Molecular Biology and Evolution 18:2298-2305 (2001)
© 2001 Society for Molecular Biology and Evolution
Exploring the Demographic History of DNA Sequences Using the Generalized Skyline Plot
Department of Zoology, University of Oxford
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.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  V. N. Minin, E. W. Bloomquist, and M. A. Suchard Smooth Skyride through a Rough Skyline: Bayesian Coalescent-Based Inference of Population Dynamics Mol. Biol. Evol., July 1, 2008; 25(7): 1459 - 1471. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. Wirth, G. Morelli, B. Kusecek, A. van Belkum, C. van der Schee, A. Meyer, and M. Achtman The rise and spread of a new pathogen: Seroresistant Moraxella catarrhalis Genome Res., November 1, 2007; 17(11): 1647 - 1656. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 N. Jimenez-Hernandez, M. Torres-Puente, M. A. Bracho, I. Garcia-Robles, E. Ortega, J. del Olmo, F. Carnicer, F. Gonzalez-Candelas, and A. Moya Epidemic dynamics of two coexisting hepatitis C virus subtypes J. Gen. Virol., January 1, 2007; 88(1): 123 - 133. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. M. Goodreau Assessing the Effects of Human Mixing Patterns on Human Immunodeficiency Virus-1 Interhost Phylogenetics Through Social Network Simulation. Genetics, April 1, 2006; 172(4): 2033 - 2045. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Nakano, L. Lu, Y. He, Y. Fu, B. H. Robertson, and O. G. Pybus Population genetic history of hepatitis C virus 1b infection in China J. Gen. Virol., January 1, 2006; 87(1): 73 - 82. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Salemi, S. L. Lamers, S. Yu, T. de Oliveira, W. M. Fitch, and M. S. McGrath Phylodynamic Analysis of Human Immunodeficiency Virus Type 1 in Distinct Brain Compartments Provides a Model for the Neuropathogenesis of AIDS J. Virol., September 1, 2005; 79(17): 11343 - 11352. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 D. Field, E. J. Feil, and G. A. Wilson Databases and software for the comparison of prokaryotic genomes Microbiology, July 1, 2005; 151(7): 2125 - 2132. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. J. Drummond, A. Rambaut, B. Shapiro, and O. G. Pybus Bayesian Coalescent Inference of Past Population Dynamics from Molecular Sequences Mol. Biol. Evol., May 1, 2005; 22(5): 1185 - 1192. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. F. Wilkins A Separation-of-Timescales Approach to the Coalescent in a Continuous Population Genetics, December 1, 2004; 168(4): 2227 - 2244. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 B. Shapiro, A. J. Drummond, A. Rambaut, M. C. Wilson, P. E. Matheus, A. V. Sher, O. G. Pybus, M. T. P. Gilbert, I. Barnes, J. Binladen, et al. Rise and Fall of the Beringian Steppe Bison Science, November 26, 2004; 306(5701): 1561 - 1565. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. Lemey, O. G. Pybus, A. Rambaut, A. J. Drummond, D. L. Robertson, P. Roques, M. Worobey, and A.-M. Vandamme The Molecular Population Genetics of HIV-1 Group O Genetics, July 1, 2004; 167(3): 1059 - 1068. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 N. S. Flanagan, A. Tobler, A. Davison, O. G. Pybus, D. D. Kapan, S. Planas, M. Linares, D. Heckel, and W. O. McMillan Historical demography of Mullerian mimicry in the neotropical Heliconius butterflies PNAS, June 29, 2004; 101(26): 9704 - 9709. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. F. Sarkar and D. S. Guttman Evolution of the Core Genome of Pseudomonas syringae, a Highly Clonal, Endemic Plant Pathogen Appl. Envir. Microbiol., April 1, 2004; 70(4): 1999 - 2012. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. Arnason Mitochondrial Cytochrome b DNA Variation in the High-Fecundity Atlantic Cod: Trans-Atlantic Clines and Shallow Gene Genealogy Genetics, April 1, 2004; 166(4): 1871 - 1885. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. Lemey, O. G. Pybus, B. Wang, N. K. Saksena, M. Salemi, and A.-M. Vandamme Tracing the origin and history of the HIV-2 epidemic PNAS, May 27, 2003; 100(11): 6588 - 6592. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
O. G. Pybus, A. J. Drummond, T. Nakano, B. H. Robertson, and A. Rambaut The Epidemiology and Iatrogenic Transmission of Hepatitis C Virus in Egypt: A Bayesian Coalescent Approach Mol. Biol. Evol., March 1, 2003; 20(3): 381 - 387. [Abstract] [Full Text] [PDF]
|
|