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Disentangling the genetic effects of refugial isolation and range expansion in a trans-continentally distributed species

Heredityvolume 122pages441457 (2019) | Download Citation


In wide-ranging taxa with historically dynamic ranges, past allopatric isolation and range expansion can both influence the current structure of genetic diversity. Considering alternate historical scenarios involving expansion from either a single refugium or from multiple refugia can be useful in differentiating the effects of isolation and expansion. Here, we examined patterns of genetic variability in the trans-continentally distributed painted turtle (Chrysemys picta). We utilized an existing phylogeographic dataset for the mitochondrial control region and generated additional data from nine populations for the mitochondrial control region (n = 302) and for eleven nuclear microsatellite loci (n = 247). We created a present-day ecological niche model (ENM) for C. picta and hindcast this model to three reconstructions of historical climate to define three potential scenarios with one, two, or three refugia. Finally, we employed spatially-explicit coalescent simulations and an approximate Bayesian computation (ABC) framework to test which scenario best fit the observed genetic data. Simulations indicated that phylogeographic and multilocus population-level sampling both could differentiate among refugial scenarios, although inferences made using mitochondrial data were less accurate when a longer coalescence time was assumed. Furthermore, all empirical genetic datasets were most consistent with expansion from a single refugium based on ABC. Our results indicate a stronger role for post-glacial range expansion, rather than isolation in allopatric refugia followed by range expansion, in structuring diversity in this species. To distinguish among complex historical scenarios, we recommend explicitly modeling the effects of range expansion and evaluating alternate refugial scenarios for wide-ranging taxa.

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  1. Aiello-Lammens ME, Boria RA, Radosavljevic A, Vilela B, Anderson RP (2015) spThin: an R package for spatial thinning of species occurrence records for use in ecological niche models. Ecography 38:541–545

  2. Anderson RP, Raza A (2010) The effect of the extent of the study region on GIS models of species distributions and estimates of niche evolution: preliminary tests with montane rodents (genus Nephelomys) in Venezuela. J Biogeogr 37:1378–1393

  3. Alvarado-Serrano DF, Knowles LL (2014) Ecological niche models in phylogeographic studies: applications, advances and precautions. Mol Ecol Resour 14:233–248

  4. Ballard JW, Whitlock MC (2004) The incomplete natural history of mitochondria. Mol Ecol 13:729–744

  5. Beatty GE, Provan J (2010) Refugial persistence and postglacial recolonization of North America by the cold-tolerant herbaceous plant Orthilia secunda. Mol Ecol 19:5009–5021

  6. Bishop SC, Schmidt FJW (1931) The painted turtles of the genus. Chrysemys Field Mus Nat Hist Publ Zool Ser 18:123–139

  7. Bleakney S (1958) Postglacial dispersal of the turtle Chrysemys picta. Herpetologica 14:101–104

  8. Blum MGB, François O (2017) Non-linear regression models for approximate Bayesian computation. Stat Comp 20:63–73

  9. Buckley TR, Marske K, Attanayake D (2010) Phylogeography and ecological niche modelling of the New Zealand stick insect Clitarchus hookeri (White) support survival in multiple coastal refugia. J Biogeogr 37:682–695

  10. Byun SA, Koop BF, Reimchen TE (1997) North American black bear mtDNA phylogeography: implications for morphology and the Haida Gwaii glacial refugium controversy. Evolution 51:1647–1653

  11. Csilléry K, Francois O, Blum MGB (2012) ABC: an R package for approximate Bayesian computation (ABC). Methods Ecol Evol 3:475–479

  12. Dahl-Jensen D, Albert MR, Aldahan A et al. (2013) Eemian interglacial reconstructed from a Greenland folded ice core. Nature 493:489–494

  13. van Dijk PP (2011) Chrysemys picta. The IUCN Red List of Threatened Species. Accessed 13 February 2018.

  14. Drummond AJ, Ho SY, Phillips MJ, Rambaut A (2006) Relaxed phylogenetics and dating with confidence. PLoS Biol 4:e88

  15. Drummond AJ, Rambaut A (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 7:214

  16. Earl DA, vonHoldt BM (2012) Structure Harvester: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet Resour 4:359–361

  17. Eckert CG, Samis KE, Lougheed SC (2008) Genetic variation across species’ geographical ranges: the central-marginal hypothesis and beyond. Mol Ecol 17:1170–1188

  18. Edmonds CA, Lillie SA, Cavalli-Sforza LL (2004) Mutations arising in the wave front of an expanding population. PNAS 101:975–979

  19. Elith J, Kearney M, Phillips S (2010) The art of modelling range-shifting species. Methods Ecol Evol 1:330–342

  20. Ernst CH, Lovich JE (2009) Turtles of the United States and Canada, 2nd ed. Johns Hopkins University Press, Baltimore

  21. Excoffier L, Smouse PE, Quattro JM (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131:479–491

  22. Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software structure: a simulation study. Mol Ecol 14:2611–2620

  23. Excoffier L, Foll M, Petit RJ (2009) Genetic consequences of range expansions. Ann Rev Ecol Evol S 40:481–501

  24. Excoffier L, Lischer HEL (2010) Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour 10:564–567

  25. Excoffier L, Ray N (2008) Surfing during population expansions promotes genetic revolutions and structuration. Trends Ecol Evol 23:347–351

  26. Fontanella FM, Feldman CR, Siddall ME, Burbrink FT (2008) Phylogeography of Diadophis punctatus: extensive lineage diversity and repeated patterns of historical demography in a trans-continental snake. Mol Phylogenet Evol 3:1049–1070

  27. Formia A, Godley BJ, Dontaine J-F, Bruford MW (2006) Mitochondrial DNA diversity and phylogeography of endangered green turtle (Chelonia mydas) populations in Africa. Conserv Genet 7:353–369

  28. Frazer NB, Gibbons JW, Greene JL (1991) Growth, survivorship, and longevity of painted turtles Chrysemys picta in a southwestern Michigan marsh. Am Midl Nat 125:245–258

  29. Graciá E, Botella F, Anadón JD, Edelaar P, Harris DJ, Giménez A (2013) Surfing in tortoises? Empirical signs of genetic structuring owing to range expansion. Biol Lett 9:20121091

  30. Greenwood PJ (1980) Mating systems, philopatry and dispersal in birds and mammals. Anim Behav 28:1140–1162

  31. He Q, Edwards DL, Knowles LL (2013) Integrative testing of how environments from the past to the present shape genetic structure across landscapes. Evolution 67:3386–3402

  32. Hellberg ME, Balch DP, Roy K (2001) Climate-driven range expansion and morphological evolution in a marine gastropod. Science 292:1707–1710

  33. Heller R, Chikhi L, Siegismund HR (2013) The confounding effect of population structure on Bayesian skyline plot inferences of demographic history. PLoS ONE 8:e62992

  34. Hewitt G (2000) The genetic legacy of the Quaternary ice ages. Nature 405:907–913

  35. Hijmans RJ, Cameron SE, Parra JL, Jones PG, Jarvis A (2005) Very high resolution interpolated climate surfaces for global land areas. Int J Climatol 25:1965–1978

  36. Hijmans RJ, Phillips S, Leathwick J, Elith J (2016) Package “dismo”. R package.

  37. Ho SYW, Phillips MJ, Cooper A, Drummond AJ (2005) Time dependency of molecular rate estimates and systematic overestimation of recent divergence times. Mol Biol Evol 22:1561–1568

  38. Hoareau TB (2016) Late glacial demographic expansion motivates a clock overhaul for population genetics. Syst Biol 65:449–464

  39. Iverson JB, Smith GR (1993) Reproductive ecology of the painted turtle (Chrysemys picta) in the Nebraska Sandhills. Copeia 1993:1–21

  40. Jakobsson M, Rosenberg NA (2007) CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23:1801–1806

  41. Jensen EL, Govindarajulu P, Russello MA (2014) When the shoe doesn’t fit: applying conservation unit concepts to western painted turtles at their northern periphery. Conserv Genet 15:261–274

  42. Jensen EL, Govindarajulu P, Russello MA (2015) Genetic assessment of taxonomic uncertainty in painted turtles. J Herpetol 49:314–324

  43. Johnson JA, Toepfer JE, Dunn PO (2003) Contrasting patterns of mitochondrial and microsatellite population structure in fragmented populations of greater prairie-chickens. Mol Ecol 12:3335–3347

  44. Kass R, Raftery A (1995) Bayes factors. J Am Stat Assoc 90:773–795

  45. Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S et al. (2012) Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28:1647–1649

  46. Kierepka EM, Latch EK (2016) Fine-scale landscape genetics of the American badger (Taxidea taxus): disentangling landscape effects and sampling artifacts in a poorly understood species. Heredity 116:33–43

  47. Knowles LL, Alvarado-Serrano DF (2010) Exploring the population genetic consequences of the colonization process with spatio-temporally explicit models: insights from coupled ecological, demographic and genetic models in montane grasshoppers. Mol Ecol 19:3727–3745

  48. Knowles LL, Massatti R (2017) Distributional shifts-not geographic isolation-as a probable driver of montane species divergence. Ecography.

  49. Lindeman PV (1997) Does life-history variation in the turtle Chrysemys picta have a subspecific component? J Herpetol 31:155–161

  50. Liu C, White M, Newell G (2013) Selecting thresholds for the prediction of species occurrence with presence-only data. J Biogeogr 40:778–789

  51. Lougheed SC, Campagna L, Dávila JA, Tubaro PL, Lijtmaer DA, Handford P (2013) Continental phylogeography of an ecologically and morphologically diverse Neotropical songbird, Zonotrichia capensis. BMC Evol Biol 13:58

  52. Massatti R, Knowles LL (2016) Contrasting support for alternative models of genomic variation based on microhabitat preference: species-specific effects of climate change in alpine sedges. Mol Ecol 25:3974–3986

  53. Mazet O, Rodriguez W, Grusea S, Boitard S, Chikhi L (2016) On the importance of being structured: instantaneous coalescence rates and human evolution—lessons for population size inference? Heredity 116:362–371

  54. Merow C, Smith MJ, Silander JA (2013) A practical guide to MaxEnt for modeling species’ distributions: what it does, and why input settings matter. Ecography 36:1058–1069

  55. Muscarella R, Galante PJ, Soley-Guardia M, Boria RA, Kass JM, Uriarté M, Anderson RP (2014) ENMEval: an R package for conducting spatially independent evaluations and estimating model complexity for MaxEnt ecological niche models. Methods Ecol Evol 5:1198–1205

  56. Oksanen J, Blanchet FG, Friendly M, Kindt R, Legendre P, McGlinn D et al. (2013) Package “vegan.” R package.

  57. Peakall R, Smouse PE (2012) GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research: an update. Bioinformatics 28:2537–2539

  58. Pearse DE, Janzen FJ, Avise JC (2002) Multiple paternity, sperm storage, and reproductive success of female and male painted turtles (Chrysemys picta) in nature. Behav Ecol Sociobiol 51:164–171

  59. Peery MZ, Kirby R, Reid BN, Stoelting R, Doucet-Bëer E, Robinson S, Váaquez-Carrillo C, Pauli JN, Palsbøll PJ (2012) Reliability of genetic bottleneck tests for detecting recent population declines. Mol Ecol 21:3403–3418

  60. Phillips SJ, Anderson RP, Schapire RE (2006) Maximum entropy modeling of species geographic distributions. Ecol Model 190:231–259

  61. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959

  62. Provan J, Bennett KD (2008) Phylogeographic insights into cryptic glacial refugia. Trends Ecol Evol 23:564–571

  63. R Core Team (2015). R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.

  64. Ray N, Currat M, Foll M, Excoffier L (2010) SPLATCHE2: a spatially explicit simulation framework for complex demography, genetic admixture and recombination. Bioinformatics 26:2993–2994

  65. Reid BN, Peery MZ (2014) Land use patterns skew sex ratios, decrease genetic diversity and trump the effects of recent climate change in an endangered turtle. Divers Distrib 20:1425–1437

  66. Reid BN, Mladenoff DJ, Peery MZ (2016) Genetic effects of landscape, habitat preference and demography on three co-occurring turtle species. Mol Ecol 26:781–798

  67. Rice WR (1989) Analyzing tables of statistical tests. Evolution 43:223–225

  68. Richards CL, Carstens BC, Knowles LL (2007) Distribution modelling and statistical phylogeography: an integrative framework for generating and testing alternative biogeographical hypotheses. J Biogeogr 34:1833–1845

  69. Riddle BR (2016) Comparative phylogeography clarifies the complexity and problems of continental distribution that drove A.R. Wallace to study islands. P Natl Acad Sci USA 113:7970–7977

  70. Rödder D, Lawing AM, Flecks M, Ahmadzadeh F, Dambach J, Engler JO et al. (2013) Evaluating the significance of paleophylogeographic species distribution models in reconstructing Quaternary range-shifts of Nearctic chelonians. PLoS ONE 8:e72855

  71. Rosenberg NA (2004) DISTRUCT: a program for the graphical display of population structure. Mol Ecol Notes 4:137–138

  72. Rousset F (2008) genepop’007: a complete re-implementation of the genepop software for Windows and Linux. Mol Ecol Resour 8:103–106

  73. Sandel B, Arge L, Dalsgaard B, Davies RG, Gaston KJ, Sutherland WJ, Svenning J-C (2011) The influence of late Quaternary climate-change velocity on species endemism. Science 334:660–664

  74. Shaffer HB, Minx P, Warren DE, Shedlock AM, Thompson RC, Valenzuela N et al. (2013) The Western Painted Turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage. Genome Biol 14:R28

  75. Slatkin M, Excoffier L (2012) Serial founder effects during range expansion: a spatial analog of genetic drift. Genetics 191:171–181

  76. Starkey DE, Shaffer HB, Burke RL, Forstner MRJ, Iverson JB, Janzen FJ, Rhodin AGJ, Ultsch GR (2003) Molecular systematics, phylogeography, and the effects of Pleistocene glaciation in the painted turtle (Chrysemys picta) complex. Evolution 57:119–128

  77. Streicher JW, McEntee JP, Drzich LC, Card DC, Schield DR, Smart U, Parkinson CL, Jezkova T, Smith EN, Castoe TA (2016) Genetic surfing, not allopatric divergence, explains spatial sorting of mitochondrial haplotypes in venomous coral snakes. Evolution 70:1435–1449

  78. TTWG (Turtle Taxonomy Working Group), Rhodin AGJ, Iverson JB, Bour R, Fritz U, Georges A, Shaffer HB, van Dijk PP (2017) Turtles of the World. Annotated checklist and atlas of taxonomy, synonymy, distribution, and conservation status, 8th ed. Chelonian Research Foundation, Lunenburg, MA.

  79. Van Oosterhout C, Hutchinson WF, Wills DPM, Shipley P (2004) MICRO-CHECKER: software for identifying and correcting genotyping errors in microsatellite data. Mol Ecol Notes 4:535–538

  80. Waltari E, Guralnick RP (2009) Ecological niche modelling of montane mammals in the Great Basin, North America: examining past and present connectivity of species across basins and ranges. J Biogeogr 36:148–161

  81. Waltari E, Hijmans RJ, Peterson AT, Nyári ÁS, Perkins SL, Guralnick RP (2007) Locating Pleistocene refugia: comparing phylogeographic and ecological niche model predictions PLoS ONE 2:e563

  82. Wilbur HM (1975) The evolutionary and mathematical demography of the turtle Chrysemys picta. Ecology 56:64–77

  83. Katalin Csilléry, Michael G.B. Blum, Oscar E. Gaggiotti, Olivier François (2010) Approximate Bayesian Computation (ABC) in practice. Trends in Ecology & Evolution 25:410–418

  84. L. Lacey Knowles, Bryan C. Carstens, Marcia L. Keat (2007) Coupling Genetic and Ecological-Niche Models to Examine How Past Population Distributions Contribute to Divergence. Current Biology 17:940–946

  85. David R. Roberts, Volker Bahn, Simone Ciuti, Mark S. Boyce, Jane Elith, Gurutzeta Guillera-Arroita, Severin Hauenstein, José J. Lahoz-Monfort, Boris Schröder, Wilfried Thuiller, David I. Warton, Brendan A. Wintle, Florian Hartig, Carsten F. Dormann (2017) Cross-validation strategies for data with temporal, spatial, hierarchical, or phylogenetic structure. Ecography 40:913–929

  86. Ronan Ledevin, Virginie 2013 (2013) Congruent morphological and genetic differentiation as a signature of range expansion in a fragmented landscape. Ecology and Evolution 3:4172–4182

  87. Beaumont MA, Zhang W, Balding DJ (2002) Approximate Bayesian Computation in population genetics. Genetics 162:2025–2035

  88. Engstrom TN, Edwards T, Osentoski MF, Myers EM (2007) A compendium of PCR primers for mtDNA, microsatellites, and other nuclear loci for freshwater turtles and tortoises. Chel Res Mono 4:124–141

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Blood and tissue samples were collected under the appropriate permits (IACUC permits from Earlham College and the University of Wisconsin-Madison; Indiana Scientific Purposes license #16-030; Scientific Collecting Permit #135 from the Wisconsin Department of Natural Resources; New York License to Collect and Possess #1757; UBC Animal Care Certificate # A11-0163 and BC Ministry of Environment sampling permit # VI11-71744). The Sackler Institute of Comparative Genomics and George Amato provided lab facilities and materials. Simulations and other computationally intensive analyses were carried out through the CUNY High Performance Computing Core, College of Staten Island, City University of New York. JBI was supported by the Earlham College Summer Research Fund. BNR was supported by a Gerstner Foundation postdoctoral fellowship and the Russ Gilder Graduate School at the American Museum of Natural History. Finally, comments provided by the editorial staff and three anonymous reviewers greatly improved the manuscript, and we thank them for their hard work and insight.

Author information


  1. W.K. Kellogg Biological Station, Michigan State University, Hickory Corners, MI, USA

    • B. N. Reid
  2. American Museum of Natural History, New York, NY, USA

    • B. N. Reid
    •  & C. J. Raxworthy
  3. The Graduate Center, City University of New York, New York, NY, USA

    • J. M. Kass
    •  & S. Wollney
  4. City College of the City University of New York, New York, NY, USA

    • J. M. Kass
  5. City University of New York- College of Staten Island, New York, NY, USA

    • S. Wollney
    • , E. M. Viola
    •  & J. Pantophlet
  6. University of British Columbia-Okanagan, Kelowna, BC, Canada

    • E. L. Jensen
    •  & M. A. Russello
  7. Earlham College, Richmond, IN, USA

    • J. B. Iverson
  8. University of Wisconsin, Madison, WI, USA

    • M. Z. Peery
  9. New York University, New York, NY, USA

    • E. Naro-Maciel


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Correspondence to B. N. Reid.

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