Landscape genetics of alpine Sierra Nevada salamanders reveal extreme population subdivision in space and time

Molecular Ecology

Volumn 19, Issue 16, 2010, Pages 3301-3314

  Savage, Wesley K ^a   Fremier, Alexander K ^b   Shaffer, H Bradley ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF IDAHO   (United States)

Author keywords

Ambystoma; landscape genetics; least cost analyses; microsatellites; population structure; temporal resampling

Indexed keywords

MICROSATELLITE DNA;

AMPHIBIA; ANIMAL; ARTICLE; BIOLOGICAL MODEL; CLUSTER ANALYSIS; DNA SEQUENCE; ENVIRONMENT; GENE FLOW; GENETIC VARIABILITY; GENETICS; GEOGRAPHY; POPULATION GENETICS; UNITED STATES; URODELA;

ANIMALS; CALIFORNIA; CLUSTER ANALYSIS; ENVIRONMENT; GENE FLOW; GENETIC VARIATION; GENETICS, POPULATION; GEOGRAPHY; MICROSATELLITE REPEATS; MODELS, GENETIC; SEQUENCE ANALYSIS, DNA; URODELA;

AMBYSTOMA; AMBYSTOMA MACRODACTYLUM SIGILLATUM; AMPHIBIA; SALAMANDROIDEA;

EID: 77955364515     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2010.04718.x     Document Type: Article

References (71)

1. Adriaensen F, Chardon JP, De Blust G et al. (2003) The application of 'least-cost' modelling as a functional landscape model. Landscape and Urban Planning, 64, 233 247.
2. Anderson JD (1967) A comparison of the life histories of coastal and montane populations of Ambystoma macrodactylum in California. The American Midland Naturalist, 77, 323 355.
3. Avise JC (2004) Molecular Markers, Natural History, and Evo-lution. Sinauer Associates, Sunderland, MA.
4. Broquet T, Ray N, Petit E, Fryxell J, Burel F (2006) Genetic isolation by distance and landscape connectivity in the American marten (Martes americana). Landscape Ecology, 21, 877 889.
5. Calhoun AJK, deMaynadier PG (2008) Science and Conservation of Vernal Pools in Northeastern North America. CRC Press, Boca Raton, Florida.
6. CaSIL (2006) California Spatial Information Library. Information Center for the Environment, Unviersity of California, Davis, CA.
7. Chapuis M-P, Estoup A (2007) Microsatellite null alleles and estimation of population differentiation. Molecular Biology and Evolution, 24, 621 631.
8. 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.
9. Clobert J, Danchin E, Dhondt AA, Nichols JD (Eds 2001) Dispersal. Oxford University Press, Oxford, UK.
10. Compton BW, McGarigal K, Cushman SA, Gamble LR (2007) A resistant-kernel model of connectivity for amphibians that breed in vernal pools. Conservation Biology, 21, 788 799.
11. Dieringer D, Schlotterer C (2003) Microsatellite analyser (MSA): a platform independent analysis tool for large microsatellite data sets. Molecular Ecology Notes, 3, 167 169.
12. Dionne M, Caron F, Dodson JJ, Bernatchez L (2008) Landscape genetics and hierarchical genetic structure in Atlantic Salmon: the interaction of gene flow and local adaptation. Molecular Ecology, 17, 2382 2396.
13. Elliott-Fisk DL, Rowntree RA, Cahill TA et al. (1996) Lake Tahoe Case Study. Centers for Water and Wildland Resources, University of California, Davis, CA, pp. 217 276.
14. Erman DC, Barbour M, Christensen N et al. (1996) Plants and Terrestrial Wildlife. Sierra Nevada Ecosystem Project, Final Report to Congress. Centers for Water and Wildland Resources, University of California, Davis, CA, pp. 71 91.
15. 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.
16. Fahrig L (1998) When does fragmentation of breeding habitat affect population survival? Ecological Modelling, 105, 273 292.
17. Falush D, Stephens M, Pritchard JK (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics, 164, 1567 1587.
18. Faubet P, Gaggiotti OE (2008) A new bayesian method to identify the environmental factors that influence recent migration. Genetics, 178, 1491 1504.
19. Flather CH, Bevers M (2002) Patchy reaction-diffusion and population abundance: the relative importance of habitat amount and arrangement. The American Naturalist, 159, 40 56.
20. FRAP (2008) Land Cover Mapping and Monitoring Program, Vegetation Data. Fire and Resource Assessment Program (FRAP), California Department of Forestry and Fire Protection, Sacramento, CA.
21. Funk WC, Dunlap WW (1999) Colonization of high-elevation lakes by long-toed salamanders (Ambystoma macrodactylum) after the extinction of introduced trout populations. Canadian Journal of Zoology, 77, 1759 1767.
22. Funk WC, Tallmon DA, Allendorf FW (1999) Small effective population size in the long-toed salamander. Molecular Ecology, 8, 1633 1640.
23. Gamble LR, McGarigal K, Compton BW (2007) Fidelity and dispersal in the pond-breeding amphibian, Ambystoma opacum: implications for spatio-temporal population dynamics and conservation. Biological Conservation, 139, 247 257.
24. Giordano AR, Ridenhour BJ, Storfer A (2007) The influence of altitude and topography on genetic structure in the long-toed salamander (Ambystoma macrodactulym). Molecular Ecology, 16, 1625 1637.
25. Goudet J (1995) fstat (Version 1.2): a computer program to calculate F-statistics. Journal of Heredity, 86, 485 486.
26. Goudet J (2001) fstat (version 2.9.3.2): A Program to Estimate and Test Gene Diversities and Fixation Indices. Lausanne University, Lausanne, Switzerland.
27. Greenwald KR, Gibbs HL, Waite TH (2009a) Efficacy of land-cover models in predicting isolation of marbled salamander populations in a fragmented landscape. Conservation Biology, 23, 1232 1241.
28. Greenwald KR, Purrenhage JL, Savage WK (2009b) Landcover predicts isolation in Ambystoma salamanders across region and species. Biological Conservation, 142, 2493 2500.
29. Hogg JT, Forbes SH, Steele BM, Luikart G (2006) Genetic rescue of an insular population of large mammals. Proceedings of the Royal Society B: Biological Sciences, 273, 1491 1499.
30. Howard JH, Wallace RL (1981) Microgeographical variation of electrophoretic loci in populations of Ambystoma macrodactylum columbianum (Caudata: Ambystomatidae). Copeia, 1971, 466 471.
31. Howard JH, Wallace RL (1985) Life history characteristics of populations of the long-toed salamander (Ambystoma macrodactylum) from different altitudes. The American Midland Naturalist, 113, 361 373.
32. Julian SE, King TL, Savage WK (2003) Isolation and characterization of novel tetranucleotide microsatellite DNA markers for the spotted salamander, Ambystoma maculatum. Molecular Ecology Notes, 3, 7 9.
33. Kalinowski ST, Wagner AP, Taper ML (2006) ml-relate: a computer program for maximum likelihood estimation of relatedness and relationship. Molecular Ecology Notes, 6, 576 579.
34. Koizumi I, Yamamoto S, Maekawa K (2006) Decomposed pairwise regression analysis of genetic and geographic distances reveals a metapopulation structure of stream-dwelling Dolly Varden charr. Molecular Ecology, 15, 3175 3189.
35. McGarigal K, Cushman SA (2002) Comparative evaluation of experimental approaches to the study of habitat fragmentation effects. Ecological Applications, 12, 335 345.
36. 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. Molecular Ecology, 13, 55 65.
37. Park SDE (2001) Trypanotolerance in West African Cattle and the Population Genetic Effects of Selection. University of Dublin, Ireland.
38. Pérez-Espona S, Pérez-Barberia FJ, McLeod JE, Jiggins CD, Gordon IJ, Pemberton JM (2008) Landscape features affect gene flow of Scottish Highland red deer (Cervus elaphus). Molecular Ecology, 17, 981 996.
39. Petranka J (1998) Salamanders of the United States and Canada. Smithsonian Institution Press, Washington.
40. Pilliod DS, Fronzuto JA (Eds 2005) Ambystoma macrodactylum, Long-toed salamander. Species account, University of California Press, Berkeley, CA.
41. Piry S, Alapetite A, Cornuet JM, Paetkau D, Baudouin L, Estoup A (2004) Geneclass2: a software for genetic assignment and first-generation migrant detection. Journal of Heredity, 95, 536 539.
42. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics, 155, 945 959.
43. Purrenhage JL, Niewiarowski PH, Moore FBG (2009) Population structure of spotted salamanders (Ambystoma maculatum) in a fragmented landscape. Molecular Ecology, 18, 235 247.
44. Queller DC, Goodnight KF (1989) Estimating relatedness using genetic markers. Evolution, 43, 258 275.
45. Rannala B, Mountain JL (1997) Detecting immigration by using multilocus genotypes. Proceedings of the National Academy of Sciences, USA, 94, 9197 9201.
46. Raymond M, Rousset F (1995) An exact test for population differentiation. Evolution, 49, 1280 1283.
47. Rousset F (1997) Genetic differentiation and estimation of gene flow from F-statistics under isolation by distance. Genetics, 145, 1219 1228.
48. Sambrook J, Russell D (2001) Molecular Cloning: a Laboratory Manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
49. Savage WK (2008) Tandem repeat markers for population genetic studies of the protected California tiger salamander (Ambystoma californiense). Conservation Genetics, 9, 1707 1710.
50. Savage WK (2009) Microsatellite loci for the critically endangered Santa Cruz long-toed salamander (Ambystoma macrodactylum croceum) and other Ambystoma taxa. Conservation Genetics, 10, 619 622.
51. Searcy CA, Shaffer HB (2008) Calculating biologically accurate mitigation credits: Insights from the California tiger salamander. Conservation Biology, 22, 997 1005.
52. Semlitsch RD (2008) Differentiating migration and dispersal processes for pond-breeding amphibians. Journal of Wildlife Management, 72, 260 267.
53. Sheppard RF (1977) The Ecology and Home Range Movements of Ambystoma Macrodactylum krausei (Amphibia: Urodela). Biology. University of Calgary, Calgary, Alberta, Canada.
54. Slatkin M (1987) Gene flow and the geographic structure of natural populations. Science, 236, 787 792.
55. Spear SF, Peterson CR, Matocq MD, Storfer A (2005) Landscape genetics of the blotched tiger salamander (Ambystoma tigrinum melanostictum). Molecular Ecology, 14, 2553 2564.
56. Stebbins RC (2003) Amphibians of Western North America. Houghton Mifflin Company, Boston, MA.
57. Tallmon DA, Funk WC, Dunlap WW, Allendorf FW (2000) Genetic differentiation among long-toed salamander (Ambystoma macrodactylum) populations. Copeia, 2000, 27 35.
58. Tallmon DA, Luikart G, Waples RS (2004) The alluring simplicity and complex reality of genetic rescue. Trends in Ecology and Evolution, 19, 489 496.
59. Trenham PC (2001) Terrestrial habitat use by adult California tiger salamanders. Journal of Herpetology, 35, 343 346.
60. Trenham PC, Shaffer HB (2005) Amphibian upland habitat use and its consequences for population viability. Ecological Applications, 15, 1158 1168.
61. Trenham PC, Koenig WD, Shaffer HB (2001) Spatially autocorrelated demography and interpond dispersal in the salamander Ambystoma californiense. Ecology, 82, 3519 3530.
62. Van Oosterhout C, Hutchinson WF, Wills DPM, Shipley P (2004) Micro-checker: software for identifying and correcting genotyping errors in microsatellite data. Molecular Ecology Notes, 4, 535 538.
63. Vences M, Wake DB (2007) Speciation, species boundaries and phylogeography of amphibians. In : Amphibian Biology (eds Heatwole H, Tyler M pp. 2613 2669. Surrey Beatty and Sons, Chipping Norton, Australia.
64. Wang IJ, Savage WK, Shaffer HB (2009) Landscape genetics and least-cost path analysis reveal unexpected dispersal routes in the California tiger salamander (Ambystoma californiense). Molecular Ecology, 18, 1365 1374.
65. Waples RS (2006) A bias correction for estimates of effective population size based on linkage disequilibrium at unlinked gene loci. Conservation Genetics, 7, 167 184.
66. Waples RS, Do C (2008) ldne: a program for estimating effective population size from data on linkage disequilibrium. Molecular Ecology Resources, 8, 753 756.
67. Waples RS, Gaggiotti O (2006) What is a population? An empirical evaluation of some genetic methods for identifying the number of gene pools and their degree of connectivity. Molecular Ecology, 15, 1419 1439.
68. Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution, 38, 1358 1370.
69. st ≠ 1/(4 Nm + 1). Heredity, 82, 117 125.
70. Wright S (1943) Isolation by distance. Genetics, 28, 114 138.
71. Zamudio KR, Wieczorek AM (2007) Fine-scale spatial genetic structure and dispersal among spotted salamander (Ambystoma maculatum) breeding populations. Molecular Ecology, 16, 257 274.