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Lab members

Francois Balloux
Group leader


Maziar Ashrafian Bonab
Graduate student

J A [Afsaneh] Jahan-Far
[e-mail to be advised]

Lori Lawson-Handley

Laurent Lehmann

Hua Liu
Graduate student

Towfique Raj
Graduate student

Camille Szmaragd
Graduate student

Past Group members

Ben Gantenbein
Postdoctoral fellow 2003/04

Franck Prugnolle
Postdoctoral fellow 2004/05

Dr Francois Balloux
Department of Genetics, Downing Street, Cambridge, CB2 3EH, England
+44 1223 333964
Fax: +44 1223 333992
Email: fb255[at]

Balloux Lab
Theoretical and Molecular Population Genetics

Outline of the Lab

Keywords: Population Genetics, Statistical Genetics, Bioinformatics, Infectious Diseases, Immunity Genes, Hepatitis B Virus, Phylogenetics, Molecular Epidemiology

Our group is working on the genetic makeup of human populations and their pathogens. Currently, our research projects focus on the geographic distribution of human genetic variation and the genetic bases of clinical outcome of Hepatitis B virus infection.

Geographic patterns of human genetic diversity: Over recent years, there has been an increasing recognition of the importance of human settlement history to medicine. We are working on characterising worldwide geographic patterns of human genetic variation, focusing in particular on disease resistance/susceptibility genes. We are also interested in genetic patterns at a smaller geographic scale. A key human migration is the spread of agriculture in Europe during the Neolithic from the Fertile Crescent. Previous studies addressing this question have yielded conflicting results and there is heated debate about whether agriculturalists replaced other populations, or instead if people remained static and it was only the practice that spread. To address this question, we have recently collected 2.500 blood samples from the Eastern part of the Fertile Crescent.

Figure 1: Shortest colonisation routes through landmasses from East Africa to 51 populations typed at 377 autosomal microsatellite markers. Inset: correlation between geographic distance from East Africa with genetic diversity of the populations (Modified from Prugnolle et al. 2005 Current Biology 15: R159-R160).

Modelling clinical outcome of infectious diseases: Understanding the factors influencing the clinical outcome of infectious diseases is crucial for early diagnosis and optimised treatment. Despite widespread recognition of the importance of the genetic composition of infecting strains and host factors such as age or sex, most efforts so far have focused narrowly on characterising disease and susceptibility genes in humans. Our work aims at developing an integrated and powerful statistical framework to characterise mutations in the pathogen influencing clinical outcome (including drug and vaccine resistance) jointly with specific risk factors of the patient (e.g. sex, age, geographic origin, susceptibility factors in the host genome). Our current study organism is the hepatitis B virus (HBV).

Figure 2: Phylogenetic tree of 600 hepatitis B virus strains based on the polymerase gene (Szmaragd, unpublished).

Latest publications

[Lab members in bold type]


  • Charpentier M, M Setchell, F Prugnolle, J Wickings, P Peignot, F Balloux and M Hossaert-McKey (2006) Life-history correlates of inbreeding depression in mandrills (Mandrillus sphinx). Molecular Ecology 15: 21-28
  • De Meeus T, L Lehmann and F Balloux (2006) The population genetics of clonal diploids: a short DIY notice. Infection Genetics Evolution 6: 163-170
  • Hammond R L, L J Lawson Handley, B J Winney, M W Bruford and N Perrin (2006) Genetic evidence for female-biased dispersal and gene-flow in a polygynous primate. Proc. Roy. Soc. Lond. B 273: 479-484.
  • Lawson Handley L J, L Braendli, and N Perrin (2006) Disentangling reasons for low Y chromosome variation in the greater-white toothed shrew (Crocidura russula). Genetics 173: 935-942
  • Lawson Handley L J, R L Hammond, G Emaresi, A Reber and N Perrin (2006) Low Y chromosome variation in Saudi-Arabian hamadryas baboons (Papio hamadryas hamadryas). Heredity 96: 298-303.
  • Lawson Handley L J, and N Perrin (2006) Y chromosome microsatellite isolation from BAC clones in the greater white-toothed shrew (Crocidura russula). Molecular Ecology Notes 6: 276-279
  • Lehmann L and L Keller (2006) The evolution of cooperation and altruism. A general framework and a classification of models. Journal of Evolutionary Biology [in press]
  • Lehmann L, N Perrin and F Rousset (2006) Population demography and the evolution of helping behaviors. Evolution [in press]
  • Lehmann L and N Perrin (2006) On metapopulation resistance to drift and extinction. Ecology [in press]
  • Lehmann L, K Bargum and M Reuter (2006) An evolutionary analysis of the relationship between spite and altruism. Journal of Evolutionary Biology [in press]
  • Liu H, F Prugnolle, A Manica and F Balloux (2006) A geographically explicit genetic model of worldwide human settlement history. American Journal of Human Genetics 79: 230-237
  • Manica A, H Liu, F Prugnolle and F Balloux (2006) Worldwide genetic patterns in human population genetics. In "Simulations, Genetics and Human Prehistory - A Focus on Islands" Editors: S Matsumura, P Forster and C Renfrew. McDonald Institute Press, University of Cambridge [in press]
  • Sazanov A A, A L Sazanova, V A Stekolnikova, A V Trukhina, A A Kozyreva, A F Smirnov, M N Romanov, L J Lawson Handley, T Malewski, and J B Dodgson (2006) Chromosomal localization of the UBAP2Z and UBAP2W genes in chicken. Animal Genetics 37: 72-73
  • Szmaragd C, G Foster, A Manica, A Bartholomeusz, RA Nichols and F Balloux (2006) Genome-wide characterisation of Hepatitis B mutations involved in clinical outcome. Heredity [in press]
  • Szmaragd C, R A Nichols and F Balloux (2006) A novel method to characterize pathogen candidate genetic polymorphisms involved in clinical outcome. Infection Genetics Evolution 6: 38-45


  • Bettencourt-Dias M, A Rodrigues-Martins, L Carpenter, M Riparbelli, L Lehmann, M K Gatt, N Carno, F Balloux, G Callaini and D M Glover (2005) SAK/PLK4 is required for centriole duplication and flagella development Current Biology 15: 2199-2207
  • De Meeus T and F Balloux (2005) F-statistics of clonal diploids structured in numerous demes. Molecular Ecology 14: 2695-2702
  • Gantenbein B, V Fet, I Gantenbein and F Balloux (2005) Evidence for recombination in scorpion mitochondrial DNA. Proc. R. Soc. London B 272: 697-704
  • Halkett F, J C Simon and F Balloux (2005) Tackling the population genetics of clonal and partially clonal organisms. Trends in Ecology and Evolution 20: 194-201
  • Manica A, F Prugnolle and F Balloux (2005) Geography is a better determinant of human genetic differentiation than ethnicity. Human Genetics 118: 366-371
  • Prugnolle F, H Liu, T De Meeus and F Balloux (2005) The population genetics of complex life cycle parasites: the case of monoecious digenetic trematodes. International Journal for Parasitology 35: 255-263
  • Prugnolle F, A Manica and F Balloux (2005) Geography predicts neutral genetic diversity of human populations. Current Biology 15: R159-R160
  • Prugnolle F, A Manica, M Charpentier, J F Guégan, V Guernier and F Balloux (2005) Worldwide HLA diversity: human colonisation history and pathogen-driven selection. Current Biology 15: 1022-1027
  • Prugnolle F, D Roze, A Theron and T De Meeus (2005) F-statistics under alternation of sexual and asexual reproduction: a model and data from schistosomes (platyhelminth parasites). Molecular Ecology 14: 1355-1365
  • Prugnolle F, A Manica, M Charpentier, JF Guégan, V Guernier, F Balloux (2005) Pathogen-driven selection and worldwide HLA class I diversity. Current Biology 15: 1022-1027
  • Prugnolle F, A Theron, J P Poitier, R Jabbour-Zahad, P Jarne, P Durand and T De Meeus (2005) Dispersal in a parasitic worm and its two hosts and its consequences for local adaptation. Evolution 59: 296-303

A listing of publications 2003 - 2004 can be found HERE