Estimating Effective Population Size and Mutation Rate From Sequence Data Using Metropolis-Hastings Sampling

INVESTIGATIONS

Estimating Effective Population Size and Mutation Rate From Sequence Data Using Metropolis-Hastings Sampling

M. K. Kuhner, J. Yamato and J. Felsenstein
Department of Genetics, University of Washington, Seattle, Washington 98195-7360

We present a new way to make a maximum likelihood estimate of the parameter 4N(e){mu} (effective population size times mutation rate per site, or {theta}) based on a population sample of molecular sequences. We use a Metropolis-Hastings Markov chain Monte Carlo method to sample genealogies in proportion to the product of their likelihood with respect to the data and their prior probability with respect to a coalescent distribution. A specific value of {theta} must be chosen to generate the coalescent distribution, but the resulting trees can be used to evaluate the likelihood at other values of {theta}, generating a likelihood curve. This procedure concentrates sampling on those genealogies that contribute most of the likelihood, allowing estimation of meaningful likelihood curves based on relatively small samples. The method can potentially be extended to cases involving varying population size, recombination, and migration.

This article has been cited by other articles:

D. A. Vasco
A Fast and Reliable Computational Method for Estimating Population Genetic Parameters
Genetics, June 1, 2008; 179(2): 951 - 963.
[Abstract] [Full Text] [PDF]

C. P. Burridge, D. Craw, D. Fletcher, and J. M. Waters
Geological Dates and Molecular Rates: Fish DNA Sheds Light on Time Dependency
Mol. Biol. Evol., April 1, 2008; 25(4): 624 - 633.
[Abstract] [Full Text] [PDF]

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]

M. G. B. Blum and N. A. Rosenberg
Estimating the Number of Ancestral Lineages Using a Maximum-Likelihood Method Based on Rejection Sampling
Genetics, July 1, 2007; 176(3): 1741 - 1757.
[Abstract] [Full Text] [PDF]

A. RoyChoudhury and M. Stephens
Fast and Accurate Estimation of the Population-Scaled Mutation Rate, {theta}, From Microsatellite Genotype Data
Genetics, June 1, 2007; 176(2): 1363 - 1366.
[Abstract] [Full Text] [PDF]

X. Liu and Y.-X. Fu
Test of Genetical Isochronism for Longitudinal Samples of DNA Sequences
Genetics, May 1, 2007; 176(1): 327 - 342.
[Abstract] [Full Text] [PDF]

J. Hey and R. Nielsen
Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics
PNAS, February 20, 2007; 104(8): 2785 - 2790.
[Abstract] [Full Text] [PDF]

M. K. Kuhner and L. P. Smith
Comparing Likelihood and Bayesian Coalescent Estimation of Population Parameters
Genetics, January 1, 2007; 175(1): 155 - 165.
[Abstract] [Full Text] [PDF]

M. K. Kuhner
Robustness of Coalescent Estimators to Between-Lineage Mutation Rate Variation
Mol. Biol. Evol., December 1, 2006; 23(12): 2355 - 2360.
[Abstract] [Full Text] [PDF]

M. M. Tanaka, A. R. Francis, F. Luciani, and S. A. Sisson
Using Approximate Bayesian Computation to Estimate Tuberculosis Transmission Parameters From Genotype Data
Genetics, July 1, 2006; 173(3): 1511 - 1520.
[Abstract] [Full Text] [PDF]

M. K. Kuhner
LAMARC 2.0: maximum likelihood and Bayesian estimation of population parameters
Bioinformatics, March 15, 2006; 22(6): 768 - 770.
[Abstract] [Full Text] [PDF]

J. Felsenstein
Accuracy of Coalescent Likelihood Estimates: Do We Need More Sites, More Sequences, or More Loci?
Mol. Biol. Evol., March 1, 2006; 23(3): 691 - 700.
[Abstract] [Full Text] [PDF]

P. Beerli
Comparison of Bayesian and maximum-likelihood inference of population genetic parameters
Bioinformatics, February 1, 2006; 22(3): 341 - 345.
[Abstract] [Full Text] [PDF]

B. W. Bowen, A. Muss, L. A. Rocha, and W. S. Grant
Shallow mtDNA Coalescence in Atlantic Pygmy Angelfishes (Genus Centropyge) Indicates a Recent Invasion from the Indian Ocean
J. Hered., January 1, 2006; 97(1): 1 - 12.
[Abstract] [Full Text] [PDF]

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]

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]

H. Li and W. Stephan
Maximum-Likelihood Methods for Detecting Recent Positive Selection and Localizing the Selected Site in the Genome
Genetics, September 1, 2005; 171(1): 377 - 384.
[Abstract] [Full Text] [PDF]

E. M. Rauch and Y. Bar-Yam
Estimating the total genetic diversity of a spatial field population from a sample and implications of its dependence on habitat area
PNAS, July 12, 2005; 102(28): 9826 - 9829.
[Abstract] [Full Text] [PDF]

E. C. Anderson
An Efficient Monte Carlo Method for Estimating Ne From Temporally Spaced Samples Using a Coalescent-Based Likelihood
Genetics, June 1, 2005; 170(2): 955 - 967.
[Abstract] [Full Text] [PDF]

D. Lavillette, Y. Morice, G. Germanidis, P. Donot, A. Soulier, E. Pagkalos, G. Sakellariou, L. Intrator, B. Bartosch, J.-M. Pawlotsky, et al.
Human Serum Facilitates Hepatitis C Virus Infection, and Neutralizing Responses Inversely Correlate with Viral Replication Kinetics at the Acute Phase of Hepatitis C Virus Infection
J. Virol., May 15, 2005; 79(10): 6023 - 6034.
[Abstract] [Full Text] [PDF]

W. Maury, R. J. Thompson, Q. Jones, S. Bradley, T. Denke, P. Baccam, M. Smazik, and J. L. Oaks
Evolution of the Equine Infectious Anemia Virus Long Terminal Repeat during the Alteration of Cell Tropism
J. Virol., May 1, 2005; 79(9): 5653 - 5664.
[Abstract] [Full Text] [PDF]

S. Hue, D. Pillay, J. P. Clewley, and O. G. Pybus
Genetic analysis reveals the complex structure of HIV-1 transmission within defined risk groups
PNAS, March 22, 2005; 102(12): 4425 - 4429.
[Abstract] [Full Text] [PDF]

K. J. Schmid, S. Ramos-Onsins, H. Ringys-Beckstein, B. Weisshaar, and T. Mitchell-Olds
A Multilocus Sequence Survey in Arabidopsis thaliana Reveals a Genome-Wide Departure From a Neutral Model of DNA Sequence Polymorphism
Genetics, March 1, 2005; 169(3): 1601 - 1615.
[Abstract] [Full Text] [PDF]

P. Fearnhead, R. M. Harding, J. A. Schneider, S. Myers, and P. Donnelly
Application of Coalescent Methods to Reveal Fine-Scale Rate Variation and Recombination Hotspots
Genetics, August 1, 2004; 167(4): 2067 - 2081.
[Abstract] [Full Text] [PDF]

L. B. Beheregaray, J. P. Gibbs, N. Havill, T. H. Fritts, J. R. Powell, and A. Caccone
Giant tortoises are not so slow: Rapid diversification and biogeographic consensus in the Galapagos
PNAS, April 27, 2004; 101(17): 6514 - 6519.
[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]

D. Shriner, R. Shankarappa, M. A. Jensen, D. C. Nickle, J. E. Mittler, J. B. Margolick, and J. I. Mullins
Influence of Random Genetic Drift on Human Immunodeficiency Virus Type 1 env Evolution During Chronic Infection
Genetics, March 1, 2004; 166(3): 1155 - 1164.
[Abstract] [Full Text] [PDF]

G. T. Marth, E. Czabarka, J. Murvai, and S. T. Sherry
The Allele Frequency Spectrum in Genome-Wide Human Variation Data Reveals Signals of Differential Demographic History in Three Large World Populations
Genetics, January 1, 2004; 166(1): 351 - 372.
[Abstract] [Full Text] [PDF]

P. L. Morrell, K. E. Lundy, and M. T. Clegg
Distinct geographic patterns of genetic diversity are maintained in wild barley (Hordeum vulgare ssp. spontaneum) despite migration
PNAS, September 16, 2003; 100(19): 10812 - 10817.
[Abstract] [Full Text] [PDF]

M. A. Beaumont
Estimation of Population Growth or Decline in Genetically Monitored Populations
Genetics, July 1, 2003; 164(3): 1139 - 1160.
[Abstract] [Full Text] [PDF]

N. Yu, Y.-X. Fu, and W.-H. Li
DNA Polymorphism in a Worldwide Sample of Human X Chromosomes
Mol. Biol. Evol., December 1, 2002; 19(12): 2131 - 2141.
[Abstract] [Full Text] [PDF]

S.-L. Liu, J. E. Mittler, D. C. Nickle, T. M. Mulvania, D. Shriner, A. G. Rodrigo, B. Kosloff, X. He, L. Corey, and J. I. Mullins
Selection for Human Immunodeficiency Virus Type 1 Recombinants in a Patient with Rapid Progression to AIDS
J. Virol., October 2, 2002; 76(21): 10674 - 10684.
[Abstract] [Full Text] [PDF]

S. Williamson and M. E. Orive
The Genealogy of a Sequence Subject to Purifying Selection at Multiple Sites
Mol. Biol. Evol., August 1, 2002; 19(8): 1376 - 1384.
[Abstract] [Full Text] [PDF]

A. J. Drummond, G. K. Nicholls, A. G. Rodrigo, and W. Solomon
Estimating Mutation Parameters, Population History and Genealogy Simultaneously From Temporally Spaced Sequence Data
Genetics, July 1, 2002; 161(3): 1307 - 1320.
[Abstract] [Full Text] [PDF]

G. F. O. Sanson, S. Y. Kawashita, A. Brunstein, and M. R. S. Briones
Experimental Phylogeny of Neutrally Evolving DNA Sequences Generated by a Bifurcate Series of Nested Polymerase Chain Reactions
Mol. Biol. Evol., February 1, 2002; 19(2): 170 - 178.
[Abstract] [Full Text] [PDF]

J. P. Huelsenbeck, F. Ronquist, R. Nielsen, and J. P. Bollback
Bayesian Inference of Phylogeny and Its Impact on Evolutionary Biology
Science, December 14, 2001; 294(5550): 2310 - 2314.
[Abstract] [Full Text] [PDF]

K. Strimmer and O. G. Pybus
Exploring the Demographic History of DNA Sequences Using the Generalized Skyline Plot
Mol. Biol. Evol., December 1, 2001; 18(12): 2298 - 2305.
[Abstract] [Full Text] [PDF]

P. Fearnhead and P. Donnelly
Estimating Recombination Rates From Population Genetic Data
Genetics, November 1, 2001; 159(3): 1299 - 1318.
[Abstract] [Full Text] [PDF]

R. Nielsen
Mutations as Missing Data: Inferences on the Ages and Distributions of Nonsynonymous and Synonymous Mutations
Genetics, September 1, 2001; 159(1): 401 - 411.
[Abstract] [Full Text] [PDF]

L. Chikhi, M. W. Bruford, and M. A. Beaumont
Estimation of Admixture Proportions: A Likelihood-Based Approach Using Markov Chain Monte Carlo
Genetics, July 1, 2001; 158(3): 1347 - 1362.
[Abstract] [Full Text] [PDF]

A. Drummond, R. Forsberg, and A. G. Rodrigo
The Inference of Stepwise Changes in Substitution Rates Using Serial Sequence Samples
Mol. Biol. Evol., July 1, 2001; 18(7): 1365 - 1371.
[Abstract] [Full Text] [PDF]

R. Nielsen and J. Wakeley
Distinguishing Migration From Isolation: A Markov Chain Monte Carlo Approach
Genetics, June 1, 2001; 158(2): 885 - 896.
[Abstract] [Full Text] [PDF]

M. A. Suchard, R. E. Weiss, and J. S. Sinsheimer
Bayesian Selection of Continuous-Time Markov Chain Evolutionary Models
Mol. Biol. Evol., June 1, 2001; 18(6): 1001 - 1013.
[Abstract] [Full Text]

R. Nielsen, D. K. Mattila, P. J. Clapham, and P. J. Palsbøll
Statistical Approaches to Paternity Analysis in Natural Populations and Applications to the North Atlantic Humpback Whale
Genetics, April 1, 2001; 157(4): 1673 - 1682.
[Abstract] [Full Text]

P. Beerli and J. Felsenstein
Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach
PNAS, March 29, 2001; (2001) 81068098.
[Abstract] [Full Text]

A. D. Kelleher, C. Long, E. C. Holmes, R. L. Allen, J. Wilson, C. Conlon, C. Workman, S. Shaunak, K. Olson, P. Goulder, et al.
Clustered Mutations in HIV-1 gag Are Consistently Required for Escape from HLA-B27-restricted Cytotoxic T Lymphocyte Responses
J. Exp. Med., February 5, 2001; 193(3): 375 - 386.
[Abstract] [Full Text] [PDF]

M. K. Kuhner, J. Yamato, and J. Felsenstein
Maximum Likelihood Estimation of Recombination Rates From Population Data
Genetics, November 1, 2000; 156(3): 1393 - 1401.
[Abstract] [Full Text]

L. Markovtsova, P. Marjoram, and S. Tavaré
The Effects of Rate Variation on Ancestral Inference in the Coalescent
Genetics, November 1, 2000; 156(3): 1427 - 1436.
[Abstract] [Full Text]

M. H. Schierup and J. Hein
Consequences of Recombination on Traditional Phylogenetic Analysis
Genetics, October 1, 2000; 156(2): 879 - 891.
[Abstract] [Full Text]

M. L. Cain, B. G. Milligan, and A. E. Strand
Long-distance seed dispersal in plant populations
Am. J. Botany, September 1, 2000; 87(9): 1217 - 1227.
[Abstract] [Full Text]

L. Markovtsova, P. Marjoram, and S. Tavaré
The Age of a Unique Event Polymorphism
Genetics, September 1, 2000; 156(1): 401 - 409.
[Abstract] [Full Text]

M. K. Kuhner, P. Beerli, J. Yamato, and J. Felsenstein
Usefulness of Single Nucleotide Polymorphism Data for Estimating Population Parameters
Genetics, September 1, 2000; 156(1): 439 - 447.
[Abstract] [Full Text]

S. C. Thomas and W. G. Hill
Estimating Quantitative Genetic Parameters Using Sibships Reconstructed From Marker Data
Genetics, August 1, 2000; 155(4): 1961 - 1972.
[Abstract] [Full Text]

O. G. Pybus, A. Rambaut, and P. H. Harvey
An Integrated Framework for the Inference of Viral Population History From Reconstructed Genealogies
Genetics, July 1, 2000; 155(3): 1429 - 1437.
[Abstract] [Full Text]

N. Galtier, F. Depaulis, and N. H. Barton
Detecting Bottlenecks and Selective Sweeps From DNA Sequence Polymorphism
Genetics, June 1, 2000; 155(2): 981 - 987.
[Abstract] [Full Text]

R. Nielsen
Estimation of Population Parameters and Recombination Rates From Single Nucleotide Polymorphisms
Genetics, February 1, 2000; 154(2): 931 - 942.
[Abstract] [Full Text]

M. A. Beaumont
Detecting Population Expansion and Decline Using Microsatellites
Genetics, December 1, 1999; 153(4): 2013 - 2029.
[Abstract] [Full Text]

H. Kaessmann, V. Wiebe, and S. Pääbo
Extensive Nuclear DNA Sequence Diversity Among Chimpanzees
Science, November 5, 1999; 286(5442): 1159 - 1162.
[Abstract] [Full Text]

P. M. d. A. Zanotto, E. G. Kallas, R. F. de Souza, and E. C. Holmes
Genealogical Evidence for Positive Selection in the nef Gene of HIV-1
Genetics, November 1, 1999; 153(3): 1077 - 1089.
[Abstract] [Full Text]

A. D. Long and C. H. Langley
The Power of Association Studies to Detect the Contribution of Candidate Genetic Loci to Variation in Complex Traits
Genome Res., August 1, 1999; 9(8): 720 - 731.
[Abstract] [Full Text]

S. Schneider and L. Excoffier
Estimation of Past Demographic Parameters From the Distribution of Pairwise Differences When the Mutation Rates Vary Among Sites: Application to Human Mitochondrial DNA
Genetics, July 1, 1999; 152(3): 1079 - 1089.
[Abstract] [Full Text]

P. Beerli and J. Felsenstein
Maximum-Likelihood Estimation of Migration Rates and Effective Population Numbers in Two Populations Using a Coalescent Approach
Genetics, June 1, 1999; 152(2): 763 - 773.
[Abstract] [Full Text]

N. C. Grassly, P. H. Harvey, and E. C. Holmes
Population Dynamics of HIV-1 Inferred From Gene Sequences
Genetics, February 1, 1999; 151(2): 427 - 438.
[Abstract] [Full Text]

I. J. Wilson and D. J. Balding
Genealogical Inference From Microsatellite Data
Genetics, September 1, 1998; 150(1): 499 - 510.
[Abstract] [Full Text] [PDF]

				C. P. Burridge, D. Craw, D. Fletcher, and J. M. Waters Geological Dates and Molecular Rates: Fish DNA Sheds Light on Time Dependency Mol. Biol. Evol., April 1, 2008; 25(4): 624 - 633. [Abstract] [Full Text] [PDF]

				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]

				M. G. B. Blum and N. A. Rosenberg Estimating the Number of Ancestral Lineages Using a Maximum-Likelihood Method Based on Rejection Sampling Genetics, July 1, 2007; 176(3): 1741 - 1757. [Abstract] [Full Text] [PDF]

				A. RoyChoudhury and M. Stephens Fast and Accurate Estimation of the Population-Scaled Mutation Rate, {theta}, From Microsatellite Genotype Data Genetics, June 1, 2007; 176(2): 1363 - 1366. [Abstract] [Full Text] [PDF]

				X. Liu and Y.-X. Fu Test of Genetical Isochronism for Longitudinal Samples of DNA Sequences Genetics, May 1, 2007; 176(1): 327 - 342. [Abstract] [Full Text] [PDF]

				J. Hey and R. Nielsen Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics PNAS, February 20, 2007; 104(8): 2785 - 2790. [Abstract] [Full Text] [PDF]

				M. K. Kuhner and L. P. Smith Comparing Likelihood and Bayesian Coalescent Estimation of Population Parameters Genetics, January 1, 2007; 175(1): 155 - 165. [Abstract] [Full Text] [PDF]

				M. K. Kuhner Robustness of Coalescent Estimators to Between-Lineage Mutation Rate Variation Mol. Biol. Evol., December 1, 2006; 23(12): 2355 - 2360. [Abstract] [Full Text] [PDF]

				M. M. Tanaka, A. R. Francis, F. Luciani, and S. A. Sisson Using Approximate Bayesian Computation to Estimate Tuberculosis Transmission Parameters From Genotype Data Genetics, July 1, 2006; 173(3): 1511 - 1520. [Abstract] [Full Text] [PDF]

				M. K. Kuhner LAMARC 2.0: maximum likelihood and Bayesian estimation of population parameters Bioinformatics, March 15, 2006; 22(6): 768 - 770. [Abstract] [Full Text] [PDF]

				J. Felsenstein Accuracy of Coalescent Likelihood Estimates: Do We Need More Sites, More Sequences, or More Loci? Mol. Biol. Evol., March 1, 2006; 23(3): 691 - 700. [Abstract] [Full Text] [PDF]

				P. Beerli Comparison of Bayesian and maximum-likelihood inference of population genetic parameters Bioinformatics, February 1, 2006; 22(3): 341 - 345. [Abstract] [Full Text] [PDF]

				B. W. Bowen, A. Muss, L. A. Rocha, and W. S. Grant Shallow mtDNA Coalescence in Atlantic Pygmy Angelfishes (Genus Centropyge) Indicates a Recent Invasion from the Indian Ocean J. Hered., January 1, 2006; 97(1): 1 - 12. [Abstract] [Full Text] [PDF]

				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]

				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]

				H. Li and W. Stephan Maximum-Likelihood Methods for Detecting Recent Positive Selection and Localizing the Selected Site in the Genome Genetics, September 1, 2005; 171(1): 377 - 384. [Abstract] [Full Text] [PDF]

				E. M. Rauch and Y. Bar-Yam Estimating the total genetic diversity of a spatial field population from a sample and implications of its dependence on habitat area PNAS, July 12, 2005; 102(28): 9826 - 9829. [Abstract] [Full Text] [PDF]

				E. C. Anderson An Efficient Monte Carlo Method for Estimating Ne From Temporally Spaced Samples Using a Coalescent-Based Likelihood Genetics, June 1, 2005; 170(2): 955 - 967. [Abstract] [Full Text] [PDF]

				D. Lavillette, Y. Morice, G. Germanidis, P. Donot, A. Soulier, E. Pagkalos, G. Sakellariou, L. Intrator, B. Bartosch, J.-M. Pawlotsky, et al. Human Serum Facilitates Hepatitis C Virus Infection, and Neutralizing Responses Inversely Correlate with Viral Replication Kinetics at the Acute Phase of Hepatitis C Virus Infection J. Virol., May 15, 2005; 79(10): 6023 - 6034. [Abstract] [Full Text] [PDF]

				W. Maury, R. J. Thompson, Q. Jones, S. Bradley, T. Denke, P. Baccam, M. Smazik, and J. L. Oaks Evolution of the Equine Infectious Anemia Virus Long Terminal Repeat during the Alteration of Cell Tropism J. Virol., May 1, 2005; 79(9): 5653 - 5664. [Abstract] [Full Text] [PDF]

				S. Hue, D. Pillay, J. P. Clewley, and O. G. Pybus Genetic analysis reveals the complex structure of HIV-1 transmission within defined risk groups PNAS, March 22, 2005; 102(12): 4425 - 4429. [Abstract] [Full Text] [PDF]

				K. J. Schmid, S. Ramos-Onsins, H. Ringys-Beckstein, B. Weisshaar, and T. Mitchell-Olds A Multilocus Sequence Survey in Arabidopsis thaliana Reveals a Genome-Wide Departure From a Neutral Model of DNA Sequence Polymorphism Genetics, March 1, 2005; 169(3): 1601 - 1615. [Abstract] [Full Text] [PDF]

				P. Fearnhead, R. M. Harding, J. A. Schneider, S. Myers, and P. Donnelly Application of Coalescent Methods to Reveal Fine-Scale Rate Variation and Recombination Hotspots Genetics, August 1, 2004; 167(4): 2067 - 2081. [Abstract] [Full Text] [PDF]

				L. B. Beheregaray, J. P. Gibbs, N. Havill, T. H. Fritts, J. R. Powell, and A. Caccone Giant tortoises are not so slow: Rapid diversification and biogeographic consensus in the Galapagos PNAS, April 27, 2004; 101(17): 6514 - 6519. [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]

				D. Shriner, R. Shankarappa, M. A. Jensen, D. C. Nickle, J. E. Mittler, J. B. Margolick, and J. I. Mullins Influence of Random Genetic Drift on Human Immunodeficiency Virus Type 1 env Evolution During Chronic Infection Genetics, March 1, 2004; 166(3): 1155 - 1164. [Abstract] [Full Text] [PDF]

				G. T. Marth, E. Czabarka, J. Murvai, and S. T. Sherry The Allele Frequency Spectrum in Genome-Wide Human Variation Data Reveals Signals of Differential Demographic History in Three Large World Populations Genetics, January 1, 2004; 166(1): 351 - 372. [Abstract] [Full Text] [PDF]

				P. L. Morrell, K. E. Lundy, and M. T. Clegg Distinct geographic patterns of genetic diversity are maintained in wild barley (Hordeum vulgare ssp. spontaneum) despite migration PNAS, September 16, 2003; 100(19): 10812 - 10817. [Abstract] [Full Text] [PDF]

				M. A. Beaumont Estimation of Population Growth or Decline in Genetically Monitored Populations Genetics, July 1, 2003; 164(3): 1139 - 1160. [Abstract] [Full Text] [PDF]

				N. Yu, Y.-X. Fu, and W.-H. Li DNA Polymorphism in a Worldwide Sample of Human X Chromosomes Mol. Biol. Evol., December 1, 2002; 19(12): 2131 - 2141. [Abstract] [Full Text] [PDF]