Dr Mary O'Connell

BSc (Hons) PhD
University Academic Fellow in Biology
School of Biology

Background: My PhD (2005) addressed the role of positive selection in molecular evolution and assessed rate heterogeneity in protein coding regions of mammals - primarily the human and mouse genomes. Following on from this I took a position as an SFI postdoctoral fellow in University College Cork working primarily on the evolution of genomic imprinting in mammals and plants from an analytical and quantitative perspective. Six Months later (2006) and following open competition, I moved to my first fully tenured academic post at Dublin City University. There I established my own independent research team. I have continued to expand and develop my interests in both the analytical/empirical analyses of genomic data from a molecular evolutionary perspective and also in the more theoretical concepts around evolution of life on the planet. My research group (www.mol-evol.org) work on specific aspects of evolutionary genomics and we are primarily computational based with some wet bench collaborations/aspects to our work. We are currently 2 PhD students and 1 postdoctoral associate and have 2 further PhD positions available (see below).

Contact: Miall 9.05, +44(0) 113 34 34890, email address for  

You can read more about Dr O'Connell's interests here:

Research Interests

Molecular Mechanisms of Evolution: Understanding the patterns and processes of evolution and the relationship between genotype, phenotype and fitness.

Current Projects



Faculty Research and Innovation

Studentship information

Undergraduate project topics:

  • None

Postgraduate studentship areas:

  • Currently recruiting 2 PhD students on the following projects:
  • "Genomic Innovation and the Emergence of Placentation in Mammals" http://www.findaphd.com/search/ProjectDetails.aspx?PJID=68382&LID=735
  • "Gene Fusion and the animal tree of life" - link to follow shortly.
  • Email me at m.oconnell@leeds.ac.uk for further details.

See also:

Modules taught

BLGY1124/1128 - The Diversity of Life/Living Planet


Peter Mulhair (Primary supervisor) 80% FTE
Alysha Taylor (Primary supervisor) 60% FTE
Georgios Nikolopoulos (Co-supervisor) 28% FTE
David Orr (Co-supervisor) 50% FTE
Ioannis Tsagakis (Co-supervisor) 10% FTE

Foley NM, Hughes GM, Huang Z, Clarke M, Jebb D, Whelan CV, Petit EJ, Touzalin F, Farcy O, Jones G, Ransome RD, Kacprzyk J, O'Connell MJ, Kerth G, Rebelo H, Rodrigues L, Puechmaille SJ, Teeling EC Growing old, yet staying young: The role of telomeres in bats' exceptional longevity Science Advances 4, 2018
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McInerney JO, McNally A, O'Connell MJ Reply to 'The population genetics of pangenomes' NATURE MICROBIOLOGY 2 1575-1575, 2017

Morgan CC, Loughran NB, Walsh TA, Harrison AJ, O'Connell MJ Erratum to: Positive selection neighboring functionally essential sites and disease-implicated regions of mammalian reproductive proteins. BMC evolutionary biology 17 170-, 2017

Lynch M, Walsh TA, Marszalowska I, Webb AE, Mac Aogáin M, Rogers TR, Windle H, Kelleher D, O’Connell MJ, Loscher CE Erratum to: Surface layer proteins from virulent Clostridium difficile ribotypes exhibit signatures of positive selection with consequences for innate immune response BMC Evolutionary Biology 17, 2017
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Webb AE, Walsh TA, O'Connell MJ VESPA: Very large-scale Evolutionary and Selective Pressure Analyses PEERJ COMPUTER SCIENCE, 2017

McInerney JO, McNally A, O'Connell MJ Why prokaryotes have pangenomes NATURE MICROBIOLOGY 2, 2017

Lynch M, Walsh TA, Marszalowska I, Webb AE, MacAogain M, Rogers TR, Windle H, Kelleher D, O'Connell MJ, Loscher CE Surface layer proteins from virulent Clostridium difficile ribotypes exhibit signatures of positive selection with consequences for innate immune response BMC EVOLUTIONARY BIOLOGY 17, 2017

McInerney JO, O'Connell MJ Microbiology: Mind the gaps in cellular evolution Nature 541 297-299, 2017
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Williams JM, Bezak T, Das M, Ning Z, Lucking EF, Kelly VP, Harrison P, Young P, O'Connell MJ, Dockery P, O'Halloran KD, Moore T Psg22 null mouse embryos develop normally under normoxic and hypoxic conditions of pregnancy Science Matters, 2016
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McRae KM, Good B, Hanrahan JP, McCabe MS, Cormican P, Sweeney T, O'Connell MJ, Keane OM Transcriptional profiling of the ovine abomasal lymph node reveals a role for timing of the immune response in gastrointestinal nematode resistance. Veterinary parasitology 224 96-108, 2016
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Tarver JE, dos Reis M, Mirarab S, Moran RJ, Parker S, O'Reilly JE, King BL, O'Connell MJ, Asher RJ, Warnow T, Peterson KJ, Donoghue PCJ, Pisani D The Interrelationships of Placental Mammals and the Limits of Phylogenetic Inference Genome Biology and Evolution 8 330-344, 2016
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Gunn L, Collins PJ, O'Connell MJ, O'shea H Phylogenetic investigation of enteric bovine coronavirus in Ireland reveals partitioning between European and global strains Irish Veterinary Journal 68, 2015
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McInerney J, Pisani D, O Connell MJ The ring of life hypothesis for eukaryote origins is supported by multiple kinds of data Philosophical Transactions of the Royal Society B: Biological Sciences 370, 2015
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Hughes L, Carton R, Minguzzi S, McEntee G, Deinum EE, O'Connell MJ, Parle-McDermott A An active second dihydrofolate reductase enzyme is not a feature of rat and mouse, but they do have activity in their mitochondria FEBS Letters 589 1855-1862, 2015
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Webb AE, Gerek ZN, Morgan CC, Walsh TA, Loscher CE, Edwards SV, O'Connell MJ Adaptive Evolution as a Predictor of Species-Specific Innate Immune Response Molecular Biology and Evolution 32 1717-1729, 2015
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Keane M, Semeiks J, Webb AE, Li YI, Quesada V, Craig T, Madsen LB, Van Dam S, Brawand D, Marques PI, Michalak P, Kang L, Bhak J, Yim H-S, Grishin NV, Nielsen NH, Heide-Jørgensen MP, Oziolor EM, Matson CW, Church GM, Stuart GW, Patton JC, George JC, Suydam R, Larsen K, López-Otín C, O'Connell MJ, Bickham JW, Thomsen B, De Magalhães JP Insights into the evolution of longevity from the bowhead whale genome Cell Reports 10 112-122, 2015
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O'Connell MJ, Moran RJ, Morgan CC A guide to phylogenetic reconstruction using heterogeneous models– a case study from the root of the placental mammal tree Computation 177-196, 2015

McInerney JO, O'Connell MJ Evolutionary developmental biology: Ghost locus appears Nature 514 570-571, 2014

Baldwin MW, Toda Y, Nakagita T, O'Connell MJ, Klasing KC, Misaka T, Edwards SV, Liberles SD Evolution of sweet taste perception in hummingbirds by transformation of the ancestral umami receptor Science 345 929-933, 2014
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Liu S, Lorenzen ED, Fumagalli M, Li B, Harris K, Xiong Z, Zhou L, Korneliussen TS, Somel M, Babbitt C, Wray G, Li J, He W, Wang Z, Fu W, Xiang X, Morgan CC, Doherty A, O'Connell MJ, McInerney JO, Born EW, Dalén L, Dietz R, Orlando L, Sonne C, Zhang G, Nielsen R, Willerslev E, Wang J Population genomics reveal recent speciation and rapid evolutionary adaptation in polar bears Cell 157 785-794, 2014
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Haggerty LS, Jachiet P-A, Hanage WP, Fitzpatrick DA, Lopez P, O'Connell MJ, Pisani D, Wilkinson M, Bapteste E, McInerney JO A pluralistic account of homology: Adapting the models to the data Molecular Biology and Evolution 31 501-516, 2014
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Collins LE, Lynch M, Marszalowska I, Kristek M, Rochfort K, O'Connell MJ, Windle H, Kelleher D, Loscher CE Surface Layer Proteins isolated from Clostridium difficile induce clearance responses in Macrophages Microbes and Infection, 2014

Morgan CC, Creevey CJ, O Connell MJ Mitochondrial data are not suitable for resolving placental mammal phylogeny Mammalian Genome 25 636-647, 2014
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McRae KM, Good B, Hanrahan JP, Glynn A, O'Connell MJ, Keane OM Response to Teladorsagia circumcincta infection in Scottish Blackface lambs with divergent phenotypes for nematode resistance Veterinary Parasitology 206 200-207, 2014
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Loughran NB, O'Connell MJ, O'Connor B,Ó'Fágáin C Stability properties of an ancient plant peroxidase Biochimie 104 156-159, 2014
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McInerney JO, O'Connell MJ, Pisani D The hybrid nature of the Eukaryota and a consilient view of life on Earth Nature Reviews Microbiology 12 449-455, 2014
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Morgan CC, Mc Cartney AM, Donoghue MTA, Loughran NB, Spillane C, Teeling EC, O'Connell MJ Molecular adaptation of telomere associated genes in mammals BMC Evolutionary Biology 13, 2013
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Morgan CC, Foster PG, Webb AE, Pisani D, McInerney JO, O'Connell MJ Heterogeneous models place the root of the placental mammal phylogeny Molecular Biology and Evolution 30 2145-2156, 2013
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Dmitriev P, Barat A, Polesskaya A, O'Connell MJ, Robert T, Dessen P, Walsh TA, Lazar V, Turki A, Carnac G, Laoudj-Chenivesse D, Lipinski M, Vassetzky YS Simultaneous miRNA and mRNA transcriptome profiling of human myoblasts reveals a novel set of myogenic differentiation-associated miRNAs and their target genes BMC Genomics 14, 2013
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Loughran NB, Hinde S, McCormick-Hill S, Leidal KG, Bloomberg S, Loughran ST, O'Connor B,Ó'Fágáin C, Nauseef WM, O'Connell MJ Functional consequence of positive selection revealed through rational mutagenesis of human myeloperoxidase Molecular Biology and Evolution 29 2039-2046, 2012
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O'Connell MJ, Doyle AM, Juenger TE, Donoghue MTA, Keshavaiah C, Tuteja R, Spillane C In Arabidopsis thaliana codon volatility scores reflect GC3 composition rather than selective pressure BMC Research Notes 5, 2012
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Morgan CC, Shakya K, Webb A, Walsh TA, Lynch M, Loscher CE, Ruskin HJ, O'Connell MJ Colon cancer associated genes exhibit signatures of positive selection at functionally significant positions. BMC evolutionary biology 12 114-, 2012
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Shakya K, O'Connell MJ, Ruskin HJ The landscape for epigenetic/epigenomic biomedical resources Epigenetics 7 982-986, 2012
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McInerney JO, Pisani D, Bapteste E, O'Connell MJ The public goods hypothesis for the evolution of life on Earth Biology Direct 6, 2011
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Ryan A, Lynch M, Smith SM, Amu S, Nel HJ, McCoy CE, Dowling JK, Draper E, O'Reilly V, McCarthy C, O'Brien J, Eidhin D, O'Connell MJ, Keogh B, Morton CO, Rogers TR, Fallon PG, O'Neill LA, Kelleher D, Loscher CE A role for TLR4 in clostridium difficile infection and the recognition of surface layer proteins PLoS Pathogens 7, 2011
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Mccole RB, Loughran NB, Chahal M, Fernandes LP, Roberts RG, Fraternali F, O'Connell MJ, Oakey RJ A Case-By-Case Evolutionary Analysis Of Four Imprinted Retrogenes Evolution 65 1413-1427, 2011
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O'Connell MJ Selection and the cell cycle: Positive darwinian selection in a well-Known DNA damage response pathway Journal of Molecular Evolution 71 444-457, 2010
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O'Connell MJ, Loughran NB, Walsh TA, Donoghue MTA, Schmid KJ, Spillane C A phylogenetic approach to test for evidence of parental conflict or gene duplications associated with protein-encoding imprinted orthologous genes in placental mammals Mammalian Genome 21 486-498, 2010
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Morgan CC, Loughran NB, Walsh TA, Harrison AJ, O'Connell MJ Positive selection neighboring functionally essential sites and disease-implicated regions of mammalian reproductive proteins BMC Evolutionary Biology 10, 2010
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O'Connell MJ, McInerney JO Reconstructing the ancestral eukaryote: lessons from the past In Ancestral Sequence Reconstruction, 2008
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Ryan BJ, O'Connell MJ,Ó'Fágáin C Consensus mutagenesis reveals that non-helical regions influence thermal stability of horseradish peroxidase Biochimie 90 1389-1396, 2008
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Loughran NB, O'Connor B,Ó'Fágáin C, O'Connell MJ The phylogeny of the mammalian heme peroxidases and the evolution of their diverse functions BMC Evolutionary Biology 8, 2008
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Haun WJ, Laoueillé-Duprat S, O'Connell MJ, Spillane C, Grossniklaus U, Phillips AR, Kaeppler SM, Springer NM Genomic imprinting, methylation and molecular evolution of maize Enhancer of zeste (Mez) homologs Plant Journal 49 325-337, 2007
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O'Connell MJ, McInerney JO Adaptive evolution of the human fatty acid synthase gene: Support for the cancer selection and fat utilization hypotheses? Gene 360 151-159, 2005
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O'Connell MJ, McInerney JO Gamma chain receptor interleukins: Evidence for positive selection driving the evolution of cell-to-cell communicators in the mammalian immune system Journal of Molecular Evolution 61 608-619, 2005
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Travers SA, O'Connell MJ, McCormack G, McInerney JO Evidence for heterogeneous selective pressures in the evolution of the env gene in different human immunodeficiency virus type 1 subtypes Journal of Virology, 2005

Creevey CJ, Fitzpatrick DA, Philip GK, Kinsella RJ, O'Connell MJ, Pentony MM, Travers SA, Wilkinson M, McInerney JO A tree-like phylogeny only exists at the tips in the prokaryotes Proceedings of the Royal Society of London Biology, 2004