Category Archives: editorial

Postdoc Positions Available

I am looking for two highly motivated computational evolutionary biologists with excellent programming and computing skills to join my team at the University of Nottingham. Both positions are fully funded for two years with an option to extend pending grant success.

Both positions are computational in nature and require strong programming, molecular evolution and genome data analytical skills. Closing Date 30th November 2018.

Please see the following links for more information and how to apply.

“Minding the gaps in cellular evolution”

Our latest article we discuss some recent work from Thijis Ettema’s group on discovery of a new member of the Asgard group of Archaea. The Asgard “superphylum” is a group of archaea that provide us with important information about the origin of eukaryotes. The image from our news and views article shown here summarises the relationship between Bacteria and Archaea and Eukaryotes – showing the two domains of life and the result of their merger i.e. the Eukaryotes..

News and Views article is here ….”Eukaryotic cells, with complex features such as membrane-bound nuclei, evolved from prokaryotic cells that lack these components. A newly identified prokaryotic group reveals intermediate steps in eukaryotic-cell evolution.” …

Click here for the research article by Katarzyna Zaremba-Niedzwiedzka et al in Nature (11th Jan 2017).

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.

Heterogeneous Models place the Root of the Placental Mammal Phylogeny.

How are mammals related to one another ? This question has puzzled biologists for decades. In our most recent publication we describe how, using sequence data and sophisticated phylogenetic models, we have resolved this issue. Our analysis shows that the root of the placental mammal phylogeny is the common ancestor of the xenarthra (e.g. armadillo) and the Afrotheria (e.g. elephant) lineages. This root position is known in the literature as the Atlantogenata position. If you are interested in reading more about what data and models we used to come to this conclusion please access our paper (open access) here.

Abstract: Heterogeneity among life traits in mammals has resulted in considerable phylogenetic conflict, particularly concerning the position of the placental root. Layered upon this are gene- and lineage-specific variation in amino acid substitution rates and compositional biases. Life trait variations that may impact upon mutational rates are longevity, metabolic rate, body size and germ line generation time. Over the past 12 years, three main conflicting hypotheses have emerged for the placement of the placental root. These hypotheses place: the Atlantogenata (common ancestor of Xenarthra plus Afrotheria), the Afrotheria, or the Xenarthra as the sister group to all other placental mammals. Model adequacy is critical for accurate tree reconstruction and by failing to account for these compositional and character exchange heterogeneities across the tree and dataset, previous studies have not provided a strongly supported hypothesis for the placental root. For the first time, models that accommodate both tree and dataset heterogeneity have been applied to mammal data. Here we show the impact of accurate model assignment and the importance of datasets in accommodating model parameters while maintaining the power to reject competing hypotheses. Through these sophisticated methods, we demonstrate the importance of model adequacy, dataset power and provide strong support for the Atlantogenata over other competing hypotheses for the position of the placental root.