Genetics, Vol. 150, 499-510, September 1998, Copyright © 1998

Genealogical Inference From Microsatellite Data

Ian J. Wilsona,b and David J. Baldingb
a School of Biological Sciences, Queen Mary and Westfield College, University of London, London E1 4NS, England
b Department of Applied Statistics, University of Reading, Reading RG6 6FN, England

Corresponding author: David J. Balding, Department of Applied Statistics, University of Reading, PO Box 240, Reading RG6 6FN, England., d.j.balding{at}reading.ac.uk (E-mail).

Communicating editor: R. R. HUDSON

Ease and accuracy of typing, together with high levels of polymorphism and widespread distribution in the genome, make microsatellite (or short tandem repeat) loci an attractive potential source of information about both population histories and evolutionary processes. However, microsatellite data are difficult to interpret, in particular because of the frequency of back-mutations. Stochastic models for the underlying genetic processes can be specified, but in the past they have been too complicated for direct analysis. Recent developments in stochastic simulation methodology now allow direct inference about both historical events, such as genealogical coalescence times, and evolutionary parameters, such as mutation rates. A feature of the Markov chain Monte Carlo (MCMC) algorithm that we propose here is that the likelihood computations are simplified by treating the (unknown) ancestral allelic states as auxiliary parameters. We illustrate the algorithm by analyzing microsatellite samples simulated under the model. Our results suggest that a single microsatellite usually does not provide enough information for useful inferences, but that several completely linked microsatellites can be informative about some aspects of genealogical history and evolutionary processes. We also reanalyze data from a previously published human Y chromosome microsatellite study, finding evidence for an effective population size for human Y chromosomes in the low thousands and a recent time since their most recent common ancestor: the 95% interval runs from ~15,000 to 130,000 years, with most likely values around 30,000 years.




This article has been cited by other articles:


Home page
 GeneticsHome page
Y. Wang and J. Hey
Estimating Divergence Parameters With Small Samples From a Large Number of Loci
Genetics, February 1, 2010; 184(2): 363 - 379.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
J. S. Lopes, D. Balding, and M. A. Beaumont
PopABC: a program to infer historical demographic parameters
Bioinformatics, October 15, 2009; 25(20): 2747 - 2749.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
S. Mona, K. E. Grunz, S. Brauer, B. Pakendorf, L. Castri, H. Sudoyo, S. Marzuki, R. H. Barnes, J. Schmidtke, M. Stoneking, et al.
Genetic Admixture History of Eastern Indonesia as Revealed by Y-Chromosome and Mitochondrial DNA Analysis
Mol. Biol. Evol., August 1, 2009; 26(8): 1865 - 1877.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
V. C. Sousa, M. Fritz, M. A. Beaumont, and L. Chikhi
Approximate Bayesian Computation Without Summary Statistics: The Case of Admixture
Genetics, April 1, 2009; 181(4): 1507 - 1519.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
M. Navascues, O. J. Hardy, and C. Burgarella
Characterization of Demographic Expansions From Pairwise Comparisons of Linked Microsatellite Haplotypes
Genetics, March 1, 2009; 181(3): 1013 - 1019.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
M. Kayser, Y. Choi, M. van Oven, S. Mona, S. Brauer, R. J. Trent, D. Suarkia, W. Schiefenhovel, and M. Stoneking
The Impact of the Austronesian Expansion: Evidence from mtDNA and Y Chromosome Diversity in the Admiralty Islands of Melanesia
Mol. Biol. Evol., July 1, 2008; 25(7): 1362 - 1374.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
K. Zhang and N. A. Rosenberg
On the Genealogy of a Duplicated Microsatellite
Genetics, December 1, 2007; 177(4): 2109 - 2122.
[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
 GeneticsHome page
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]

Home page
 GeneticsHome page
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]

Home page
 GeneticsHome page
X. Didelot and D. Falush
Inference of Bacterial Microevolution Using Multilocus Sequence Data
Genetics, March 1, 2007; 175(3): 1251 - 1266.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
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]

Home page
 Syst BiolHome page
R. Nielsen and M. Matz
Statistical Approaches for DNA Barcoding
Syst Biol, February 1, 2006; 55(1): 162 - 169.
[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
 Phil Trans R Soc BHome page
J. Wang
Estimation of effective population sizes from data on genetic markers
Phil Trans R Soc B, July 29, 2005; 360(1459): 1395 - 1409.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
L. Excoffier, A. Estoup, and J.-M. Cornuet
Bayesian Analysis of an Admixture Model With Mutations and Arbitrarily Linked Markers
Genetics, March 1, 2005; 169(3): 1727 - 1738.
[Abstract] [Full Text] [PDF]

Home page
 Syst BiolHome page
M. Pagel, A. Meade, and D. Barker
Bayesian Estimation of Ancestral Character States on Phylogenies
Syst Biol, October 1, 2004; 53(5): 673 - 684.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
D. G. Hwang and P. Green
Inaugural Article: Bayesian Markov chain Monte Carlo sequence analysis reveals varying neutral substitution patterns in mammalian evolution
PNAS, September 28, 2004; 101(39): 13994 - 14001.
[Abstract] [Full Text] [PDF]

Home page
 Syst BiolHome page
M. Pagel and A. Meade
A Phylogenetic Mixture Model for Detecting Pattern-Heterogeneity in Gene Sequence or Character-State Data
Syst Biol, August 1, 2004; 53(4): 571 - 581.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
J. Hey and R. Nielsen
Multilocus Methods for Estimating Population Sizes, Migration Rates and Divergence Time, With Applications to the Divergence of Drosophila pseudoobscura and D. persimilis
Genetics, June 1, 2004; 167(2): 747 - 760.
[Abstract] [Full Text] [PDF]

Home page
 Am. J. Bot.Home page
V. L. Semerikov and M. Lascoux
Nuclear and cytoplasmic variation within and between Eurasian Larix (Pinaceae) species
Am. J. Botany, August 1, 2003; 90(8): 1113 - 1123.
[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]

Home page
 GeneticsHome page
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]

Home page
 GeneticsHome page
G. Laval, M. SanCristobal, and C. Chevalet
Maximum-Likelihood and Markov Chain Monte Carlo Approaches to Estimate Inbreeding and Effective Size From Allele Frequency Changes
Genetics, July 1, 2003; 164(3): 1189 - 1204.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
R. Leblois, A. Estoup, and F. Rousset
Influence of Mutational and Sampling Factors on the Estimation of Demographic Parameters in a "Continuous" Population Under Isolation by Distance
Mol. Biol. Evol., April 1, 2003; 20(4): 491 - 502.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
M. A. Beaumont, W. Zhang, and D. J. Balding
Approximate Bayesian Computation in Population Genetics
Genetics, December 1, 2002; 162(4): 2025 - 2035.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
J. F. Storz, M. A. Beaumont, and S. C. Alberts
Genetic Evidence for Long-Term Population Decline in a Savannah-Dwelling Primate: Inferences from a Hierarchical Bayesian Model
Mol. Biol. Evol., November 1, 2002; 19(11): 1981 - 1990.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
T. Jansen, P. Forster, M. A. Levine, H. Oelke, M. Hurles, C. Renfrew, J. Weber, and K. Olek
Mitochondrial DNA and the origins of the domestic horse
PNAS, August 6, 2002; 99(16): 10905 - 10910.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
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]

Home page
 Mol Biol EvolHome page
M. E. Weale, D. A. Weiss, R. F. Jager, N. Bradman, and M. G. Thomas
Y Chromosome Evidence for Anglo-Saxon Mass Migration
Mol. Biol. Evol., July 1, 2002; 19(7): 1008 - 1021.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
M. E. Hurles, J. Nicholson, E. Bosch, C. Renfrew, B. C. Sykes, and M. A. Jobling
Y Chromosomal Evidence for the Origins of Oceanic-Speaking Peoples
Genetics, January 1, 2002; 160(1): 289 - 303.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
A. Estoup, I. J. Wilson, C. Sullivan, J.-M. Cornuet, and C. Moritz
Inferring Population History From Microsatellite and Enzyme Data in Serially Introduced Cane Toads, Bufo marinus
Genetics, December 1, 2001; 159(4): 1671 - 1687.
[Abstract] [Full Text] [PDF]

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

Home page
 Proc. Natl. Acad. Sci. USAHome page
P. Michalak, I. Minkov, A. Helin, D. N. Lerman, B. R. Bettencourt, M. E. Feder, A. B. Korol, and E. Nevo
Genetic evidence for adaptation-driven incipient speciation of Drosophilamelanogaster along a microclimatic contrast in ""Evolution Canyon,"" Israel
PNAS, October 25, 2001; (2001) 231478298.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
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]

Home page
 GeneticsHome page
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]

Home page
 GeneticsHome page
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]

Home page
 GeneticsHome page
B. Walsh
Estimating the Time to the Most Recent Common Ancestor for the Y chromosome or Mitochondrial DNA for a Pair of Individuals
Genetics, June 1, 2001; 158(2): 897 - 912.
[Abstract] [Full Text] [PDF]

Home page
 ScienceHome page
M. P. H. Stumpf and D. B. Goldstein
Genealogical and Evolutionary Inference with the Human Y Chromosome
Science, March 2, 2001; 291(5509): 1738 - 1742.
[Abstract] [Full Text]

Home page
 Hum Mol GenetHome page
U. Holtkemper, B. Rolf, C. Hohoff, P. Forster, and B. Brinkmann
Mutation rates at two human Y-chromosomal microsatellite loci using small pool PCR techniques
Hum. Mol. Genet., March 1, 2001; 10(6): 629 - 633.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
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]

Home page
 GeneticsHome page
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]

Home page
 Proc. Natl. Acad. Sci. USAHome page
R. Thomson, J. K. Pritchard, P. Shen, P. J. Oefner, and M. W. Feldman
Recent common ancestry of human Y chromosomes: Evidence from DNA sequence data
PNAS, June 20, 2000; 97(13): 7360 - 7365.
[Abstract] [Full Text] [PDF]

Home page
 Am. J. Bot.Home page
C. M. Clark, T. R. Wentworth, and D. M. O'Malley
Genetic discontinuity revealed by chloroplast microsatellites in eastern North American Abies (Pinaceae)
Am. J. Botany, June 1, 2000; 87(6): 774 - 782.
[Abstract] [Full Text]

Home page
 GeneticsHome page
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]

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

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

Home page
 Proc. Natl. Acad. Sci. USAHome page
G. Cooper, N. J. Burroughs, D. A. Rand, D. C. Rubinsztein, and W. Amos
Markov Chain Monte Carlo analysis of human Y-chromosome microsatellites provides evidence of biased mutation
PNAS, October 12, 1999; 96(21): 11916 - 11921.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
P. Michalak, I. Minkov, A. Helin, D. N. Lerman, B. R. Bettencourt, M. E. Feder, A. B. Korol, and E. Nevo
Genetic evidence for adaptation-driven incipient speciation of Drosophilamelanogaster along a microclimatic contrast in "Evolution Canyon," Israel
PNAS, November 6, 2001; 98(23): 13195 - 13200.
[Abstract] [Full Text] [PDF]