Follow me on ResearchGate

I am the Principal Investigator of the group, Chair in Evolutionary Biology at The University of Manchester and Fellow of the American Academy of Microbiology.

I am also the Director for the research domain of "Evolution, Systems and Genomics" at the University of Manchester, which is a research grouping of approximately 120 principal investigators and 500 researchers.

My surname sounds like "Mack-And-Ernie".  Many people ask.

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.

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 since 2009 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.

Research Focus:

The work in the lab is entirely computational molecular evolution.  We make software tools for carrying out new analyses, we analyse genomes and we contribute to theory.

Eukaryote Origins:

We have used "Omics" data in an effort to augment phylogenetic approaches for understanding the origin of eukaryotes.  There is a wealth of information from proteomics, transcriptomics and genomics and all these data contain useful information about organismal and genomic history.  We are investigating ways in which these data can be profitably used to answer questions on Eukaryotic Origins.

Horizontal Gene Transfer:

Genes create phenotypes and therefore, given what we know about inter-species gene transfer, it makes sense to try to understand phenotypes by understanding gene flow.  We are investigating how genes move from one organisms to another and trying to understand what the advantages of such moves might be and what effect they produced.


Evolution is not linear and genes are quite often mosaic - being formed by the merging of DNA sequences with different histories.  We are investigating the extent of this process and we are gaining an understanding of how often it happens and why it happens.

N-Rooted Fusion Graphs:

Clearly, it is not possible to accurately display or analyse mosaic sequences using standard phylogenetic trees.  Therefore, we have invented N-Rooted Fusion Graphs for visualising these historical events.  N-Rooted Fusion Graphs differ from phylogenetic trees by having more than one root and having at least one node with an in-degree of 2 (this represents the merging of two unrelated or distantly related entities).  Current work involves the development of methods for constructing such graphs.


We have developed several software programs for evolutionary analyses.  The list is to be found in the "Software" menu at the top of the website.

Other information:

In 2002, at the Pasteur Institute in Paris, I was presented with a medal for my research at MEEGID VI and a year later I was recognized by NUI Maynooth for my research achievements when I was awarded the NUI Maynooth Young Investigator Award.  In 2009, I was a guest-editor, along with Prof James Lake and Prof. Mark Ragan of a special issue of Philosophical Transactions of the Royal Society of London (Biology Series), which is the world's oldest continuously-published journal.  In 2011, I gave the "Ernst Mayr" Keynote lecture at the Mechanisms of Protein Evolution meeting in Denver Colorado.

I was one of the founding directors of the Irish Centre for High End Computing. I am an Associate Editor of Molecular Biology and Evolution, Biology Direct, Journal of Experimental Zoology and am currently serving as the secretary for the Society for Molecular Biology and Evolution.  I am also a regular commentator on scientific matters on TV, Radio and in the print media.

I have supervised 25 PhD students, been awarded Marie Curie fellowships, been funded to the tune of more than €3.5 million in direct research funding and been involved in more than €39 Million in programme grants. In addition, my group has published in Science, Nature, CellPNAS, Current Biology, TREE, Trends in Genetics, Proceedings of the Royal Society of London and so on. In total we have published more than 100 articles and I have been an invited speaker at more than 70 conferences.

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 burgdorferi. Proceedings 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:

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.