Bayesian Coalescent Inference of Past Population Dynamics from Molecular Sequences Export

@article{citeulike:162412, abstract = {We introduce the Bayesian skyline plot, a new method for estimating past population dynamics through time from a sample of molecular sequences without dependence on a prespecified parametric model of demographic history. We describe a Markov chain Monte Carlo sampling procedure that efficiently samples a variant of the generalized skyline plot, given sequence data, and combines these plots to generate a posterior distribution of effective population size through time. We apply the Bayesian skyline plot to simulated data sets and show that it correctly reconstructs demographic history under canonical scenarios. Finally, we compare the Bayesian skyline plot model to previous coalescent approaches by analyzing two real data sets (hepatitis C virus in Egypt and mitochondrial DNA of Beringian bison) that have been previously investigated using alternative coalescent methods. In the bison analysis, we detect a severe but previously unrecognized bottleneck, estimated to have occurred 10,000 radiocarbon years ago, which coincides with both the earliest undisputed record of large numbers of humans in Alaska and the megafaunal extinctions in North America at the beginning of the Holocene. 10.1093/molbev/msi103}, author = {Drummond, A. J. and Rambaut, A. and Shapiro, B. and Pybus, O. G.}, citeulike-article-id = {162412}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/molbev/msi103}, citeulike-linkout-1 = {http://mbe.oxfordjournals.org/content/22/5/1185.abstract}, citeulike-linkout-2 = {http://mbe.oxfordjournals.org/content/22/5/1185.full.pdf}, citeulike-linkout-3 = {http://mbe.oxfordjournals.org/cgi/content/abstract/22/5/1185}, citeulike-linkout-4 = {http://www.ingentaconnect.com/content/oup/molbev/2005/00000022/00000005/art01185}, citeulike-linkout-5 = {http://view.ncbi.nlm.nih.gov/pubmed/15703244}, citeulike-linkout-6 = {http://www.hubmed.org/display.cgi?uids=15703244}, day = {1}, doi = {10.1093/molbev/msi103}, issn = {0737-4038}, journal = {Mol Biol Evol}, keywords = {coalescence, demographics, egypt, evolution-rate, finding-parameters, hepatitis, phylogenetics, skyline}, month = {May}, number = {5}, pages = {1185--1192}, posted-at = {2009-11-05 22:22:33}, priority = {0}, publisher = {Oxford University Press}, title = {Bayesian Coalescent Inference of Past Population Dynamics from Molecular Sequences}, url = {http://dx.doi.org/10.1093/molbev/msi103}, volume = {22}, year = {2005} }

TY - JOUR ID - citeulike:162412 L3 - citeulike-article-id:162412 N2 - We introduce the Bayesian skyline plot, a new method for estimating past population dynamics through time from a sample of molecular sequences without dependence on a prespecified parametric model of demographic history. We describe a Markov chain Monte Carlo sampling procedure that efficiently samples a variant of the generalized skyline plot, given sequence data, and combines these plots to generate a posterior distribution of effective population size through time. We apply the Bayesian skyline plot to simulated data sets and show that it correctly reconstructs demographic history under canonical scenarios. Finally, we compare the Bayesian skyline plot model to previous coalescent approaches by analyzing two real data sets (hepatitis C virus in Egypt and mitochondrial DNA of Beringian bison) that have been previously investigated using alternative coalescent methods. In the bison analysis, we detect a severe but previously unrecognized bottleneck, estimated to have occurred 10,000 radiocarbon years ago, which coincides with both the earliest undisputed record of large numbers of humans in Alaska and the megafaunal extinctions in North America at the beginning of the Holocene. 10.1093/molbev/msi103 IS - 5 JF - Mol Biol Evol SN - 0737-4038 EP - 1192 TI - Bayesian Coalescent Inference of Past Population Dynamics from Molecular Sequences PB - Oxford University Press VL - 22 SP - 1185 KW - coalescence KW - demographics KW - egypt KW - evolution-rate KW - finding-parameters KW - hepatitis KW - phylogenetics KW - skyline AU - Drummond, AJ AU - Rambaut, A AU - Shapiro, B AU - Pybus, OG PY - 2005/05/01/ UR - http://dx.doi.org/10.1093/molbev/msi103 ER -