Genetic effects of habitat fragmentation and population isolation on Etheostoma raneyi (Percidae)

Conservation Genetics

Volumn 13, Issue 3, 2012, Pages 859-872

  Sterling, Ken A ^a,d   Reed, David H ^b   Noonan, Brice P ^a   Warren Jr , Melvin L ^c  

^a UNIVERSITY OF MISSISSIPPI   (United States)

^b UNIVERSITY OF LOUISVILLE   (United States)

^c CENTER FOR BOTTOMLAND HARDWOODS RESEARCH   (United States)

^d UTAH STATE UNIVERSITY   (United States)

Author keywords

Barrier; Etheostoma; Excess heterozygosity; Genetic structure; Habitat fragmentation; Population isolation

Indexed keywords

ANTHROPOGENIC EFFECT; FLOOD CONTROL; GENE FLOW; GENETIC MARKER; HABITAT FRAGMENTATION; HABITAT MANAGEMENT; HUMAN SETTLEMENT; PERCIFORM; POPULATION STRUCTURE; RIVER DISCHARGE;

MISSISSIPPI; UNITED STATES;

ETHEOSTOMA; ETHEOSTOMA RANEYI; PERCIDAE;

EID: 84860474646     PISSN: 15660621     EISSN: 15729737     Source Type: Journal    
DOI: 10.1007/s10592-012-0335-0     Document Type: Article

References (65)

1. Adams SB, Warren ML Jr, Haag WR (2004) Spatial and temporal patterns of fish assemblages of upper coastal plain streams, Mississippi, USA. Hydrobiology 528: 45-61.
2. Beerli P (2010) MIGRATE version 3. 2: a maximum likelihood and Bayesian estimator of gene flow using the coalescent. http://popgen. scs. edu/migrate. html. Accessed 5 December 2010.
3. Beerli P, Felsenstein J (1999) Maximum likelihood estimation of migration rates and population numbers of two populations using a coalescent approach. Genetics 152: 763-773.
4. Beneteau CL, Mandrak NE, Heath DD (2007) Characterization of eight polymorphic microsatellite DNA markers for the greenside darter, Etheostoma blennioides (Percidae). Mol Ecol Notes 7: 641-643.
5. Beneteau CL, Mandrak NE, Heath DD (2009) The effects of river barriers and range expansion of the population genetic structure and stability in greenside darter (Etheostoma blennioides) populations. Conserv Genet 10: 477-487.
6. Benjamini Y, Yekutieli D (2001) The control of false discovery rate under dependency. Ann Stat 29: 1165-1188.
7. Bensch S, Andren H, Hansson B, Pedersen HC, Sand H, Sejberg D, Wabakken P, Akesson M, Liberg O (2006) Selection for heterozygosity gives hope to a wild population of inbred wolves. PLoS ONE. doi: 10. 1371/journal. pone. 0000072.
8. Bohonak AJ (2002) IBD (isolation by distance): a program for analyses of isolation by distance. J Hered 93: 153-154.
9. Chapman SS, Griffith GE, Omernik JM, Comstock JA, Beiser MC, Johnson D (2004) Ecoregions of Mississippi, (color poster with map, descriptive text, summary tables, and photographs): Reston, Virginia, U. S. Geological Survey (map scale 1: 1, 000, 000). http://www. epa. gov/wed/pages/ecoregions/ms_eco. htm. Accessed 20 February 2011.
10. Chiucchi JE, Gibbs HL (2010) Similarity of contemporary and historical gene flow among highly fragmented populations of and endangered rattlesnake. Mol Ecol 19: 5345-5358.
11. Cooper CM, Knight SS (1991) Water quality cycles in two hill land streams subjected to natural, municipal, and non-point agricultural stresses in the Yazoo Basin of Mississippi, USA (1985-1987). Organ Int Ver Theor Angew Limnol 24: 1654-1663.
12. Edberg KL (2009) The effects of a reservoir on genetic isolation in two species of darters. Thesis, Western Kentucky University.
13. Estes-Zumpf WA, Rachlow JL, Waits LP, Warheit KI (2010) Dispersal, gene flow, and population genetic structure in the pygmy rabbit (Brachylagus idahoensis). J Mammal 91: 208-219.
14. Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14: 2611-2620.
15. Excoffier L, Smouse PE, Quattro JM (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131: 479-491.
16. Excoffier L, Laval G, Schneider S (2005) Arlequin ver. 3. 0: an integrated software package for population genetic analysis. Evol Bioinform Online 1: 47-50.
17. Falush D, Stephens M, Pritchard JK (2003) Inference of population structure: extensions to linked loci and correlated allele frequencies. Genetics 164: 1567-1587.
18. Fluker BL, Kuhajda BR, Lang NJ, Harris PM (2010) Low genetic diversity and small long-term population sizes in the spring endemic watercress darter, Etheostoma nuchale. Conserv Genet 11: 2267-2279.
19. Gabel JM, Dakin EE, Freeman BJ, Porter BA (2008) Isolation and identification of eight microsatellite loci in the Cherokee darter (Etheostoma scotti) and their variability in other members of the genera Etheostoma, Ammocrypta, and Percina. Mol Ecol Res 8: 149-151.
20. George AL, Caldieraro JB, Chartrand KM, Mayden RL (2008) Population genetics of the blue shiner, Cyprinella caerulea. Southeast Nat 7: 637-650.
21. Goudet J (2001) FSTAT version 2. 9. 3, a program to estimate and test gene diversities and fixation indices. http//: unil. ch/izea/softwares/fstat. html. Accessed 5 December 2010.
22. Guillot G, Santos F (2009) A computer program to simulate multilocus genotype data with spatially auto-correlated allele frequencies. Mol Ecol Res 9: 1112-1120.
23. Guillot G, Estoup A, Mortier F, Cosson J-F (2005) A spatial model for landscape genetics. Genetics 170: 1261-1280.
24. Hallerman E, Brown B, Epifanio J (2003) An overview of classical and molecular genetics. In: Hallerman EM (ed) Population genetics: principles and applications for fisheries scientists. American Fisheries Society, Bethesda, pp 3-20.
25. Haponski AE, Bollin TL, Jedlicka MA, Stepien CA (2009) Landscape genetic patterns of the rainbow darter Etheostoma caeruleum: a catchment analysis of mitochondrial DNA sequences and nuclear microsatellites. J Fish Biol 75: 2244-2268.
26. Hubisz M, Falush D, Stephens M, Pritchard JK (2009) Inferring weak population structure with the assistance of sample group information. Mol Ecol Res 9: 1322-1332.
27. Hudman SP, Grose MJ, Landis JB, Skalski GT, Wiley EO (2008) Twenty-three microsatellite DNA loci for population genetic studies and parentage assignment in orangethroat darter, Etheostoma spectabile. Mol Ecol Res 8: 1483-1485.
28. Jelks HL, Walsh SJ, Burkhead NM, Contreras-Balderas S, Diaz-Pardo E, Hendrickson DA, Lyons J, Mandrak NE, McCormick F, Nelson JS, Plantania SP, Porter BA, Renaud CB, Schmitter-Soto JJ, Taylor EB, Warren ML Jr (2008) Conservation status of imperiled North American freshwater and diadromous fishes. Fisheries 33: 372-407.
29. Jensen JL, Bohonak AJ, Kelley ST (2005) Isolation by distance, web service. BMC Genet 6: 13. Version 3. 16. http://ibdws. sdsu. edu/. Accessed 1 March 2011.
30. Johnson RL (2007) Geneflow and genetic structuring of yellow cheek darters (Etheostoma moorei) in the little Red River watershed. Final report submitted to the Arkansas Game and Fish Commission, Little Rock, AR.
31. Johnston CE, Haag WR (1996) Life history of the Yazoo darter (Percidae: Etheostoma raneyi), a species endemic to north-central Mississippi. Tulane Stud Zool Bot 30: 47-60.
32. Khudamrongsawat J, Heath LS, Heath HE, Harris PM (2007) Microsatellite DNA primers for the endangered vermilion darter, Etheostoma chermocki, and cross-species amplification in other darters (Percidae: Etheostoma). Mol Ecol Notes 7: 811-813.
33. Kuhajda BR, George AL, Williams JD (eds) (2008) The desperate dozen: southeastern freshwater fishes on the brink. Southeast Fish Counc Proc 51: 10-30.
34. Lamphere BA, Blum MJ (2012) Genetic estimates of population structure and dispersal in a benthic stream fish. Ecol Fresh Fish 21: 75-86.
35. Mantel N (1967) The detection of disease clustering and a generalized regression approach. Cancer Res 27: 209-220.
36. Narum S (2006) Beyond Bonferroni: less conservative analyses for conservation genetics. Conserv Genet 7: 783-787.
37. NatureServe (2011) http://www. natureserve. org/explorer/servlet/NatureServe?sourceTemplate=tabular_report. wmt&loadTemplate=species_RptComprehensive. wmt&selectedReport=RptComprehensive. wmt&summaryView=tabular_report. wmt&elKey=100184&paging=home&save=true&startIndex=1&nextStartIndex=1&reset=false&offPageSelectedElKey=100184&offPageSelectedElType=species&offPageYesNo=true&post_processes=&radiobutton=radiobutton&selectedIndexes=100184. Accessed 19 February 2011.
38. Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New York.
39. Powers SL, Warren ML Jr (2009) Phylogeography of three snubnose darters (Percidae: Subgenus Ulocentra) endemic to the southeastern U. S. Coastal Plain. Copeia 2009: 523-528.
40. Powers SL, Mayden RL, Etnier DA (2004) Conservation genetics of the ashy darter, Etheostoma cinereum (Percidae: subgenus Allohistium), in the Cumberland and Tennessee Rivers of the southeastern United States. Copeia 2004: 632-637.
41. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945-959.
42. Pudovkin AI, Zaykin DV, Hedgecock D (1996) On the potential for estimating the effective number of breeders from heterozygosity excess in progeny. Genetics 144: 383-387.
43. Rasmussen DI (1979) Sibling clusters and genotypic frequencies. Am Nat 113: 948-951.
44. Raymond M, Rousset F (1995) GENEPOP (version 1. 2): population genetics software for exact tests and ecumenicism. J Hered 86: 248-249.
45. Reed DH (2007) Natural selection and genetic diversity. Heredity 99: 1-2.
46. Reed DH (2008) Effects of population size on population viability: from mutation to environmental catastrophes. In: Carroll SP, Fox CW (eds) Conservation biology. Oxford University Press, New York, pp 16-34.
47. Reed DH, Teoh VH, Stratton GE, Hataway JA (2011) Levels of gene flow among populations of a wolf spider in a fragmented habitat: current versus historical rates. Conserv Genet 12: 331-335.
48. Rousset F (2008) GENEPOP '007: a complete reimplementation of the Genepop software for Windows and Linux. Mol Ecol Res 8: 103-106.
49. Shields FD, Knight SS, Cooper CM (1994) Effects of channel incision on base flow stream habitats and fishes. Environ Manag 18: 43-57.
50. Shields FD, Knight SS, Cooper CM (1998) Rehabilitation of aquatic habitats in warmwater streams damaged by channel incision in Mississippi. Hydrobiology 382: 63-86.
51. Simon A, Darby SE (1997) Disturbance, channel evolution and erosion rates: Hotophia Creek, Mississippi. In: Wang SSY, Langendoen EJ, Shields FD Jr (eds) Management of landscapes disturbed by channel incision: stabilization, rehabilitation, restoration. University of Mississippi Press, Oxford, pp 476-481.
52. Skalski GT, Landis JB, Grose MJ, Hudman SP (2008) Genetic structure of creek chub, a headwater minnow, in an impounded river system. Trans Am Fish Soc 137: 962-975.
53. Spiegelhalter DJ (2002) Bayesian measures of model complexity and fit. J R Stat Soc Ser B (Methodol) 64: 583-639.
54. Sterling K, Warren ML Jr, Noonan BP, Reed DH, Henderson LG (2011) Yazoo darter, Etheostoma raneyi: population and demographic status, distributional changes, and habitat use of an endemic, nongame species. Final report submitted to the Mississippi Museum of Natural Science, Jackson MS.
55. Storz JF (1999) Genetic consequences of mammalian social structure. J Mammal 80: 553-569.
56. Storz JF, Bhat HR, Kunz TH (2001) Genetic consequences of polygyny and social structure in an Indian fruit bat, Cynopterus sphinx. I. Inbreeding, outbreeding, and population subdivision. Evolution 55: 1215-1223.
57. Suttkus RD, Bailey RM, Bart HL Jr (1994) Three new species of Etheostoma, subgenus Ulocentra, from the Gulf Coastal Plain of southeastern United States. Tulane Stud Zool Bot 29: 97-126.
58. Switzer JF, Welsh SA, King TL (2008) Microsatellite DNA primers for the candy darter, Etheostoma osburni, and variegate darter, Etheostomavariatum, and cross-species amplification in other darters (Percidae). Mol Ecol Res 8: 335-338.
59. Taggart JB, Haynes RA, Prodohl PA, Ferguson A (1992) A simplified protocol for routine total DNA isolation from salmonid fishes. J Fish Biol 40: 963-965.
60. Thompson KW, Muncy RJ (1986) Darters of the Little Tallahatchie watershed in northern Mississippi. J Miss Acad Sci 31: 63-77.
61. Tonnis BD (2006) Microsatellite DNA markers for the rainbow darter, Etheostoma caeruleum (Percidae), and their potential utility for other darter species. Mol Ecol Notes 6: 230-232.
62. Turner TF, Robison HW (2006) Genetic diversity of the Caddo madtom, Noturus taylori, with comments on factors that promote genetic divergence in fishes endemic to the Ouachita highlands. Southwest Nat 51: 338-345.
63. Turner TF, Trexler JC (1998) Ecological and historical associations of gene flow in darters (Teleostei: Percidae). Evolution 52: 1781-1801.
64. Warren ML Jr, Burr BM, Walsh SJ, Bart HL Jr, Cashner RC, Etnier DA, Freeman BJ, Kuhajda BR, Mayden RL, Robison HW, Ross ST, Starnes WC (2000) Diversity, distribution, and conservation status of the native freshwater fishes of the southern United States. Fisheries 25: 7-29.
65. Wilson GA, Rannala B (2003) Bayesian inference of recent migration rates using multilocus genotypes. Genetics 163: 1177-1191.