Bermingham E, Moritz C: Comparative phylogeography: concepts and applications. Mol Ecol 1998, 7: 367–369. 10.1046/j.1365-294x.1998.00424.x
Article
Google Scholar
Arbogast BS, Kenagy GJ: Comparative phylogeography as an integrative approach to historical biogeography. J Biogeogr 2001, 28: 819–825. 10.1046/j.1365-2699.2001.00594.x
Article
Google Scholar
Coyne JA, Orr HA: Speciation. Sunderland, MA: Sinauer Associates Inc; 2004.
Google Scholar
Avise JC: Phylogeography: The history and formation of species. Cambridge: Harvard University Press; 2000.
Google Scholar
Hubbell SP: The Unified Neutral Theory of Biodiversity and Biogeography. Princeton, NJ: Princeton University Press; 2001.
Google Scholar
Vera C, Wheat CW, Fescemyer HW, Frilander MJ, Crawford DL, Hanski I, Marden JH: Rapid transcriptome characterization for a non-model organism using massively parallel 454 pyrosequencing. Mol Ecol 2008., 2371:
Google Scholar
Graham CH, Parra JL, Rahbek C, McGuire JA: Phylogenetic structure in tropical hummingbird communities. Proceedings of the National Academy of Sciences 2009, 106(Supplement 2):19673–19678. 10.1073/pnas.0901649106
Article
CAS
Google Scholar
Nielsen R, Beaumont MA: Statistical inferences in phylogeography. Mol Ecol 2009, 18: 1034–1047. 10.1111/j.1365-294X.2008.04059.x
Article
CAS
PubMed
Google Scholar
Tallmon DA, Luikart G, Beaumont BA: Comparative evaluation of a new effective population size estimator based on approximate Bayesian computation. Genetics 2004, 167: 977–988. 10.1534/genetics.103.026146
Article
PubMed Central
PubMed
Google Scholar
Excoffier L, Estoup A, Cornuet J-M: Bayesian analysis of an admixture model with mutations and arbitrarily linked markers. Genetics 2005, 169: 1727–1738. 10.1534/genetics.104.036236
Article
PubMed Central
CAS
PubMed
Google Scholar
Hickerson MJ, Stahl E, Lessios HA: Test for simultaneous divergence using approximate Bayesian computation. Evolution 2006, 60: 2435–2453.
Article
CAS
PubMed
Google Scholar
Beaumont MA: Approximate Bayesian Computation in Evolution and Ecology. Annual Review of Ecology, Evolution, and Systematics 2010, 41(1):379–406. 10.1146/annurev-ecolsys-102209-144621
Article
Google Scholar
Csilléry K, Blum MGB, Gaggiotti OE, Francois O: Approximate Bayesian Computation (ABC) in practice. Trends Ecol Evol 2010, 25(7):410–418. 10.1016/j.tree.2010.04.001
Article
PubMed
Google Scholar
Bertorelle G, Benazzo A, S M: ABC as a flexible framework to estimate demography over space and time: some cons, many pros. Mol Ecol 2010, 19(13):2609–2625. 10.1111/j.1365-294X.2010.04690.x
Article
CAS
PubMed
Google Scholar
Carnaval A, Hickerson MJ, Haddad CFB, Rodrigues MT, Moritz C: Stability predicts genetic diversity in the Brazilian Atlantic Forest Hotspot. Science 2009, 323: 785–789. 10.1126/science.1166955
Article
CAS
PubMed
Google Scholar
Lopes JS, Balding D, Beaumont MA: PopABC: a program to infer historical demographic parameters. Bioinformatics 2009, 25(20):2747–2749. 10.1093/bioinformatics/btp487
Article
CAS
PubMed
Google Scholar
Anderson CNK, Ramakrishnan U, Chan YL, Hadly EA: Serial SimCoal: A population genetic model for data from multiple populations and points in time. Bioinformatics 2005, 21: 1733–1734. 10.1093/bioinformatics/bti154
Article
CAS
PubMed
Google Scholar
Cornuet J-M, Santos F, Beaumont MA, Robert CP, Marin J-M, Balding DJ, Guillemaud T, Estoup A: Inferring population history with DIY ABC: a user-friendly approach to Approximate Bayesian Computation. Bioinformatics 2008, 24(23):2713–2719. 10.1093/bioinformatics/btn514
Article
PubMed Central
CAS
PubMed
Google Scholar
Jobin MJ, Mountain JL: REJECTOR: software for population history inference from genetic data via a rejection algorithm. Bioinformatics 2008, 24: 2936–2937. 10.1093/bioinformatics/btn540
Article
PubMed Central
CAS
PubMed
Google Scholar
Thornton K: Automating approximate Bayesian computation by local linear regression. BMC Genet 2009, 10(1):35. 10.1186/1471-2156-10-35
Article
PubMed Central
PubMed
Google Scholar
Wegmann D, Leuenberger C, Neuenschwander S, Excoffier L: ABCtoolbox: a versatile toolkit for approximate Bayesian computations. BMC Bioinformatics 2010, 11(1):116. 10.1186/1471-2105-11-116
Article
PubMed Central
PubMed
Google Scholar
Palero F, Lopes J, Abello P, Macpherson E, Pascual M, Beaumont M: Rapid radiation in spiny lobsters (Palinurus spp) as revealed by classic and ABC methods using mtDNA and microsatellite data. BMC Evol Biol 2009, 9(1):263. 10.1186/1471-2148-9-263
Article
PubMed Central
PubMed
Google Scholar
Storz JF, Beaumont BA: Testing for genetic evidence of population expansion and contraction: an empirical analysis of microsattelite DNA variation using a hierarchical Bayesian model. Evolution 2002, 56: 154–166.
Article
CAS
PubMed
Google Scholar
Hickerson MJ, Stahl E, Takebayashi N: msBayes: Pipeline for testing comparative phylogeographic histories using hierarchical approximate Bayesian computation. BMC Bioinformatics 2007, 8: 268. 10.1186/1471-2105-8-268
Article
PubMed Central
PubMed
Google Scholar
Fagundes NJR, Ray N, Beaumont M, Neuenschwander S, Salzano FM, Bonatto SL, Excoffier L: Statistical evaluation of alternative models of human evolution. Proceedings of the National Academy of Sciences of the United States of America 2007, 104: 17614–17619. 10.1073/pnas.0708280104
Article
PubMed Central
CAS
PubMed
Google Scholar
Estoup A, Beaumont BA, Sennedot F, Moritz C, Cornuet J-M: Genetic analysis of complex demographic scenarios: spatially expanding populations of the cane toad, Bufo marinus . Evolution 2004, 58: 2021–2036.
Article
PubMed
Google Scholar
Tavaré S, Balding DJ, Griffiths RC, Donnelly P: Inferring coalescence times from DNA sequence data. Genetics 1997, 145: 505–518.
PubMed Central
PubMed
Google Scholar
Weiss G, von Haeseler A: Inference of population history using a likelihood approach. Genetics 1998, 149: 1539–1546.
PubMed Central
CAS
PubMed
Google Scholar
Pritchard JK, Seielstad MT, P-L A, Feldman MW: Population growth of human Y chromosomes: a study of Y chromosome microsatellites. Mol Biol Evol 1999, 16: 1791–1798.
Article
CAS
PubMed
Google Scholar
Marjoram PM, Molitor J, Plagnol V, Tavaré S: Markov chain Monte Carlo without likelihoods. Proc Natl Acad Sci USA 2003, 100: 15324–15328. 10.1073/pnas.0306899100
Article
PubMed Central
CAS
PubMed
Google Scholar
Beaumont MA, Zhang W, Balding DJ: Approximate Bayesian computation in population genetics. Genetics 2002, 162: 2025–2035.
PubMed Central
PubMed
Google Scholar
Beaumont MA: Joint determination of topology, divergence time and immigration in population trees. In Simulations, Genetics and Human Prehistory. Edited by: Matsumura S, Forster P, Renfrew C. Cambridge: McDonald Institute for Archaeological Research; 2008:135–154.
Google Scholar
François O, Blum MGB, Jakobsson M, Rosenberg NA: Demographic history of european populations of arabidopsis thaliana . PLoS Genet 2008, 4: e1000075.
Article
PubMed Central
PubMed
Google Scholar
Leuenberger C, Wegmann D: Bayesian Computation and Model Selection Without Likelihoods. Genetics 184(1):243–252. 10.1534/genetics.109.109058
Blum MGB, François O: Non-linear regression models for Approximate Bayesian Computation. Statistics and Computing 2010, 20(1):63–73. 10.1007/s11222-009-9116-0
Article
Google Scholar
Hudson RR: Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 2002, 18: 337–338. 10.1093/bioinformatics/18.2.337
Article
CAS
PubMed
Google Scholar
Jukes TH, Cantor CH: Evolution of protein molecules. In Mammalian protein metabolism. Edited by: Munro HM. New York: Academic Press; 1969:21–123.
Chapter
Google Scholar
Felsenstein J: Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981, 17: 368–376. 10.1007/BF01734359
Article
CAS
PubMed
Google Scholar
Hasegawa M, Kishino H, Yano TA: Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol 1985, 22: 160–174. 10.1007/BF02101694
Article
CAS
PubMed
Google Scholar
Nei N, Kumar S: Molecular Evolution and Phylogenetics. Oxford: Oxford University Press; 2000.
Google Scholar
Watterson GA: On the number of segregating sites in genetic models without recombination. Theor Popul Biol 1975, 7: 256–276. 10.1016/0040-5809(75)90020-9
Article
CAS
PubMed
Google Scholar
Sherwin WB, Jabot F, Rush R, Rossetto M: Measurement of biological information with applications from genes to landscapes. Mol Ecol 2006, 15: 2857–2869. 10.1111/j.1365-294X.2006.02992.x
Article
PubMed
Google Scholar
Wakeley J: Distinguishing migration from isolation using the variance of pairwise differences. Theor Popul Biol 1996, 49: 369–386. 10.1006/tpbi.1996.0018
Article
CAS
PubMed
Google Scholar
Nei M, Li W: Mathematical model for studying variation in terms of restriction endonucleases. Proceedings of the National Academy of Sciences of the United States of America 1979, 76: 5269–5273. 10.1073/pnas.76.10.5269
Article
PubMed Central
CAS
PubMed
Google Scholar
Wakeley J: The variance of pairwise nucleotide differences in two populations with migration. Theor Popul Biol 1996, 49: 39–57. 10.1006/tpbi.1996.0002
Article
CAS
PubMed
Google Scholar
Bazin E, Dawson KJ, Beaumont MA: Likelihood-free Inference of Population Structure and Local Adaptation in a Bayesian Hierarchical Model. Genetics 2010. genetics. 109.112391 genetics. 109.112391
Google Scholar
Papoulis A: Probability, Random Variables, and Stochastic Processes. 2nd edition. New York: McGraw-Hill; 1984.
Google Scholar
Takahata N, Nei M: Gene genealogy and variance of interpopulational nucleotide differences. Genetics 1985, 110: 325–344.
PubMed Central
CAS
PubMed
Google Scholar
Hey J, Nielsen R: Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis . Genetics 2004, 167: 747–760. 10.1534/genetics.103.024182
Article
PubMed Central
CAS
PubMed
Google Scholar
Cook SR, Gelman A, Rubin DB: Validation of Software for Bayesian Models Using Posterior Quantiles. Journal of Computational and Graphical Statistics 2006, 15(3):675–692. 10.1198/106186006X136976
Article
Google Scholar
Jennings WB, Edwards SV: Speciational history of australian grass finches ( poephila ) inferred from thirty gene trees. Evolution 2005, 59: 2033–2047.
CAS
PubMed
Google Scholar
Lee JY, Edwards SV: Divergence Across Australia's Carpentarian Barrier: Statistical Phylogeography of the Red-Backed Fairy Wren ( Malurus melanocephalus ). Evolution 2008, 62(12):3117–3134. 10.1111/j.1558-5646.2008.00543.x
Article
PubMed
Google Scholar
Sousa VC, Fritz M, Beaumont MA, Chikhi L: Approximate Bayesian Computation Without Summary Statistics: The Case of Admixture. Genetics 2009, 181(4):1507–1519. 10.1534/genetics.108.098129
Article
PubMed Central
CAS
PubMed
Google Scholar
Rosenberg NA, Feldman MW: The relationship between coalescence times and population divergence times. In Modern Developments in Theoretical Population Genetics. Edited by: Slatkin M, Veuille M. Oxford: University Press; 2002:130–164.
Google Scholar
Arbogast BS, Edwards SV, Wakeley J, Beerli P, Slowinski JB: Estimating divergence times from molecular data on phylogenetic and population genetic timescales. Annu Rev Ecol Syst 2002, 33: 707–740. 10.1146/annurev.ecolsys.33.010802.150500
Article
Google Scholar
Nielsen R, Wakeley J: Distinguishing migration from isolation: A Markov chain Monte Carlo approach. Genetics 2001, 158(2):885–896.
PubMed Central
CAS
PubMed
Google Scholar
Carstens BC, Stoute HN, Reid NM: An information-theoretical approach to phylogeography. Mol Ecol 2009, 18(20):4270–4282. 10.1111/j.1365-294X.2009.04327.x
Article
PubMed
Google Scholar
Verdu P, Austerlitz F, Estoup A, Vitalis R, Georges M, ThÈry S, Froment A, Le Bomin S, Gessain A, Hombert J: Origins and Genetic Diversity of Pygmy Hunter-Gatherers from Western Central Africa. Curr Biol 2009, 19(4):312–318. 10.1016/j.cub.2008.12.049
Article
CAS
PubMed
Google Scholar
Kass RE, Raftery A: Bayes factors. Journal of the American Statistical Association 1995, 90: 773–795. 10.2307/2291091
Article
Google Scholar
Rannala B, Yang ZH: Bayes Estimation of Species Divergence Times and Ancestral Population Sizes Using DNA Sequences From Multiple Loci. Genetics 2003, 164: 1645–1656.
PubMed Central
CAS
PubMed
Google Scholar
Lee JY, Edwards SV: Divergence Across Australia's Carpentarian Barrier: Statistical Phylogeography of the Red-Backed Fairy Wren (Malurus melanocephalus). Evolution 2009, 62(12):3117–3134. 10.1111/j.1558-5646.2008.00543.x
Article
Google Scholar
Knowles LL: Statistical Phylogeography. Annual Review of Ecology, Evolution, and Systematics 2009, 40(1):593–612. 10.1146/annurev.ecolsys.38.091206.095702
Article
Google Scholar
Hickerson MJ, Carstens BC, Cavender-Bares J, Crandall KA, Graham CH, Johnson JB, Rissler L, Victoriano PF, Yoder AD: Phylogeography's past, present, and future: 10 years after. Mol Phylogen Evol 2010, 54(1):291–301. 10.1016/j.ympev.2009.09.016
Article
CAS
Google Scholar
Moyle LC: Ecological and evolutionary genomics in the wild tomatoes (solanum sect. Lycopersicon). Evolution 2008, 62(12):2995–3013. 10.1111/j.1558-5646.2008.00487.x
Article
PubMed
Google Scholar
Dolman G, Moritz C: A multilocus perspective on refugial isolation and divergence in rainforest skinks ( carlia ). Evolution 2006, 60(3):573–582.
Article
CAS
PubMed
Google Scholar
Hurt C, Anker A, Knowlton N: A multilocus test of simultaneous divergence across the isthmus of panama using snapping shrimp in the genus alpheus. Evolution 2009, 63(2):514–530. 10.1111/j.1558-5646.2008.00566.x
Article
CAS
PubMed
Google Scholar
Rogers S, Bernatchez L: The Genetic Architecture of Ecological Speciation and the Association with Signatures of Selection in Natural Lake Whitefish (Coregonus sp. Salmonidae) Species Pairs. Mol Biol Evol 2007, 24(6):1423–1438. 10.1093/molbev/msm066
Article
CAS
PubMed
Google Scholar
Becquet Cl, Przeworski M: Learning about Modes of Speciation by Computational Approaches. Evolution 2009, 63(10):2547–2562. 10.1111/j.1558-5646.2009.00662.x
Article
PubMed
Google Scholar