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PLOS ONE  2014 

Unexpectedly Low Rangewide Population Genetic Structure of the Imperiled Eastern Box Turtle Terrapene c. carolina

DOI: 10.1371/journal.pone.0092274

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Abstract:

Rangewide studies of genetic parameters can elucidate patterns and processes that operate only over large geographic scales. Herein, we present a rangewide population genetic assessment of the eastern box turtle Terrapene c. carolina, a species that is in steep decline across its range. To inform conservation planning for this species, we address the hypothesis that disruptions to demographic and movement parameters associated with the decline of the eastern box turtle has resulted in distinctive genetic signatures in the form of low genetic diversity, high population structuring, and decreased gene flow. We used microsatellite genotype data from (n = 799) individuals from across the species range to perform two Bayesian population assignment approaches, two methods for comparing historical and contemporary migration among populations, an evaluation of isolation by distance, and a method for detecting barriers to gene flow. Both Bayesian methods of population assignment indicated that there are two populations rangewide, both of which have maintained high levels of genetic diversity (HO = 0.756). Evidence of isolation by distance was detected in this species at a spatial scale of 300 – 500 km, and the Appalachian Mountains were identified as the primary barrier to gene flow across the species range. We also found evidence for historical but not contemporary migration between populations. Our prediction of many, highly structured populations across the range was not supported. This may point to cryptic contemporary gene flow, which might in turn be explained by the presence of rare transients in populations. However these data may be influenced by historical signatures of genetic connectivity because individuals of this species can be long-lived.

References

[1]  Frankham R, Ballou JD, Briscoe DA (2002) Introduction to Conservation Genetics. Cambridge University Press. Cambridge. 642 p.
[2]  Whitlock MC, McCauley DE (1999) Indirect measures of gene flow and migration: FST≠1/(4Nm+1). Heredity 82: 117–125. doi: 10.1038/sj.hdy.6884960
[3]  Avise JC, Ball RM, Arnold J (1988) Current versus historical population sizes in vertebrate species with high gene flow: a comparison based on mitochondrial DNA lineages and inbreeding theory for neutral mutations. Mol Biol Evol 5: 331–344.
[4]  Kuo C-H, Janzen FJ (2004) Genetic effects of a persistent bottleneck on a natural population of Ornate Box Turtles (Terrapene ornata). Conserv Genet 5: 425–437. doi: 10.1023/b:coge.0000041020.54140.45
[5]  Lowe WH, Allendorf FW (2010) What can genetics tell us about population connectivity? Mol Ecol 19: 3038–3051. doi: 10.1111/j.1365-294x.2010.04688.x
[6]  Ewers RM, Didham RK (2006) Confounding factor in the detection of species responses to habitat fragmentation. Biol Rev 81: 117–142. doi: 10.1017/s1464793105006949
[7]  Steen DA, Gibbs JP (2004) Effects of roads on the structure of freshwater turtle populations. Conserv Biol 18: 1143–1148. doi: 10.1111/j.1523-1739.2004.00240.x
[8]  Aresco MJ (2005) Mitigation measures to reduce highway mortality of turtles and other herpetofauna at a north Florida lake. J Wildl Manage 69: 549–560. doi: 10.2193/0022-541x(2005)069[0549:mmtrhm]2.0.co;2
[9]  Hartl DL, Clark AG (2007) Principles of Population Genetics, 4th edn. Sinauer Associates, Sunderland, Massachusetts.
[10]  Rousset F (1997) Genetic differentiation and estimation of gene flow from F-statistics under isolation by distance. Genetics 145: 1219–1228.
[11]  Pearse DE, Arndt AD, Valenzuela N, Miller BA, Cantarelli V, et al. (2006) Estimating population structure under nonequilibrium conditions in a conservation context: continent-wide population genetics of the giant Amazon river turtle, Podocnemis expansa (Chelonia; Podocnemididae). Mol Ecol 15: 985–1006. doi: 10.1111/j.1365-294x.2006.02869.x
[12]  Nei M, Maruyama T, Chakraborty R (1975) The bottleneck effect and genetic variability in populations. Evol 29: 1–10. doi: 10.2307/2407137
[13]  Lesica O, Allendorf FW (1999) Ecological genetics and the restoration of plant communities: mix or match? Restor Ecol 7: 42–50. doi: 10.1046/j.1526-100x.1999.07105.x
[14]  McKay JK, Christian CE, Harrison S, Rice KJ (2005) “How local is local? – A review of practical and conceptual issues in the genetics of restoration. Restor Ecol. 13: 432–440. doi: 10.1111/j.1526-100x.2005.00058.x
[15]  Waples RS (1995) Evolutionary significant units and the conservation of biological diversity under the Endangered Species Act. Amer Fish Soc Symp 17: 8–27.
[16]  Alacs EA, Janzen FJ, Scribner KT (2007) Genetic issues in freshwater turtle and tortoise conservation. Chel Res Mon 4: 107–123.
[17]  Gibbons JW, Scott DE, Ryan TJ, Buhlmann KA, Tuberville TD, et al. (2000) The global decline of reptiles, déjà vu amphibians. Biosci 50: 653–666. doi: 10.1641/0006-3568(2000)050[0653:tgdord]2.0.co;2
[18]  Cook RP, Brothernon DK, Behler JL (2010) Inventory of amphibians and reptiles at the Williams Floyd Estate, Fire Island National Seashore. Natural Resouce Report NPS/NCBN/NRTR-2010/380. U.S. Department of the Interior, National Park Service, Fort Collins, Colorado.
[19]  Dodd CK (2001) North American Box Turtles: A Natural History. University of Oklahoma Press, Norman, Oklahoma. 231 p.
[20]  Stickel LF (1978) Changes in a box turtle population during three decades. Copeia 1978: 221–225. doi: 10.2307/1443554
[21]  Williams EC, Parker WS (1987) A long-term study of a box turtle (Terrapene carolina) population at Allee Memorial Woods, Indiana, with emphasis on survivorship. Herpetol 43: 328–335.
[22]  Hall RJ, Henry PFP, Bunck CM (1999) Fifty-year trends in a box turtle population in Maryland. Biol Cons 88: 165–172. doi: 10.1016/s0006-3207(98)00107-4
[23]  Hagood S (2009) Genetic differentiation of selected Eastern Box Turtle (Terrapene carolina carolina) populations in fragmented habitats, and a comparison of road-based mortality rates to population size. PhD Dissertation, University of Maryland.
[24]  Marsack K, Swanson BJ (2009) A genetic analysis of the impact of generation time and road-based habitat fragmentation on Eastern box turtles (Terrapene c. carolina). Copeia 4: 647–652. doi: 10.1643/ce-08-233
[25]  Butler JM, Dodd Jr CK, Aresco M, Austin JD (2011) Morphological and molecular evidence indicates that the Gulf Coast box turtle (Terrapene carolina major) is not a distinct evolutionary lineage in the Florida Panhandle. Biol J Linn Soc Lond 102: 889–901. doi: 10.1111/j.1095-8312.2011.01625.x
[26]  Miller BK (1993) Wildlife trends in Indiana. Hoosier Farmland Wildlife Notes 1: 2.
[27]  Kimble SJA, Williams RN (2012) Temporal variance in hematologic and plasma biochemical reference intervals for free-ranging eastern box turtle (Terrapene carolina carolina). J Wildl Dis 48: 799–802. doi: 10.7589/0090-3558-48.3.799
[28]  Ernst CH, Barbour RW, Hershey MF (1974) A new coding system for hardshelled turtles. J Ky Acad Sci 35: 27–28.
[29]  Sambrook J, Russell DW (2001) Molecular Cloning: A Laboratory Manual, 3rd edn. Cold Springs Harbor Press, Cold Springs Harbor, New York. 2344 p.
[30]  Kimble SJA, Fike JA, Rhodes Jr OE, Williams RN (2011) Identification of 12 polymorphic microsatellite loci for the eastern box turtle (Terrapene carolina carolina). Conserv Genet Resour 3: 65–67. doi: 10.1007/s12686-010-9291-5
[31]  Kalinowski ST, Taper ML, Marshall TC (2007) Revising how the computer program C accommodates genotyping error increases success in paternity assignment. Mol Ecol 16: 1099–1006. doi: 10.1111/j.1365-294x.2007.03089.x
[32]  Van Oosterhout C, Hutchinson WF, Wills DPM, Shipley P (2004) M: software for identifying and correcting genotyping errors in microsatellites. Mol Ecol Notes 4: 535–538. doi: 10.1111/j.1471-8286.2004.00684.x
[33]  Raymond M, Rousset F (1995a) G (version 1.2): Population genetics software for exact tests and ecuminicism. J Hered 86: 248–249.
[34]  Raymond M, Rousset F (1995b) An exact test for population differentiation. Evol 49: 1280–1283. doi: 10.2307/2410454
[35]  Guo SW, Thompson EA (1992) Performing the exact test of Hardy-Weinberg proportion for multiple alleles. Biometrics 48: 361–372. doi: 10.2307/2532296
[36]  Mantel N (1967) Detection of disease clustering and a generalized regression approach. Cancer Res 27: 209–220.
[37]  Miller MP (2005) Alleles in Space (A): computer software for the joint analysis of interindividual spatial and genetic information. J Hered 96: 722–724. doi: 10.1093/jhered/esi119
[38]  Nei M (1972) Genetic distance between populations. Am Nat 106: 283–292. doi: 10.1086/282771
[39]  Dharmarajan G, Beasley JC, Fike JA, Rhodes Jr OE (2009) Population genetic structure of raccoons (Procyon lotor) inhabiting a highly fragmented landscape. Can J Zool 87: 814–827. doi: 10.1139/z09-072
[40]  Latch EK, Scognamillo DG, Fike JA, Chamberlain MJ, Rhodes Jr OE (2008) Deciphering ecological barriers to North American River Otter (Lontra canadensis) gene flow in the Louisiana landscape. J Hered 99: 265–274. doi: 10.1093/jhered/esn009
[41]  Guillot G, Mortier F, Estoup A (2005) G: a computer package for landscape genetics. Mol Ecol Notes 5: 712–715. doi: 10.1111/j.1471-8286.2005.01031.x
[42]  R Development Core Team (2009) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. http://www.r-project.org.
[43]  Serre D, P??bo S (2004) Evidence for gradients of human genetic diversity within and among continents. Genome Res 14: 1679–1685. doi: 10.1101/gr.2529604
[44]  Falush D, Stephens M, Pritchard JK (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genet 164: 1567–1587.
[45]  Dupanloup I, Schneider S, Excoffier L (2002) A simulated annealing approach to define the genetic structure of populations. Mol Ecol 11: 2571–2581. doi: 10.1046/j.1365-294x.2002.01650.x
[46]  Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genet 155: 945–959.
[47]  Earl DA, vonHoldt BM (2012) S H: a website and program for visualizing S output and implementing the Evanno method. Conserv Genet Resour 4: 359–361. doi: 10.1007/s12686-011-9548-7
[48]  Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software S: a simulation study. Mol Ecol 14: 2611–2620. doi: 10.1111/j.1365-294x.2005.02553.x
[49]  Monmonier MS (1973) Maximum-difference barriers: an alternative numerical regionalization method. Geo Anal 3: 245–261. doi: 10.1111/j.1538-4632.1973.tb01011.x
[50]  Manel S, Schwartz L, Luikart L, Taberlet P (2003) Landscape genetics: combining landscape ecology and population genetics. Trends Ecol Evol 18: 189–197. doi: 10.1016/s0169-5347(03)00008-9
[51]  Palmé AE, Su Q, Rautenberg A, Manni F, Lascoux M (2003) Postglacial recolonization and cpDNA variation of silver birch, Betula pendula. Mol Ecol 12: 201–212. doi: 10.1046/j.1365-294x.2003.01724.x
[52]  Tsai Y-H E, Manos PS (2010) Host density drives the postglacial migration of the tree parasite, Epifagus virginiana. Proc Natl Acad Sci USA 107: 17035–17040. doi: 10.1073/pnas.1006225107
[53]  Wilson GA, Rannala B (2003) Bayesian inference of recent migration rates using multilocus genotypes. Genet 163: 1177–1191.
[54]  Rambaut A, Drummond AJ (2007) T v.5, available at beast.bio.ed.ac.uk/Tracer.
[55]  Beerli P, Felsenstein J (2001) Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach. Proc Natl Acad Sci USA 98: 4563–4568. doi: 10.1073/pnas.081068098
[56]  Wright S (1943) Isolation by distance. Genet 25: 114–138.
[57]  Sokal RR, Wartenberg DE (1983) A test of spatial autocorrelation analysis using an isolation-by-distance model. Genet 105: 219–237.
[58]  Lemer S, Rochel E, Planes S (2011) Correction method for null alleles in species with variable microsatellite flanking regions, a case study of the black-lipped pearl oyster Pinctada margaritifera. J Hered 102: 243–246. doi: 10.1093/jhered/esq123
[59]  Dharamarajan GD, Beatty WS, Rhodes OE Jr (2013) Heterozygote deficiencies caused by a Wahlund effect: dispelling unfounded expectations. J Wild Manag 77: 226–234. doi: 10.1002/jwmg.458
[60]  Metcalf E, Metcalf AL (1970) Observations on ornate box turtles (Terrapene ornata ornata Agassiz). Trans Kans Acad Sci 73: 96–117. doi: 10.2307/3627283
[61]  Currylow AF, MacGowan BJ, Williams RN (2012) Short-term forest management effects on a long-lived ectotherm. Plos One 7(7): e40473. doi: 10.1371/journal.pone.0040473
[62]  Madden R (1975) Home range, movements, and orientation in the eastern box turtle Terrapene carolina carolina. PhD dissertation, City University of New York.
[63]  Burke RL, Capitano W (2012) Eastern box turtle, Terrapene carolina, neonate overwintering ecology on Long Island.New York. Chel Conserv Biol 10: 256–259. doi: 10.2744/ccb-0855.1
[64]  Schwartz CW, Schwartz ER (1974) The three-toed box turtle in central Missouri: its population, home range, and movements. Part I. Missouri Department of Conservation, Jefferson City, Missouri.
[65]  Kiester AR, Schwartz CW, Schwartz ER (1982) Promotion of gene flow by transient individuals in an otherwise sedentary population of box turtles (Terrapene carolina triunguis). Evol 36: 617–619. doi: 10.2307/2408108
[66]  Richtsmeier RJ, Bernstein NP, Demastes JW, Black RW (2008) Migration, gene flow, and genetic diversity within and among Iowa populations of Ornate Box Turtles (Terrapene ornata ornata). Chel Conserv Biol 7: 3–11. doi: 10.2744/ccb-0653.1
[67]  Latch EK, Boarman WI, Walde A, Fleischer RC (2011) Fine-scale analysis reveals cryptic landscape genetic structure in desert tortoises. Plos One 6: e27794. doi: 10.1371/journal.pone.0027794
[68]  Steyaert LT, Knox RG (2008) Reconstructed historical land cover and biophysical parameters for studies of land-atmosphere interactions within the eastern United States. J Geophys Res 113: 1–27. doi: 10.1029/2006jd008277
[69]  Bishop JM, Leslie AJ, Bourquin SL, O’Ryan C (2009) Reduced effective population size in an overexploited population of the Nile crocodile (Crocodylus niloticus) Biol Cons. 142: 2335–2341. doi: 10.1016/j.biocon.2009.05.016
[70]  Lerner HR, Johnson JA, Lindsay AR, Kiff LF, Mindell DP (2009) It's not too late for the harpy eagle (Harpia harpyja): high levels of genetic diversity and differentiation can fuel conservation programs. PLOS One 4: e7336. doi: 10.1371/journal.pone.0007336
[71]  Victory ER, Glaubitz JC, Rhodes Jr OE, Woeste KE (2006) Genetic homogeneity in Jugland nigra (Juglandaceae) at nuclear microsatellites. Am J Bot 93: 118–126. doi: 10.3732/ajb.93.1.118

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