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Department of Genetics



John retrained as a biologist after a music degree and a job as a programmer. Following postdoctoral work at University of Sussex, University of Edinburgh and Université de Montpellier, John joined the Department of Genetics as a lecturer in 2010.

John’s doctoral work was in mathematical population genetics, and this is still a large part of his research, but he now combines this with empirical approaches, especially evolutionary inference from microbial genealogies, and cross-species comparative analyses.

Research Interests

John has wide interests within the field of evolutionary genetics, but his current research is focussed on two themes.

The first theme is evolution of reproductive isolation. When different populations or species hybridise, their divergent alleles are brought together in new combinations. The fitness of these combinations will help to determine the outcome of the hybridisation, and might also contain information about the mode of evolutionary divergence between the populations, and shed light on broader patterns of gene interaction. Decades of work on hybridisation has revealed a number of robust patterns that appear predictably in very distantly related groups (“Haldane’s Rule” is probably the best known). We have been trying to develop a theoretical framework that might to help to explain these patterns in a unified way, and combine simplicity and flexibility so as to be useful for data analysis.

The second theme involves evolutionary inference from the genomes of microbial pathogens. The aim here is to use the tools of classical population genetics and molecular phylogenetics to make inferences about pathogen ecology and epidemiology, that might be useful in combatting infectious disease.

Research Group Links

Welch Group


Key publications: 

Publications on Group website

Representative publications:

Schneemann H*, De Sanctis B*, Roze D, Bierne N, Welch JJ (2020). The geometry and genetics of hybridization. Evolution 74: 2575-2590. doi:10.1111/evo.14116

Simon A, Bierne N, Welch JJ (2018). Coadapted genomes and selection on hybrids: Fisher's geometric model explains a variety of empirical patterns. Evolution Letters 2: 472-498.doi:10.1002/evl3.66

Fraïsse C, Gunnarsson PA, Roze D, Bierne N, Welch JJ (2016). The genetics of speciation: insights from Fisher’s geometric model. Evolution 70: 1450-1464. doi:10.1111/evo.12968.

Weinert LA, Welch JJ (2017). Why might bacterial pathogens have small genomes? Trends Ecol Evol 32: 936-947. doi:10.1016/j.tree.2017.09.006

Hadjirin NF, Miller EL, Murray GGR, Yen PLK, Phuc HD, Wileman TM, Hernandez-Garcia J, Williamson SM, Parkhill J, Maskell DJ, Zhou R, Fittipaldi N, Gottschalk N, Tucker AW, Hoa NT, Welch JJ, Weinert LA (2021). Large scale genomic analysis of antimicrobial resistance in the zoonotic pathogen Streptococcus suis. BMC Biology (in press).

University Associate Professor
Dr John  Welch
Areas of Interest: 
Molecular evolution
Email address: 
Department of Genetics,
University of Cambridge,
Downing Street,
Cambridge CB2 3EH,
United Kingdom
Office phone: 
+44 (0)1223 333959
Takes PhD students