Population structure and conservation genetic assessment of the endangered Pugnose Shiner, Notropis anogenus (original) (raw)
Abell R (2002) Conservation biology for the biodiversity crisis: a freshwater follow-up. Conserv Biol 16:1435–1437 Article Google Scholar
Austin JD, Jelks HL, Tate B, Johnson AR, Jordan F (2011) Population genetic structure and conservation genetics of threatened Okaloosa darters (Etheostoma okaloosae). Conserv Genet 12:981–989 Article Google Scholar
Bailey RM (1959) Distribution of the American cyprinid fish Notropis anogenus. Copeia 1959:119–123 Article Google Scholar
Becker GC (1983) Fishes of Wisconsin. University of Wisconsin Press, Madison Google Scholar
Beneteau CL, Walter RP, Mandrak NE, Heath DD (2012) Range expansion by invasion: genetic characterization of invasion of the greenside darter (Etheostoma blennioides) at the northern edge of its distribution. Biol Invasions 14:191–201 Article Google Scholar
Bernard AM, Ferguson MM, Noakes DLG, Morrison BJ, Wilson CC (2009) How different is different? Defining management and conservation units for a problematic exploited species. Can J Fish Aquat Sci 66:1617–1630 Article Google Scholar
Bonin A, Bellemain E, Bronken Eidesen P, Pompanon C, Brochmann C, Taberlet P (2004) How to track and assess genotyping errors in population genetic studies. Mol Ecol 13:3261–3273 ArticleCASPubMed Google Scholar
Broquet T, Angelone S, Jaquiery J, Joly P, Lena J-P, Lengagne T, Plenet S, Luquet E (2010) Genetic bottlenecks driven by population disconnection. Conserv Biol 24:1596–1605 ArticlePubMed Google Scholar
Burridge CP, Gold JR (2003) Conservation genetic studies of the endangered Cape Fear shiner, Notropis mekistocholas (Teleostei: cyprinidae). Conserv Genet 4:219–225 ArticleCAS Google Scholar
Cavalli-Sforza LL, Edwards AWF (1967) Phylogenetic analysis: models and estimation procedures. Evolution 21:550–570 Article Google Scholar
Chapuis M-P, Estoup A (2007) Microsatellite null alleles and estimation of population differentiation. Mol Biol Evol 24:621–631 ArticleCASPubMed Google Scholar
Chikhi L, Sousa VC, Luisi P, Goossens B, Beaumont MA (2010) The confounding effects of population structure, genetic diversity and the sampling scheme on the detection and quantification of population size changes. Genetics 186:983–995 ArticlePubMed CentralPubMed Google Scholar
Cornuet J-M, Luikart G (1996) Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. Genetics 144:2001–2014 CASPubMed CentralPubMed Google Scholar
COSEWIC (2013) COSEWIC assessment and update status report on the Pugnose Shiner Notropis anogenus in Canada. In: Committee on the Status of Endangered Wildlife in Canada.Ottawa
de Guia APO, Saitoh T (2007) The gap between the concept and definitions in the Evolutionarily Significant Unit: the need to integrate neutral genetic variation and adaptive variation. Ecol Res 22:604–612 Article Google Scholar
DeHaan PW, Scheerer PD, Rhew R, Ardren WR (2012) Analyses of genetic variation in populations of Oregon Chub, a threatened floodplain minnow in a highly altered environment. Trans Am Fish Soc 141:533–549 Article Google Scholar
DFO (2010) Recovery Potential Assessment of Pugnose Shiner (Notropis anogenus) in Canada. DFO Canadian Science Advisory Secretariat Science Advisory Report 2010/025
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 ArticleCASPubMed Google Scholar
Excoffier L, Lischer H (2010) Arlequin suite ver 35: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Res 10:564–567 Article Google Scholar
Faurby S, Pertoldi C (2012) The consequences of the unlikely but critical assumption of stepwise mutation in the population genetic software, MSVAR. Evol Ecol Res 14:859–879 Google Scholar
Favé M-J, Turgeon J (2008) Patterns of genetic diversity in great lakes bloaters (Coregonus hoyi) with a view to future reintroduction in Lake Ontario. Conserv Genet 9:281–293 Article Google Scholar
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 Article Google Scholar
Frankham R (2005) Genetics and Extinction. Biol Conserv 126:131–140 Article Google Scholar
Frankham R, Ballou JD, Briscoe DA (2002) Introduction to Conservation Genetics. Cambridge University Press, Cambridge Book Google Scholar
Franklin I (1980) Evolutionary changes in small populations. In: Soule ME, Wilcox BA (eds) Conservation biology: an evolutionary-ecological perspective. Sinauer Associates, Sunderland, pp 135–140 Google Scholar
Franklin IR, Frankham R (1998) How large must populations be to retain evolutionary potential? Anim Conserv 1:69–73 Article Google Scholar
Garza JC, Williamson EG (2001) Detection of reduction in population size using data from microsatellite loci. Mol Ecol 10:305–318 ArticleCASPubMed Google Scholar
Girod C, Vitalis R, Leblois R, Freville H (2011) Inferring population decline and expansion from microsatellite data: a simulation-based evaluation of the Msvar method. Genetics 188:165–179 ArticlePubMed CentralPubMed Google Scholar
Gold JR, Saillant E, Burridge CP, Blanchard A, Patton JC (2004) Population structure and effective size in critically endangered Cape Fear shiners Notropis mekistocholas. Southeast Nat 3:89–102 Article Google Scholar
Goudet J (1995) FSTAT (Version 12): a computer program to calculate F-statistics. J Hered 86:485–486 Google Scholar
Green DM (2005) Designatable units for status assessment of endangered species. Conserv Biol 19:1813–1820 Article Google Scholar
Holm E, Mandrak NE (2002) COSEWIC status report on the pugnose shiner Notropis anogenus in Canada: In Committee on the status of endangered wildlife in Canada, pp 1-15
Hubisz MJ, Falush D, Stephens M, Pritchard JK (2009) Inferring weak population structure with the assistance of sample group information. Mol Ecol Res 9:1322–1332 Article Google Scholar
Ingvarsson PK (2001) Restoration of genetic variation lost- the genetic rescue hypothesis. Trends Ecol Evol 16:62–63 ArticlePubMed Google Scholar
IUCN (2013) IUCN Red List of Threatened Species. Version 2013.1. http://www.iucnredlist.org. Accessed 21 Oct 2013
Jelks HL, Walsh SJ, Burkhead NM, Contreras-Balderas S, Diaz-Pardo E, Hendrickson DA, Lyons J, Mandrak N, McCormick F, Platania SP, Porter BA, Renaud CB, Schmitter-Soto JJ, Taylor EB, Warren MLJ (2008) Conservation status of imperiled North American freshwater and diadromous fishes. Fisheries 33:372–407 Article Google Scholar
McCraney WT, Goldsmith G, Jacobs DK, Kinziger AP (2010) Rampant drift in artificially fragmented populations of the endangered tidewater goby (Eucyclogobius newberryi). Mol Ecol 19:3315–3327 ArticleCASPubMed Google Scholar
Miller MP (1997) Tools for population genetic analyses (TFPGA) v 13 A windows program for the analysis of allozyme and molecular population genetic data. http://www.marksgeneticsoftware.net/. Accessed 12 May 2012
Moritz C (1994) Defining ‘ Evolutionarily Significant Units’ for conservation. TREE 9:373–375 CASPubMed Google Scholar
NatureServe (2013) NatureServe Explorer: an online encyclopedia of life [web application]. Version 7.1. NatureServe, Arlington, Virginia. http://www.natureserve.org/explorer. Accessed 21 Oct 2013
Page LM, Burr BM (2011) A field guide to freshwater fishes of North America north of Mexico. The Peterson Field Guide Series, 2nd ed edn. Houghton Mifflin Co, Boston Google Scholar
Peery MZ, Kirby R, Reid BN, Stoelting R, Douct-Beer E, Robinson S, Vasquez-Carrillo C, Pauli JN, Palsboll PJ (2012) Reliability of genetic bottleneck tests for detecting recent population declines. Mol Ecol 21:3403–3418 ArticlePubMed Google Scholar
Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959 CASPubMed CentralPubMed Google Scholar
Raymond M, Rousset F (1995) GENEPOP (version 12): population genetics software for exact tests and ecumenicism. J Hered 86:248–249 Google Scholar
Renshaw M, Carson E, Hanna A, Rexroad CEI, Krabbenhoft T, Gold J (2009) Microsatellite markers for species of the genus Dionda (Cyprinidae) from the American southwest. Conserv Genet 10:1569–1575 ArticleCAS Google Scholar
Robinson JD, Simmons JW, Williams AS, Moyer GR (2013) Population structure and genetic diversity in the endangered Bluemask Darter (Etheostoma akatulo). Conserv Genet 14:79–92 Article Google Scholar
Rosenberg NA (2004) DISTRUCT: a program for the graphical display of population structure. Mol Ecol Notes 4:137–138 Article Google Scholar
Rosenberg NA, Pritchard JK, Weber JL, Cann HM, Kidd KK, Zhivotovsky LA, Feldman MW (2002) Genetic structure of human populations. Science 298:2381–2385 ArticleCASPubMed Google Scholar
Schonhuth S, Doadrio I (2003) Phylogenetic relationships of Mexican minnows of the genus Notropis (Actinopterygii, Cyprinidae). Biol J Linn Soc 80:323–337 Article Google Scholar
Sepulveda-Villet OJ, Stepien CA (2011) Fine-scale population genetic structure of the yellow perch Perca flavescens in Lake Erie. Can J Fish Aquat Sci 68:1435–1453 Article Google Scholar
Sousa VC, Penha F, Pala I, Chikhi L, Coelho MM (2010) Conservation genetics of a critically endangered Iberian minnow: evidence of population decline and extirpations. Anim Conserv 13:162–171 Article Google Scholar
Spielman D, Brook BW, Frankham R (2004) Most species are not driven to extinction before genetic factors impact them. Proc Nat Acad Sci 101:15261–15264 ArticleCASPubMed CentralPubMed Google Scholar
Stepien CA, Murphy DJ, Strange RM (2007) Broad.to fine-scale population genetic patterning in the smallmouth bass Micropterus dolomieu across the Laurentian Great Lakes and beyond: an interplay of behaviour and geography. Mol Ecol 16:1605–1624 ArticleCASPubMed Google Scholar
Stepien CA, Murphy DJ, Lohner RN, Sepulveda-Villet OJ, Haponski AE (2009) Signatures of vicariance, postglacial dispersal and spawning philopatry: population genetics of the walleye Sander vitreus. Mol Ecol 18:3411–3428 ArticleCASPubMed Google Scholar
Sterling KA, Reed DH, Noonan BP, Warren ML Jr (2012) Genetic effects of habitat fragmentation and population isolation on Etheostoma raneyi (Percidae). Conserv Genet 13:859–872 Article Google Scholar
Storz JF, Beamont MA (2002) Testing for genetic evidence of population expansion and contraction: an empirical analysis of microsatellite DNA variation using a hierarchical Bayesian model. Evolution 56:154–166 CASPubMed Google Scholar
Takezaki N, Nei M (1996) Genetic distances and reconstruction of phylogenetic trees from microsatellite DNA. Genetics 144:389–399 CASPubMed CentralPubMed Google Scholar
Underhill JC (1957) The distribution of Minnesota minnows and darters in relation to Pleistocene glaciation. Minn Mus Nat Hist Occ Pap 7:1–45 Google Scholar
Van Oosterhout C, Hutchinson WF, Wills DPM, Shipley P (2004) MICRO-CHECKER: software for identifying and correcting genotyping errors in microsatellite data. Mol Ecol Notes 4:535–538 Article Google Scholar
Vila C, Sundqvist A-K, Flagstad O, Seddon J, Bjornerfeldt S, Kojola I, Casulli A, Sand H, Wabakken P, Ellegren H (2003) Rescue of a severely bottlenecked wolf (Canis lupus) population by a single immigrant. Proc Royal Soc London B 270:91–97 Article Google Scholar
Waples RS (1991) Pacific Salmon, Oncorhynchus spp., and the definition of “Species” under the Endangered Species Act. Mar Fish Rev 53:11–22 Google Scholar
Waples RS (1998) Evolutionarily significant units, distinct population segments, and the Endangered Species Act: reply to Pennock and Dimmick. Conserv Bio 12:718–721 Article Google Scholar
Waples RS, Do C (2008) LDNE: a program for estimating effective population size from data on linkage disequilibrium. Mol Ecol Res 8:753–756 Article Google Scholar
Waples RS, Do C (2010) Linkage disequilibrium estimates of contemporary Ne using highly variable genetic markers: a largely untapped resource for applied conservation and evolution. Evol App 3:244–262 Article Google Scholar
Waples RS, Gaggiotti O (2006) What is a population? An empirical evaluation of some genetic methods for identifying the number of gene pools and their degree of connectivity. Mol Ecol 15:1419–1439 ArticleCASPubMed Google Scholar
Whitlock MC, McCauley DE (1999) Indirect measures of gene flow and migration: F ST ≠ 1/(4Nm + 1). Heredity 82:117–125 ArticlePubMed Google Scholar
Willi Y, Van Buskirk J, Hoffman AA (2006) Limits to the adaptive potential of small populations. Annu Rev Ecol Sys 37:433–458 Article Google Scholar
Willi Y, Griffin P, Van Buskirk J (2013) Drift load in populations of small size and low density. Hered 110:296–302 ArticleCAS Google Scholar