Prof. James McInerney BSc PhD DSc FLS

I am the Head of the School of Life Sciences at The University of Nottingham (since Feb 1st, 2018) and principal investigator of this research group. I am also an elected Fellow of the American Academy of Microbiology and in 2020 I was elected President of the Society for Molecular Biology and Evolution, a position I will take up for the duration of 2022.

My surname sounds like “Mack-And-Ernie”.  I thought I’d mention it, since many people ask.

Before coming to Nottingham, I was Chair in Evolutionary Biology at The University of Manchester and also the Director for the research domain of “Evolution, Systems and Genomics” at the University of Manchester.

My BSc and PhD were awarded by University College Galway, where I studied from 1987 until 1994. Subsequently I worked as a post-doc at the National Diagnostics Centre in Galway and in the Department of Zoology at The Natural History Museum, London. In 1999 I set up the bioinformatics research group at NUI Maynooth and became the director of the Genetics and Bioinformatics degree course. For the academic year 2012-2013, I took a sabbatical at the Center for Communicable Disease Dynamics at Harvard University, USA.  In 2015 I moved my research to The University of Manchester to take up a chair in evolutionary biology. In 2016 I was appointed as the director of the research domain of “Evolution, Systems and Genomics” in the Faculty of Biology, Medicine and Health at the University of Manchester. In 2018, I became the Head of the School of Life Sciences at the University of Nottingham and moved my research group to the Life Sciences Building on University Campus.

I was elected Fellow of the American Academy of Microbiology in 2015 and as a Fellow of the Linnean Society in 2016.  In 2015, I was recognised by the Irish government with a conference ambassador award by the Minister for Tourism.  I was elected secretary of the Society for Molecular Biology and Evolution for the period 2013-2017.  In 2013, I was awarded a DSc by the National University of Ireland for a thesis entitled “Studies on the evolution of genes and genomes”.  I have served as an Associate Editor of Molecular Biology and Evolution from 2009 until I stepped down in 2018, and as an Associate Editor of the Journal of Experimental Zoology since 2011.  I am also a scientific associate of The Natural History Museum, London.

Selected Publications


McInerney, J.O., McNally, A and O’Connell, M.J. (2017) Why Prokaryotes have Pangenomes. Nature Microbiology 2, 17040.

McInerney, J.O. and O’Connell, M.J. (2017) Minding the gaps in cellular evolution. Nature 541, 297–299 doi:10.1038/nature21113  doi:10.1038/nature21113

McInerney, J.O. (2016) Evolution: A four billion year old metabolism. Nature Microbiology. 1, Art. No. 16139.

Ku, C., Nelson-Sathi, S., Roettger, M., Sousa, F.L., Lockhart, P., Bryant, D., Hazkani-Covo,E., McInerney, J.O., Landan, G., and Martin, W.F. (2015) Endosymbiotic origin and differential loss of eukaryotic genes Nature. 524, 427–432. doi:10.1038/nature14963

Nelson-Sathi, et al., (2015). Origins of major archaeal clades correspond to gene acquisitions from bacteria. Nature doi:10.1038/nature13805. [pdf]

McInerney, J.O. and O’Connell, M.J. (2014) Evolutionary developmental biology: Ghost locus appears. Nature 514, 570–571. doi:10.1038/514570a. [pdf]

McInerney, et al., (2014). The hybrid nature of the Eukaryota and a consilient view of life on Earth. Nature Reviews Microbiology doi:10.1038/nrmicro3271.[pdf]

Liu et al., (2014) Population Genomics Reveal Recent Speciation and Rapid Evolutionary Adaptation in Polar Bears. Cell , 157(4) 785 – 794. doi:10.1016/j.cell.2014.03.054 [pdf]

Alvarez-Ponce, et al., (2013). Gene similarity networks provide new tools for understanding eukaryote origins and evolution.Proceedings of the National Academy of Sciences USA doi: 10.1073/pnas.1211371110.[pdf]

Nelson-Sathi, et al., (2012) Acquisition of 1,000 eubacterial genes physiologically transformed a methanogen at the origin of Haloarchaea. Proceedings of the National Academy of Sciences USA. 109 (50) 20537-20542 doi: 10.1073/pnas.1209119109.[pdf]

Feuda, et al., (2012) Metazoan opsin evolution reveals a simple route to animal vision. Proceedings of the National Academy of Sciences, USA 109:(46) 18868-18872 doi: 10.1073/pnas.1204609109 [pdf]

Bapteste et al., (2012). Evolutionary analyses of non-genealogical bonds produced by introgressive descent. Proceedings of the National Academy of Sciences, USA. 109:(45) 18266-18272 doi:10.1073/pnas.1206541109.

Cotton, J.A., and McInerney, J.O. (2010) Eukaryotic genes of archaebacterial origin are more important than the more numerous eubacterial genes, irrespective of function. Proceedings of the National Academy of Sciences, USA 107:40 17252-17255. [link]

McInerney, J.O. and Pisani, D (2007) Genetics: Paradigm for Life. Science 318:1390-1391. [link]

Kinsella et al., (2003). Fatty acid biosynthesis in Mycobacterium tuberculosis: Lateral gene transfer, adaptive evolution and gene duplication. Proceedings of the National Academy of Sciences, USA, 100, 10320-10325. [link]

McInerney, J.O. (1998). Replicational and Transcriptional Selection on Codon Usage in Borrelia burgdorferiProceedings of the National Academy of Sciences, USA: 95 10698-10703. [link]


You can find more of our publications by clicking the Papers tab at the top of this page.

Research themes:

– Horizontal Gene Transfer

– Eukaryote origins and early evolution

– Network analyses of evolution

– Synonymous Codon Usage

– Phylogenetics

– Phylogenetic Supertrees

– Adaptive evolution

Research Interests

Prof. McInerney’s research group are interested in genomic evolution, particularly the influence of horizontal gene transfer on the evolution of genomes and gene duplications and losses in Vertebrates. We work on Eubacteria, Archaebacteria, Viruses, Eukaryotes.

Major Software Projects:

Coinfinder: detecting significant associations and dissociations in pangenomes


TIGER: Tree-Independent Generation of Evolutionary Rates.


TOPD/FMTS: Software to Compare Phylogenetic Trees (Developed by Pere Puigbo, during his stay in the group).


MultiPhyl: Phylogenetic Supercomputer.


Modelgenerator: Selection of Amino Acid Substitution Matrices.


DPRml: Distributed Phylogeny Reconstruction by Maximum Likelihood.


CLANN: Investigating Phylogenetic Information Through Supertree Analysis.


Crann: A Program for Detecting Adaptive Evolution in Protein-Coding DNA Sequences.


GCUA: General Codon Usage Analysis.