Similarity of contemporary and historical gene flow among highly fragmented populations of an endangered rattlesnake

Molecular Ecology

Volumn 19, Issue 24, 2010, Pages 5345-5358

  Chiucchi, James E ^a   Gibbs, H L ^a  

^a OHIO STATE UNIVERSITY   (United States)

Author keywords

eastern massasauga rattlesnake; effective population size; historical and contemporary gene flow; microsatellite DNA loci; population differentiation

Indexed keywords

MICROSATELLITE DNA;

ANIMAL; ARTICLE; GENE FLOW; GENETIC VARIABILITY; GENETICS; GENOTYPE; PHYSIOLOGY; POPULATION GENETICS; POPULATION MIGRATION; SNAKE;

ANIMAL MIGRATION; ANIMALS; CROTALUS; GENE FLOW; GENETIC VARIATION; GENETICS, POPULATION; GENOTYPE; MICROSATELLITE REPEATS;

SERPENTES; SISTRURUS; SISTRURUS CATENATUS CATENATUS;

EID: 78650155193     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2010.04860.x     Document Type: Article

References (71)

1. Anderson CD, Gibbs HL, Douglas ME, Holycross AT, (2009) Conservation genetics of the desert massasauga rattlesnake (Sistrurus catenatus edwardsii). Copeia, 2009, 740-747.
2. Anderson CS, Gibbs HL, Chiucchi J, (2010) Nineteen polymorphic microsatellite loci isolated from the Eastern Massasauga Rattlesnake, Sistrurus c. catenatus. Conservation Genetics DOI:.
3. Beerli P, (2004) Effect of unsampled populations on the estimation of population sizes and migration rates between sampled populations. Molecular Ecology, 13, 827-836.
4. Beerli P, (2008) Migrate version 3.0: a maximum likelihood and Bayesian estimator of gene flow using the coalescent. Distributed over the internet at. http://popgen.scs.edu/migrate.html.
5. Beerli P, (2009) How to use MIGRATE or why are Markov chain Monte Carlo programs difficult to use. In: Population Genetics for Animal Conservatio (Eds, Bertorell G, Bruford MW, Hauffe HC, Rizzoli A, Vernesi C,). pp. 42-79, Cambridge University Press, Cambridge.
6. Beerli P, Felsenstein J, (2001) Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach. Proceedings of the National Academy of Sciences, USA, 98, 4563-4568.
7. Benjamini Y, Yekutieli D, (2001) The control of the false discovery rate in multiple testing under dependency. The Annals of Statistics, 29, 1165-1188.
8. Bonnet E, Van de Peer Y, (2002) zt: a software tool for simple and partial Mantel tests. Journal of Statistical Software, 7, 1-12.
9. Bushar LM, Reinert HK, Gelbert L, (1998) Genetic variation and gene flow within and between local populations of the timber rattlesnake, Crotalus horridus. Copeia, 2, 411-422.
10. Chapman JR, Nakagawa S, Coltman DW, Slate J, Sheldon BC, (2009) A quantitative review of heterozygosity-fitness correlations in animal populations. Molecular Ecology, 18, 2746-2765.
11. Chapuis MP, Estoup A, (2007) Microsatellite null alleles and estimation of population differentiation. Molecular Biology and Evolution, 24, 621-631.
12. Ciofi C, Beaumont MA, Swingland IR, Bruford MW, (1999) Genetic divergence and units for conservation in the Komodo dragon Varanus komodoensis. Proceedings of the Royal Society of London Series B, 266, 2269-2274.
13. Clark RW, (2004) Kin recognition in rattlesnakes. Proceedings of the Royal Society of London Series B Biology Letters, 271, S243-S245.
14. Clark RW, Brown WS, Stechert R, Zamudio KR, (2008) Integrating individual behaviour and landscape genetics: the population structure of timber rattlesnake hibernacula. Molecular Ecology, 17, 719-730.
15. Cook FR, (1992) After an ice age: zoogeography of the massasauga within a Canadian herpetofaunal perspective. In: International Symposium and Workshop on the Conservation of the Eastern Massasauga Rattlesnak (eds, Johnson B, Menzies V,). pp. 19-25, Zoo, Toronto, ON.
16. Cornuet JM, Luikart G, (1996) Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. Genetics, 144, 2001-2014.
17. Cunningham M, Moritz C, (1998) Genetic effects of forest fragmentation on a rainforest restricted lizard (Scincidae: Gnypetoscincus queenslandiae). Biological Conservation, 83, 19-30.
18. Dieringer D, Schlötterer C, (2003) Microsatellite analyser (MSA): a platform independent analysis tool for large microsatellite data sets. Molecular Ecology Notes, 3, 167-169.
19. Earl D, (2009) Structure Harvester v0.3, from website: http://users.soe.ucsc.edu/~dearl/software/struct-harvest/
20. Evanno G, Regnaut S, Goudet J, (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology, 14, 2611-2620.
21. Faubet P, Waples RS, Gaggiotti OE, (2007) Evaluating the performance of a multilocus Bayesian method for the estimation of migration rates. Molecular Ecology, 16, 1149-1166.
22. Frankham R, (1995) Conservation Genetics. Annual Review of Genetics, 29, 305-327.
23. Frankham R, Ballou JD, Briscoe DA, (2002) Introduction to Conservation Genetics, Cambridge University Press, Cambridge.
24. Garza JC, Williamson EG, (2001) Detection of reduction in population size using data from microsatellite loci. Molecular Ecology, 10, 305-318.
25. 2 venom genes in closely related Sistrurus rattlesnakes with divergent diets. Journal of Molecular Evolution, 66, 151-166.
26. Gibbs HL, Weatherhead PJ, (2001) Insights into population ecology and sexual selection in snakes through the application of DNA-based genetic markers. Journal of Heredity, 92, 173-179.
27. Gibbs HL, Prior KA, Weatherhead PJ, Johnson G, (1997) Genetic structure of populations of the threatened eastern massasauga rattlesnake, Sistrurus c. catenatus: evidence from microsatellite DNA markers. Molecular Ecology, 6, 1123-1132.
28. Gibbs HL, Sanz L, Calvete J, (2009) Snake population venomics: Proteomics-based analyses of individual variation reveals gene regulation effects on venom protein expression in Sistrurus rattlesnakes. Journal of Molecular Evolution, 68, 113-125.
29. Goudet J, (2001) FSTAT, a program to estimate and test gene diversities and fixation indices (version 2.9.3). Available from. http://www2.unil.ch/ popgen/softwares/fstat.htm.
30. Government of Canada (2009) Species at Risk Public Registry. http://www.sararegistry.gc.ca.
31. Hansen BD, Harley KP, Lindenmayer DB, et al. (2009) Population genetic analysis reveals a long-term decline of a threatened endemic Australian marsupial. Molecular Ecology, 18, 3346-3362.
32. Hartl GB, Zachos FE, Nadlinger K, et al. (2005) Allozyme and mitochondrial DNA analysis of French red deer (Cervus elaphus) populations: genetic structure and its implications for management and conservation. Mammalian Biology, 70, 24-34.
33. Johnson G, (2000) Spatial ecology of the Eastern Massasauga Sistrurus c. catenatus) in a New York peatland. Journal of Herpetology, 34, 186-192.
34. Johnson JA, Toepfer JE, Dunn PO, (2003) Contrasting patterns of mitochondrial and microsatellite population structure in fragmented populations of greater prairie chickens. Molecular Ecology, 12, 3335-3347.
35. Keyghobadi N, (2007) The genetic implications of habitat fragmentation for animals. Canadian Journal of Zoology, 85, 1049-1064.
36. Kubatko LS, Gibbs HL, Bloomquist EW, (2010) Inferring species-level phylogenies and taxonomic distinctiveness using multi-locus data in Sistrurus rattlesnakes. Systematic Biology (in press).
37. Kuhner M, (2006) LAMARC 2.0: maximum likelihood and Bayesian estimation of population parameters. Bioinformatics, 22, 768-770.
38. Loader C, (1999) Local Regression and Likelihood, Springer Mathematics, New York.
39. Luikart G, Allendorf FW, Cornuet JM, Sherwin WB, (1998) Distortion of allele frequency distributions provides a test for recent population bottlenecks. Journal of Heredity, 89, 238-247.
40. Manier MK, Arnold SJ, (2005) Population genetic analysis identifies source-sink dynamics for two sympatric garter snake species (Thamnophis elegans and Thamnophis sirtalis). Molecular Ecology, 14, 3965-3976.
41. Marshall JCJ, Kingsbury BA, Minchella DJ, (2009) Microsatellite variation, population structure, and bottlenecks in the threatened copperbelly water snake. Conservation Genetics, 10, 465-476.
42. Martinez-Cruz B, Godoy JA, Negro JJ, (2007) Population fragmentation leads to spatial and temporal genetic structure in the endangered Spanish imperial eagle. Molecular Ecology, 16, 477-486.
43. Martinez-Solano I, Rey I, Garcia-Paris M, (2005) The impact of historical and recent factors on genetic variability in a mountain frog: the case of Rana iberica (Anura: Ranidae). Animal Conservation, 8, 431-441.
44. Middleton J, Chu JY, (2004) Population viability analysis (PVA) of the Eastern Massasauga Rattlesnake, Sistrurus catenatus catenatus, in Georgian Bay Islands National Park and elsewhere in Canada. Prepared for the Eastern Massasauga Rattlesnake Species Recovery Team, January 2004. 52pp.
45. Miller P, (2005) Population viability assessment for the Eastern Massasauga Rattlesnake (Sistrurus catenatus catenatus) on the Bruce Peninsula, Ontario, Canada. In: Third International Symposium and Workshop on Conservation of the Massasauga (Sistrurus catenatus): Population Viability and Outreach (eds Massasauga Recovery Team). 2005 October 12-14, pp. 37. Toronto Zoo, Toronto, ON.
46. Mönkkönen M, Welsh DA, (1994) A biogeographical hypothesis on the effects of human caused landscape changes on the forest bird communities of Europe and North America. Annales Zoologici Fennici, 31, 61-70.
47. Narum SR, (2006) Beyond Bonferroni: less conservative analyses for conservation genetics. Conservation Genetics, 7, 783-787.
48. Palstra FP, O'Connell MF, Ruzzante DE, (2007) Population structure and gene flow reversals in Atlantic salmon (Salmo trutto) over contemporary and long-term temporal scales: effects of population size and life history. Molecular Ecology, 16, 4504-4522.
49. Paquin MM, Wylie GD, Routman EJ, (2006) Population structure of the giant garter snake, Thamnophis gigas. Conservation Genetics, 7, 25-36.
50. Pavlacky Jr DC, Goldizen AW, Prentis PJ, et al. (2009) A landscape genetics approach for quantifying the relative influence of historic and contemporary habitat heterogeneity on the genetic connectivity of a rainforest bird. Molecular Ecology, 18, 2945-2960.
51. Pertoldi C, Bijlsma R, Loeschcke V, (2007) Conservation genetics in a globally changing environment: present problems, paradoxes and future challenges. Biodiversity and Conservation, 16, 4147-4163.
52. Pielou EC, (1991) After the Ice Age: The Return of Life to Glaciated North America, University of Chicago Press, Chicago, Illinois.
53. Piry S, Luikart G, Cornuet JM, (1999) Computer note. Bottleneck: a computer program for detecting recent reductions in the effective size using allele frequency data. Journal of Heredity, 90, 502-503.
54. Prior KA, Gibbs HL, Weatherhead PJ, (1997) Population genetic structure in the black rat snake: implications for management. Conservation Biology, 11, 1147-1158.
55. Pritchard JK, Stephens M, Donnelly P, (2000) Inference of population structure using multilocus genotype data. Genetics, 155, 945-959.
56. Prosser MR, Gibbs HL, Weatherhead PJ, (1999) Microgeographic population genetic structure in the northern water snake, Nerodia sipedon sipedon detected using microsatellite DNA loci. Molecular Ecology, 8, 329-333.
57. Raymond M, Rousset F, (1995) GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism. Journal of Heredity, 86, 248-249.
58. Redeker S, Andersen LW, Pertoldi C, et al. (2006) Genetic structure, habitat fragmentation and bottlenecks in Danish bank voles (Clethrionomys glareolus). Mammalian Biology, 71, 144-158.
59. Reed DH, Frankham R, (2003) Correlation between fitness and genetic diversity. Conservation Biology, 17, 230-237.
60. Reinert HK, Kodrich WR, (1982) Movements and habitat utilization by the massasauga, Sistrurus catenatus catenatus. Journal of Herpetology, 16, 162-171.
61. Rosenberg NA, (2004) Distruct: a program for the graphical display of population structure. Molecular Ecology Notes, 4, 137-138.
62. Schmidt KP, (1938) Herpetological evidence for the post-glacial extension of the steppe in North America. Ecology, 19, 396-407.
63. Schwartz TS, Karl SA, (2005) Population and conservation genetics of the gopher tortoise (Gopherus polyphemus). Conservation Genetics, 6, 917-928.
64. Seigel RA, Sheil CA, (1999) Population viability analysis: applications for the conservation of massasaugas. In: "Second International Symposium and Workshop on the Conservation of the Eastern Massasauga Rattlesnake, Sistrurus Catenatus Catenatus: Population and Habitat Management Issues in Urban, Bog, Prairie and Forested Ecosystems (eds, Johnson B, Wright M,). pp. 17-22, Toronto Zoo, Toronto, Ontario.
65. Spiegelhalter DJ, (2002) Bayesian measures of model complexity and fit. Journal of the Royal Statistical Society. Series B (Methodological), 64, 583-639.
66. Szymanski J, (1998) Status Assessment for Eastern Massasauga. U.S. Fish and Wildlife Service Series Status Assessment for Eastern Massasauga.
67. Ursenbacher S, Monney JC, Fumagalli L, (2009) Limited genetic diversity and high differentiation among the remnant adder (Vipera berus) populations in the Swiss and French Jura Mountains. Conservation Genetics, 10, 303-315.
68. Vandergast AG, Bohonak AJ, Weissman DB, et al. (2007) Understanding the genetic effects of recent habitat fragmentation in the context of evolutionary history: phylogeography and landscape genetics of a southern California endemic Jerusalem cricket (Orthoptera: Stenopelmatidae: Stenpelmatus). Molecular Ecology, 16, 977-992.
69. Vucetich JA, Waite TA, Nunney L, (1995) Fluctuating population size and the ratio of effective to census population size. Evolution, 51, 2017-2021.
70. Weir BS, Cockerham CC, (1984) Estimating F-statistics for the analysis of population structure. Evolution, 38, 1358-1370.
71. Wilson GA, Rannala B, (2003) Bayesian inference of recent migration rates using multilocus genotypes. Genetics, 163, 1177-1191.