Mark A Beaumont

2024

Genomics and conservation: Guidance from training to analyses and applications

Schiebelhut, L. M., Guillaume, A. S., Kuhn, A., Schweizer, R. M., Armstrong, E. E., Beaumont, M. A., Byrne, M., Cosart, T., Hand, B. K., Howard, L., Mussmann, S. M., Narum, S. R., Rasteiro, R., Rivera-Colón, A. G., Saarman, N., Sethuraman, A., Taylor, H. R., Thomas, G. W. C., Wellenreuther, M. & Luikart, G., 11 Jan 2024, In: Molecular Ecology Resources. 24, 2, e13893.

Research output: Contribution to journal › Review article (Academic Journal) › peer-review

Open Access

6 Citations (Scopus)

How admixed captive breeding populations could be rescued using local ancestry information

Lawson, D. J., Howard-McCombe, J., Beaumont, M. & Senn, H., 18 Apr 2024, (E-pub ahead of print) In: Molecular Ecology. 16 p., e17349.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

Open Access

2023

Estimating temporally variable selection intensity from ancient DNA data

He, Z., Dai, X., Lyu, W., Beaumont, M. A. & Yu, F., 1 Mar 2023, In: Molecular Biology and Evolution. 40, 3, msad008.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

Open Access

3 Citations (Scopus)

Estimating temporally variable selection intensity from ancient DNA data with the flexibility of modelling linkage and epistasis

Yu, F., He, Z., Dai, X., Lyu, W. & Beaumont, M. A., 1 Aug 2023, In: Molecular Ecology Resources. 23, 6, p. 1226-1240 15 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

Open Access

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22 Downloads (Pure)

Genetic swamping of the critically endangered Scottish wildcat was recent and accelerated by disease

Howard-McCombe, J., Jamieson, A., Carmagnini, A., Russo, I.-R. M., Ghazali, M., Campbell, R., Driscoll, C., Murphy, W. J., Nowak, C., O'Connor, T., Tomsett, L., Lyons, L. A., Muñoz-Fuentes, V., Bruford, M. W., Kitchener, A. C., Larson, G., Frantz, L., Senn, H., Lawson, D. J. & Beaumont, M. A., 6 Nov 2023, In: Current Biology. 33, 21, p. 4761-4769.e5

Research output: Contribution to journal › Article (Academic Journal) › peer-review

Open Access

11 Citations (Scopus)

Limited historical admixture between European wildcats and domestic cats

Jamieson, A., Carmagnini, A., Howard-McCombe, J., Doherty, S., Hirons, A., Dimopoulos, E., Lin, A. T., Allen, R., Anderson-Whymark, H., Barnett, R., Batey, C., Beglane, F., Bowden, W., Bratten, J., De Cupere, B., Drew, E., Foley, N. M., Fowler, T., Fox, A. & Geigl, E.-M. & 35 others, Gotfredsen, A. B., Grange, T., Griffiths, D., Groß, D., Haruda, A., Hjermind, J., Knapp, Z., Lebrasseur, O., Librado, P., Lyons, L. A., Mainland, I., McDonnell, C., Muñoz-Fuentes, V., Nowak, C., O'Connor, T., Peters, J., Russo, I.-R. M., Ryan, H., Sheridan, A., Sinding, M.-H. S., Skoglund, P., Swali, P., Symmons, R., Thomas, G., Trolle Jensen, T. Z., Kitchener, A. C., Senn, H., Lawson, D., Driscoll, C., Murphy, W. J., Beaumont, M., Ottoni, C., Sykes, N., Larson, G. & Frantz, L., 6 Nov 2023, In: Current Biology. 33, 21, p. 4751-4760.e14

Research output: Contribution to journal › Article (Academic Journal) › peer-review

Open Access

5 Citations (Scopus)

To unscramble an egg: admixed captive breeding populations can be rescued using local ancestry information

Lawson, D. J., Howard-McCombe, J., Beaumont, M. & Senn, H., 29 Jul 2023, (Submitted)

Research output: Other contribution

2022

Recommendations for improving statistical inference in population genomics

Johri, P., Aquadro, C. F., Beaumont, M., Charlesworth, B., Excoffier, L., Eyre-Walker, A., Keightley, P. D., Lynch, M., McVean, G., Payseur, B. A., Pfeifer, S. P., Stephan, W. & Jensen, J. D., 31 May 2022, In: PLoS Biology. 20, 5, p. e3001669

Research output: Contribution to journal › Article (Academic Journal) › peer-review

Open Access

62 Citations (Scopus)

Robust neural posterior estimation and statistical model criticism

Ward, D. G., Cannon, P., Beaumont, M. A., Fasiolo, M. & Schmon, S., 9 Dec 2022. 15 p.

Research output: Contribution to conference › Conference Paper › peer-review

Open Access

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2 Downloads (Pure)

2021

Inferring the timing and strength of natural selection and gene migration in the evolution of chicken from ancient DNA data

Yu, F., Lyu, W., He, Z., Beaumont, M. A. & Dai, X., 28 Sept 2021, (Accepted/In press) In: Molecular Ecology Resources.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

Open Access

On the use of genome-wide data to model and date the time of anthropogenic hybridisation: An example from the Scottish wildcat

Howard-McCombe, J., Ward, D., Kitchener, A. C., Lawson, D., Senn, H. V. & Beaumont, M., 30 Jul 2021, In: Molecular Ecology. 30, 15, p. 3688-3702 15 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

Open Access

File

18 Citations (Scopus)

110 Downloads (Pure)

The role of gene flow and chromosomal instability in shaping the bread wheat genome

Przewieslik-Allen, A. M., Wilkinson, P. A., Burridge, A. J., Winfield, M. O., Dai, X., Beaumont, M., King, J., Yang, C.-Y., Griffiths, S., Wingen, L. U., Horsnell, R., Bentley, A. R., Shewry, P., Barker, G. L. A. & Edwards, K. J., 1 Feb 2021, In: Nature Plants. 7, 2, p. 172-183 12 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

40 Citations (Scopus)

2020

Detecting and quantifying natural selection at two linked loci from time series data of allele frequencies with forward-in-time simulations

He, Z., Dai, X., Beaumont, M. & Yu, F., 6 Oct 2020, In: Genetics. 216, 2, p. 521-541 21 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

File

10 Citations (Scopus)

100 Downloads (Pure)

Estimation of natural selection and allele age from time series allele frequency data using a novel likelihood-based approach

He, Z., Dai, X., Beaumont, M. & Yu, F., 7 Aug 2020, In: Genetics. 215, 4, 36 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

6 Citations (Scopus)

Performance of a priori and a posteriori calibration strategies in divergence time estimation

Beavan, A. J. S., Donoghue, P. C. J., Beaumont, M. A. & Pisani, D., 22 May 2020, In: Genome Biology and Evolution. 12, 7, p. 1087-1098 12 p., evaa105.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

Open Access

File

8 Citations (Scopus)

75 Downloads (Pure)

Rapid homoploid hybrid speciation in British gardens: The origin of Oxford ragwort (Senecio squalidus)

Nevado, B., Harris, S. A., Beaumont, M. A. & Hiscock, S. J., 10 Sept 2020, In: Molecular Ecology. 29, 21, p. 4221-4233 13 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

18 Citations (Scopus)

2019

Approximate Bayesian computation

Beaumont, M. A., 7 Mar 2019, In: Annual Review of Statistics and Its Application. 6, p. 379-403 25 p.

Research output: Contribution to journal › Review article (Academic Journal) › peer-review

135 Citations (Scopus)

Climate-induced phenology shifts linked to range expansions in species with multiple reproductive cycles per year

Macgregor, C. J., Thomas, C. D., Roy, D. B., Beaumont, M. A., Bell, J. R., Brereton, T., Bridle, J. R., Dytham, C., Fox, R., Gotthard, K., Hoffmann, A. A., Martin, G., Middlebrook, I., Nylin, S., Platts, P. J., Rasteiro, R., Saccheri, I. J., Villoutreix, R., Wheat, C. W. & Hill, J. K., 24 Oct 2019, In: Nature Communications. 10, 10 p., 4455 (2019).

Research output: Contribution to journal › Article (Academic Journal) › peer-review

Open Access

File

107 Citations (Scopus)

255 Downloads (Pure)

Dominant words rise to the top by positive frequency-dependent selection

Pagel, M., Beaumont, M., Meade, A., Verkerk, A. & Calude, A., 9 Apr 2019, In: Proceedings of the National Academy of Sciences of the United States of America. 116, 15, p. 7397-7402 6 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

11 Citations (Scopus)

Looking for local adaptation: Convergent microevolution in aleppo pine (pinus halepensis)

Daniels, R. R., Taylor, R. S., Martínez, S. C. G., Vendramin, G. G., Fady, B., Muratorio, S. O., Piotti, A., Simioni, G., Grivet, D. & Beaumont, M. A., 4 Sept 2019, In: Genes. 10, 9, 16 p., 673.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

Open Access

File

12 Citations (Scopus)

179 Downloads (Pure)

2017

Effects of the ordering of natural selection and population regulation mechanisms on Wright-Fisher models

He, Z., Beaumont, M. & Yu, F., 5 Jul 2017, In: G3. 7, 7, p. 2095-2106 12 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

Open Access

File

8 Citations (Scopus)

359 Downloads (Pure)

2015

Calibration and evaluation of individual-based models using Approximate Bayesian Computation

van der Vaart, E., Beaumont, M. A., Johnston, A. S. A. & Sibly, R. M., 24 Sept 2015, In: Ecological Modelling. 312, p. 182-190 9 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

Open Access

File

98 Citations (Scopus)

495 Downloads (Pure)

CodABC: A computational framework to coestimate recombination, substitution, and molecular adaptation rates by approximate bayesian computation

Arenas, M., Lopes, J. S., Beaumont, M. A. & Posada, D., 1 Apr 2015, In: Molecular Biology and Evolution. 32, 4, p. 1109-1112 4 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

Open Access

File

20 Citations (Scopus)

327 Downloads (Pure)

Complex trait architecture: The pleiotropic model revisited

North, T. L. & Beaumont, M. A., 23 Mar 2015, In: Scientific Reports. 5, 9 p., 9351.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

Open Access

File

8 Citations (Scopus)

341 Downloads (Pure)

2014

Coestimation of recombination, substitution and molecular adaptation rates by approximate Bayesian computation

Lopes, J. S., Arenas, M., Posada, D. & Beaumont, M. A., Mar 2014, In: Heredity. 112, 3, p. 255-264 10 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

30 Citations (Scopus)

Detecting and measuring selection from gene frequency data

Vitalis, R., Gautier, M., Dawson, K. J. & Beaumont, M. A., Mar 2014, In: Genetics. 196, 3, p. 799-817 19 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

53 Citations (Scopus)

2013

Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates

Aeschbacher, S., Futschik, A. & Beaumont, M. A., Feb 2013, In: Molecular Ecology. 22, 4, p. 987-1002 16 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

10 Citations (Scopus)

The shaping of genetic variation in edge-of-range populations under past and future climate change.

Razgour, O. N., Juste, J., Ibanez, C., Kiefer, A., Rebelo, H. E. V., Puechmaille, S., Arlettaz, R., Burke, T., Dawson, D. A., Beaumont, M. A. & Jones, G., Oct 2013, In: Ecology Letters. 16, 10, p. 1258–1266 9 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

100 Citations (Scopus)

2012

A Novel Approach for Choosing Summary Statistics in Approximate Bayesian Computation

Aeschbacher, S., Beaumont, M. A. & Futschik, A., Nov 2012, In: Genetics. 192, 3, p. 1027-1047 21 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

77 Citations (Scopus)

Challenges and pitfalls in the characterization of anonymous outlier AFLP markers in non-model species: lessons from an ocellated lizard genome scan

Nunes, V. L., Beaumont, M. A., Butlin, R. K. & Paulo, O. S., Dec 2012, In: Heredity. 109, 6, p. 340-348 9 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

12 Citations (Scopus)

Population divergence with or without admixture: selecting models using an ABC approach

Sousa, V. C., Beaumont, M. A., Fernandes, P., Coelho, M. M. & Chikhi, L., May 2012, In: Heredity. 108, 5, p. 521-530 10 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

40 Citations (Scopus)

2011

Adaptive divergence and speciation among sexual and pseudoviviparous populations of Festuca

Chiurugwi, T., Beaumont, M., Wilkinson, M. & Battey, N., May 2011, In: Heredity. 106(5), p. 854 - 861 7 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

13 Citations (Scopus)

Association of Mc1r variants with ecologically relevant phenotypes in the European ocellated lizard, Lacerta lepida

Nunes, V., Miraldo, A., Beaumont, M., Butlin, R. & Paulo, O., Oct 2011, In: Journal of Evolutionary Biology. 24(10), p. 2289 - 2298 10 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

26 Citations (Scopus)

Effect of oceanographic barriers and overfishing on the population genetic structure of the Euroepan spiny lobster (Palinurus elephas)

Palero, F., Abelló, P., Macpherson, E., Beaumont, M. & Pascual, M., Oct 2011, In: Biological Journal of the Linnean Society. 104(2), p. 407 - 418 12 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

31 Citations (Scopus)

Mcheza: a workbench to detect selection using dominant markers

Antao, T. & Beaumont, M., Jun 2011, In: Bioinformatics. 27(12), p. 1717 - 1718 2 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

78 Citations (Scopus)

Multiple approaches to detect outliers in a genome scan for selection in ocellated lizards (Lacerta lepida) along an environmental gradient

Nunes, V., Beaumont, M., Butlin, R. & Paulo, O., Jan 2011, In: Molecular Ecology. 20(2), p. 193 - 205 13 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

43 Citations (Scopus)

2010

ABC: a useful Bayesian tool for the analysis of population data.

Lopes, J. S. & Beaumont, M. A., Aug 2010, In: Infection, Genetics and Evolution. 10, 6, p. 826-833 8 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

35 Citations (Scopus)

Approximate Bayesian computation in evolution and ecology

Beaumont, M., 2010, In: Annual Review of Ecology, Evolution, and Systematics. 41, p. 379 - 406

Research output: Contribution to journal › Article (Academic Journal) › peer-review

824 Citations (Scopus)

Combining genetic, historical and geographical data to reconstruct the dynamics of bioinvasions: application to the cane toad Bufo marinus

Estoup, A., Baird, S. J. E., Ray, N., Currat, M., Cornuet, J.-M., Santos, F., Beaumont, M. A. & Excoffier, L., Sept 2010, In: Molecular Ecology Resources. 10, 5, p. 886 - 901 6 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

53 Citations (Scopus)

Evaluating Nested Clade Phylogeographic Analysis under Models of Restricted Gene Flow

Panchal, M. & Beaumont, M. A., May 2010, In: Systematic Biology. 59, 4, p. 415 - 432 18 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

25 Citations (Scopus)

In defence of model-based inference in phylogeography REPLY

Beaumont, M., Nielsen, R., Robert, C., Hey, J., Gaggiotti, O., Knowles, L., Estoup, A., Panchal, M., Corander, J., Hickerson, M., Sisson, S., Fagundes, N., Chikhi, L., Beerli, P., Vitalis, R., Cornuet, J., Huelsenbeck, J., Foll, M., Yang, Z. & Rousset, F. & 2 others, Balding, D. & Escoffier, L., Feb 2010, In: Molecular Ecology. 19(3), p. 436 - 446 11 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

125 Citations (Scopus)

Inferring introduction routes of invasive species using approximate Bayesian computation on microsatellite data

Guillemaud, T., Beaumont, M., Ciosi, M., Cornuet, J. & Estoup, A., Jan 2010, In: Heredity. 104(1), p. 88 - 99 12 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

136 Citations (Scopus)

Likelihood-Free Inference of Population Structure and Local Adaptation in a Bayesian Hierarchical Model

Bazin, E., Dawson, K. & Beaumont, M., Jun 2010, In: Genetics. 185, issue 2, p. 587 - 602 16 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

76 Citations (Scopus)

Saving Darwin's muse: evolutionary genetics for the recovery of the Floreana mockingbird

Hoeck, P., Beaumont, M., James, K., Grant, R., Grant, P. & Keller, L., Apr 2010, In: Biology Letters. 6(2), p. 212 - 215 4 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

20 Citations (Scopus)

The Confounding Effects of Population Structure, Genetic Diversity and the Sampling Scheme on the Detection and Quantification of Population Size Changes

Chikhi, L., Sousa, V. C., Luisi, P., Goossens, B. & Beaumont, M. A., Nov 2010, In: Genetics. 186, 3, p. 983 - 995 13 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

250 Citations (Scopus)

2009

Adaptive approximate Bayesian computation

Beaumont, M., Cornuet, J., Marin, J. & Robert, C., Dec 2009, In: Biometrika. 96(4), p. 983 - 990 8 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

421 Citations (Scopus)

A novel parallel approach to the likelihood-based estimation of admixture in population genetics

Giovannini, A., Zanghirati, G., Beaumont, M., Chikhi, L. & Barbujani, G., Jun 2009, In: Bioinformatics. 25(11), p. 1440 - 1441 2 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

5 Citations (Scopus)

Approximate Bayesian Computation Without Summary Statistics: The Case of Admixture

Sousa, V., Fritz, M., Beaumont, M. & Chikhi, L., Apr 2009, In: Genetics. 179(4), p. 1507 - 1519 13 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

57 Citations (Scopus)

PopABC: a program to infer historical demographic parameters

Lopes, J., Balding, D. & Beaumont, M., Oct 2009, In: Bioinformatics. 25(20), p. 2747 - 2749 3 p.

Research output: Contribution to journal › Article (Academic Journal) › peer-review

76 Citations (Scopus)

Rapid radiation in spiny lobsters (Palinurus spp) as revealed by classic and ABC methods using mtDNA and microsatellite data

Palero, F., Lopes, J., Abelló, P., Macpherson, E., Pascual, M. & Beaumont, M., Nov 2009, In: BMC Evolutionary Biology. 9:263

Research output: Contribution to journal › Article (Academic Journal) › peer-review

34 Citations (Scopus)

Professor Mark A Beaumont

Research output

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