve as the ecological model for the evolution of drug resistance by diseases and for host–pathogen interactions in general. Revealing who wins these arms races and how they do so is critical to our understanding of these processes. Capitalizing on the geographic mosaic of species interactions, we examined the dynamics of the arms race between snakes and their toxic newt prey. Garter snakes in some populations have evolved dramatic resistance to the tetrodotoxin defense of the their local prey. By evaluating the pattern of mismatches between toxicity and resistance, we discovered that predators sometimes escape the arms race through the evolution of extreme resistance, but that prey never come out ahead. The reason for this one-sided outcome appears to depend on the molecular genetic basis of resistance in snakes, wherein changes to a single amino acid residue can confer huge differences in resistance. Who wins in the arms race between predators and prey? In the interaction between snakes and toxic newts, predators sometimes escape the arms race through the evolution of extreme resistance, but prey never come out ahead.
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Affiliation(s)
- Charles T Hanifin
- Department of Biology, Utah State University, Logan, Utah, United States of America.
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RICH KATHERINEA, THOMPSON JOHNN, FERNANDEZ CATHERINEC. Diverse historical processes shape deep phylogeographical divergence in the pollinating seed parasite Greya politella. Mol Ecol 2008; 17:2430-48. [DOI: 10.1111/j.1365-294x.2008.03754.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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A striking lack of genetic diversity across the wide-ranging amphibian Gastrophryne carolinensis (Anura: Microhylidae). Genetica 2008; 135:169-83. [DOI: 10.1007/s10709-008-9267-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2007] [Accepted: 02/20/2008] [Indexed: 11/27/2022]
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Wood DA, Fisher RN, Reeder TW. Novel patterns of historical isolation, dispersal, and secondary contact across Baja California in the Rosy Boa (Lichanura trivirgata). Mol Phylogenet Evol 2008; 46:484-502. [DOI: 10.1016/j.ympev.2007.11.014] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2007] [Revised: 11/15/2007] [Accepted: 11/20/2007] [Indexed: 11/25/2022]
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48
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Douglas ME, Douglas MR, Schuett GW, Porras LW, Thomason BL. Genealogical Concordance between Mitochondrial and Nuclear DNAs Supports Species Recognition of the Panamint Rattlesnake (Crotalus mitchellii stephensi). COPEIA 2007. [DOI: 10.1643/0045-8511(2007)7[920:gcbman]2.0.co;2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Molecular and phenotypic diversity in Chionactis occipitalis (Western Shovel-nosed Snake), with emphasis on the status of C. o. klauberi (Tucson Shovel-nosed Snake). CONSERV GENET 2007. [DOI: 10.1007/s10592-007-9482-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Haenel GJ. Phylogeography of the tree lizard,Urosaurus ornatus: responses of populations to past climate change. Mol Ecol 2007; 16:4321-34. [PMID: 17868290 DOI: 10.1111/j.1365-294x.2007.03515.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Isolation due to both geological barriers and range contractions during the Pleistocene glacial maxima has been an important cause of diversification of arid-adapted species in the North American deserts. Tree lizards, Urosaurus ornatus, are distributed across much of the southwestern arid regions and can tolerate a wide range of environments. Thus, they may have avoided large-scale shifts in distribution caused by Pleistocene climate change and any subsequent evolutionary impacts. Cytochrome b sequences were sampled from U. ornatus across the northern part of their range to test if current structure of these populations resulted from post-Pleistocene range expansion and habitat fragmentation, or prior geological isolation. Phylogenetic analyses found geographical structuring of populations consistent with a model of long-term geographical isolation corresponding to each of the desert regions. The two post-Pleistocene hypotheses were not well supported as estimated times of divergence predated the retreat of the last continental ice sheet. Populations in different regions were impacted by different processes. Southern populations of U. ornatus appear to have remained largely independent of more derived northern and eastern populations during Pleistocene climate change, while populations in regions containing more derived populations showed evidence of more recent range expansion (Colorado Plateau). As populations of U. ornatus attest to, the complex and dynamic history of the southwestern USA has left a deep-rooted and multifaceted imprint on genetic and phylogeographical structure of the species living there.
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Affiliation(s)
- G J Haenel
- CB 2625, Elon University, Elon, NC 27244, USA.
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