Category Archives: Blog

Ann successfully defends her PhD

On the 1st of August Ann had her PhD viva and did a wonderful job of bringing her hard work to life for her panel of examiners. Ann’s PhD was primarily computational, involving sequence similarity network analysis of primate genomes, the identification of gene fusions, and the analysis of their transcription and translation profiles using meta data analysis and qRT-PCR amongst other things !;-) Ann will be graduating in the November 2018 graduation ceremony. We are absolutely delighted for her and wish her every success in her future career.

Launch of Our Leeds Omics Virtual Institute

Save the date: 21st June for the launch of Leeds Omics.

You are invited to the launch of Leeds Omics on Tuesday morning (21st June) at 10.00am.

Please register for this event using the following link:

Dr Julie Aspden, Dr Mary J. O’Connell and Dr Niamh Forde (Founders of Leeds Omics).

Leeds Omics is a cross faculty initiative between the Faculty of Biological Sciences and the Faculty of Medicine and Heath Sciences. The aim is to bring together the critical mass of researchers using the omics technologies across the University of Leeds ( The launch will take place in LIDA on level 11 of the Worsley building on Tuesday the 21st of June at 10.00am. Both John Ladbury (Dean of FBS) and Paul Stewart (Dean of FMH) will be saying a few words to celebrate the launch, and we will give a short overview of the vision for Leeds Omics. Please join us for coffee and cake, and a chance to network with other researchers using or interested in using omics data and technologies here at Leeds.

To subscribe to our mailing list please click the link below:

If you are a PI and are interested in being a member of Leeds Omics (including having your research profile on the Leeds Omics website) please e-mail a member of the Leeds Omics steering committee ( and we will give you the information that we need.

Looking forward to seeing you there!

Niamh, Mary and Julie (Leeds Omics steering committee).

EMBO phylogenomics course in the Amazon


I had the tremendous pleasure of teaching a very talented and motivated bunch of students on an EMBO (European Molecular Biology Organisation) funded course. The course was delivered in the amazon jungle city of Iquitos Peru, the largest jungle city in the world unconnected by road to the rest of the world. It was hot, it was intense, it was a lot of fun.

The course was organised by Dr Karen Siu Ting and Dr Chris Creevey (both from the University of Aberystwyth) and myself. The team of international experts included Dr Claire Morgan (Imperial College London), Dr Mark Wilkinson (Natural History Museum, London), Dr Omar Rota-Stabelli (Fondazione Edmund Mach, Italy), Dr Claudia Russo (Universidade Federal do Rio De Janeiro (UFRJ)), and Professor James McInerney (University of Manchester). A huge thanks to all and to EMBO for facilitating this programme and to IIAP for hosting us.

Dr O’Connell becomes Associate Editor for GBE

Dr O’Connell has been invited to the board of associate editors for Genome Biology and Evolution (GBE). GBE is an Oxford University Press journal owned by the Society for Molecular Biology and Evolution, and is in the top ten evolutionary biology journals internationally and has an impact factor of 4.2.

“I feel honoured to have been invited to this role. For years I have read and cited articles from this journal. GBE publishes excellent quality articles in evolutionary genomics and I hope to contribute to continued success of the journal in my new role.”

– Dr Mary O’Connell

“Genome Biology and Evolution (GBE) publishes leading original research at the interface between evolutionary biology and genomics.” … from the GBE website.



Placental Mammals and the limits of phylogenetic inference

More support for Atlantogenata. 

This week an international collaborative effort has tackled a major challenge in phylogenetics – the interrelationships amongst placental mammals. The paper has just been published in Genome Biology and Evolution (please click here to see the paper). In work led by Dr James Tarver and Dr Davide Pisani (with contributions from our research group and a wonderful team of evolutionary biologists), we conclude that the placental mammal phylogeny is not a hard polytomy as previously thought.

Using a variety of data types and approaches we show that the effects of incomplete lineage sorting and rapid radiation (while having some impact in early placental evolution) do not make the phylogeny of mammals impossible. Here we show that all datasets applied converge on a single position for the rooting – the Atlantogenata position. We estimate that the crown Atlantogenata diverged approx. 84-97 MYA.

This is further support for the Atlantogenata position for the root of placental mammals published here (Morgan et al MBE 2013).


Results from three of the phylogenetic analyses with each one providing support for Atlantogenata as the sister taxon to all other eutherians.

The origin of Eukaryotes and the Ring of Life

In our latest work on the origin of eukaryotes published in a special issue of Philosophical Transactions of the Royal Society B (link to full issue) compiled and edited by Professor Martin Embley and Dr Tom Williams, we advocate a ‘domain-free’ view of the history of life. Debates about whether there should be two domains or three are essentialist and moot.
“In a pluralistic view of cellular life on the planet, we can see that the merging of eubacterial genes with archaebacterial genes gave rise to the halophiles and indeed it made an enormous contribution to the origins of most of the major groups of Archaebacteria. We see that photosynthesis can only be interpreted as a series of gene flows around the prokaryotic and eukaryotic worlds. We see that eukaryotes have arisen as a consequence of major flows between prokaryotes initially (eukaryogenesis), and later, between a prokaryote group and a eukaryotic group (plastid origins)…Life’s history is complex and we should not try to simplify it to suit our need for orderly nomenclatural systems.”

Sandwalk blog on the special issue can be found here:

Dr Mary O’Connell on Extinction at TEDx DCU

So I took to the stage to talk about evolution and mass extinction for the TEDx DCU event in 2015. It was pitched for the general audience and was really good fun. It is a real challenge to get these concepts across and not bore people to death ! I am not sure I have managed it entirely – but I tried !;-)

If you would like to watch it :

Graduation time for Dr Andrew Webb and Dr Kathryn McRae

It was freezing and there was a northerly wind whipping through DCU campus but that wasn’t going to keep us from smiling ! We had a double celebration in our group today with the graduation of Dr Andrew Webb and Dr Kathryn McRae photographed here with our president Prof Brian Mac Craith. Kathryn was supervised jointly by Dr Orla Keane at Teagasc (Ireland’s agriculture research centre). Kathryn and Andrew are heading off to Postdoc in New Zealand and the USA. Flying my nest !;-) I wish them every success in their futures.

Of mice and men

Super treat in the lab this week.  The journal Science decided to feature one of our publications in its “Editor’s Choice” section.  The author of the little piece is Laura Zahn and she chose to feature the work, which was published in Molecular Biology and Evolution.


It is always a real thrill to have work highlighted and appreciated in this way.


The manuscript in question involved a comparative analysis of the innate immune systems between humans and mice.  We use methods that compare the rates of non-synonymous and synonymous substitutions in protein-coding genes, as well as using population genomic data (from the 1,000 human genomes projects and the 17 mouse genomes project).


What we found was that the innate immune systems of human and mouse have undergone divergent selective pressures in their 200 million years of independent evolution (100 million years on each lineage – give or take a few million years). Linking this information with known differences in phenotype between human and mouse brings us closer to better modeling of human diseases.


You can find the paper at


Of mice and men
Of mice and men