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An Interdisciplinary Research Centre at the University of Cambridge

Understanding adaptive evolution in bacterial pathogens using genomic data.


2022-present: Senior Research Fellow & Group Leader, Department of Genetics, Evolution and Environment, UCL
2022: Senior Bioinformatician, Wellcome Sanger Institute
2018-2022: Wheldale Onslow Junior Research Fellow in Evolutionary Biology, Newnham College
2018-2022: Research Associate, Department of Veterinary Medicine, University of Cambridge
2016-2018: Postdoctoral Scholar, Department of Ecology and Evolution, University of California, Santa Cruz
2012-2016: PhD, Department of Genetics, University of Cambridge
2010-2011: MSc Quantitative Genetics and Genome Analysis, Institute of Evolutionary Biology, University of Edinburgh
2009-2010: MPhil Philosophy, University of Cambridge
2007-2008: MA Philosophy, Western University
2001-2006: MPhys Theoretical Physics, University of St Andrews



My research aims at understanding adaptive evolution in bacterial pathogens. I am interested in how and why bacteria evolve to cause disease, colonise and infect new host species, evade vaccines, and resist antibiotic treatments. To address these questions, I develop phylogenetic methodology and population genetic theory, and apply these to genomic and phenotypic data from wild populations and laboratory experiments. My research is inherently collaborative and I work closely with wet-lab microbiologists, epidemiologists, vets and clinicians. 

A common theme in my research is the need to understand bacterial pathogens in their broader evolutionary and ecological context. Advances in sequencing technologies have led to an increasing appreciation of the genetic and ecological diversity within pathogens and more broadly across the microbiome. Studying the drivers of this diversity and the relationship between pathogens and other members of the microbiome could lead to a deeper understanding of the ecology and evolution of pathogens that could inform control and treatment strategies.


Current areas of research:

  • The evolution and ecology of bacterial pathogens: how and why bacterial ecologies change over time and how these changes influence broader evolutionary dynamics.
  • The role of commensal populations in pathogen evolution, particularly the evolution of antibiotic resistance.
  • The impact of purifying selection on bacterial evolution: how changes in mutation rate, genome size or recombination rate influence the burden imposed by deleterious mutations, how this translates to changes in the shape and depth of bacterial phylogenies, and how it influences the emergence and persistence of pathogens.


Key publications: 

Matuszewska M, Murray GGR, Ba X, Wood R, Holmes M & Weinert LA. 2022. Stable antibiotic resistance and rapid human adaptation in livestock-associated MRSA. eLife. 11:e74819. DOI: 10.7554/eLife.74819

Murray GGR, Balmer A, Herbert J, Hadjirin N, Kemp C, Matuszewska M, Bruchmann S, Hossain ASMM, Gottschalk M, Tucker AW, Miller EL & Weinert LA. 2021. Mutation rate dynamics reflect ecological change in an emerging zoonotic pathogen. PLOS Genetics. 17(11): e1009864. DOI: 10.1371/journal.pgen.1009864

Murray GGR, Charlesworth J, Miller EL, Casey MJ, Lloyd CT, Gottschalk M, Tucker AW, Welch JJ & Weinert LA. 2021. Genome reduction is associated with bacterial pathogenicity across different scales of temporal and ecological divergence. Molecular Biology and Evolution. 38 (4): 1570–1579. DOI: 10.1093/molbev/msaa323

Murray GGR, Soares AER, Novak BJ, Schaefer NK, Cahill JA, Baker AJ, Demboski J, Doll A, Da Fonseca RR, Fulton TL, Gilbert MTP, Heintzman PD, Letts B, McIntosh G, O’Connell BL, Peck M, Pipes M-L, Rice ES, Santos KM, Sohrweide AG, Vohr SH, Corbett-Detig RB, Green RE & Shapiro B (2017).  Natural selection shaped the rise and fall of passenger pigeon genomic diversity. Science. 358 (6375). DOI: 10.1126/science.aao0960.

Murray GGR, Weinert LA, Rhule EL, Welch JJ. (2016) The Phylogeny of Rickettsia Using Different Evolutionary Signatures: How Tree-Like is Bacterial Evolution? Systematic biology 65:2, 265-279. DOI: 10.1093/sysbio/syv084.

Murray GGR, Wang F, Harrison EM, Paterson GK, Mather AE, Harris SR, Holmes MA, Rambaut A & Welch JJ (2016). The effect of genetic structure on molecular dating and tests for temporal signal. Methods in Ecology and Evolution. 7 (1). DOI: 10.1111/2041-210X.12466.

Other publications: 

Wang M-S, Murray GGR, Mann D, Groves P,  Corbett-Detig R,  Vershinina AO,  Supple M , Kapp JD, Crump S, Stirling I, Laidre K, Kunz M, Dalén L , Green RE & Shapiro B. 2022. A polar bear paleogenome reveals extensive ancient gene flow from polar bears into brown bears. Nature Ecology and Evolution. 6(7):936-944. DOI: 10.1038/s41559-022-01753-8

Hadjirin N, Miller EL, Murray GGR, Yen PLK, Phuc HD, Wileman TM, Hernandez-Garcia J, Williamson SM, Parkhill J, Maskell DJ, Zhou R, Fittipaldi N, Gottschalk M, Tucker AW, Hoa NT, Welch JJ & Weinert LA. 2021. Large scale genomic analysis of antimicrobial resistance in the zoonotic pathogen Streptococcus suis. BMC Biology 19, 191. DOI: 10.1186/s12915-021-01094-1

Funck J, Heintzman PD, Murray GGR, Shapiro B, McKinney H, Bigelow N, Huchet J-B, Druckenmiller P, Wooller KJ. 2020. A detailed life history of a Pleistocene steppe bison (Bison priscus) skeleton unearthed in Arctic Alaska. Quaternary Science Reviews. DOI: 10.1016/j.quascirev.2020.106578

Dehasque M, Ávila-Arcos MC, Díez-del-Molino D, Fumagalli M, Guschanski K, Lorenzen  ED, Malaspinas A-S, Marques-Bonet T, Martin MD, Murray GGR, Papadopulos  AST, Therkildsen NO, Wegmann D, Dalén L, Foote AD†. 2020. Inference of natural selection from ancient DNA. Evolution Letters. DOI: 10.1002/evl3.165

Matuszewska M, Murray GGR, Harrison EM, Holmes MA & Weinert LA. 2020. The evolutionary genomics of host specificity in Staphylococcus aureus. Trends in Microbiology. DOI: 10.1016/j.tim.2019.12.007

Eerkens J, Nichols R, Murray GGR, Perez K, Murga E, Kaijankoski P, Rosentahl J, Engbring L & Shapiro B. 2018. A probable prehistoric case of meningococcal disease from San Francisco Bay: next generation sequencing of Neisseria meningitidis from dental calculus and osteological evidence. International Journal of Paleopathology. 22. DOI: 10.1016/j.ijpp.2018.05.001.

Cotoras DD, Murray GGR, Kapp J, Gillespie RG, Griswold C, Simison WB, Green RE & Shapiro B (2017). Ancient DNA resolves the history of Tetragnatha (Araneae, Tetragnathidae) spiders on Rapa Nui. Genes. 8 (12). DOI: 10.3390/genes8120403.

Longdon B, Murray GGR, Palmer W, Day J, Parker D, Welch JJ, Obbard DJ & Jiggins FJ (2015). The evolution, diversity and host associations of rhabdoviruses. Virus Evolution. 1 (1). DOI: 10.1093/ve/vev014.

Paterson GK, Harrison EM, Murray GGR, Welch JJ, Warland JH, Holden MTG, Morgan FJE, Ba X, Koop G, Harris SR, Maskell DJ, Peacock SJ, Herrtage ME, Parkhill J & Holmes MA. 2015. Capturing the cloud of MRSA diversity after transmission and during infection reveals complex and heterogenous carriage and transmission. Nature Communications. 6 (6560). DOI: 10.1038/ncomms7560.        

Woolhouse MEJ, Thumbi SM, Jennings A, Chase-Topping M, Callaby R, Kiara H, Oosthuizen M, Ndila M, Conradie I, Handel IG, Poole EJ, Njiri E, Collins NE, Murray G, Tapio M, Tosas Auguet O, Weir W, Morrison WI, Kruuk LEB, Bronsvoort BM de C, Hanotte O, Coetzer K & Toye PG (2015). Coinfections determine patterns of mortality in populations exposed to parasite infection. Science Advances. 1 (2). DOI: 10.1126/sciadv.1400026.

Murray GGR, Woolhouse MEJ, Tapio M, Mbole-Kariuki MN, Sonstegard TS, Thumbi SM, Jennings AE, Conradie van Wyk I, Chase-Topping M, Kiara H, Toye P, Coetzer K, Bronsvoort BM deC & Hanotte O. 2013. Genetic susceptibility to infectious disease in East African Shorthorn Zebu: a genome-wide analysis of the effect of heterozygosity and exotic introgression. BMC Evolutionary Biology. 13 (246). DOI: 10.1186/1471-2148-13-246.

Murray GGR, Kosakovsky Pond SL & Obbard DJ. Proceedings of the Royal Society B (2013).  Suppressors of RNAi from plant viruses are subject to episodic positive selection. 280 (1765). DOI: 10.1098/rspb.2013.0965.

Group Leader in the Department of Genetics, Evolution and Environment, UCL
Photo of Gemma Murray
Available for consultancy


Person keywords: 
Host-Pathogen Interaction
Pathogen Evolution
Innate Immunity
Cross-species transmission
Bacterial evolution and ecology