Population structure and gene flow in a heavily disturbed habitat: Implications for the management of the imperilled Red Hills salamander (Phaeognathus hubrichti)

Conservation Genetics

Volumn 13, Issue 4, 2012, Pages 913-923

  Apodaca, Joseph J ^a,b   Rissler, Leslie J ^a   Godwin, James C ^c  

^a UNIVERSITY OF ALABAMA   (United States)

^b FLORIDA STATE UNIVERSITY   (United States)

^c AUBURN UNIVERSITY   (United States)

Author keywords

Conservation genetics; Gene flow; Landscape genetics; Phaeognathus hubrichti; Red Hills salamander

Indexed keywords

AMPHIBIAN; CONSERVATION GENETICS; CONSERVATION MANAGEMENT; GENE FLOW; GENETIC VARIATION; HABITAT FRAGMENTATION; HUMAN ACTIVITY; INBREEDING; ISOLATED POPULATION; POPULATION BOTTLENECK; POPULATION STRUCTURE;

PHAEOGNATHUS; PHAEOGNATHUS HUBRICHTI; SALAMANDROIDEA;

EID: 84864303835     PISSN: 15660621     EISSN: 15729737     Source Type: Journal    
DOI: 10.1007/s10592-012-0340-3     Document Type: Article

References (76)

1. Anderson CD, Epperson BK, Fortin MJ, Holderegger R, James PMA, Rosenberg MS, Scribner KT, Spear S (2010) Considering spatial and temporal scale in landscape-genetic studies of gene flow. Mol Ecol 19: 3565-3575.
2. Apodaca JJ (2010) Prioritizing regions for the conservation of amphibians with special emphasis on the Red Hills salamander (Phaeognathus hubrichti). Dissertation, The University of Alabama, Tuscaloosa.
3. Avise JC (2004) Molecular markers, natural history and evolution, 2nd edn. Sinauer, Sunderland.
4. Beebee TJC (2005) Conservation genetics of amphibians. Heredity 95: 423-427.
5. Beerli P (2006) Comparison of Bayesian and maximum-likelihood inference of population genetic parameters. Bioinformatics 22: 341-345.
6. Beerli P, Felsenstein J (1999) Maximum-likelihood estimation of migration rates and effective population numbers in two populations using a coalescent approach. Genetics 152: 763-773.
7. 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.
8. Berry O, Tocher MD, Sarre SD (2004) Can assignment tests measure dispersal? Mol Evol 13: 551-561.
9. Blaustein AR, Wake DB, Sousa WP (1994) Amphibian declines: judging stability, persistence, and susceptibility of populations to local and global extinctions. Conserv Biol 8: 60-71.
10. Blouin MS, Phillipsen IC, Monsen KJ (2010) Population structure and conservation genetics of the Oregon spotted frog, Rana pretiosa. Conserv Genet 11: 2179-2194.
11. Busch JD, Waser PM, DeWoody JA (2007) Recent demographic bottlenecks are not accompanied by a genetic signature in banner-tailed kangaroo rats (Dipodomys spectabilis). Mol Ecol 16: 2450-2462.
12. Cabe PR, Page RB, Hanlon TJ, Aldrich ME, Connors L, Marsh DM (2006) Fine-scale population differentiation and gene flow in a terrestrial salamander (Plethodon cinereus) living in continuous habitat. Heredity 98: 53-60.
13. Chen C, Durand E, Forbes F, Francois O (2007) Bayesian clustering algorithms ascertaining spatial population structure: a new computer program and a comparison study. Mol Ecol Notes 7: 747-756.
14. 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.
15. Coulon A, Guillot G, Cosson JF, Angibault JMA, Aulagnier S, Cargnelutti B, Galan M, Hewison AJM (2006) Genetic structure is influenced by landscape features: empirical evidence from a roe deer population. Mol Ecol 15: 1669-1679.
16. Cushman SA (2006) Effects of habitat loss and fragmentation on amphibians: a review and prospectus. Biol Conserv 128: 231-240.
17. Dixon JD, Oli MK, Wooten MC, Eason TH, McCown JW, Paetkau D (2006) Effectiveness of a regional corridor in connecting two Florida black bear populations. Conserv Biol 20: 155-162.
18. Dodd CK (1991) The status of the Red Hills salamander Phaeognathus hubrichti, Alabama, USA, 1976-1988. Biol Conserv 55: 57-75.
19. Epps CW, Palsboll PJ, Wehausen JD, Roderick GK, Ramey RR, McCullough DR (2005) Highways block gene flow and cause a rapid decline in genetic diversity of desert bighorn sheep. Ecol Lett 8: 1029-1038.
20. 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.
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. Excoffier L, Laval G, Schneider S (2005) Arlequin (version 3. 0): an integrated software package for population genetics data analysis. Evol Bioinform 1: 47-50.
23. Frankham R, Ballou JD, Briscoe DA (2002) Introduction to conservation genetics. Cambridge University Press, Cambridge.
24. French TW, Mount RH (1978) Current status of the Red Hills salamander, Phaeognathus hubrichti (Highton), and factors affecting its distribution. J Alabama Acad Sci 49: 172-179.
25. Funk WC, Tallmon DA, Allendorf FW (1999) Small effective population size in the long-toed salamander. Mol Ecol 8: 1633-1640.
26. Funk WC, Greene AE, Corn PS, Allendorf FW (2005) High dispersal in a frog species suggests that it is vulnerable to habitat fragmentation. Biol Lett 1: 13-16.
27. Geist J, Kuehn R (2005) Genetic diversity and differentiation of central European freshwater pearl mussel (Margaritifera margaritifera L.) populations: implications for conservation and management. Mol Ecol 14: 425-439.
28. Gilpin ME, Hanski IA (1991) Metapopulation dynamics: empirical and theoretical investigations. Academic Press, London.
29. Godwin JC (2008) Red Hills salamander habitat delineation, breeding bird surveys, and habitat restoration recommendations on commercial timberlands (Unpublished report prepared for The Alabama Department of Conservation and Natural Resources, Montgomery).
30. Goldberg CS, Waits LP (2010) Comparative landscape genetics of two pond-breeding amphibian species in a highly modified agricultural landscape. Mol Ecol 19: 3650-3663.
31. Goldstein DB, Linares AR, Cavallisforza LL, Feldman MW (1995) Genetic absolute dating based on microsatellites and the origin of modern humans. Proc Natl Acad Sci USA 92: 6723-6727.
32. Guo SW, Thompson EA (1992) Performing the exact test of Hardy-Weinberg proportion for multiple alleles. Biometrics 48: 361-372.
33. Harding EK, Crone EE, Elderd BD, Hoekstra JM, McKerrow AJ, Perrine JD, Regetz J, Rissler LJ, Stanley AG, Walters EL, NCEAS Habitat Conservation Plan Working Group (2001) The scientific foundations of habitat conservation plans: a quantitative assessment. Conserv Biol 15: 488-500.
34. Harrison RG (1991) Molecular changes at speciation. Annu Rev Ecol Syst 22: 281-308.
35. Howes BJ, Brown JW, Gibbs HL, Herman TB, Mockford SW, Prior KA, Weatherhead PJ (2009) Directional gene flow patterns in disjunct populations of the black ratsnake (Pantheropis obsoletus) and the Blanding's turtle (Emydoidea blandingii). Conserv Genet 10: 407-417.
36. 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.
37. Jehle R, Arntzen W, Burke T, Krupa AP, Hodl W (2001) The annual number of breeding adults and the effective population size of syntopic newts (Triturus cristatus, T. marmoratus). Mol Ecol 10: 839-850.
38. Jensen JL, Bohonak AJ, Kelley ST (2005) Isolation by distance, web service. BMC Genet 6: 13-19.
39. Jordan RJ, Mount RH (1975) The status of the Red Hills salamander, Phaeognathus hubrichti Highton. J Herpetol 9: 211-215.
40. Lance SL, Hagen C, Glenn TC, Apodaca JJ, Rissler LJ (2009) Development and characterization of twelve polymorphic microsatellite loci in the threatened Red Hills salamander, Phaeognathus hubrichti. Conserv Genet 10: 1919-1921.
41. Lee-Yaw JA, Davidson A, McRae BH, Green DM (2009) Do landscape processes predict phylogeographic patterns in the wood frog? Mol Ecol 18: 1863-1874.
42. Manel S, Schwartz MK, Luikart G, Taberlet P (2003) Landscape genetics: combining landscape ecology and population genetics. Trends Ecol Evol 18: 189-197.
43. Mantel N (1967) The detection of disease clustering and a generalized regression approach. Cancer Res 27: 209-220.
44. Marshall JCJ, Kingsbury BA, Minchella DJ (2009) Microsatellite variation, population structure, and bottlenecks in the threatened copperbelly water snake. Conserv Genet 10: 465-476.
45. Matern A, Desender K, Drees C, Gaublomme E, Paill WG, Assmann T (2009) Genetic diversity and population structure of the endangered insect species Carabus variolosus in its western distribution range: implications for conservation. Conserv Genet 10: 391-405.
46. McKnight ML, Dodd CK, Spolsky CM (1991) Protein and mitochondrial-DNA variation in the salamander Phaeognathus hubrichti. Herpetologica 47: 440-447.
47. McRae BH (2006) Isolation by resistance. Evolution 60: 1551-1561.
48. Measey GJ, Tolley KA (2011) Investigating the cause of the disjunct distribution of Amietophrynus pantherinus, the endangered South African western leopard toad. Conserv Genet 12: 61-70.
49. Morgan MJ, Hunter D, Pietsch R, Osborne W, Keogh JS (2008) Assessment of genetic diversity in the critically endangered Australian corroboree frogs, Pseudophryne corroboree and Pseudophryne pengilleyi, identifies four evolutionarily significant units for conservation. Mol Ecol 17: 3448-3463.
50. Murphy MA, Evans JS, Cushman SA, Storfer A (2008) Representing genetic variation as continuous surfaces: an approach for identifying spatial dependency in landscape genetic studies. Ecography 31: 685-697.
51. Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New York.
52. Pabijan M, Babik W, Rafinski J (2005) Conservation units in north-eastern populations of the Alpine newt (Triturus alpestris). Conserv Genet 6: 307-312.
53. Paetkau D, Strobeck C (1995) Microsatellite analysis of genetic-variation in black-bear populations. Mol Ecol 4: 133-133.
54. Paetkau D, Slade R, Burden M, Estoup A (2004) Genetic assignment methods for the direct, real-time estimation of migration rate: a simulation-based exploration of accuracy and power. Mol Ecol 13: 55-65.
55. Piry S, Luikart G, Cornuet JM (1999) BOTTLENECK: a computer program for detecting recent reductions in the effective population size using allele frequency data. J Hered 90: 502-503.
56. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945-959.
57. Proctor MF, McLellan BN, Strobeck C, Barclay RMR (2005) Genetic analysis reveals demographic fragmentation of grizzly bears yielding vulnerably small populations. Proc R Soc B Biol Sci 272: 2409-2416.
58. Reed DH, Teoh VH, Stratton GE, Hataway RA (2011) Levels of gene flow among populations of a wolf spider in a recently fragmented habitat: current versus historical rates. Conserv Genet 12: 331-335.
59. Rowe G, Beebee TJC (2004) Reconciling genetic and demographic estimators of effective population size in the anuran amphibian Bufo calamita. Conserv Genet 5: 287-298.
60. Schwaner TD, Mount RH (1970) Notes on the distribution, habits, and ecology of the salamander Phaeognathus hubrichti Highton. Copeia 1970: 571-573.
61. Schwartz MK, Luikart G, Waples RS (2007) Genetic monitoring as a promising tool for conservation and management. Trends Ecol Evol 22: 25-33.
62. Shirk AJ, Wallin DO, Cushman SA, Rice CG, Warheit KI (2010) Inferring landscape effects on gene flow: a new model selection framework. Mol Ecol 19: 3603-3619.
63. Smouse PE, Long JC, Sokal RR (1986) Multiple regression and correlation extensions of the Mantel test for matrix correspondence. Syst Zool 35: 627-632.
64. Sokal RR, Rohlf FJ (2003) Biometry, 3rd edn. W. H. Freeman, New York.
65. Spear SF, Peterson CR, Matocq MD, Storfer A (2005) Landscape genetics of the blotched tiger salamander (Ambystoma tigrinum melanostictum). Mol Ecol 14: 2553-2564.
66. Storfer A, Murphy MA, Evans JS, Goldberg CS, Robinson S, Spear SF, Dezzani R, Delmelle E, Vierling L, Waits LP (2007) Putting the "landscape" in landscape genetics. Heredity 98: 128-142.
67. Straub SC, Doyle JJ (2009) Conservation genetics of Amorpha georgiana (Fabaceae), an endangered legume of the southeastern United States. Mol Ecol 18: 4349-4365.
68. Swindell WR, Bouzat JL (2005) Modeling the adaptive potential of isolated populations: experimental simulations using Drosophila. Evolution 59: 2159-2169.
69. 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.
70. Vandergast AG, Bohonak AJ, Weissman DB, Fisher RN (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: Stenopelmatus). Mol Ecol 16: 977-992.
71. Wang IJ (2009) Fine-scale population structure in a desert amphibian: landscape genetics of the black toad (Bufo exsul). Mol Ecol 18: 3847-3856.
72. Wang IJ, Summers K (2010) Genetic structure is correlated with phenotypic divergence rather than geographic isolation in the highly polymorphic strawberry poison-dart frog. Mol Ecol 19: 447-458.
73. Wilson GA, Rannala B (2003) Bayesian inference of recent migration rates using multilocus genotypes. Genetics 163: 1177-1191.
74. Wright S (1943) An analysis of local variability of flower color in Linanthus parryae. Genetics 28: 139-156.
75. Wright S (1978) Evolution and the genetics of populations, vol IV, Variability within and among natural populations. University of Chicago Press, Chicago.
76. Zellmer AJ, Knowles LL (2009) Disentangling the effects of historic vs. contemporary landscape structure on population genetic divergence. Mol Ecol 18: 3593-3602.