Identification of polymorphic loci in Ambystoma annulatum and review of cross-species microsatellite use in the genus Ambystoma

Copeia

Volumn , Issue 3, 2012, Pages 570-577

  Peterman, William E ^a   Connette, Grant M ^a   Spatola, Brett N ^a   Eggert, Lori S ^a   Semlitsch, Raymond D ^a  

^a UNIVERSITY OF MISSOURI   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMPHIBIAN; GENETIC MARKER; IDENTIFICATION METHOD; POLYMORPHISM; REPRODUCTIVE SUCCESS;

AMBYSTOMA; AMBYSTOMA ANNULATUM;

EID: 84867068436     PISSN: 00458511     EISSN: None     Source Type: Journal    
DOI: 10.1643/CH-11-001     Document Type: Article

References (55)

1. Bartoszek, J., and K. R. Greenwald. 2009. A population divided: railroad tracks as barriers to gene flow in an isolated population of marbled salamanders (Ambystoma opacum). Herpetological Conservation and Biology 4:191-197.
2. Beerli, P. 2006. Comparison of Bayesian and maximum-likelihood inference of population genetic parameters. Bioinformatics 22:341-345.
3. Bogart, J. P., J. Bartoszek, D. W. A. Noble, and K. Bi. 2009. Sex in unisexual salamanders: discovery of a new sperm donor with ancient affinities. Heredity 103:483-493.
4. Bogart, J. P., K. Bi, J. Z. Fu, D. W. A. Noble, and J. Niedzwiecki. 2007. Unisexual salamanders (genus Ambystoma) present a new reproductive mode for eukaryotes. Genome 50:119-136.
5. Bos, D. H., D. Gopurenko, R. N. Williams, and J. A. Dewoody. 2008. Inferring population history and demography using microsatellites, mitochondrial DNA, and major histocompatibility complex (MHC) genes. Evolution 62:1458-1468.
6. Bulut, Z., C. R. Mccormick, D. Gopurenko, R. N. Williams, D. H. Bos, and J. A. Dewoody. 2009. Microsatellite mutation rates in the eastern tiger salamander (Ambystoma tigrinum tigrinum) differ 10-fold across loci. Genetica 136:501-504.
7. Castoe, T. A., A. W. Poole, W. Gu, A. P. Jason de Koning, J. M. Daza, E. N. Smith, and D. D. Pollock. 2010. Rapid identification of thousands of copperhead snake (Agkistrodon contortrix) microsatellite loci from modest amounts of 454 shotgun genome sequence. Molecular Ecology Resources 10:341-347.
8. Cosentino, B. J., C. A. Phillips, R. L. Schooley, W. H. Lowe, and M. R. Douglas. 2011. Linking extinction-colonization dynamics to genetic structure in a salamander metapopulation. Proceedings of the Royal Society B: Biological Sciences 279:1575-1582.
9. Croshaw, D. A. 2010. Quantifying sexual selection: a comparison of competing indices with mating system data from a terrestrially breeding salamander. Biological Journal of the Linnean Society 99:73-83.
10. Croshaw, D. A., N. A. Schable, M. B. Peters, and T. C. Glenn. 2005. Isolation and characterization of microsatellite DNA loci from Ambystoma salamanders. Conservation Genetics 6:473-479.
11. Demastes, J. W., J. M. Eastman, J. S. East, and C. Spolsky. 2007. Phylogeography of the blue-spotted salamander, Ambystoma laterale (Caudata: Ambystomatidae). American Midland Naturalist 157:149-161.
12. Eastman, J. M., T. A. Spradling, and J. W. Demastes. 2007. Conservation genetic assessment of the blue-spotted salamander in Iowa. American Midland Naturalist 158: 233-239.
13. Eggert, L. S., J. S. Beadell, A. Mcclung, C. E. Mcintosh, and R. C. Fleischer. 2009. Evolution of microsatellite loci in the adaptive radiation of Hawaiian honeycreepers. Journal of Heredity 100:137-147.
14. Ellegren, H., C. R. Primmer, and B. C. Sheldon. 1995. Microsatellite 'evolution': directionality or bias? Nature Genetics 11:360-362.
15. Faircloth, B. C. 2008. MSATCOMMANDER: detection of microsatellite repeat arrays and automated, locus-specific primer design. Molecular Ecology Resources 8:92-94.
16. Faubet, P., and O. E. Gaggiotti. 2008. A new Bayesian method to identify the environmental factors that influence recent migration. Genetics 178:1491-1504.
17. Gardner, M. G., A. J. Fitch, T. Bertozzi, and A. J. Lowe. 2011. Rise of the machines - recommendations for ecologists when using next generation sequencing for micro-satellite development. Molecular Ecology Resources 11: 1093-1101.
18. Giordano, A. R., B. J. Ridenhour, and A. Storfer. 2007. The influence of altitude on genetic structure in the long-toed salamander (Ambystoma macrodactylum). Molecular Ecology 16:1625-1637.
19. Goldberg, C. S., and L. P. Waits. 2010a. Comparative landscape genetics of two pond-breeding amphibian species in a highly modified agricultural landscape. Molecular Ecology 19:3650-3663.
20. Goldberg, C. S., and L. P. Waits. 2010b. Quantification and reduction of bias from sampling larvae to infer population and landscape genetic structure. Molecular Ecology Resources 10:304-313.
21. Gopurenko, D., R. N. Williams, C. R. Mccormick, and J. A. Dewoody. 2006. Insights into the mating habits of the tiger salamander (Ambystoma tigrinum tigrinum) as revealed by genetic parentage analyses. Molecular Ecology 15: 1917-1928.
22. Greenwald, K. R., H. L. Gibbs, and T. A. Waite. 2009. Efficacy of land-cover models in predicting isolation of marbled salamander populations in a fragmented landscape. Conservation Biology 25:1232-1241.
23. Hamilton, M. B., E. L. Pincus, A. Di Fiore, and R. C. Fleischer. 1999. Universal linker and ligation procedures for construction of genomic DNA libraries enriched for microsatellites. Bio Techniques 27:500-507.
24. Hutter, C., M. Schug, and C. Aquadro. 1998. Microsatellite variation in Drosophila melanogaster and Drosophila simulans: a reciprocal test of the ascertainment bias hypothesis. Molecular Biology and Evolution 15:1620-1636.
25. Jarne, P., and P. J. L. Lagoda. 1996. Microsatellites, from molecules to populations and back. Trends in Ecology and Evolution 11:424-429.
26. Julian, S. E., T. L. King, and W. K. Savage. 2003a. Isolation and characterization of novel tetranucleotide microsatellite DNA markers for the spotted salamander, Ambystoma maculatum. Molecular Ecology Notes 3:7-9.
27. Julian, S. E., T. L. King, and W. K. Savage. 2003b. Novel Jefferson salamander, Ambystoma jeffersonianum, microsatellite DNA markers detect population structure and hybrid complexes. Molecular Ecology Notes 3:95-97.
28. Kalinowski, S. 2002. How many alleles per locus should be used to estimate genetic distances? Heredity 88:62-65.
29. Keever, C. C., J. Sunday, C. Wood, M. Byrne, and M. W. Hart. 2008. Discovery and cross-amplification of micro-satellite polymorphisms in asterinid sea stars. The Biological Bulletin 215:164-172.
30. Kim, K.-S., M.-S. Min, J.-H. An, and H. Lee. 2004. Crossspecies amplification of Bovidae microsatellites and low diversity of the endangered Korean goral. Journal of Heredity 95:521-525.
31. Manel, S., O. E. Gaggiotti, andR. S.Waples. 2005. Assignment methods: matching biological questions with appropriate techniques. Trends in Ecology and Evolution 20:136-142.
32. Mech, S. G., A. Storfer, J. A. Ernst, M. W. Reudink, and S. C. Maloney. 2003. Polymorphic microsatellite loci for tiger salamanders, Ambystoma tigrinum. Molecular Ecology Notes 3:79-81.
33. Murphy, M. A., J. S. Evans, and A. Storfer. 2010. Quantifying Bufo boreas connectivity in Yellowstone National Park with landscape genetics. Ecology 91:252-261.
34. Park, S. D. E. 2001. Trypanotolerance in West African cattle and the population genetic effects of selection. Unpubl. Ph.D. diss., University of Dublin, Dublin.
35. Parra-Olea, G., E. Recuero, and K. R. Zamudio. 2007. Polymorphicmicrosatellitemarkers forMexican salamanders of the genus Ambystoma.Molecular EcologyNotes 7:818-820.
36. Petranka, J. W. 1998. Salamanders of the United States and Canada. Smithsonian Institution Press, Washington, D.C.
37. Ramsden, C. 2008. Population genetics of Ambystoma jeffersonianum and sympatric unisexuals reveal signatures of both gynogenetic and sexual reproduction. Copeia 2008:586-594.
38. Ramsden, C., K. Beriault, and J. P. Bogart. 2006. A nonlethal method of identification of Ambystoma laterale, Ambystoma jeffersonianum and sympatric unisexuals. Molecular Ecology Notes 6:261-264.
39. Raymond, M., and F. Rousset. 1995. GenePop (version 1.2): population genetics software for exact tests and ecumenicism. Journal of Hereditiy 86:248-249.
40. Rice, W. R. 1989. Analyzing tables of statistical tests. Evolution 43:223-225.
41. Rousset, F. 2008. Genepop9007: a complete re-implementation of the Genepop software for Windows and Linux. Molecular Ecology Resources 8:103-106.
42. Savage, W. K. 2008. Tandem repeat markers for population genetic studies of the protected California tiger salamander (Ambystoma californiense). Conservation Genetics 9:1707-1710.
43. Savage, W. K. 2009. Microsatellite loci for the critically endangered Santa Cruz long-toed salamander (Ambystoma macrodactylum croceum) and other Ambystoma taxa. Conservation Genetics 10:619-622.
44. Shaffer, H. B., J. M. Clark, and F. Kraus. 1991. When molecules and morphology clash: a phylogenetic analysis of the North American ambystomatid (Caudata: Ambystomatidae) salamanders. Systematic Zoology 40:284-303.
45. Spear, S. F., C. R. Peterson, M. D. Matocq, and A. Storfer. 2006. Molecular evidence for historical and recent population size reductions of tiger salamanders (Ambystoma tigrinum) in Yellowstone National Park. Conservation Genetics 7:605-611.
46. Stevens, V. M., C. Verkenne, S. Vandewoestijne, R. A. Wesselingh, and M. Baguette. 2006. Gene flow and functional connectivity in the natterjack toad. Molecular Ecology 15:2333-2344.
47. Tennessen, J. A., and K. R. Zamudio. 2003. Early male reproductive advantage, multiple paternity and sperm storage in an amphibian aggregate breeder. Molecular Ecology 12:1567-1576.
48. Van Oosterhout, C., W. F. Hutchinson, D. P. M. Wills, and P. Shipley. 2004. MICRO-CHECKER: software for identifying and correcting genotyping errors in microsatellite data. Molecular Ecology Notes 4:535-538.
49. Wang, I. J., and K. Summers. 2010. Genetic structure is correlated with phenotypic divergence rather than geographic isolation in the highly polymorphic strawberry poison-dart frog. Molecular Ecology 19:447-458.
50. Wieczorek, A. M., K. R. Zamudio, T. L. King, and B. Gjetvaj. 2002. Isolation of microsatellite loci in spotted salamanders (Ambystoma maculatum). Molecular Ecology Notes 2:313-315.
51. Williams, R. N., D. H. Bos, D. Gopurenko, and J. A. Dewoody. 2008. Amphibian malformations and inbreeding. Biology Letters 4:549-552.
52. Williams, R. N., and J. A. DeWoody. 2004. Fluorescent dUTP helps characterize 10 novel tetranucleotide microsatellites from an enriched salamander (Ambystoma texanum) genomic library. Molecular Ecology Notes 4:17-19.
53. Williams, R. N., D. Gopurenko, K. R. Kemp, B. Williams, and J. A. DeWoody. 2009. Breeding chronology, sexual dimorphism, and genetic diversity of congeneric ambystomatid salamanders. Journal of Herpetology 43:438-449.
54. Zamudio, K. R., and W. K. Savage. 2003. Historical isolation, range expansion, and secondary contact of two highly divergent mitochondrial lineages in spotted salamanders (Ambystoma maculatum). Evolution 57:1631-1652.
55. Zamudio, K. R., and A. M. Wieczorek. 2007. Fine-scale spatial genetic structure and dispersal among spotted salamander (Ambystoma maculatum) breeding populations. Molecular Ecology 16:257-274.