Genetics, Vol. 163, 395-404, January 2003, Copyright © 2003

Estimating Ancestral Population Sizes and Divergence Times

Jeffrey D. Walla
a Department of Human Genetics, University of Chicago, Chicago, Illinois 60637

Corresponding author: Jeffrey D. Wall, 920 E. 58th St.--CLSC 507, Chicago, IL 60637., jwall{at}genetics.bsd.uchicago.edu (E-mail)

Communicating editor: N. TAKAHATA

This article presents a new method for jointly estimating species divergence times and ancestral population sizes. The method improves on previous ones by explicitly incorporating intragenic recombination, by utilizing orthologous sequence data from closely related species, and by using a maximum-likelihood framework. The latter allows for efficient use of the available information and provides a way of assessing how much confidence we should place in the estimates. I apply the method to recently collected intergenic sequence data from humans and the great apes. The results suggest that the human-chimpanzee ancestral population size was four to seven times larger than the current human effective population size and that the current human effective population size is slightly >10,000. These estimates are similar to previous ones, and they appear relatively insensitive to assumptions about the recombination rates or mutation rates across loci.




This article has been cited by other articles:


Home page
 Mol Biol EvolHome page
C. M. Miller-Butterworth, J. R. Kaplan, J. Shaffer, B. Devlin, S. B. Manuck, and R. E. Ferrell
Sequence Variation in the Primate Dopamine Transporter Gene and Its Relationship to Social Dominance
Mol. Biol. Evol., January 1, 2008; 25(1): 18 - 28.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
R. Zhou, K. Zeng, W. Wu, X. Chen, Z. Yang, S. Shi, and C.-I Wu
Population Genetics of Speciation in Nonmodel Organisms: I. Ancestral Polymorphism in Mangroves
Mol. Biol. Evol., December 1, 2007; 24(12): 2746 - 2754.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
C. Becquet and M. Przeworski
A new approach to estimate parameters of speciation models with application to apes
Genome Res., October 1, 2007; 17(10): 1505 - 1519.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
I. Ebersberger, P. Galgoczy, S. Taudien, S. Taenzer, M. Platzer, and A. von Haeseler
Mapping Human Genetic Ancestry
Mol. Biol. Evol., October 1, 2007; 24(10): 2266 - 2276.
[Abstract] [Full Text] [PDF]

Home page
 J. Virol.Home page
R. Belshaw, J. Watson, A. Katzourakis, A. Howe, J. Woolven-Allen, A. Burt, and M. Tristem
Rate of Recombinational Deletion among Human Endogenous Retroviruses
J. Virol., September 1, 2007; 81(17): 9437 - 9442.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
S. C. Leman, M. K. Uyenoyama, M. Lavine, and Y. Chen
The evolutionary forest algorithm
Bioinformatics, August 1, 2007; 23(15): 1962 - 1968.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
M. A. Bakewell, P. Shi, and J. Zhang
More genes underwent positive selection in chimpanzee evolution than in human evolution
PNAS, May 1, 2007; 104(18): 7489 - 7494.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
J. A. Shapiro, W. Huang, C. Zhang, M. J. Hubisz, J. Lu, D. A. Turissini, S. Fang, H.-Y. Wang, R. R. Hudson, R. Nielsen, et al.
Adaptive genic evolution in the Drosophila genomes
PNAS, February 13, 2007; 104(7): 2271 - 2276.
[Abstract] [Full Text] [PDF]

Home page
 J. Virol.Home page
L. A. Shackelton, A. Rambaut, O. G. Pybus, and E. C. Holmes
JC Virus Evolution and Its Association with Human Populations.
J. Virol., October 1, 2006; 80(20): 9928 - 9933.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
K. L. Bubb, D. Bovee, D. Buckley, E. Haugen, M. Kibukawa, M. Paddock, A. Palmieri, S. Subramanian, Y. Zhou, R. Kaul, et al.
Scan of Human Genome Reveals No New Loci Under Ancient Balancing Selection
Genetics, August 1, 2006; 173(4): 2165 - 2177.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
G. H. Perry, J. Tchinda, S. D. McGrath, J. Zhang, S. R. Picker, A. M. Caceres, A. J. Iafrate, C. Tyler-Smith, S. W. Scherer, E. E. Eichler, et al.
Hotspots for copy number variation in chimpanzees and humans
PNAS, May 23, 2006; 103(21): 8006 - 8011.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
H. Innan and H. Watanabe
The Effect of Gene Flow on the Coalescent Time in the Human-Chimpanzee Ancestral Population
Mol. Biol. Evol., May 1, 2006; 23(5): 1040 - 1047.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
J. Taylor, S. Tyekucheva, M. Zody, F. Chiaromonte, and K. D. Makova
Strong and Weak Male Mutation Bias at Different Sites in the Primate Genomes: Insights from the Human-Chimpanzee Comparison
Mol. Biol. Evol., March 1, 2006; 23(3): 565 - 573.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
H. E. Walsh, I. L. Jones, and V. L. Friesen
A Test of Founder Effect Speciation Using Multiple Loci in the Auklets (Aethia spp.)
Genetics, December 1, 2005; 171(4): 1885 - 1894.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
S. C. Leman, Y. Chen, J. E. Stajich, M. A. F. Noor, and M. K. Uyenoyama
Likelihoods From Summary Statistics: Recent Divergence Between Species
Genetics, November 1, 2005; 171(3): 1419 - 1436.
[Abstract] [Full Text] [PDF]

Home page
 J. Virol.Home page
R. Belshaw, A. L. A. Dawson, J. Woolven-Allen, J. Redding, A. Burt, and M. Tristem
Genomewide Screening Reveals High Levels of Insertional Polymorphism in the Human Endogenous Retrovirus Family HERV-K(HML2): Implications for Present-Day Activity
J. Virol., October 1, 2005; 79(19): 12507 - 12514.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
F. A. Reed, J. M. Akey, and C. F. Aquadro
Fitting background-selection predictions to levels of nucleotide variation and divergence along the human autosomes
Genome Res., September 1, 2005; 15(9): 1211 - 1221.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
N. Osada and C.-I Wu
Inferring the Mode of Speciation From Genomic Data: A Study of the Great Apes
Genetics, January 1, 2005; 169(1): 259 - 264.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
S. I. Wright and B. Charlesworth
The HKA Test Revisited: A Maximum-Likelihood-Ratio Test of the Standard Neutral Model
Genetics, October 1, 2004; 168(2): 1071 - 1076.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
J. M. Comeron
Selective and Mutational Patterns Associated With Gene Expression in Humans: Influences on Synonymous Composition and Intron Presence
Genetics, July 1, 2004; 167(3): 1293 - 1304.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
S. E. Ptak, K. Voelpel, and M. Przeworski
Insights Into Recombination From Patterns of Linkage Disequilibrium in Humans
Genetics, May 1, 2004; 167(1): 387 - 397.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
A. Fischer, V. Wiebe, S. Paabo, and M. Przeworski
Evidence for a Complex Demographic History of Chimpanzees
Mol. Biol. Evol., May 1, 2004; 21(5): 799 - 808.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
B. Rannala and Z. Yang
Bayes Estimation of Species Divergence Times and Ancestral Population Sizes Using DNA Sequences From Multiple Loci
Genetics, August 1, 2003; 164(4): 1645 - 1656.
[Abstract] [Full Text] [PDF]