msBayes: Pipeline for testing comparative phylogeographic histories using hierarchical approximate Bayesian computation

BMC Bioinformatics

Volumn 8, Issue , 2007, Pages

  Hickerson, Michael J ^a   Stahl, Eli ^b   Takebayashi, Naoki ^c  

^a CITY UNIVERSITY OF NEW YORK   (United States)

^b UNIVERSITY OF MASSACHUSETTS DARTMOUTH   (United States)

^c UNIVERSITY OF ALASKA FAIRBANKS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCEPTANCE/REJECTION; APPROXIMATE BAYESIAN; DEGREE OF VARIABILITY; DEMOGRAPHIC PARAMETERS; EVOLUTIONARY BIOLOGY; OPEN SOURCE LICENSE; PHYLOGEOGRAPHIC HISTORY; RESEARCH QUESTIONS;

BAYESIAN NETWORKS; BIOLOGY; C (PROGRAMMING LANGUAGE); COMPUTER OPERATING SYSTEMS; FORESTRY; HIERARCHICAL SYSTEMS; PIPELINES; SOFTWARE PACKAGES;

POPULATION STATISTICS;

ARTICLE; BAYES THEOREM; COMPUTER PROGRAM; COMPUTER SYSTEM; DATA ANALYSIS; DEMOGRAPHY; EVOLUTIONARY DEVELOPMENTAL BIOLOGY; GENE ISOLATION; GENE LOCUS; GENE TRANSFER; GENETIC DATABASE; GENETIC VARIABILITY; PHYLOGENY; STATISTICAL ANALYSIS; ALGORITHM; BIOLOGICAL MODEL; CHROMOSOME MAP; COMPUTER SIMULATION; GENETICS; METHODOLOGY; MOLECULAR EVOLUTION; QUANTITATIVE TRAIT LOCUS;

ALGORITHMS; CHROMOSOME MAPPING; COMPUTER SIMULATION; EVOLUTION, MOLECULAR; MODELS, GENETIC; PHYLOGENY; QUANTITATIVE TRAIT LOCI; SOFTWARE; VARIATION (GENETICS);

EID: 34548065664     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-8-268     Document Type: Article

References (30)

1. Avise JC Phylogeography: The history and formation of species Cambridge: Harvard University Press 2000
2. Wen J Origin and the evolution of the eastern North American distinct distributions of flowering plants Annu Rev Ecol Syst 1999 30 421-455 10.1146/annurev.ecolsys.30.1.421
3. Lessios HA The first stage of speciation as seen in organisms separated by the Isthmus Panama Endless Forms: Species and speciation Oxford, U.K.: Oxford University Press Howard DJ, Berlocher S 1998 186-201
4. Barraclough TG Nee S Phylogenetics and speciation Trends Ecol Evol 2001 16 7 391-399 10.1016/S0169-5347(01)02161-9 11403872
5. Knowles LL Maddison WP Statistical phylogeography Mol Ecol 2002 11 12 2623-2635 10.1046/j.1365-294X.2002.01637.x 12453245
6. Edwards SV Liu L Pearl DK High-resolution species trees without concatination Proc Natl Acad Sci USA 2007 104 5936-5941 10.1073/ pnas.0607004104 17392434
7. 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 1462670 12930768
8. Hey J Nielsen R Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics Proc Natl Acad Sci USA 2007 104 2785-2790 10.1073/pnas.0611164104 17301231
9. Edwards SV Beerli P Perspective: Gene divergence, population divergence, and the variance in coalescence time in phylogeographic studies Evolution 2000 54 6 1839-1854 11209764
10. Hickerson MJ Stahl E Lessios HA Test for simultaneous divergence using approximate Bayesian computation Evolution 2006 60 2435-2453 17263107
11. Thornton K Andolfatto P Approximate Bayesian inference reveals evidence for a recent, severe bottleneck in a Netherlands population of Drosophila melanogaster Genetics 2005 172 1607-1619 1456302 16299396 10.1534/genetics.105.048223
12. Excoffier L Estoup A Cornuet J-M Bayesian analysis of an admixture model with mutations and arbitrarily linked markers Genetics 2005 169 1727-1738 1449551 15654099 10.1534/genetics.104.036236
13. 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 15521459
14. 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 1470910 15238546 10.1534/ genetics.103.026146
15. Beaumont MA Zhang W Balding DJ Approximate Bayesian computation in population genetics Genetics 2002 162 2025-2035 1462356 12524368
16. Weiss G von Haeseler A Inference of population history using a likelihood approach Genetics 1998 149 1539-1546 1460236 9649540
17. 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 1145509
18. Nei M Li W Mathematical model for studying variation in terms of restriction endonucleases Proc Natl Acad Sci USA 1979 76 5269-5273 413122 291943 10.1073/pnas.76.10.5269
19. Hickerson MJ Dolman G Moritz C Comparative phylogeographic summary statistics for testing simultaneous vicariance across taxon-pairs Mol Ecol 2006 15 209-224 10.1111/j.1365-294X.2005.02718.x 16367841
20. Hudson RR Generating samples under a Wright-Fisher neutral model of genetic variation Bioinformatics 2002 18 337-338 10.1093/bioinformatics/ 18.2.337 11847089
21. 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 1470901 15238526 10.1534/genetics.103.024182
22. Beaumont MA Rannala B The Bayesian revolution in genetics Nat Rev Genet 2004 5 251-261 10.1038/nrg1318 15131649
23. James W Stein C Estimation with quadradic loss Proceedings of the Fourth Berkeley Symposium on Mathematical Statistics and Probability: 1960 Berkeley, CA: University of California Press 1960
24. Gelman A Carlin JB Stern HS Rubin DB Bayesian Data Analysis London, UK: Chapman and Hall/CRC 1995
25. Hugall A Moritz C Moussalli A Stanisic J Reconciling paleodistribution models and comparative phylogeography in the Wet Tropics rainforest land snail Gnarosophia bellendenkerensis (Brazier 1875) Proc Natl Acad Sci USA 2002 99 9 6112-6117 122911 11972064 10.1073/pnas.092538699
26. Kass RE Raftery A Bayesian factors Journal of the American Statistical Association 1995 90 773-795 10.2307/2291091
27. Kalinowski ST Evolutionary and statistical properties of three genetic distances Mol Ecol 2002 11 8 1263-1273 10.1046/j.1365-294X.2002.01520.x 12144649
28. Slatkin M Gene flow in natural populations Ann Rev Ecol Syst 1985 16 393-430 10.1146/annurev.ecolsys.16.1.393
29. 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 8813013
30. Wakeley J Distinguishing migration from isolation using the variance of pairwise differences Theor Popul Biol 1996 49 369-386 10.1006/ tpbi.1996.0018 8693431