Neutrality tests of molecular markers and the connection between DNA polymorphism, demography, and conservation biology

Conservation Biology

Volumn 10, Issue 2, 1996, Pages 665-671

  Rand, David M ^a  

^a BROWN UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0000195233     PISSN: 08888892     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1523-1739.1996.10020665.x     Document Type: Article

References (53)

1. Aguadé, M., N. Miyashita, and C. H. Langley. 1989. Reduced variation in the yellow-achete-scute region in natural populations of Drosophila melanogaster. Genetics 122:607-615.
2. Aquadro, C. F., and D. J. Begun, 1993 Evidence for and implications of genetic hitchhiking in the Drosophila genome. Pages 159-178 in N. Takahata and A. G. Clark, editors. Mechanisms of molecular evolution. Japan Scientific Societies Press and Sinauer Associates, Sunderland, Massachusetts.
3. Aquadro, C. F., K. M. Lado, and W. A. Noon. 1988. The rosy region of Drosophila melanogaster and Drosophila simulans. I. Contrasting levels of naturally occurring DNA restriction map variation and divergence. Genetics 119:1165-1190.
4. Avise, J. C. 1992. Molecular population structure and the biogeographic history of a regional fauna: a case history with lessons for conservation biology. Oikos 63:62-76.
5. Avise, J. C. 1994. Molecular markers, natural history and evolution. Chapman and Hall, New York.
6. Avise, J. C. 1995. Mitochondrial DNA polymorphism and a connection between genetics and demography of relevance to conservation. Conservation Biology 9:686-690.
7. Avise, J. C., and R. M. Ball, Jr. 1990. Principles of genealogical concordance in species concepts and biological taxonomy. Oxford Surveys in Evolutionary Biology 7:45-67.
8. Avise, J. C., and W. S. Nelson. 1989. Molecular genetic relationships of the extinct Dusky Seaside Sparrow. Science 243:646-648.
9. Ballard, J. W. O., and M. E. Kreitman. 1994. Unraveling selection in the mitochondrial genome of Drosophila. Genetics 138:757-772.
10. Ballard, J. W. O., and M. E. Kreitman. 1995. Is mitochondrial DNA a strictly neutral marker? Trends in Ecology and Evolution 10:485-488.
11. Begun, D. J., and C. F. Aquadro. 1991. Molecular population genetics of the distal portion of the X chromosome in Drosophila: Evidence for genetic hitchhiking of the yellow-achaete region. Genetics 129: 1147-1158.
12. Begun, D. J., and C. F. Aquadro. 1992. Levels of naturally occurring DNA polymorphism correlate with recombination rates in D. melanogaster. Nature 356:519-520.
13. Begun, D. J., and C. F. Aquadro. 1993. African and North American populations of Drosophila melanogaster are very different at the DNA level. Nature 356:519-520.
14. Berry, A. J., J. W. Ajioka, and M. Kreitman. 1991. Lack of polymorphism on the Drosophila fourth chromosome resulting from selection. Genetics 129:1111-1117.
15. Berry, A. J., and M. Kreitman. 1993. Molecular analysis of an allozyme cline: alcohol dehydrogenase in Drosophila melanogaster on the east coast of North America. Genetics 134:869-893.
16. Braverman, J. M., R. R. Hudson, N. L. Kaplan, C. H. Langley, and W. Stephan. 1995. The hitchhiking effect on the site frequency spectrum of DNA polymorphisms. Genetics 140:783-796.
17. Charlesworth, B., M. T. Morgan, and D. Charlesworth. 1993. The effect of deleterious mutations on neutral molecular variation. Genetics 134:1289-1303.
18. Cronin, M. 1993. Mitochondrial DNA in wildlife taxonomy and conservation biology: cautionary notes. Wildlife Society Bulletin 21:339-348.
19. Degnan, S. M. 1993 The perils of single gene trees - mitochondrial versus single-copy nuclear DNA variation in white-eyes (Aves:Zosteropidae). Molecular Ecology 2:219-225.
20. Fleischer, R. C., C. L. Tarr, and T. K. Pratt. 1994. Genetic structure and mating system in the palila, and endangered Hawaiian honey creeper, as assessed by DNA fingerprinting. Molecular Ecology 3: 383-392.
21. Fu, Y.-X., and W.-H. Li. 1993. Statistical tests of neutrality of mutations. Genetics 133:693-709.
22. Fu, Y.-X. 1994. A phylogenetic estimator of effective population size or mutation rate. Genetics 136:685-692.
23. Gibbs, H. L., K. A. Prior, and P. J. Weatherhead. 1994. Genetic analysis of populations of threatened snake species using RAPD markers. Molecular Ecology 3:329-338.
24. Hudson, R. R., M. Kreitman, and M. Aguadé. 1987. A test of neutral molecular evolution based on nucleotide data. Genetics 116:153-159.
25. Hudson, R. R. 1990. Gene genealogies and the coalescent process. Pages 1-44 in D. Futuyma and J. Antonovics, editors. Oxford surveys in evolutionary biology, volume 7. Oxford University Press, Oxford England.
26. Hudson, R. R, D. D. Boos, and N. L. Kaplan. 1992. A statistical test for detecting geographic subdivision. Molecular Biology and Evolution. 9:138-151.
27. Hudson, R. R, M. Slatkin, and W. P. Maddison. 1992. Estimation of levels of gene flow from DNA sequence data. Genetics 132:583-589.
28. Hughes, A. L., and M. Nei. 1988. Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection. Nature 335:167-170.
29. Karl, S. A., and J. C. Avise. 1992. Balancing selection at allozyme loci in oysters: implications from nuclear RFLPs. Science 256:100-102.
30. Kilpatrick, S. T., and D. M. Rand. 1995. Conditional hitchhiking of mitochondrial DNA: Frequency shifts of Drosophila melanogaster mtDNA haplotypes depend on nuclear genetic back ground. Genetics 141:1113-1124.
31. Kimura, M., 1983. The neutral theory of molecular evolution. Cambridge University Press, Cambridge, United Kingdom.
32. Kreitman, M., and R. R. Hudson. 1991. Inferring the evolutionary histories of the Adh and Adh-dup loci in Drosophila melanogaster from patterns of polymorphism and divergence. Genetics 127:565-582.
33. Kuhner, M. K., J. Yamato, and J. Felsenstein. 1995. Estimating effective population size and mutation rate from sequence data using Metropolis-Hastings sampling. Genetics 140:1421-1430.
34. Lewontin, R. C., and J. Krakauer. 1973. Distribution of gene frequency as a test of the theory of selective neutrality of polymorphism. Genetics 74:175-195.
35. McDonald, J. H. 1994. Detecting natural selection by comparing geographic variation in protein and DNA polymorphisms. Pages 88-100 in B. Golding, editor. Non-neutral evolution: theories and molecular data. Chapman and Hall, New York.
36. Melnick, D. J., and G. A. Hoelzer. 1992. Differences in male and female macaque dispersal lead to contrasting distributions of nuclear and mitochondrial DNA variation. International Journal of Primatology 13:379-393.
37. Milligan, B. G., J. Leebens-Mack, and A. E. Strand. 1994. Conservation genetics: beyond the maintenance of marker diversity. Molecular Ecology 3:423-435.
38. Moritz, C. 1994. Applications of mitochondrial DNA analysis in conservation: a critical review. Molecular Ecology 3:401-411.
39. Nachman, M. W., S. N. Boyer, and C. F. Aquadro. 1994. Non-neutral evolution at the mitochondrial ND3 gene in mice Proceedings of the National Academy of Sciences, USA 91:6364-6368.
40. Nei, M. 1987. Molecular evolutionary genetics. Columbia University Press, New York.
41. Palumbi, S., A. Martin, S. Romano, W. O. McMillan, L. Stice, and G. Grabowski. 1991. The simple fool's guide to PCR. Department of Zoology, Kewalo Marine Laboratory, University of Hawaii, Honolulu.
42. Pamilo, P., and M. Nei. 1988. Relationships between gene trees and species trees. Molecular Biology and Evolution 5:568-583.
43. Pogson, G. H., K. A. Mesa, and R. G. Boutilier. 1995. Genetic population structure and gene flow in the Atlantic cod Gadus morhua: a comparison of allozyme and nuclear RFLP loci. Genetics 139:375-385.
44. Rand, D. M., M. Dorfsman, and L. M. Kann. 1994. Neutral and non-neutral evolution of Drosophila mitochondrial DNA. Genetics 138: 741-756.
45. Ryder, O. A. 1986. Species conservation and systematics: the dilemma of subspecies. Trends in Ecology and Evolution 1:9-10
46. Rojas, M. 1992. The species status and conservation: what are we protecting? Conservation Biology 6:170-178.
47. Sambrook, J., E. F. Fritsch and T. Maniatis. 1989. Molecular cloning: a laboratory manual, second edition. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York.
48. Simon, C., F. Frati, A. Bechenbach, B. Crespi, H. Liu, and P. Flook. 1994. Evolution, weighting, and phylogenetic utility of mitochondrial gene sequences and a compilation of conserved polymerase chain reaction primers. Annals of the Entomological Society of America 87:651-701.
49. Simonsen, K. L., G. C. Churchill, and C. F. Aquadro. 1995. Properties of statistical tests of neutrality for DNA polymorphism data. Genetics 141:413-429.
50. Tajima, F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585-595.
51. Taylor, A. C., W. B. Sherwin, and R. K. Wayne. 1994. Genetic variation of microsatellite loci in a bottlenecked species: the northern hairy-nosed wombat Lasiorhinus kreftii. Molecular Ecology 3:277-290.
52. Utter, F. 1991. Biochemical genetics and fisheries management: an historical perspective. Journal of Fish Biology 39A:1-20.
53. Watterson, G. A. 1975. On the number of segregating sites in genetical models without recombination. Theoretical Population Biology 7: 256-276.