Affiliation: University of Reading
- Approximate Bayesian computation in population geneticsMark A Beaumont
School of Animal and Microbial Sciences, The University of Reading, Whiteknights, Reading RG6 6AJ, United Kingdom
Genetics 162:2025-35. 2002..We also compare the relative efficiency of inferences obtained using methods based on summary statistics with those obtained directly from the data using MCMC...
- Detecting population expansion and decline using microsatellitesM A Beaumont
Institute of Zoology, Zoological Society of London, London NW1 4RY, United Kingdom
Genetics 153:2013-29. 1999..The method is then applied to published microsatellite data from two populations. Data from the northern hairy-nosed wombat show strong evidence of decline. Data from European humans show weak evidence of expansion...
- On the validity of nested clade phylogeographical analysisMark A Beaumont
School of Biological Sciences, University of Reading, Reading RG6 6BX, UK
Mol Ecol 17:2563-5. 2008
- Rapid radiation in spiny lobsters (Palinurus spp) as revealed by classic and ABC methods using mtDNA and microsatellite dataFerran Palero
Departament de Genetica, Facultat de Biologia, Universitat de Barcelona, Av Diagonal 645, Barcelona, Spain
BMC Evol Biol 9:263. 2009....
- Recent developments in genetic data analysis: what can they tell us about human demographic history?M A Beaumont
School of Animal and Microbial Sciences, University of Reading, Whiteknights, PO Box 228, Reading RG6 6AJ, UK
Heredity (Edinb) 92:365-79. 2004....
- The Bayesian revolution in geneticsMark A Beaumont
School of Animal and Microbial Sciences, University of Reading, Whiteknights, P O Box 228, Reading RG6 6AJ, UK
Nat Rev Genet 5:251-61. 2004
- Estimation of population growth or decline in genetically monitored populationsMark A Beaumont
School of Animal and Microbial Sciences, Reading RG6 6AJ, United Kingdom
Genetics 164:1139-60. 2003..The method is used on three example data sets and problems in interpreting the posterior densities are highlighted and discussed...
- Selection and sticklebacksMark A Beaumont
School of Biological Sciences, University of Reading, Reading RG6 6BX, UK
Mol Ecol 17:3425-7. 2008..They identify a further two independent candidates for local selection, and, most intriguingly, they further suggest that up to 15% of their loci may provide evidence of balancing selection...
- Genetic diversity and introgression in the Scottish wildcatM Beaumont
Institute of Zoology, Zoological Society of London, Regents Park, London NW 1RY, UK
Mol Ecol 10:319-36. 2001..However, from the morphological data it is highly likely that this gene pool also contains a contribution from earlier introgression of domestic cat genes...
- Likelihood-free inference of population structure and local adaptation in a Bayesian hierarchical modelEric Bazin
School of Biological Sciences, University of Reading, Whiteknights, Reading RG6 6BX, United Kingdom
Genetics 185:587-602. 2010..We demonstrate using receiver operating characteristic (ROC) analysis that this approach has comparable performance to a full-likelihood method and outperforms it when mutation rates are variable across loci...
- PopABC: a program to infer historical demographic parametersJoao S Lopes
School of Biological Sciences, University of Reading, Whiteknights, PO Box 228, Reading RG66AJ, UK
Bioinformatics 25:2747-9. 2009..PopABC can also be used to perform Bayesian model choice to discriminate between different demographic scenarios. The program can be used either for research or for education and teaching purposes...
- Identifying adaptive genetic divergence among populations from genome scansMark A Beaumont
School of Animal and Microbial Sciences, The University of Reading, Whiteknights, PO Box 228, Reading RG6 6AJ, UK
Mol Ecol 13:969-80. 2004..Neither method could reliably distinguish loci under balancing selection in our simulations, even when the selection coefficient is twenty times the migration rate...
- The automation and evaluation of nested clade phylogeographic analysisMahesh Panchal
School of Biological Sciences, University of Reading, Whiteknights, Reading, UK
Evolution 61:1466-80. 2007..However, published datasets typically yield a richer set of inferences with NCPA than obtained in our random-mating simulations, and further testing of NCPA with models of structured populations is necessary to examine its accuracy...
- Evaluating nested clade phylogeographic analysis under models of restricted gene flowMahesh Panchal
School of Biological Sciences, University of Reading, Whiteknights, PO Box 228, Reading RG6 6AJ, UK
Syst Biol 59:415-32. 2010..We suggest that the NCPA method should not be used without objective simulation-based testing by independent researchers...
- Microsatellites reveal heterosis in red deerT N Coulson
Institute of Zoology, Zoological Society of London, Regent s Park, London, UK
Proc Biol Sci 265:489-95. 1998..We suggest that, together, individual heterozygosity and mean d2, estimated using microsatellites, are useful tools for exploring inbreeding and outbreeding in natural population...
- Comparative evaluation of a new effective population size estimator based on approximate bayesian computationDavid A Tallmon
Laboratoire d Ecologie Alpine, UMR Centre National de la Recherche Scientifique 5553, Universite Joseph Fourier, F38041 BP 53 Cedex 09, Grenoble, France
Genetics 167:977-88. 2004..The greatest strength of the SummStat estimator is its flexible structure. This flexibility allows it to incorporate any potentially informative summary statistic from population genetic data...
- An approximate Bayesian computation approach to overcome biases that arise when using amplified fragment length polymorphism markers to study population structureMatthieu Foll
Laboratoire d Ecologie Alpine LECA, CNRS UMR 5553, 38041 Grenoble Cedex 09, France
Genetics 179:927-39. 2008..The software is available at our web site (http://www-leca.ujf-grenoble.fr/logiciels.htm). Finally, we provide advice on how to avoid the effects of ascertainment bias...
- Genetic evidence for long-term population decline in a savannah-dwelling primate: inferences from a hierarchical bayesian modelJay F Storz
Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, 85721, USA
Mol Biol Evol 19:1981-90. 2002..These results indicate that savannah baboons apparently did not share a common demographic history with other codistributed primate species...
- Y genetic data support the Neolithic demic diffusion modelLounes Chikhi
Department of Biology, University College London, Darwin Building, London WC1E 6BT, United Kingdom
Proc Natl Acad Sci U S A 99:11008-13. 2002..J. & Cavalli-Sforza, L. L. (1984) The Neolithic Transition and the Genetics of Populations in Europe (Princeton Univ. Press, Princeton)] captures the major features of this dramatic episode in European prehistory...
- Testing for genetic evidence of population expansion and contraction: an empirical analysis of microsatellite DNA variation using a hierarchical Bayesian modelJay F Storz
Department of Ecology and Evolutionary Biology, University of Arizona, Biosciences West, Tucson 85721, USA
Evolution 56:154-66. 2002..Genetic evidence for population decline may reflect the consequences of habitat destruction on a more recent time scale...
- Likelihood-based estimation of the effective population size using temporal changes in allele frequencies: a genealogical approachPierre Berthier
Laboratoire de Biologie des populations d Altitude, UMR CNRS 5553, Universite Joseph Fourier, F38041 BP53 Cedex 9 Grenoble, France
Genetics 160:741-51. 2002..It will be especially useful in conservation biology because it less often overestimates N(e) than does N(eLB) and thus is less likely to erroneously suggest that a population is large and has a low extinction risk...