Journal
MOLECULAR BIOLOGY AND EVOLUTION
Volume 18, Issue 12, Pages 2298-2305Publisher
SOC MOLECULAR BIOLOGY EVOLUTION
DOI: 10.1093/oxfordjournals.molbev.a003776
Keywords
coalescent process; corrected Akaike criterion; HIV-1 model selection; likelihood; red panda; skyline plot
Ask authors/readers for more resources
We present an intuitive visual framework, the generalized skyline plot, to explore the demographic history of sampled DNA sequences. This approach is based on a genealogy inferred from the sequences and provides a nonparametric estimate of effective population size through time. In contrast to previous related procedures, the generalized skyline plot is more applicable to cases where the underlying tree is not fully resolved and the data is not highly variable. This is achieved by the grouping of adjacent coalescent intervals. We employ a small-sample Akaike information criterion to objectively choose the optimal grouping strategy. We investigate the performance of our approach using simulation and subsequently apply it to HIV-1 sequences from central Africa and mtDNA sequences from red pandas.
Authors
I am an author on this paper
Click your name to claim this paper and add it to your profile.
Reviews
Recommended
No Data Available