Mark Beaumont
Research Fellow, School of Animal and Microbial Sciences

Glas Llyn, Machynlleth, Sep 2000 CONTACT DETAILS
School of Animal and Microbial Sciences
University of Reading
Whiteknights
P.O. Box 228
Reading, RG6 6AJ, UK

Tel: 0118 987 5123 X 7707
Fax: 0118 931 0180
E-mail:   m.a.beaumont@reading.ac.uk


RESEARCH INTERESTS
I am a NERC Advanced Fellow in the School of Animal and Microbial Sciences, University of Reading. I am interested in using gene frequency information to infer the demographic history of populations. I have developed a number of statistical methods to estimate changes in effective population size and patterns of gene-flow and admixture, and also to identify discrepant loci, possibly under selection.


GENERAL FILE DOWNLOADS
You can download some files from here. These include more recent versions of the Msvar program, the Dfdist package, and a distribution of R functions that may be helpful for analysing the output of MCMC methods, and for carrying out Approximate Bayesian Computation (ABC). Other files can be downloaded from the software and data sections below.



RECENTLY FUNDED PROJECTS
(BBSRC) Bayesian methods for quantifying levels of adaptive divergence between populations from gene frequency data, with Kevin Dawson (Rothamsted)

(NERC) The influence of propagule banks on demography and genetic diversity in freshwater invertebrates and plants, with Beth Okamura (Reading) and Joanna Freeland (Open University)

(BBSRC/NERC) Development of statistical methods to infer gene flow from crop plants into wild relatives, with Mike Shaw (Agricultural Botany, Reading).

(BBSRC) Development of statistical tools to infer demographic history using linked microsatellite markers, with David Balding (Department of Epidemiology and Public Health, Imperial College)

(NERC) Estimating genetic admixture using a likelihood approach, with Richard Nichols (Biology, QMW) and Lounes Chikhi (Biology, UCL).

(NERC) Reconstructing the abundance histories of endangered species - a molecular genetics approach, with Ken Norris (AMS, Reading) and Mike Bruford (Biology, Cardiff)


CURRENT PHD STUDENTS
Mahesh Panchal. Testing cladistic/network-based methods of genetic data analysis, and development of approximate Bayesian methods to infer demographic history from DNA sequence data.

Darran Singleton. Development of methods to identify loci under selection from genome scans.

Kate Ciborowski (External | Institute of Zoology). Patterns of genetic variability during the decline of Iberian-Atlantic salmon populations.



RECENT VISITING RESEARCHERS
David Talmon. Development of methods to infer demographic parameters using ABC.

Jean-Marie Cornuet. Development of computer intensive methods for genetic data analysis.

Claire Calmet. Inferring parameters in demographic models using microsatellite markers.



BACKGROUND
Current post
University of Reading, NERC Advanced Fellow, School of Animal and Microbial Sciences

1999-2002
University of Reading, University Fellow, School of Animal and Microbial Sciences

1995-1999
Institute of Zoology, London, Research Fellow in conservation genetics

1992-1995
Queen Mary and Westfield College, London, Wellcome Research Fellow in Mathematical Biology

1991-1992
Queen Mary and Westfield College, London, PDRA with Richard Nichols and Peter Donnelly

1988-1991
University of Nottingham, PDRA with Bryan Clarke

1986-1988
University of East Anglia, PDRA with Godfrey Hewitt

1988
University of Nottingham Ph.D. Genetics

1983
University of Manchester B.Sc Zoology


SOFTWARE
Click here for a list of freely available software arising from my work on various population genetics problems - all programs run on a PC and are supplied as zip archives with executables, READMEs, and example data.


DATA SETS
Click here for a list of freely available data, arising from my collaborations.


PUBLICATIONS
Some recent publications are given below - full list here.

Beaumont, M.A. (2005)
Adaptation and speciation: what can FST tell us? Trends in Ecology and Evolution. In Press (available online).

Hamilton, G., Currat, M., Ray, N., Heckel, G., Beaumont, M. and L. Excoffier. (2005)
Bayesian estimation of recent migration rates after a spatial expansion. Genetics 170: 409-417

Chikhi, L., Beaumont, M.A. (2005)
Modelling human genetic history, in The Encyclopedia of Genetics, Genomics, Proteomics & Bioinformatics, John Wiley, New York.

Estoup, A., Beaumont, M., Sennedot, F., Moritz, C., Cornuet, J-M. (2004)
Genetic analysis of complex demographic scenarios: spatially expanding populations of the cane toad, Bufo marinus. Evolution. 58: 2021-2036.

Beaumont, M.A. and B. Rannala (2004)
The Bayesian revolution in genetics. Nature Reviews Genetics. 5: 251-261.

Tallmon, D., G. Luikart, M.A. Beaumont (2004)
Comparative evaluation of a new effective population size estimator based on approximate Bayesian computation. Genetics. 167: 977-988.

Beaumont, M.A. (2004)
Recent developments in genetic data analysis: what can they tell us about human demographic history? Heredity. 92: 365-379

Beaumont, M.A., and D.J. Balding (2004).
Identifying adaptive genetic divergence among populations from genome scans. Molecular Ecology. 13: 969-980

Vogl, C., A. Das, M.A. Beaumont, S. Mohanty, and W. Stephan. (2003)
Population subdivision and molecular sequence variation: Theory and analysis of Drosophila ananassae data. Genetics 165: 1385-1395.

Beaumont, M.A. (2003)
Estimation of population growth or decline in genetically monitored populations. Genetics 164: 1139-1160.

Beaumont, M.A. (2003)
Conservation Genetics, in Balding, D.J., Bishop, M., and Cannings, C. (eds) The Handbook of Statistical Genetics 2nd Edition, pp. 751-792. John Wiley, New York.

Chikhi, L., Nichols, R.A., Barbujani, G. and Beaumont, M.A. (2002)
Y genetic data support the Neolithic demic diffusion model. Proc. Natl. Acad. Sci. U.S.A., 99: 11008-11013.

Beaumont, M.A., Zhang, W., and Balding, D.J. (2002)
Approximate Bayesian Computation in Population Genetics. Genetics, 162: 2002, 2025-2035.

Storz, J.F., Beaumont, M.A., and Alberts, S.C. (2002)
Genetic evidence for long-term population decline in a savannah-dwelling primate: inferences from a hierarchical Bayesian model. Mol. Biol. Evol. 19: 1981-1990.

Storz, J.F. and Beaumont, M.A. (2002)
Testing for genetic evidence of population expansion and contraction: an empirical analysis of microsatellite DNA variation using a hierarchical Bayesian model. Evolution. 56: 154-166.

Berthier, P., Beaumont, M.A., Cornuet, J.M., Luikart, G. (2002)
Likelihood-based estimation of the effective population size using temporal changes in allele frequencies: a genealogical approach. Genetics. 160: 741 751.

(c) M.A. Beaumont, 2004 Last updated: August 2004