References
- Chung Y, Hey J. Bayesian analysis of evolutionary divergence with genomic data under diverse demographic models. Mol Biol Evol 2017;34:1517-1528. https://doi.org/10.1093/molbev/msx070
- 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. https://doi.org/10.1534/genetics.103.024182
- Hey J, Nielsen R. Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics. Proc Natl Acad Sci U S A 2007;104:2785-2790. https://doi.org/10.1073/pnas.0611164104
- Nielsen R, Wakeley J. Distinguishing migration from isolation: a Markov chain Monte Carlo approach. Genetics 2001;158:885-896. https://doi.org/10.1093/genetics/158.2.885
- Drummond AJ, Suchard MA, Xie D, Rambaut A. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol 2012;29:1969-1973. https://doi.org/10.1093/molbev/mss075
- Kubatko LS, Carstens BC, Knowles LL. STEM: species tree estimation using maximum likelihood for gene trees under coalescence. Bioinformatics 2009;25:971-973. https://doi.org/10.1093/bioinformatics/btp079
- Liu L. BEST: Bayesian estimation of species trees under the coalescent model. Bioinformatics 2008;24:2542-2543. https://doi.org/10.1093/bioinformatics/btn484
- Liu L, Pearl DK. Species trees from gene trees: reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions. Syst Biol 2007;56:504-514. https://doi.org/10.1080/10635150701429982
- Liu L, Yu L, Kubatko L, Pearl DK, Edwards SV. Coalescent methods for estimating phylogenetic trees. Mol Phylogenet Evol 2009;53:320-328. https://doi.org/10.1016/j.ympev.2009.05.033
- Rannala B, Yang Z. Efficient Bayesian species tree inference under the multispecies coalescent. Syst Biol 2017;66:823-842. https://doi.org/10.1093/sysbio/syw119
- Degnan JH, Rosenberg NA. Gene tree discordance, phylogenetic inference and the multispecies coalescent. Trends Ecol Evol 2009;24:332-340. https://doi.org/10.1016/j.tree.2009.01.009
- Chung Y, Ane C. Comparing two Bayesian methods for gene tree/species tree reconstruction: simulations with incomplete lineage sorting and horizontal gene transfer. Syst Biol 2011;60:261-275. https://doi.org/10.1093/sysbio/syr003
- Leache AD, Harris RB, Rannala B, Yang Z. The influence of gene flow on species tree estimation: a simulation study. Syst Biol 2014;63:17-30. https://doi.org/10.1093/sysbio/syt049
- Muller NF, Ogilvie HA, Zhang C, Drummond A, Stadler T. Inference of species histories in the presence of gene flow. Cold Spring Harbor: bioRxiv, Cold Spring Harbor Laboratory, 2018. Accessed 2019 Aug 3. Available from: https://doi.org/10.1101/348391.
- Bouckaert R, Vaughan TG, Barido-Sottani J, Duchene S, Fourment M, Gavryushkina A, et al. BEAST 2.5: an advanced software platform for Bayesian evolutionary analysis. PLoS Comput Biol 2019;15:e1006650. https://doi.org/10.1371/journal.pcbi.1006650
- Hey J, Chung Y, Sethuraman A, Lachance J, Tishkoff S, Sousa VC, et al. Phylogeny estimation by integration over isolation with migration models. Mol Biol Evol 2018;35:2805-2818.
- Hey J. Isolation with migration models for more than two populations. Mol Biol Evol 2010;27:905-920. https://doi.org/10.1093/molbev/msp296
- Wakeley J, Hey J. Testing speciation models with DNA sequence data. In: Molecular Approaches to Ecology and Evolution (DeSalle R, Schierwater B, eds.). Basel: Birkhauser, 1998. pp. 157-175.
- Becquet C, Przeworski M. A new approach to estimate parameters of speciation models with application to apes. Genome Res 2007;17:1505-1519. https://doi.org/10.1101/gr.6409707
- Dalquen DA, Zhu T, Yang Z. Maximum likelihood implementation of an isolation-with-migration model for three species. Syst Biol 2017;66:379-398.
- Mailund T, Halager AE, Westergaard M, Dutheil JY, Munch K, Andersen LN, et al. A new isolation with migration model along complete genomes infers very different divergence processes among closely related great ape species. PLoS Genet 2012;8:e1003125. https://doi.org/10.1371/journal.pgen.1003125
- Muller NF, Rasmussen DA, Stadler T. The structured coalescent and its approximations. Mol Biol Evol 2017;34:2970-2981. https://doi.org/10.1093/molbev/msx186
- Craiu RV, Rosenthal JS. Bayesian computation via Markov chain Monte Carlo. Annu Rev Stat Its Appl 2014;1:179-201. https://doi.org/10.1146/annurev-statistics-022513-115540
- Sousa V, Hey J. Understanding the origin of species with genome-scale data: modelling gene flow. Nat Rev Genet 2013;14:404-414. https://doi.org/10.1038/nrg3446
- Nascimento FF, Reis MD, Yang Z. A biologist's guide to Bayesian phylogenetic analysis. Nat Ecol Evol 2017;1:1446-1454. https://doi.org/10.1038/s41559-017-0280-x
- Chatzou M, Magis C, Chang JM, Kemena C, Bussotti G, Erb I, et al. Multiple sequence alignment modeling: methods and applications. Brief Bioinform 2016;17:1009-1023. https://doi.org/10.1093/bib/bbv099
- Hudson RR, Kaplan NL. Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics 1985;111:147-64. https://doi.org/10.1093/genetics/111.1.147
- Kimura M. The number of heterozygous nucleotide sites maintained in a finite population due to steady flux of mutations. Genetics 1969;61:893-903. https://doi.org/10.1093/genetics/61.4.893
- Jukes TH, Cantor CR. Evolution of protein molecules. In: Mammalian Protein Metabolism (Munro HN, ed.). New York: Academic Press, 1969. pp. 21-132.
- Hasegawa M, Kishino H, Yano T. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol 1985;22:160-174. https://doi.org/10.1007/BF02101694
- Tavare S. Some probabilistic and statistical problems in the analysis of DNA sequences. Am Math Soc Lect Math Life Sci 1986;17:57-86.
- Kingman JF. On the genealogy of large populations. J Appl Probab 1982;19:27-43. https://doi.org/10.1017/S0021900200034446
- Hudson RR. Properties of a neutral allele model with intragenic recombination. Theor Popul Biol 1983;23:183-201. https://doi.org/10.1016/0040-5809(83)90013-8
- Hudson RR. Testing the constant-rate neutral allele model with protein sequence data. Evolution 1983;37:203-217. https://doi.org/10.2307/2408186
- Felsenstein J. Phylogenies from molecular sequences: inference and reliability. Annu Rev Genet 1988;22:521-565. https://doi.org/10.1146/annurev.ge.22.120188.002513
- Yang Z. Molecular Evolution: A Statistical Approach. Oxford: Oxford University Press, 2014.
- Robert CP. Bayesian computational tools. Annu Rev Stat Its Appl 2014;1:153-177. https://doi.org/10.1146/annurev-statistics-022513-115543
- Robert CP, Casella G. Monte Carlo Statistical Methods. New York: Springer, 2004.
- Sethuraman A, Hey J. IMa2p: parallel MCMC and inference of ancient demography under the Isolation with migration (IM) model. Mol Ecol Resour 2016;16:206-215. https://doi.org/10.1111/1755-0998.12437
- Knoblauch J, Sethuraman A, Hey J. IMGui-A Desktop GUI application for isolation with migration analyses. Mol Biol Evol 2017;34:500-504. https://doi.org/10.1093/molbev/msw252
- Cruickshank TE, Hahn MW. Reanalysis suggests that genomic islands of speciation are due to reduced diversity, not reduced gene flow. Mol Ecol 2014;23:3133-3157. https://doi.org/10.1111/mec.12796
- Hey J, Chung Y, Sethuraman A. On the occurrence of false positives in tests of migration under an isolation-with-migration model. Mol Ecol 2015;24:5078-5083. https://doi.org/10.1111/mec.13381
- Bouckaert R, Heled J, Kuhnert D, Vaughan T, Wu CH, Xie D, et al. BEAST 2: a software platform for Bayesian evolutionary analysis. PLoS Comput Biol 2014;10:e1003537. https://doi.org/10.1371/journal.pcbi.1003537
- Ogilvie HA, Bouckaert RR, Drummond AJ. StarBEAST2 brings faster species tree inference and accurate estimates of substitution rates. Mol Biol Evol 2017;34:2101-2114. https://doi.org/10.1093/molbev/msx126
- Barido-Sottani J, Boskova V, Plessis LD, Kuhnert D, Magnus C, Mitov V, et al. Taming the BEAST-A community teaching material resource for BEAST 2. Syst Biol 2018;67:170-174. https://doi.org/10.1093/sysbio/syx060
- Wilkinson-Herbots HM. The distribution of the coalescence time and the number of pairwise nucleotide differences in a model of population divergence or speciation with an initial period of gene flow. Theor Popul Biol 2012;82:92-108. https://doi.org/10.1016/j.tpb.2012.05.003
- Lan S, Palacios JA, Karcher M, Minin VN, Shahbaba B. An efficient Bayesian inference framework for coalescent-based nonparametric phylodynamics. Bioinformatics 2015;31:3282-3289. https://doi.org/10.1093/bioinformatics/btv378