Simulating gene trees under the multispecies coalescent and time-dependent migration

BMC Evolutionary Biology

Volumn 13, Issue 1, 2013, Pages

  Heled, Joseph ^a   Bryant, David ^b,c   Drummond, Alexei J ^a,b  

^a UNIVERSITY OF AUCKLAND   (New Zealand)

^b Allan Wilson Centre for Molecular Ecology & Evolution   (New Zealand)

^c UNIVERSITY OF OTAGO   (New Zealand)

Author keywords

[No Author keywords available]

Indexed keywords

COALESCENCE; DATA SET; FRACTIONATION; GENE EXPRESSION; GENETIC ANALYSIS; MIGRATION; NUMERICAL MODEL; PHYLOGENY; POPULATION SIZE; SOFTWARE; SPECIATION (BIOLOGY); TIME DEPENDENT BEHAVIOR; TOPOLOGY;

ARTICLE; BIOLOGICAL MODEL; COMPUTER PROGRAM; COMPUTER SIMULATION; EQUIPMENT; EVALUATION STUDY; GENE FLOW; METHODOLOGY; MOLECULAR EVOLUTION; PHYLOGENY; POPULATION GENETICS; SPECIES DIFFERENTIATION; STATISTICAL MODEL;

COMPUTER SIMULATION; EVOLUTION, MOLECULAR; GENE FLOW; GENETIC SPECIATION; GENETICS, POPULATION; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; PHYLOGENY; SOFTWARE;

EID: 84873939892     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-13-44     Document Type: Article

References (36)

1. Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Rannala B, Yang Z, Genetics 2003 164 4 1645 1656 12930768
2. The probability distribution of ranked gene trees on a species tree. Degnan J, Rosenberg N, Stadler T, Math Biosci 2012 235 45 55 10.1016/j.mbs.2011.10.006 22075548
3. Inconsistency of phylogenetic estimates from concatenated data under coalescence. Kubatko L, Degnan J, Syst Biol 2007 56 17 24 10.1080/ 10635150601146041 17366134
4. STEM: species tree estimation using maximum likelihood for gene trees under coalescence. Kubatko L, Carstens B, Knowles L, Bioinformatics 2009 25 7 971 973 10.1093/bioinformatics/btp079 19211573
5. Bayesian inference of species trees from multilocus data. Heled J, Drummond A, Mol Biol Evol 2010 27 3 570 10.1093/molbev/msp274 19906793
6. Estimating Species Trees Using Multiple-Allele DNA Sequence Data. Liu L, Pearl D, Brumfield R, Edwards S, Evolution 2008 62 8 2080 2091 10.1111/j.1558-5646.2008.00414.x 18462214
7. BEST: Bayesian estimation of species trees under the coalescent model. Liu L, Bioinformatics 2008 24 21 2542 2543 10.1093/bioinformatics/btn484 18799483
8. BUCKy: Gene tree/species tree reconciliation with Bayesian concordance analysis. Larget B, Kotha S, Dewey C, Ané C, Bioinformatics 2010 26 22 2910 2911 10.1093/bioinformatics/btq539 20861028
9. The accuracy of species tree estimation under simulation: a comparison of methods. Leaché A, Rannala B, Syst Biol 2011 60 2 126 137 10.1093/sysbio/syq073 21088009
10. Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics. Hey J, Nielsen R, Proc Natl Acad Sci 2007 104 8 2785 10.1073/pnas.0611164104 17301231
11. Isolation by distance. Wright S, Genetics 1943 28 2 114 17247074
12. Stepping stone. Kimura M, Model Popul Annu Rep Natl Inst Genet Jpn 1953 3 62 63
13. The stepping stone model of population structure and the decrease of genetic correlation with distance. Kimura M, Weiss G, Genetics 1964 49 4 561 17248204
14. A migration matrix model for the study of random genetic drift. Bodmer W, Cavalli-Sforza L, Genetics 1968 59 4 565 5708302
15. Generating samples under a Wright-Fisher neutral model of genetic variation. Hudson R, Bioinformatics 2002 18 2 337 338 10.1093/bioinformatics/18. 2.337 11847089
16. SIMCOAL 2.0: a program to simulate genomic diversity over large recombining regions in a subdivided population with a complex history. Laval G, Excoffier L, Bioinformatics 2004 20 15 2485 2487 10.1093/bioinformatics/bth264 15117750
17. Calibrating a coalescent simulation of human genome sequence variation. Schaffner S, Foo C, Gabriel S, Reich D, Daly M, Altshuler D, Genome Research 2005 15 11 1576 1583 10.1101/gr.3709305 16251467
18. GENOME: a rapid coalescent-based whole genome simulator. Liang L, Zöllner S, Abecasis G, Bioinformatics 2007 23 12 1565 1567 10.1093/bioinformatics/btm138 17459963
19. A flexible forward simulator for populations subject to selection and demography. Hernandez R, Bioinformatics 2008 24 23 2786 2787 10.1093/bioinformatics/btn522 18842601
20. MSMS: a coalescent simulation program including recombination, demographic structure and selection at a single locus. Ewing G, Hermisson J, Bioinformatics 2010 26 16 2064 2065 10.1093/bioinformatics/btq322 20591904
21. fastsimcoal: a continuous-time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios. Excoffier L, Foll M, Bioinformatics 2011 27 9 1332 1334 10.1093/bioinformatics/btr124 21398675
22. How robust are "isolation with migration" analyses to violations of the IM model? A simulation study. Strasburg J, Rieseberg L, Mol Biol Evol 2010 27 2 297 10.1093/molbev/msp233 19793831
23. Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis. Hey J, Nielsen R, Genetics 2004 167 2 747 10.1534/genetics.103.024182 15238526
24. Isolation with migration models for more than two populations. Hey J, Mol Biol Evol 2009
25. Evolution in Mendelian populations. Wright S, Genetics 1931 16 2 97 17246615
26. Gene flow in natural populations. Slatkin M, Ann Rev Ecol Syst 1985 16 393 430
27. Sampling Theory for Neutral Alleles in a Varying Environment. Griffiths RC, Tavare S, R Soc Lond Philos Trans Ser B 1994 344 403 410 10.1098/rstb.1994.0079
28. Bayesian inference of population size history from multiple loci. Heled J, Drummond A, BMC Evol Biol 2008 8 289 10.1186/1471-2148-8-289 18947398
29. Gene genealogy and the coalescent process. Hudson R, Oxford Surv Evol Biol 1990 7 1 44
30. The coalescent and the genealogical process in geographically structured population. Notohara M, J Math Biol 1990 29 59 75 2277236
31. Branch lengths on birth-death trees and the expected loss of phylogenetic diversity. Mooers A, Gascuel O, Stadler T, Li H, Steel M, Syst Biol 2012 61 2 195 203 10.1093/sysbio/syr090 21865336
32. A statistical approach for distinguishing hybridization and incomplete lineage sorting. Joly S, McLenachan P, Lockhart P, Am Nat 2009 174 2 54-70 19519219
33. JML: testing hybridization from species trees. JOLY S, Mol Ecol Resour 2011 12 179 184 21899723
34. Sequence diversity under the multispecies coalescent with Yule process and constant population size. Heled J, Theor Popul Biol 2011 81 2 97 101 22210390
35. On the convolution of exponential distributions. Akkouchi M, J Chungcheong Math Soc 2008 21 4 501 510
36. Evaluation of a Bayesian coalescent method of species delimitation. Zhang C, Zhang D, Zhu T, Yang Z, Syst Biol 2011 60 6 747 761 10.1093/sysbio/syr071 21876212