Analysis of genetic diversity in geographically structured populations: A Bayesian perspective

Hereditas

Volumn 130, Issue 3, 1999, Pages 245-255

  Holsinger, Kent E ^a  

^a UNIVERSITY OF CONNECTICUT   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALLELE; ARTICLE; BAYES THEOREM; GENE LOCUS; GENETIC VARIABILITY; NONHUMAN; POPULATION GENETICS;

ARGANIA SPINOSA;

EID: 0032832829     PISSN: 00180661     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1601-5223.1999.00245.x     Document Type: Article

References (53)

1. Allendorf FW and Waples RS. (1996). Conservation and genetics of salmonid fishes. In Conservation Genetics: Case Histories from Nature (eds JC Avise and JL Hamrick), NY: Chapman & Hall, p. 238-280. New York.
2. Balding DJ and Nichols RA, (1995). A method for quantifying differentiation between populations at multi-allelic loci and its implications for investigating identity and paternity. Genetica 96: (1-2), 3-12.
3. Barton NH, Halliday RB and Hewitt GB, (1983). Rare electrophoretic variants in a hybrid zone. Heredity 50: 139-146.
4. Charlesworth B, (1998). Measures of divergence between populations and the effect of forces that reduce variability. Mol. Biol. Evol. 15: 538-543.
5. Cockerham CC, (1969). Variance of gene frequencies. Evolution 23: 72-84.
6. Cockerham CC and Weir BS, (1993). Estimation of gene flow from F-statistics. Evolution 47: 855-863.
7. Crow JF and Kimura M, (1970). An Introduction to Population Genetics Theory. Burgess Publishing Company, Minneapolis, Minn.
8. Edwards AWF, (1972). Likelihood. Cambridge Univ. Press, Cambridge.
9. Efron B and Tibshirani RJ, (1993). An introduction to the Bootstrap, Volume 57 of Monographs on Statistics and Applied Probability. NY: Chapman & Hall, New York.
10. Ewens WJ, (1979). Mathematical Population Genetics. Springer-Verlag, Berlin.
11. Falconer DS and Mackay TFC, (1996). Introduction to Quantitative Genetics (4th ed.). Longman. Essex.
12. Gelfand AE and Ghosh SK, (1998). Model choice: a minimum posterior predictive loss approach. Biometrika 85: 1-11.
13. Gelfand AE and Smith AFM, (1990). Sampling-based approaches to calculating marginal densities. J. Am. Statist. Ass. 85: 398-409.
14. Gilks WR. Thomas A and Spiegelhalter DJ, (1994). A language and program for complex Bayesian modeling. The Statistican 43: 169-178.
15. Goldstein J, (1995). Multilevel Statistical Models. Kendall's Library of Statistics. Edward Arnold, London.
16. Govindjaru DR, (1989). Estimates of gene flow in forest trees. Biol. J. Linn. Soc. 37: 345-357.
17. Hamrick JL, (1987). Gene flow and distribution of genetic variation in plant populations. In Differentiation Patterns in Higher Plants, (ed K Urbanska) p. 53-67. Academic Press, New York.
18. Hamrick JL and Godt MJW, (1990). Allozyme diversity in plant species. In Plant Population Genetics Breeding, and Genetic Resources (eds AHD Brown, MT Clegg, AT Kahler and BS Weir), Sinauer Associates, Sunderland, MA p. 43-63
19. Hamrick JL and Godt MJW, (1996). Conservation genetics of endemic plant species. In Conservation Genetics: Case Histories from Nature, (eds JC Avise and JL Hamrick) Chapman & Hall, New York, NY, p. 281-304.
20. Hamrick JL, Linhart YB and Mitton JB, (1979). Relationships between life history characteristics and electrophoretically deterctable genetic variation in plants. Ann. Rev. Ecol. Syst. 10: 173-200.
21. Holsinger KE and Mason-Gamer RJ, (1996). Hierarchical analysis of nucleotide diversity in goegraphically structured populations. Genetics 142: 629-639.
22. Holsinger KE and Vitt P, (1997). The future of conservation biology: what's a geneticist to do? In Enhancing the Ecological Basis of Conservation: Heterogeneity, Ecosystem Function, and Biodiversity, (eds SA Pickett, R Ostfeld, M Shachak and G Likens), Chapman & Hall, New York, NY.
23. Kuhner MK, Yamato J and Felsenstein J, (1995). Estimating effective population size and mutation rate from sequence data using Metropolis-Hastings sampling. Genetics 140: 1421-1430.
24. Kuhner MK, Yamato J and Felsenstein J, (1998). Maximum likelihood estimation of population growth rates based on the coalescent. Genetics 149: 429-434.
25. Lange K, (1995). Applications of the dirichlet distribution to forensic match probabilities. Genetica 96: 107-117.
26. Lee PM, (1989). Bayesian Statistics: An Introduction. Edward Arnold, London.
27. Lee PO and Whitkus R, (1989). GENESTAT for microcomputers. Am. Soc. Plant Taxon. Newsl. 2: 15-16.
28. Lewis PO and Zaykin D, (1999). Genetic Data Analysis: computer program for the analysis of allelic data. Version 1.0 (d12). Available from http:// alleyn.eeb.uconn.edu/gda/.
29. Lynch M and Crease TJ, (1990). The analysis of population survey data on DNA sequence variation. Mol. Biol. Evol. 7: 377-394.
30. Lynch M and Walsh B, (1998). Genetics and Analysis of Quantitative Traits. Sinauer Associates, Sunderland, MA.
31. Millar CI and Libby WJ, (1991). Strategies for conserving clinal, ecotypic and disjunct population diversity in widespread species. In Genetics and Conservation of Rare Plants (eds DA Falk and KE Holsinger), Oxford University Press, New York, p. 149-170.
32. Nei M, (1973). Analysis of gene diversity in subdivided populations. Proc. Natl. Acad. Sci. USA 70: 3321-3321.
33. Nei M and Chester RK, (1983). Estimation of fixation indices and gene diversities. Ann. Human Genetics 47: 253-259.
34. Nevo E, Beiles A and Ben-Shlomo R, (1984). The evolutionary significance of genetic diversity: ecological, demographic, and life history correlates. In Evolutionary Dynamics of Genetic Diversity (ed G S Mani), Springer-Verlag, Berlin, p. 13-213.
35. Nunney L, (1999). The effective size of a hierarchically structured population. Evolution 53: 1-10.
36. O'Hagan A, (1994). Kendall's Advanced Theory of Statistics, Volume 2B. Bayesian Inference. Edward Arnold, London.
37. Petit RJ, El Mousadik A and Pons O, (1998). Identifying populations for conservation on the basis of gentic markers. Conserv. Biol. 12: 844-855.
38. Rannala B and Hartigan JA, (1995). Identity by descent in island-mainland populations. Genetics 139: 429-437.
39. Riggs LA, (1990). Conserving genetic resources on-site in forest ecosystems. Forest Ecol. and Manag. 35: 45-68.
40. Roeder K, Escobar M, Kadane JB and Balazs, I (1998). Measuring heterogeneity in forensic databases using hierarchical Bayes models. Biometrika 85: 269-287.
41. Schoen DJ and Brown AHD, (1993). Conservation of allelic richness in wild crop relatives is aided by assessment of genetic markers. Proc. Natl. Aca. Sci. USA 90: 10623-10627.
42. Searle SR, Casella G and McCulloch CE, (1992). Variance Components. John Wiley & Sons, Inc., New York, NY.
43. Slatkin M, (1991). Inbreeding coefficients and coalescence times. Genet. Res. 58: 167-175.
44. Slatkin M and Barton NH, (1989). A comparison of three indirect methods for estimation average levels of gene flow. Evolution 43: 1349-1368.
45. Wehrhahn CF and Powell R, (1987). Electrophoretic variation, regional differences, and gene flow in the coho salmon (Onchorhyncus kisutch) of southern British Columbia. Can. J. Fish. Aquat. Sci. 44: 822-831.
46. Wehrhahn CR, (1989). Proceedings of the ecological genetics workshop. Genome 31: 1098-1099.
47. Weir BS, (1996). Genetic Data Analysis II: Methods for Discrete Population Genetic Data. Sinauer Associates, Sunderland, MA.
48. Weir BS and Cockerham CC , (1984). Estimating F-statistics for the analysis of population structure. Evolution 38: 1358-1370.
49. Whtlock MC and Barton NH, (1997). The effective size of a subdivided population. Genetics 146: 427-441.
50. Wright S, (1931). Evolution in Mendelian populations. Genetics 16: 97-159.
51. Wright S, (1951). The genetical structure of populations. Ann. Eugenics 15: 323-354.
52. Wright S, (1965). The interpretation of population structure by F-statistics with special regard to systems of mating. Evolution 19: 395-420.
53. Wright S, (1969). Evolution and the Genetics of Populations, Volume 2. The Theory of Gene Frequencies. University of Chicago Press, Chicago, IL.