Bayesian Coalescent Inference of Past Population Dynamics from Molecular Sequences

2005/02/09 by Alexei J. Drummond · 3,273 citations
Biochemistry, Genetics and Molecular Biology · Environmental Science · Mathematics · #Forensic and Genetic Research #Genetic diversity and population structure #Isotope Analysis in Ecology #Coalescent theory #Skyline #Population #Biology #Markov chain Monte Carlo #Bayesian probability #Plot (graphics) #Markov chain #Inference #Effective population size #Evolutionary biology #Statistics #Computer science #Mathematics #Artificial intelligence #Data mining #Genetics #Phylogenetic tree #Demography #Genetic diversity

paper · pdf · doi:10.1093/molbev/msi103

published in Molecular Biology and Evolution 22(5), 1185-1192 (Oxford University Press)

openalex publication_date 2005/02/09 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/01

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.

Citations

• Dating of the human-ape splitting by a molecular clock of mitochondrial DNA
• Estimating effective population size from samples of sequences: inefficiency of pairwise and segregating sites as compared to phylogenetic estimates
• Rise and Fall of the Beringian Steppe Bison
• Sampling theory for neutral alleles in a varying environment
• Genetic evidence for a Paleolithic human population expansion in Africa
• A new look at the statistical model identification
• Measurably evolving populations

Cited by

• Detecting past changes of effective population size
• Phylogeography of the North American red fox: vicariance in Pleistocene forest refugia
• Range‐wide multilocus phylogeography of the red fox reveals ancient continental divergence, minimal genomic exchange and distinct demographic histories
• Out of America: Ancient DNA Evidence for a New World Origin of Late Quaternary Woolly Mammoths
• Insights into human genetic variation and population history from 929 diverse genomes
• Prehistoric demography [wikipedia]