Skip to main content
SpringerLink
Log in

Beyond FST: Analysis of population genetic data for conservation

  • Published:
Conservation Genetics Aims and scope Submit manuscript

Abstract

Both the ability to generate DNA data and the variety of analytical methods for conservation genetics are expanding at an ever-increasing pace. Analytical approaches are now possible that were unthinkable even five years ago due to limitations in computational power or the availability of DNA data, and this has vastly expanded the accuracy and types of information that may be gained from population genetic data. Here we provide a guide to recently developed methods for population genetic analysis, including identification of population structure, quantification of gene flow, and inference of demographic history. We cover both allele-frequency and sequence-based approaches, with a special focus on methods relevant to conservation genetic applications. Although classical population genetic approaches such as F st (and its derivatives) have carried the field thus far, newer, more powerful, methods can infer much more from the data, rely on fewer assumptions, and are appropriate for conservation genetic management when precise estimates are needed.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  • Abdo Z, Crandall KA, Joyce P (2004) Evaluating the performance of likelihood methods for detecting population structure and migration. Mol. Ecol., 13, 837–852.

    Google Scholar 

  • Anderson EC, Williamson EG, Thompson EA (2000) Monte Carlo evaluation of the likelihood for Ne from temporally spaced samples. Genetics, 156, 2109–2118.

    Google Scholar 

  • Anderson EC, Thompson EA (2002) A model-based method for identifiying species hybrids using multilocus genetic data. Genetics 160, 1217–1229.

    Google Scholar 

  • Arbogast BS, Edwards SV, Wakely J, Beerli P, Slowinski JB (2002) Estimating divergence times from molecular data on phylogenetic and population genetic timescales. Annu. Rev. Ecol. Syst., 33, 707–740.

    Google Scholar 

  • Avise JC, Arnold J, Ball RM, Bermingham E, Lamb T, Neigel JE, Reeb CA, Saunders NC (1987) Intraspecific phylogeography: The mitochondrial DNA bridge between population genetics and systematics. Annu. Rev. Ecol. Syst. 18, 489–522.

    Google Scholar 

  • Avise JC (2000) Phylogeography: The history and formation of species. Harvard University Press, Cambridge, Mass.

    Google Scholar 

  • Bahlo M, Griffiths RC (2000) Inference from gene trees in a subdivided population. Theor. Pop. Biol., 57, 79–95.

    Google Scholar 

  • Balloux F, Goudet J (2002) Statistical properties of population differentiation estimators under stepwise mutation in a finite island model. Mol. Ecol. 11, 771–783.

    Google Scholar 

  • Balloux F, Lugon-Moulin N (2002) The estimation of population differentiation with microsatellite markers. Mol. Ecol., 11, 155–165.

    Google Scholar 

  • Banks, MA, Eichert W (2000) WHICHRUN (Version 3. 2) a computer program for population assignment of individuals based on multilocus genotype data. J. Hered., 91, 87–89.

    Google Scholar 

  • Beaumont MA (1999) Detecting population expansion and decline using microsatellites. Genetics, 153, 2013–2029.

    Google Scholar 

  • Beaumont MA, Rannala B (2004) The Bayesian revolution in genetics. Nature Rev. Genet 5, 251–261.

    Google Scholar 

  • Beebee T, Rowe G (2001) Application of genetic bottleneck testing to the investigation of amphibian declines: a case study with natterjack toads. Cons. Biol. 15, 266–270.

    Google Scholar 

  • Beerli P (1998) Estimation of migration rates and population sizes in geographically structured populations. In: Advances in Molecular Ecology (ed, Carvalho GR), pp. 39–54. IOS Press, Amsterdam.

    Google Scholar 

  • Beerli P, Felsenstein J (1999) Maximum likelihood estimation of migration rates and effective population umbers in two populations using a coalescent approach. Genetics, 152, 763–773.

    Google Scholar 

  • Beerli P, Felsenstein J (2001) Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach. Proc. Natl. Acad. Sci. USA, 98, 4563–4568.

    Google Scholar 

  • Berry O, Tocher MD, Sarrre SD (2004) Can assignment tests measure dispersal?Mol. Ecol., 13, 551–561.

    Google Scholar 

  • Bossart JL, Prowell DP (1998) Genetic estimates of population structure and gene flow: limitations, lessons, and new directions. TREE, 13, 202–206.

    Google Scholar 

  • Brumffeld RT, Beerli P, Nickerson DA, Edwards SV (2003) The utility of single nucleotide polymorphisms in inferences of population history. TREE, 18, 249–256.

    Google Scholar 

  • Clement M, Posada D, Crandall KA (2000) TCS: a computer program to estimate gene genealogies. Mol. Ecol., 9, 1657–1659.

    Google Scholar 

  • Colson I, Goldstein DB (1999) Evidence for complex mutations at microsatellie loci in Drosophila. Genetics, 152, 617–627.

    Google Scholar 

  • Corander J, Waldmann P, Sillanpa ¨a ¨ MJ (2003) Bayesian analysis of genetic differentiation between populations. Genetics, 163, 367–374.

    Google Scholar 

  • Cornuet JM, Luikart G (1996) Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. Genetics, 144, 2001–14.

    Google Scholar 

  • Cornuet J-M, Piry S, Luikart G, Estoup A, Solignac M (1999) New methods employing multilocus genotypes to select or exclude population as origins of individuals. Genetics, 153, 1989–2000.

    Google Scholar 

  • Courtois R, Bernatchez L, Ouellet J-P, Breton L (2003) Significance of caribou (Rangifer tarandus) ecotypes from a molecular genetics viewpoint. Conserv. Genet., 4, 393–404.

    Google Scholar 

  • Crandall KA, Posada D and Vasco D (1999) Effective population sizes: missing measures and missing concepts. Animal Conserv., 2, 317–319.

    Google Scholar 

  • Crandall KA, Bininda-Emonds ORP, Mace GM, Wayne RK (2000) Considering evolutionary processes in conservation biology. TREE, 15, 290–295.

    Google Scholar 

  • Davies N, Villablanca FX, Roderick GK (1999) Determining the source of individuals: multilocus genotyping in non-equilibrium population genetics. TREE, 14, 17–21.

    Google Scholar 

  • Dawson KJ, Belkhir K (2001) A Bayesian approach to the identification of panmictic populations and the assignment of individuals. Genet. Res., 78, 59–77.

    Google Scholar 

  • Dieringer D, Schlo ¨tterer C (2003) MICROSATELLITE ANA-LYSER(MSA): a platform independent analysis tool for large microsatellite data sets. Mol. Ecol. Notes, 3, 167–169.

    Google Scholar 

  • Diniz-Filho JAF, Telles MPC (2002) Spatial autocorrelation analysis and the identi cation of operational units for conservation in continuous populations. Conserv. Biol., 16, 924–935.

    Google Scholar 

  • Dupanloup I, Schneider S, Excoffer L (2002) A simulated annealing approach to de ne the genetic structure of populations. Mol. Ecol., 11, 2571–2581.

    Google Scholar 

  • Emerson BC, Paradis E, Thebaud C (2001) Revealing the demographic histories of species using DNA sequences. TREE, 16, 707–716.

    Google Scholar 

  • Emery AM, Wilson IJ, Craig S, Boyle PR, Noble LR (2001) Assignment of paternity groups without access to parental genotypes: multiple mating and developmental plasticity in squid. Mol. Ecol., 10, 1265–1278.

    Google Scholar 

  • Estoup A, Clegg SM (2003) Bayesian inferences on the recent island colonization history by the bird Zosterops lateralis lateralis. Mol. Ecol., 12, 657–674.

    Google Scholar 

  • Estoup A, Wilson IJ, Sullivan C, Cornuet J-M, Moritz C (2001) Inferring population history from microsatellite and enzyme data in serially introduced cane toads, Bufo marinus. Genet., 159, 1671–1687.

    Google Scholar 

  • Excoffer 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.

    Google Scholar 

  • Fabiani A, Hoelzel AR, Galimberti F, Muelbert MMC (2003) Long-range paternal gene. ow in the southern elephant seal. Science, 299, 676.

    Google Scholar 

  • Falush D, Wirth T, Linz B, Pritchard JK, Stephens M, Kidd M, Blaser MJ, Graham DY, Vacher S, Perez-Perez GI, Yamaoka Y, Me ´graud F, Otto K, Reichard U, Katzowitsch E, Wang X, Achtman M, Suerbaum S (2003) Traces of human migrations in Helicobacer pylori populations. Science, 299, 1582–1585.

    Google Scholar 

  • Fisher RA (1930) The Genetical Theory of Natural Selection. Clarendon Press, Oxford.

    Google Scholar 

  • Ford MJ (2002) Applications of selective neutrality tests to molecular ecology. Mol. Ecol., 11, 1245–1262.

    Google Scholar 

  • Friar EA, Boose DL, LaDoux T, Roalson EH, Robichaux RH (2001) Population structure in the engangered Mauna Loa silversword, Argyroxiphium kauenese (Aseracea), and its bearing on reintroduction. Mol. Ecol., 10, 1657–1663.

    Google Scholar 

  • Gaggiotti OE, Lange O, Rassmann K, and Gliddon C (1999) A comparison of two indirect methods for estimating average levels of gene flow using microsatellite data. Mol. Ecol., 8, 1513–1520.

    Google Scholar 

  • Gaggiotti OE, Jones F, Lee WM, Amos W, Harwood J, Nichols RA (2002) Patterns of colonization in a metapopulation of grey seals. Nature, 416, 424–427.

    Google Scholar 

  • Gardner MG, Bull CM, Cooper SJB, Duffeld GA (2000) Microsatellite mutations in litters of the Australian lizard Egernia stokesii. J. Evol. Biol., 13, 551–560.

    Google Scholar 

  • Garza C, Williamson EG (2001) Detection of reduction in population size using data from microsatellite loci. Mol. Ecol., 10, 305–318.

    Google Scholar 

  • Glaubitz JC (2004) CONVERT: A user-friendly program to reformat diploid genotypic data for commonly used population genetic software packages. Molecular Ecology Notes, 4 (2), 309–310.

    Google Scholar 

  • Goldstein DB, Linares AR, Cavalli-Sforza LL, Feldman MW (1995) Genetic absolute dating based on microsatellites and the origin of modern humans. Proc. Natl. Acad. Sci. USA, 92, 623–6727.

    Google Scholar 

  • Griffiths RC, Tavare ´ S (1994) Sampling theory for neutral alleles in a varying environment. Phil. Trans. R. Soc. Lond. B, 344, 403–410.

    Google Scholar 

  • Harpending H, Rogers AR (2000) Genetic perspectives on human origins and differentiation. Ann. Rev. Hum. Gen., 1, 361–385.

    Google Scholar 

  • Holsinger KE, Mason-Gamer RJ (1996) Hierarchical analysis of nucleotide diversity in geographically structured populations. Genetics, 142, 629–639.

    Google Scholar 

  • Holsinger KE, Lewis PO, Dey DK (2002) A Bayesian approach to inferring population structure from dominant markers. Mol. Ecol., 11, 1157–1164.

    Google Scholar 

  • Hudson RR (1990) In: Oxford Surveys in Evolutionary Biology (eds. Futuyma D, Antonovics J), Oxford University Press, Oxford.

    Google Scholar 

  • Huelsenbeck JP, Larget B, Miller RE, Ronquist F (2002) Potential applications and pitfalls of Bayesian inference of phylogeny. Syst. Biol., 51, 673–688.

    Google Scholar 

  • Jones AG, Ardren WR (2003) Methods of parentage analysis in natural populations. Mol. Ecol., 12, 2511–2523.

    Google Scholar 

  • Kimmel M, Chakraborty R, King JP, Bamshad M, Watkins WS et al. (1998) Signatures of population expansion in microsatellite repeat data. Genetics, 148, 1921–1930.

    Google Scholar 

  • Kingman JFC (1982) The coalescent. Stoc. Proc. App., 13, 235–248.

    Google Scholar 

  • Kinnison MT, Bentzen P, Unwin MJ, Quinn TP (2002) Reconstructing recent divergence: evaluating nonequilibrium population structure in New Zealand chinook salmon. Mol. Ecol., 11, 739–754.

    Google Scholar 

  • Knowles LL, Maddison WP (2002) Statistical phylogeography. Mol. Ecol., 11, 2623–2635.

    Google Scholar 

  • Kuhner MK, Yamato J, Felsenstein J (1995) Estimating effective population size and mutation rate from sequence data using Metropolis-Hastings sampling. Genetics, 140, 1421–1430.

    Google Scholar 

  • Kuhner MK, Yamato J, Felsenstein J (1998) Maximum likeli-hood estimation of population growth rates based on the coalescent. Genetics, 149, 429–434.

    Google Scholar 

  • Larson S, Jameson R, Etnier M, Fleming M, Bentzen P. (2002) Loss of genetic diversity in sea otters (Enhydra lutris) associated with the fur trade of the 18 th and 19 th centuries. Mol. Ecol., 11, 1899–1903.

    Google Scholar 

  • Lewis PO (2001) Phylogenetic systematics turns over a new leaf. TREE, 16, 30–37.

    Google Scholar 

  • Luikart G, Cornuet JM (1998) Empirical evaluation of a test for identifying recently bottlenecked populations from allele frequency data. Conserv. Biol., 12, 28–233.

    Google Scholar 

  • Lynch M, Crease TJ (1990) The analysis of population survey data on DNA sequence variation. Mol. Biol. Evol., 7, 377–394.

    Google Scholar 

  • Malone CL, Knapp CR, Taylor JF, Davis SK (2003) Genetic consequences of Pleistocene fragmentation: Isolation, drift, and loss of diversity in rock iguanas (Cyclura). Conserv. Genet., 4, 1–15.

    Google Scholar 

  • Manel S, Berthier P, Luikart (2002) Detecting wildlife poaching: identifying the origin of individuals with bayesian assignment tests and multilocus genotypes. Conserv. Biol., 16, 650–659.

    Google Scholar 

  • Manel, S, Schwartz MK, Luikart P, Taberlet P (2003) Landscapge genetics: combining landscape ecology and popula-tion genetics. TREE, 18, 189–197.

    Google Scholar 

  • Masta SE, Laurent NM, Routman EJ (2003) Population genetic structure of the toad Bufo woodhousii: an empirical assesment of the effects of haplotype extinction on nested cladistic analysis. Mol. Ecol., 12, 1541–1554.

    Google Scholar 

  • Michalakis Y, Excoffer L (1996) A generic estimation of population subdivision using distances between alleles with special reference for microsatellite loci. Genetics, 142, 1061–1064.

    Google Scholar 

  • Milligan BG (2003) Maximum-likelihood estimation of relatedness. Genetics, 163, 1153–1167.

    Google Scholar 

  • Mills LS, Citta JJ, Lair KP, Schwarz MK, Tallmon DA (2000) Estimating animal abundance using noninvasive DNA sampling: promise and pitfalls. Ecol. Apps., 10, 283–294.

    Google Scholar 

  • Moazami-Goudarzi K Laloe D (2002) Is a multivariate consensus representation of genetic relationships among popu-lations always meaningful?Genetics, 162, 473–484.

    Google Scholar 

  • Moritz C (1994) Defining ''evolutionary signi cant units ''for conservation. TREE, 9, 373–375.

    Google Scholar 

  • Nee S, Holmes EC, Rambaut A, Harvey PH (1995) Inferring population history from molecular phylogenies. Phil. Trans. Roy. Soc. Lond., 349, 25–31.

    Google Scholar 

  • Nei M (1973) Analysis of gene diversity in subdivided populations. Proc. Nat. Acad. Sci. USA, 70, 3321–3323.

    Google Scholar 

  • Neigel JE (1997) A comparison of alternative strategies for estimating gene flow from genetic markers. Annu. Rev. Ecol. Syst., 28, 105–128.

    Google Scholar 

  • Neigel JE (2002) Is FST ST obsolete?Conserv. Genet., 3, 167–173.

    Google Scholar 

  • Nielsen R (2001) Statistical tests of selective neutrality in the age of genomics. Heredity, 86, 641–647.

    Google Scholar 

  • Nielsen R, Slatkin M (2000) Analysis of population subdivision using diallelic models. Evolution, 54, 44–50.

    Google Scholar 

  • Nielsen R, Wakeley J (2001) Distinguishing migration from isolation: A markov chain monte carlo approach. Genetics, 158, 885–896.

    Google Scholar 

  • Nordborg M (2001) Coalescent theory. In: Handbook of Sta-tistical Genetics (eds. Balding, DJ, Bishop M, Cannings C), Wiley, England.

    Google Scholar 

  • Ortý ´G, Pearse DE, Avise JC (1997) Phylogenetic assessment of length variation at a microsatellite locus. Proc. Natl. Acad. Sci. USA, 94, 10745–10749.

    Google Scholar 

  • Paetkau D, Calvert W, Sterling I, Strobeck C (1995) Micro-satellite analysis of population structure in Canadian polar bears. Mol. Ecol., 4, 347–354.

    Google Scholar 

  • Palsbøll PJ, Allen J, Be ´rube ´ M, Clapham PJ, Feddersen TP, Hammond P, Hudson RR, Jørgensen J, Katona S, Larsen AH, Larsen F, Lien J, Mattila DK, Sigurjo ´nsson J, Sears R, Smith T, Sponer R, Stevick P, Øien N (1997) Genetic tagging of humpback whales. Nature, 388, 767–769.

    Google Scholar 

  • Pearse DE, Eckerman CM, Janzen FJ, Avise JC (2001) A genetic analogue of 'mark-recapture 'methods for estimating population size: an approach based on molecular parentage assessments. Mol. Ecol., 10, 2711–2718.

    Google Scholar 

  • Pella JJ, Milner GB (1987) Use of genetic marks in stock composition analysis. In: Population genetics and shery management (eds. Ryman N, Utter F), pp. 247–276. University of Washington.

  • Piry S, Luikart G, Cornuet JM (1999) BOTTLENECK: A computer program for detecting recent reductions in the effective population size using allele frequency data. J. Heredity, 90, 502–503.

    Google Scholar 

  • Posada D, Crandall KA, Templeton AR (2000) GeoDis: a program for the cladistic nested analysis of the geographical distribution of genetic haplotypes. Mol. Ecol., 9, 487–488.

    Google Scholar 

  • Primmer CR, Koskinen MT, Piironen J (2000) The one that did not get away: individual assignment using microsatellite data detects a case of shing competition fraud. Proc. Roy. Soc. Lond., 267, 1699–1704.

    Google Scholar 

  • Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics, 155, 945–959.

    Google Scholar 

  • Pybus OG, Rambaut A, Harvey PH (2000) An integrated framework for the inference of viral population history from reconstructed genealogies. Genetics, 155, 1429–1437.

    Google Scholar 

  • Pybus OG, Rambaut A (2002) GENIE: estimating demographic history from molecular phylogenies. Bioinformatics, 18, 1404–1405.

    Google Scholar 

  • Randi E, Lucchini V (2002) Detecting rare introgression of domestic dog genes into wild wolf (Canis lupus) populations by Bayesian admixture analyses of microsatellite variation. Conserv. Genet., 3, 31–45.

    Google Scholar 

  • Rannala B, Mountain JL (1997) Detecting immigration by using multilocus genotypes. Proc. Natl. Acad. Sci. USA, 94, 9197–9201.

    Google Scholar 

  • Ray, N, Currat M, Excoffer L (2003) Intra-deme molecular diversity in spatially expanding populations. Mol. Biol. Evol., 20, 76–86.

    Google Scholar 

  • Raymond M and Rousset F (1995) An exact test for population differentiation. Evolution, 49, 1280–1283.

    Google Scholar 

  • Rogers AR and Harpending H (1992) Population growth makes waves in the distribution of pairwise genetic differences. Mol. Biol. Evol., 9, 552–569.

    Google Scholar 

  • Roman J, Palumbi SR (2003) Whales before whaling in the north atlantic. Science, 301, 508–510.

    Google Scholar 

  • Rooney AP, Honeycutt RL, Derr JN (2001) Historical population size change of bowhead whales inferred from DNA sequence polymorphism data. Evolution, 55, 1678–1685.

    Google Scholar 

  • Rousset F (1996) Equilibrium values of measures of population subdivision for stepwise mutation processes. Genetics, 142, 1357–1362.

    Google Scholar 

  • Saint-Laurent R, Legault M, Bernatchez L (2003) Divergent selection maintains adaptive di. erentiation despite high gene flow between sympatric rainbow smelt ecotypes (Osmerus mordax Mitchill). Mol. Ecol., 12, 315–330.

    Google Scholar 

  • Schnabel A, Beerli P, Estoup A, Hillis D. (1998) A guide to software packages for data analysis in molecular ecology. In: Advances in Molecular Ecology (ed. Carvalho GR), pp. 291–303. IOS Press, Amsterdam.

    Google Scholar 

  • Schneider S, Excoffer L (1999) Estimation of past demographic parameters from the distribution of pairwise differences when the mutation rates vary among sites: application to human mitochondrial DNA. Genetics, 152, 1079–1089.

    Google Scholar 

  • Shoemaker JS, Painter IS, Weir BS (1999) Bayesian statistics in genetics. TIG, 15, 354–358.

    Google Scholar 

  • Sites JW Jr., FitzSimmons NN, DA Silva NJ Jr., Cantarelli VH (1999) Conservation genetics of the giant amazon river turtle (Podocnemis expansa; Pelomedusidae)-inferences from two classes of molecular markers. Chelonian Conserv. Biol., 3, 454–463.

    Google Scholar 

  • Slatkin M (1993) Isolation by distance in equilibrium and non-equilibrium populations. Evolution, 47, 264–279.

    Google Scholar 

  • Slatkin M(1995) A measure of population subdivision based on microsatellite allele frequencies. Genetics, 139, 457–462.

    Google Scholar 

  • Slatkin M, Barton NH (1989) Methods for estimating gene flow. Evolution, 43, 1349–1368.

    Google Scholar 

  • Smouse PE, Waples RS, Tworek JA (1990) A mixed shery model for use with incomplete source population data. Can. J. Fish. Aquat. Sci., 47, 620–634.

    Google Scholar 

  • Spencer CC, Neigel JE, Leberg PL (2000) Experimental evaluation of the usefulness of microsatellite DNA for detecting demographic bottlenecks. Mol. Ecol., 9, 1517–1528.

    Google Scholar 

  • Stephens M (2001) Inference under the coalescent. In: Handbook of Statistical Genetics (eds. Balding, DJ, Bishop M, Cannings C), Wiley, England.

    Google Scholar 

  • Storz JF, Beaumont MA (2002) Testing for genetic evidence of population expantion and contraction: an empirical analysis of microsatellite DNA variation using a hierarchical Bayesian model. Evolution 56, 154–166.

    Google Scholar 

  • Storz JF, Beaumont MA, Alberts SC (2002) Genetic evidence for long-term population decline in a savannah-dwelling primate: inferences from a hierarchical Bayesian model. Mol. Biol. Evol., 19, 1981–1990.

    Google Scholar 

  • Strimmer K and Pybus OG (2001) Exploring the demographic history of DNA sequences using the generalized skyline plot. Mol. Biol. Evol., 18, 2298–2305.

    Google Scholar 

  • Sunnucks P (2000) Efficient genetic markers for population biology. TREE, 15, 199–203.

    Google Scholar 

  • Tajima F (1989) Statistical methods for testing the neutral mutation hypothesis by DNA polymorphisms. Genetics, 123, 585–595.

    Google Scholar 

  • Templeton AR, Routman E, Phillips C (1995) Separating population structure from population history: a cladistic analysis of the geographical distribution of mitochondrial DNA haplotypes in the tiger salamander, Ambystoma tigrinum. Genetics, 140, 767–782.

    Google Scholar 

  • Templeton AR (1998) Nested clade analyses of phylogeo-graphic data: testing hypotheses about gene. ow and population history. Mol. Ecol., 7, 381–397.

    Google Scholar 

  • Templeton AR (2004) Statistical phylogeography: methods of evaluating and minimizing inference errors. Mol. Ecol., 13, 789–810.

    Google Scholar 

  • Turner TF, Wares JP, Gold JR (2002) Genetic effective size is three orders of magnitude smaller than adult census size in an abundant, estuarine-dependent marine sh (Sciaenops ocellatus) Genetics, 162, 1329–1339.

    Google Scholar 

  • Utter F and Ryman N (1993) Genetic markers and mixed stock sheries. Fisheries, 18, 11–21.

    Google Scholar 

  • Van Oppen MJH, Rico C, Turner GF, Hewitt GM (2000) Extensive homoplasy, nonstepwise mutations, and shared ancestral polymorphism at a complex microsatellite locus in Lake Malawi cichlids. Mol. Biol. Evol., 17, 489–498.

    Google Scholar 

  • Vila`et al. (2003) Rescue of a severely bottlenecked wolf (Canis lupus) population by a single immigrant. Proc. Roy. Soc. Lond., 270, 91–97.

    Google Scholar 

  • Wakeley J (1996) Distinguishing migration from isolation using the variance of pairwise dierences. Theor. Pop. Biol., 49, 369–386.

    Google Scholar 

  • Waldick RC, Kraus S, Brown M, White BN (2002) Evaluating the effects of historic bottleneck events: an assessment of microsatellite variability in the endangered North Atlantic right whale. Mol. Ecol., 11, 2241–2249.

    Google Scholar 

  • Wall JD (2003) Estimating ancestral population sizes and divergence times. Genetics, 163, 395–404.

    Google Scholar 

  • Waples RS (1989) A generalized approach for estimating e. ective population size from temporal changes in allele frequency. Genetics, 121, 379–391.

    Google Scholar 

  • Waples RS (1998) Separating the wheat from the chaff: patterns of genetic di. erentiation in high gene flow species. J. Hered., 89, 438–450.

    Google Scholar 

  • Waser PM, Strobeck C (1998) Genetic signatures of interpop-ulation dispersal. TREE, 13, 43–44.

    Google Scholar 

  • Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution, 38, 1358–1370.

    Google Scholar 

  • Weir BS, Hill WG (2002) Estimating F-statistics. Annu. Rev. Gen., 36, 721–750.

    Google Scholar 

  • Whitlock M, McCauley DE (1999) Indirect estimation of gene flow and migration: FST≠1/(4Nm+1). Heredity, 82, 117–125.

    Google Scholar 

  • Williamson EG, Slatkin M (1999) Using maximum likelihood to estimate population size from temporal changes in allele frequencies. Genetics, 152, 755–761.

    Google Scholar 

  • Wilson GA, Rannala B (2003) Bayesian inference of recent migration rates using multilocus genotypes. Genetics, 163, 1177–1191.

    Google Scholar 

  • Wilson IJ, Balding DJ (1998) Genealogical inference from mi-crosatellite data. Genetics, 150, 499–510.

    Google Scholar 

  • Wilson IJ, Weale, Balding DJ (2003) Inferences from DNAdata: population histories, evolutionary processes and forensic match probabilities. J. Roy. Stat. Soc. A, 166, 155–188.

    Google Scholar 

  • Wright S (1931) Evolution in Mendelian population. Genetics, 16, 97–159.

    Google Scholar 

  • Wright S (1951) The genetical structure of populations. Ann. Eugen., 15, 323–354.

    Google Scholar 

  • Yang Z (2002) Likelihood and Bayes estimation of ancestral population sizes in hominoids using data from multiple loci. Genetics, 162, 1811–1823.

    Google Scholar 

  • Zhivotovsky LA (1999) A new genetic distance with application to constrained variation at microsatellite loci. Mol. Biol. Evol., 16, 467–471.

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Integrative Biology, Brigham Young University, Provo, UT, 84602, USA

    Devon E. Pearse & Keith A. Crandall

  2. National Marine Fisheries Service, Southwest Fisheries Science Center, Santa Cruz, CA, 95060, USA

    Devon E. Pearse

Authors
  1. Devon E. Pearse
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Keith A. Crandall
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Devon E. Pearse.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Pearse, D.E., Crandall, K.A. Beyond FST: Analysis of population genetic data for conservation. Conservation Genetics 5, 585–602 (2004). https://doi.org/10.1007/s10592-003-1863-4

Download citation

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10592-003-1863-4

Keywords

Search

Navigation