- THIS ARTICLE
- Full Text
- Full Text (PDF)
- Alert me when this article is cited
- Alert me if a correction is posted
- SERVICES
- Email this article to a friend
- Similar articles in this journal
- Similar articles in PubMed
- Alert me to new issues of the journal
- Download to citation manager
- Reprints & Permissions
- CITING ARTICLES
- Citing Articles via HighWire
- Citing Articles via Google Scholar
- GOOGLE SCHOLAR
- Articles by Adams, A. M.
- Articles by Hudson, R. R.
- Search for Related Content
- PUBMED
- PubMed Citation
- Articles by Adams, A. M.
- Articles by Hudson, R. R.
Genetics, Vol. 168, 1699-1712, November 2004, Copyright © 2004
doi:10.1534/genetics.104.030171
Maximum-Likelihood Estimation of Demographic Parameters Using the Frequency Spectrum of Unlinked Single-Nucleotide Polymorphisms
Alison M. Adams*,1 and
Richard R. Hudson
* Committee on Genetics, University of Chicago, Chicago, Illinois 60637
Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637
1 Corresponding author: Department of Ecology and Evolution, 1101 E. 57th St., Room Z302, University of Chicago, Chicago, IL 60637.
E-mail: alison1{at}uchicago.edu
A maximum-likelihood method for demographic inference is applied to data sets consisting of the frequency spectrum of unlinked single-nucleotide polymorphisms (SNPs). We use simulation analyses to explore the effect of sample size and number of polymorphic sites on both the power to reject the null hypothesis of constant population size and the properties of two- and three-dimensional maximum-likelihood estimators (MLEs). Large amounts of data are required to produce accurate demographic inferences, particularly for scenarios of recent growth. Properties of the MLEs are highly dependent upon the demographic scenario, as estimates improve with a more ancient time of growth onset and smaller degree of growth. Severe episodes of growth lead to an upward bias in the estimates of the current population size, and that bias increases with the magnitude of growth. One data set of African origin supports a model of mild, ancient growth, and another is compatible with both constant population size and a variety of growth scenarios, rejecting greater than fivefold growth beginning >36,000 years ago. Analysis of a data set of European origin indicates a bottlenecked population history, with an 85% population reduction occurring 
30,000 years ago.
This article has been cited by other articles:
 |
|
 |
|
  R. Nielsen, M. J. Hubisz, I. Hellmann, D. Torgerson, A. M. Andres, A. Albrechtsen, R. Gutenkunst, M. D. Adams, M. Cargill, A. Boyko, et al. Darwinian and demographic forces affecting human protein coding genes Genome Res., May 1, 2009; 19(5): 838 - 849. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. Stadler, B. Haubold, C. Merino, W. Stephan, and P. Pfaffelhuber The Impact of Sampling Schemes on the Site Frequency Spectrum in Nonequilibrium Subdivided Populations Genetics, May 1, 2009; 182(1): 205 - 216. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. E. Lohmueller, C. D. Bustamante, and A. G. Clark Methods for Human Demographic Inference Using Haplotype Patterns From Genomewide Single-Nucleotide Polymorphism Data Genetics, May 1, 2009; 182(1): 217 - 231. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 G. V. Kryukov, A. Shpunt, J. A. Stamatoyannopoulos, and S. R. Sunyaev Power of deep, all-exon resequencing for discovery of human trait genes PNAS, March 10, 2009; 106(10): 3871 - 3876. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
I. Hellmann, Y. Mang, Z. Gu, P. Li, F. M. de la Vega, A. G. Clark, and R. Nielsen Population genetic analysis of shotgun assemblies of genomic sequences from multiple individuals Genome Res., July 1, 2008; 18(7): 1020 - 1029. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. D. Keightley and A. Eyre-Walker Joint Inference of the Distribution of Fitness Effects of Deleterious Mutations and Population Demography Based on Nucleotide Polymorphism Frequencies Genetics, December 1, 2007; 177(4): 2251 - 2261. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
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]
|
|
|
|
 |
|
 S. Seixas, G. Suriano, F. Carvalho, R. Seruca, J. Rocha, and A. Di Rienzo Sequence Diversity at the Proximal 14q32.1 SERPIN Subcluster: Evidence for Natural Selection Favoring the Pseudogenization of SERPINA2 Mol. Biol. Evol., February 1, 2007; 24(2): 587 - 598. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. P. Noonan, G. Coop, S. Kudaravalli, D. Smith, J. Krause, J. Alessi, F. Chen, D. Platt, S. Paabo, J. K. Pritchard, et al. Sequencing and Analysis of Neanderthal Genomic DNA. Science, November 17, 2006; 314(5802): 1113 - 1118. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 U.-k. Kim, S. Wooding, N. Riaz, L. B. Jorde, and D. Drayna Variation in the Human TAS1R Taste Receptor Genes Chem Senses, September 1, 2006; 31(7): 599 - 611. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Innan Modified Hudson-Kreitman-Aguade Test and Two-Dimensional Evaluation of Neutrality Tests Genetics, July 1, 2006; 173(3): 1725 - 1733. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. M. Teshima, G. Coop, and M. Przeworski How reliable are empirical genomic scans for selective sweeps? Genome Res., June 1, 2006; 16(6): 702 - 712. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Eyre-Walker, M. Woolfit, and T. Phelps The Distribution of Fitness Effects of New Deleterious Amino Acid Mutations in Humans Genetics, June 1, 2006; 173(2): 891 - 900. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. F. Voight, A. M. Adams, L. A. Frisse, Y. Qian, R. R. Hudson, and A. Di Rienzo Interrogating multiple aspects of variation in a full resequencing data set to infer human population size changes PNAS, December 20, 2005; 102(51): 18508 - 18513. [Abstract] [Full Text] [PDF]
|
|