Forward-in-Time, Spatially Explicit Modeling Software to Simulate Genetic Lineages Under Selection

Prevalence of yaws and syphilis in the Ashanti region of Ghana and occurrence of H. ducreyi, herpes simplex virus 1 and herpes simplex virus 2 in skin lesions associated with treponematoses
Agyekum Boaitey, Y., Alex Owusu-Ofori,, Amarachukwu Anyogu, Farhang Aghakhanian, Natasha Arora, Jonathan B. Parr, Philipp P. Bosshard, Saki Raheem and Pascale Gerbault 2024. Prevalence of yaws and syphilis in the Ashanti region of Ghana and occurrence of H. ducreyi, herpes simplex virus 1 and herpes simplex virus 2 in skin lesions associated with treponematoses. PLoS ONE. 19 (5) e0295088. https://doi.org/10.1371/journal.pone.0295088

Author Correction: Dairying, diseases and the evolution of lactase persistence in Europe
Evershed, R., Davey Smith, G., Roffet-Salque, M., Timpson, A., Diekmann, Y., Lyon, Matthew S, Cramp, L., Casanova, Emmanuelle, Smyth, J., Whelton, H., Dunne, J., Brychova, Veronika, Šoberl, Lucija, Gerbault, P., Gillis, Rosalind E, Heyd, Volker, Johnson, Emily, Kendall, Iain, Manning, Katie, Marciniak, Arkadiusz, Outram, A., Vigne, Jean-Denis, Shennan, Stephen, Bevan, A., Colledge, Sue, Allason-Jones, Lyndsay, Amkreutz, L., Anders, Alexandra, Arbogast, Rose-Marie, Bălăşescu, Adrian, Bánffy, E., Barclay, Alistair, Behrens, Anja, Bogucki, P., Carrancho Alonso, Ángel, Carretero, José Miguel, Cavanagh, Nigel, Claßen, E., Collado Giraldo, Hipolito, Conrad, Matthias, Csengeri, Piroska, Czerniak, Lech, Dębiec, Maciej, Denaire, A., Domboróczki, László, Donald, Christina, Ebert, Julia, Evans, Christopher, Francés-Negro, Marta, Gronenborn, Detlef, Haack, Fabian, Halle, Matthias, Hamon, Caroline, Hülshoff, Roman, Ilett, Michael, Iriarte, E., Jakucs, János, Jeunesse, Christian, Johnson, Melanie, Jones, Andy M, Karul, Necmi, Kiosak, Dmytro, Kotova, Nadezhda, Krause, Rüdiger, Kretschmer, Saskia, Krüger, Marta, Lefranc, Philippe, Lelong, Olivia, Lenneis, E., Logvin, Andrey, Lüth, Friedrich, Marton, Tibor, Marley, Jane, Mortimer, Richard, Oosterbeek, Luiz, Oross, Krisztián, Pavúk, Juraj, Pechtl, Joachim, Pétrequin, Pierre, Pollard, Joshua, Pollard, Richard, Powlesland, D., Pyzel, Joanna, Raczky, Pál, Richardson, Andrew, Rowe, Peter, Rowland, Stephen, Rowlandson, Ian, Saile, Thomas, Sebők, Katalin, Schier, Wolfram, Schmalfuß, Germo, Sharapova, Svetlana, Sharp, Helen, Sheridan, A., Shevnina, Irina, Sobkowiak-Tabaka, Iwona, Stadler, Peter, Stäuble, Harald, Stobbe, Astrid, Stojanovski, Darko, Tasić, Nenad, van Wijk, Ivo, Vostrovská, Ivana, Vuković, Jasna, Wolfram, Sabine, Zeeb-Lanz, Andrea and Thomas, M. 2022. Author Correction: Dairying, diseases and the evolution of lactase persistence in Europe. Nature.

Disentangling Immediate Adaptive Introgression from Selection on Standing Introgressed Variation in Humans
Jagoda, E., Lawson, D.J., Wall, J.D., Lambert, D., Muller, C., Westaway, M., Leavesley, M., Capellini, T.D., Lahr, M.M., Gerbault, P., Thomas, M.G., Migliano, A.B., Willerslev, E., Metspalu , M. and Pagani, L. 2018. Disentangling Immediate Adaptive Introgression from Selection on Standing Introgressed Variation in Humans. Molecular Biology and Evolution. 35 (3), pp. 623-630. https://doi.org/10.1093/molbev/msx314

Dairying history and the evolution of lactase persistence
Gerbault, P. and Roffet-Salque, M. 2017. Dairying history and the evolution of lactase persistence. Cahiers de Nutrition et de Diététique. 52 (Supp. 1), pp. S19-S24. https://doi.org/10.1016/S0007-9960(17)30195-5

World-wide distributions of lactase persistence alleles and the complex effects of recombination and selection
Liebert, A., López, S., Jones, B.L., Montalva, N., Gerbault, P., Lau, W., Thomas, M.G., Bradman, N., Maniatis, N. and Swallow, D.M. 2017. World-wide distributions of lactase persistence alleles and the complex effects of recombination and selection. Human Genetics. 136 (11-12), p. 1445–1453. https://doi.org/10.1007/s00439-017-1847-y

Accurate age estimation in small-scale societies
Diekmann, Y., Smith, D., Gerbault, P., Dyble, M., Page, A.E., Chaudhary, N., Migliano, A.B. and Thomas, M.G. 2017. Accurate age estimation in small-scale societies. Proceedings of the National Academy of Sciences. 114 (31), pp. 8205-8210. https://doi.org/10.1073/pnas.1619583114

Investigating mitochondrial DNA relationships in Neolithic Western Europe through serial coalescent simulations
Rivollat, M., Rottier, S., Couture, C., Pemonge, M.H., Mendisco, F., Thomas, M.G., Deguilloux, M.F. and Gerbault, P. 2017. Investigating mitochondrial DNA relationships in Neolithic Western Europe through serial coalescent simulations. European Journal of Human Genetics. 25, pp. 388-392. https://doi.org/10.1038/ejhg.2016.180

Genomic analyses inform on migration events during the peopling of Eurasia
Gerbault, P. 2016. Genomic analyses inform on migration events during the peopling of Eurasia. Nature. 538 (7624), pp. 238-242. https://doi.org/10.1038/nature19792

A genomic history of Aboriginal Australia
Malaspinas, A.S., Westaway, M.C., Muller, C., Sousa, V.C., Lao, O., Alves, I., Bergström, A., Athanasiadis, G., Cheng, J.Y., Crawford, J.E., Heupink, T.H., Macholdt, E., Peischl, S., Rasmussen, S., Schiffels, S., Subramanian, S., Wright, J.L., Albrechtsen, A., Barbieri, C., Dupanloup, I., Eriksson, A., Margaryan, A., Moltke, I., Pugach, I., Korneliussen, T.S., Levkivskyi, I.P., Moreno-Mayar, J.V., Ni, S., Racimo, F., Xue, Y., Sikora, M., Aghakhanian, F.A., Brucato, N., Brunak, S., Campos, P.F., Clark, W., Ellingvåg, S., Fourmile, G., Gerbault, P., Injie, D., Koki, G., Leavesley, M., Logan, B., Lynch, A., Matisoo-Smith, E.A., McAllister, P.J., Mentzer, A.J., Metspalu, M., Migliano, A.B., Murgha, L., Phipps, M.E., Pomat, W., Reynolds, D., Ricaut, F.X., Siba, P., Thomas, M.G., Wales, T., Wall, C.M., Oppenheimer, S.J., Tyler-Smith, C., Durbin, R., Dortch, J., Manica, A., Schierup, M.H., Foley, R.A., Lahr, M.M., Bowern, C., Wall, J.D., Mailund, T., Stoneking, M., Nielsen, R., Sandhu, M.S., Excoffier, L., Lambert, D.M. and Willerslev, E. 2016. A genomic history of Aboriginal Australia. Nature. 538 (7624), pp. 207-214. https://doi.org/10.1038/nature18299

Statistically robust representation and comparison of mortality profiles in archaeozoology
Gerbault, P., Gillis, R., Vigne, J.D., Tresset, A., Bréhard, S. and Thomas, M.G. 2016. Statistically robust representation and comparison of mortality profiles in archaeozoology. Journal of Archaeological Science. 71, pp. 24-32. https://doi.org/10.1016/j.jas.2016.05.001

Competition for Cooperation: variability, benefits and heritability of relational wealth in hunter-gatherers
Chaudhary, N., Salali, G.D., Thompson, J., Rey, A., Gerbault, P., Stevenson, E.G., Dyble, M., Smith, D., Mace, R., Vinicius, L. and Migliano, A.B. 2016. Competition for Cooperation: variability, benefits and heritability of relational wealth in hunter-gatherers. Scientific Reports. 6, p. 29120 29120. https://doi.org/10.1038/srep29120

Introductory Editorial: Evolutionary Genomics
Itan, Y., Pines, G. and Gerbault, P. 2016. Introductory Editorial: Evolutionary Genomics. Evolutionary Bioinformatics. 11 (Suppl 2), pp. 53-55. https://doi.org/10.4137/EBO.S39729

Greenlandic Inuit show genetic signatures of diet and climate adaptation
Fumagalli, M., Moltke, I., Grarup, N., Racimo, F., Bjerregaard, P., Jørgensen, M.E., Korneliussen, T.S., Gerbault, P., Skotte, L., Linneberg, A., Christensen, C., Brandslund, I., Jørgensen, T., Huerta-Sánchez, E., Schmidt, E.B., Pedersen, O., Hansen, T., Albrechtsen, A. and Nielsen, R. 2015. Greenlandic Inuit show genetic signatures of diet and climate adaptation. Science. 349 (6254), pp. 1343-1347. https://doi.org/10.1126/science.aab2319

Widespread exploitation of the honeybee by early Neolithic farmers
Roffet-Salque, M., Regert, M., Evershed, R.P., Outram, A.K., Cramp, L.J., Decavallas, O., Dunne, J., Gerbault, P., Mileto, S., Mirabaud, S., Paakkonen, M., Smyth, J., Soberl, L., Whelton, H.L., Alday-Ruiz, A., Asplund, H., Bartkowiak, M., Bayer-Niemeier, E., Belhouchet, L., Bernardini, F., Budja, M., Cooney, G., Cubas, M., Danaher, E.M., Diniz, M., Domboroczki, L., Fabbri, C., Gonzalez-Urquijo, J.E., Guilaine, J., Hachi, S., Hartwell, B.N., Hofmann, D., Hohle, I., Ibanez, J.J., Karul, N., Kherbouche, F., Kiely, J., Kotsakis, K., Lueth, F., Mallory, J.P., Manen, C., Marciniak, A., Maurice-Chabard, B., Mc Gonigle, M.A., Mulazzani, S., Ozdogan, M., Peric, O.S., Peric, S.R., Petrasch, J., Petrequin, A.M., Petrequin, P., Poensgen, U., Pollard, C.J., Poplin, F., Radi, G., Stadler, P., Stauble, H., Tasic, N., Urem-Kotsou, D., Vukovic, J.B., Walsh, F., Whittle, A., Wolfram, S., Zapata-Pena, L. and Zoughlami, J. 2015. Widespread exploitation of the honeybee by early Neolithic farmers. Nature. 527 (7577), pp. 226-230. https://doi.org/10.1038/nature15757

Human evolutionary genetics
Gerbault, P. and Thomas, M.G. 2015. Human evolutionary genetics. in: International encyclopedia of the social & behavioral sciences (second edition) Elsevier. pp. 289-296

Storytelling and story testing in domestication
Gerbault, P., Allaby, R.G., Boivin, N., Rudzinski, A., Grimaldi, I.M., Pires, J.C., Climer Vigueira, C., Dobney, K., Gremillion, K.J., Barton, L., Arroyo-Kalin, M., Purugganan, M.D., Rubio de Casas, R., Bollongino, R., Burger, J., Fuller, D.Q., Bradley, D.G., Balding, D.J., Richerson, P.J., Gilbert, M.T., Larson, G. and Thomas, M.G. 2014. Storytelling and story testing in domestication. Proceedings of the National Academy of Sciences of the United States of America. 111 (17), pp. 6159-6164. https://doi.org/10.1073/pnas.1400425111

Lactose malabsorption and nutrition
Gerbault, P., Liebert, A., Swallow, D.M. and Thomas, M.G. 2014. Lactose malabsorption and nutrition. in: Lomer, M. (ed.) Advanced Nutrition and Dietetics in Gastroenterology Wiley. pp. 202-209

The onset of lactase persistence in Europe
Gerbault, P. 2013. The onset of lactase persistence in Europe. Human Heredity. 76 (3-4), pp. 154-161. https://doi.org/10.1159/000360136

How long have adult humans been consuming milk?
Gerbault, P., Roffet-Salque, M., Evershed, R.P. and Thomas, M.G. 2013. How long have adult humans been consuming milk? IUBMB Life. 65 (12), pp. 983-990. https://doi.org/10.1002/iub.1227

Modeling Recent Human Evolution in Mice by Expression of a Selected EDAR Variant
Kamberov, Y.G., Wang, S., Tan, J., Gerbault, P., Wark, A., Tan, L., Yang, Y., Li, S., Tang, K., Chen, H., Powell, A., Itan, Y., Fuller, D., Lohmueller, J., Mao, J., Schachar, A., Paymer, M., Hostetter, E., Byrne, E., Burnett, M., McMahon, A.P., Thomas, M.G., Lieberman, D.E., Jin, L., Tabin, C.J., Morgan, B.A. and Sabeti, P.C. 2013. Modeling Recent Human Evolution in Mice by Expression of a Selected EDAR Variant. Cell. 152 (4), pp. 691-702. https://doi.org/10.1016/j.cell.2013.01.016

Evaluating demographic models for goat domestication using mtDNA sequences
Gerbault, P., Powell, A. and Thomas, M.G. 2012. Evaluating demographic models for goat domestication using mtDNA sequences. Anthropozoologica. 47 (2), pp. 64-76. https://doi.org/10.5252/az2012n2a5

Domestication and migrations: Using mitochondrial DNA to infer domestication processes of goats and horses
Gerbault, P., Leonardi, M., Powell, A., Weber, C., Benecke, N., Burger, J. and Thomas, M.G. 2012. Domestication and migrations: Using mitochondrial DNA to infer domestication processes of goats and horses. in: Kaiser, E., Burger, J. and Schier, Wo (ed.) Population Dynamics in Prehistory and Early History: New Approaches Using Stable Isotopes and Genetics. Berlin, Germany De Grutyer. pp. 17-30

Inferring processes of Neolithic gene-culture co-evolution using genetic and archaeological data: The case of lactase persistence and dairying
Gerbault, P., Bollongino, R., Burger, J. and Thomas, M.G. 2012. Inferring processes of Neolithic gene-culture co-evolution using genetic and archaeological data: The case of lactase persistence and dairying. in: Colledge, S., Conolly, J., Dobney, K., Manning, K. and Shennan, S. (ed.) The Origins and Spread of Domestic Animals in Southwest Asia and Europe Walnut Creek, CA Left Coast Press. pp. 37-48

The evolution of lactase persistence in Europe. A synthesis of archaeological and genetic evidence
Leonardi, M, Gerbault, P., Thomas, M.G. and Burger, J. 2012. The evolution of lactase persistence in Europe. A synthesis of archaeological and genetic evidence. International Dairy Journal. 22 (2), pp. 88-97. https://doi.org/10.1016/j.idairyj.2011.10.010

mtDNA and Y‐chromosome diversity in Aymaras and Quechuas from Bolivia: Different stories and special genetic traits of the Andean Altiplano populations
Gayà‐Vidal, M., Moral, P., Saenz‐Ruales, N., Gerbault, P., Tonasso, L., Villena, M., Vasquez, R., Bravi, C.M. and Dugoujon, J.M. 2011. mtDNA and Y‐chromosome diversity in Aymaras and Quechuas from Bolivia: Different stories and special genetic traits of the Andean Altiplano populations. American Journal of Physical Anthropology. 145 (2), pp. 215-230. https://doi.org/10.1002/ajpa.21487

Evolution of lactase persistence: an example of human niche construction
Gerbault, P., Liebert, A., Itan, Y., Powell, A., Currat, M., Burger, J., Swallow, D. and Thomas, M.G. 2011. Evolution of lactase persistence: an example of human niche construction. Philosophical Transactions of the Royal Society B: Biological Sciences. 366 (1566), pp. 863-877. https://doi.org/10.1098/rstb.2010.0268

Impact of selection and demography on the diffusion of lactase persistence
Gerbault, P., Moret, C., Currat, M. and Sanchez-Mazas, A. 2009. Impact of selection and demography on the diffusion of lactase persistence. PLoS ONE. 4 (7) e6369. https://doi.org/10.1371/journal.pone.0006369