Conservation genetics and demographic history of the endangered Cape Fear shiner (Notropis mekistocholas)

Molecular Ecology

Volumn 13, Issue 10, 2004, Pages 2947-2958

  Saillant, E ^a   Patton, J C ^a   Ross, K E ^a   Gold, J R ^a  

^a TEXAS A AND M UNIVERSITY   (United States)

Author keywords

Cape Fear shiners; Conservation genetics; Demographic history; Effective population size; Microsatellites; mtDNA

Indexed keywords

MICROSATELLITE DNA; MITOCHONDRIAL DNA;

ANIMAL; ARTICLE; BAYES THEOREM; BIOLOGICAL MODEL; COMPARATIVE STUDY; CYPRINIFORMES; DNA SEQUENCE; ENVIRONMENTAL PROTECTION; GENE FREQUENCY; GENETIC VARIABILITY; GENETICS; GEOGRAPHY; HAPLOTYPE; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; POPULATION GENETICS; UNITED STATES;

ANIMALS; BASE SEQUENCE; BAYES THEOREM; CONSERVATION OF NATURAL RESOURCES; CYPRINIDAE; DNA, MITOCHONDRIAL; GENE FREQUENCY; GENETICS, POPULATION; GEOGRAPHY; HAPLOTYPES; MICROSATELLITE REPEATS; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; NORTH CAROLINA; SEQUENCE ANALYSIS, DNA; VARIATION (GENETICS);

CYPRINIDAE; NOTROPIS; NOTROPIS MEKISTOCHOLAS; TRANSPOSONS; VERTEBRATA;

EID: 4644341840     PISSN: 09621083     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2004.02303.x     Document Type: Article

References (65)

1. Akst EP, Boersma PD, Fleischer RC (2002) A comparison of genetic diversity between the Galápagos penguin and the Magellanic penguin. Conservation Genetics, 3, 375-383.
2. Avise JC, Arnold J, Ball RM et al. (1987) Intraspecific phylogeography: the mitochondrial DNA bridge between population genetics and systematics. Annual Review of Ecology and Systematics, 18, 389-522.
3. Beaumont MA (1999) Detecting population expansion and decline using microsatellites. Genetics, 153, 2013-2029.
4. Bermingham E, McCafferty SS, Martin AP (1997) Fish biogeography and molecular clocks: perspectives from the Panamanian Isthmus. In: Molecular Systematics of Fishes (eds Kocher TD, Stepien CA), pp. 113-128. Academic Press, San Diego, CA.
5. Burridge CP, Gold JR (2003) Conservation genetic studies of the endangered Cape Fear shiner, Notroips mekistocholas (Teleostei: Cyprinidae). Conservation Genetics, 4, 219-225.
6. Caro TM, Laurenson MK (1994) Ecological and genetic factors in conservation: a cautionary tale. Science, 263, 485-486.
7. Cloutman DG, Harrell RD (1987) Life-history notes on the white-fin shiner, Notropis niveus (Pisces, Cyprinidae). Copeia, 1987, 1037-1040.
8. DeWoody JA, Avise JC (2000) Microsatellite variation in marine, freshwater and anadromous fishes compared with other animals. Journal of Fish Biology, 56, 461-473.
9. Doiron S, Bernatchez L, Blier PU (2002) A comparative mitogenomic analysis of the potential adaptative value of Arctic charr mtDNA introgression in brook charr populations (Salvelinus fontinalis Mitchill). Molecular Biology and Evolution, 19, 1902-1909.
10. Farris JS, Källersjö M, Kluge AG, Bult C (1995a) Testing for significance of incongruence. Cladistics, 10, 315-319.
11. Farris JS, Källersjö M, Kluge AG, Bult C (1995b) Constructing a significance test for incongruence. Systematic Biology, 44, 570-572.
12. Federal Register (1987) Federal Register, 52, no. 186. September 25. Office of the Federal Register, Washington DC.
13. Frankham R (1995) Inbreeding and extinction: a threshold effect. Conservation Biology, 9, 792-799.
14. Frankham R, Ballou JD, Broscoe DA (2002) Introduction to Conservation Genetics. Cambridge University Press, Cambridge, UK.
15. Franklin IR (1980) Evolutionary change in small populations. In: Conservation Biology: an Evolutionary-Ecological Perspective (eds Soulé M, Wilcox B), Chapter 8, pp. 135-149. Sinauer, Sunderland, MA.
16. Fu Y-X (1997) Statistical tests of neutrality of mutations against population growth, hitchhiking, and background selection. Genetics, 147, 915-925.
17. Fu Y-X, Li W-H (1993) Statistical tests of neutral mutations. Genetics, 133, 693-709.
18. Garza JC, Williamson EG (2001) Detection of reduction in population size using data from microsatellite loci. Molecular Ecology, 10, 305-318.
19. Gold JR, Saillant E, Burridge CP, Blanchard A, Patton JC (2004) Population structure and effective size reduction in critically endangered Cape Fear shiners Notropis mekistocholas. Southeastern Naturalist, 3, 89-102.
20. Goudet J (1995) F-STAT version 1.2: a computer program to calculate F-statistics. Journal of Heredity, 86, 485-486.
21. Guo S, Thompson E (1992) Performing the exact test of Hardy-Weinberg proportion from multiple alleles. Biometrics, 48, 361-372.
22. Harrell RD, Cloutman DG (1978) Distribution and life history of sandbar shiner, Notropis scepticus (Pisces, Cyprinidae). Copeia, 1978, 443-447.
23. Hasegawa M, Kishino H, Yano T (1985) Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. Journal of Molecular Evolution, 21, 160-174.
24. Hauser L, Adcock GJ, Smith PJ, Ramirez JHB, Carvalho GR (2002) Loss of microsatellite diversity and low effective population size in an overexploited population of New Zealand snapper (Pagrus auratus). Proceedings of the National Academy of Sciences USA, 99, 11742-11747.
25. Heath DD, Buch C, Kelly J, Atagi DY (2002) Temporal change in genetic structure and effective population size in steelhead trout (Oncorhynchis mykiss). Molecular Ecology, 11, 197-214.
26. Hedrick PW (1999) Genetics of Populations, 2nd edn. Jones and Bartlett, Sudbury, MA.
27. Hilton-Taylor C (2000) 2000 IUCN Red List of Threatened Species. IUCN, Cambridge, UK.
28. Howard AK (2003) Influence of instream physical habitat and water quality on the survival and occurrence of the endangered Cape Fear shiner. PhD Dissertation, North Carolina State University, Raleigh, NC.
29. Kimura M (1980) A simple method for estimating evolutionary rate of base substitution through comparative studies of nucleotide sequences. Journal of Molecular Evolution, 11, 424-429.
30. Koskinen M, Knizhin I, Primmer CP, Schlötterer C, Weiss S (2002) Mitochondrial and nuclear DNA phylogeography of Thymallus spp. (grayling) provides evidence of ice-age mediated environmental perturbations in the world's oldest body of fresh water, Lake Baikal. Molecular Ecology, 11, 2599-2611.
31. Kuhner MK, Yamato J, Felsenstein J (1998) Maximum likelihood estimation of population growth rates based on the coalescent. Genetics, 149, 429-434.
32. Lance SL, Maldonado JE, Bocetti CI, Pattee OH, Ballou JD, Fleischer RC (2003) Genetic variation in natural and translocated populations of the endangered Delmarva fox squirrel (Sciurus niger cinerus). Conservation Genetics, 4, 707-718.
33. Lavery S, Moritz C, Fielder DR (1996) Genetic patterns suggest exponential population growth in a declining species. Molecular Biology and Evolution, 13, 1106-1113.
34. Lessios HA, Garrido MJ, Kessing BD (2001) Demographic history of Diadema antiliarum, a keystone herbivore on Caribbean reefs. Proceedings of the Royal Society of London Series B, 268, 2347-2353.
35. Lynch M, Conery J, Bürger R (1995) Mutation meltdown and the extinction of small populations. American Naturalist, 146, 489-518.
36. Lynch M, Lande R (1998) The critical effective size for a genetically secure population. Animal Conservation, 1, 70-72.
37. Matthews MM, Heins DC (1984) Life-history of the redfin shiner, Notropis umbratilis (Pisces, Cyprinidae), in Mississipi. Copeia, 1984, 385-390.
38. Mickevich MF, Farris JS (1981) The implications of congruence in Menidia. Systematic Zoology, 30, 351-370.
39. Moran P (2002) Current conservation genetics building an ecological approach to the synthesis of molecular and quantitative genetic methods. Ecology of Freshwater Fish, 11, 30-55.
40. Nei M (1987) Molecular Evolutionary Genetics. Columbia University Press, New York, NY.
41. North Carolina Division of Water Quality (NCDWQ) (2000) Cape Fear River basinwide water quality management plan. Raleigh, NC, 2000. In: Influence of instream physical habitat and water quality on the survival and occurrence of the endangered Cape Fear shiner (ed. Howard AK), p. 133. PhD Dissertation. North Carolina State University, Raleigh, NC.
42. North Carolina Wildlife Resources Commission (1995) Cape Fear shiner (subsection). Annual Performance Report, Nongame and Endangered Wildlife Program, vol. IV (Biologist, Alderman JM), pp. 18-20. Project no. E-3, Segment no. 12, North Carolina Wildlife Resources Commission, Raleigh, NC.
43. O'Brien SJ, Martenson JS, Miththapala S et al. (1996) Conservation genetics of the Felidae. In: Conservation Genetics: Case History from Nature (eds Avise JC, Hamrick JL), pp. 50-74. Chapman & Hall, New York, NY.
44. Posada D, Crandall KA (1998) MODELTEST: testing the model of DNA substitution. Bioinformatics, 14, 817-818.
45. Pottern GB, Huish MT (1986) Supplement to the Status Survey of the Cape Fear Shiner Notropis mekistocholas. US Fish and Wildlife Service Endangered Species Office, Asheville, NC.
46. Pottern GB, Huish MT (1987) Second Supplement to the Status Survey of the Cape Fear Shiner Notropis mekistocholas. US Fish and Wild-life Service Endangered Species Office, Asheville, NC.
47. Raymond M, Rousset F (1995) GENEPOP version 1.2: a population genetics software for exact tests and eucemenicism. Journal of Heredity, 86, 248-249.
48. Rice WR (1989) Analyzing tables of statistical tests. Evolution, 43, 223-225.
49. Rogers A (1996) Population structure and modern human origins. In: Progress in Population Genetics and Human Evolution (eds Donnelly P, Tavare S), pp. 55-79. Springer-Verlag, New York, NY.
50. Rogers A, Harpending H (1992) Population growth makes waves in the distribution of pairwise genetic differences. Molecular Biology and Evolution, 9, 552-559.
51. Rozas J, Sánchez-Delbarrio JC, Messeguer X, Rozas R (2003) DNASP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics, 19, 2496-2497.
52. Schneider S, Excoffier L (1999) Estimation of demographic parameters from the distribution of pairwise differences when the mutation rates vary among sites: application to human mitochondrial DNA. Genetics, 152, 1079-1089.
53. Schneider S, Roessli D, Excoffier L (2000) ARLEQUIN Version 2000: a Software for Population Genetic Data Analysis. Genetics and Biometry Laboratory, University of Geneva, Switzerland.
54. Schultz ST, Lynch M (1997) Mutation and extinction: the role of variable mutational effects, synergistic epistasis, beneficial mutations, and degree of outcrossing. Evolution, 51, 1363-1371.
55. Sinclair EA, Costello B, Courtenay JM, Crandall KA (2002) Detecting a genetic bottleneck in Gilbert's potoroo (Potprous gilberti) (Marsulialia: Potoroidae), inferred from microsatellite and mitochondrial DNA sequence data. Conservation Genetics, 3, 191-196.
56. Snelson FF (1971) Notropis mekistocholas, a new herbivorous cyprinid fish endemic to the Cape Fear river basin, North Carolina. Copeia, 1971, 449-462.
57. Storz JF, Beaumont MA (2002) Testing for genetic evidence of population expansion and contraction: an empirical analysis of microsatellite DNA variation using a hierarchical Bayesian model. Evolution, 56, 156-166.
58. Swofford DL (1998) PAUP*: Phylogenetic Analysis Using Parsimony (*and other methods), version 4, 4.0b4a edn. Sinauer Associates, Sunderland MA.
59. Templeton AR, Crandall KA, Sing CF (1992) A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation. Genetics, 132, 619-633.
60. US Fish and Wildlife Service (1988) Cape Fear shiner recovery plan. US Fish and Wildlife Service, Atlanta, GA.
61. Vrijenhoek RC (1998) Conservation genetics of freshwater fish. Journal of Fish Biology, 53, 394-412.
62. Waldick RC, Kraus S, Brown M, White BN (2002) Evaluating the effects of historic bottlenecks: an assessment of microsatellite variability in the endangered, North Atlantic right whale. Molecular Ecology, 11, 2241-2249.
63. Warren ML, Burr BM, Walsh SJ et al. (2000) Diversity, distribution, and conservation status of the native freshwater fishes of the southern United States. Fisheries, 25, 7-31.
64. Watterson G (1975) On the number of segregating sites in genetical models without recombination. Theoretical Population Biology, 7, 256-276.
65. Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution, 38, 1358-1370.