James Mcinerney

James Mcinerney, BSc, PhD, DSc, F Am Acad Microbiol, FLS


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Personal profile


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.
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.

Research interests

Horizontal Gene Transfer - Eukaryote origins and early evolution - Network analyses of evolution - Synonymous Codon Usage - Phylogenetics - Phylogenetic Supertrees - Adaptive evolution

Major Software Projects:

TIGER: Tree-Independent Generation of Evolutionary Rates.
TOPD/FMTS: Software to Compare Phylogenetic Trees.
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.

Selected Publications:

Nelson-Sathi S., Sousa F.L., Roettger M., Lozada-Chávez N., Thiergart T., Janssen A., Bryant D., Landan G., Schönheit P., Siebers B., McInerney J.O., Martin W.F., (2015) Origins of major archaeal clades correspond to gene acquisitions from bacteria. Nature, doi:10.1038/nature13805
McInerney, J.O., O’Connell, M.J., and Pisani, D. (2014) The hybrid nature of the Eukaryota and a consilient view of life on Earth. Nature Reviews Microbiology 12(6):449-455.
Liu S., [...] McInerney J.O., [...] Wang J. (2014) Population genomics reveal recent speciation and rapid evolutionary adaptation in polar bears. Cell, 157 (4):785–794.
Alvarez-Ponce, D., Lopez, P., Bapteste, E. and McInerney, J.O. (2013). Gene similarity networks provide tools for understanding eukaryote origins and evolution. PNAS 110(17):E1594-1603.
Nelson-Sathi, S., Dagan, T., Landan, G., Janssen, A., Steel, M., McInerney, J. O., Deppenmeier, U., and Martin, W.F. (2012). Acquisition of 1,000 eubacterial genes physiologically transformed a methanogen at the origin of Haloarchaea. PNAS 109 (50) 20537-20542.
Bapteste, E., Bouchard F., Baquero F., McInerney J.O., Lopez P. and Burian R.M. (2012). Evolutionary analyses of non-genealogical bonds produced by introgressive descent. PNAS 109:45 18266-18272, doi:10.1073/pnas.1206541109.
Feuda, R., Hamilton, S.C., McInerney, J.O. and Pisani, D. (2012) Metazoan opsin evolution reveals a simple route to animal vision. PNAS 109:46 18868-18872, doi: 10.1073/pnas.1204609109.
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. PNAS 107:40 17252-17255. 
McInerney, J.O. and Pisani, D (2007) Genetics: Paradigm for Life. Science 318:1390-1391.
Kinsella, R.J., Fitzpatrick, D.A., Creevey, C.J. and McInerney J.O. (2003). Fatty acid biosynthesis in Mycobacterium tuberculosis: Lateral gene transfer, adaptive evolution and gene duplication. PNAS, 100, 10320-10325.
McInerney, J.O. (1998). Replicational and Transcriptional Selection on Codon Usage in Borrelia burgdorferi. PNAS: 95 10698-10703



My research involves understanding how genes and genomes evolve. Evolution is the simple process of replicating biological entities, but with errors occasionally entering the system. These errors can be deleterious (not a good idea), neutral or advantageous. Natural selection is the process of making the decision about the benefit or otherwise of an evolutionary change. The types of changes that can occur varies from small changes such as nucleotides being replaced in a DNA strand, all the way up to mergers of distantly-related cells and the formation of entirely new kinds of life in the process. The implications for humanity in understanding evolutionary processes include better understandings of antibiotic resistance, better appreciation and understanding of the world around us and better understanding of what might happen in the future in our ever-changing world.


Molecular Evolution, inheritance, evolutionary microbiology, bioinformatics, phylogenetics

Expertise related to UN Sustainable Development Goals

In 2015, UN member states agreed to 17 global Sustainable Development Goals (SDGs) to end poverty, protect the planet and ensure prosperity for all. This person’s work contributes towards the following SDG(s):

  • SDG 3 - Good Health and Well-being
  • SDG 14 - Life Below Water

Education/Academic qualification

Doctor of Philosophy, Analysis of Archaea in the North West Atlantic, University College - Galway

Award Date: 20 Jul 1995

Research Beacons, Institutes and Platforms

  • Digital Futures


  • bioinformatics
  • horizontal gene transfer
  • networks
  • introgression
  • phylogeny
  • genomes
  • microorganisms
  • mammals
  • python
  • programming


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