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Inadvertent Paralog Inclusion Drives Artifactual Topologies and Timetree Estimates in Phylogenomics

In work lead by Dr Karen Siu Ting she addresses an important question in phylogenomics using 18 amphibian species. She chose to work on this Lissamphibian group because there is significant conflict over their relationships to one another, and because transcriptomes are increasingly being used to overcome the lack of genomic data for this clade. In total 2656 putative single gene orthologs were identified and following the application of a novel paralog filtering approach phylogenetic reconstruction was carried out using Bayesian inference, maximum likelihood, and quartet-based supertrees. The paper describes how paralogs drive strongly supported conflicting hypotheses within the Lissamphibia (Batrachia and Procera) and older divergence time estimates even within groups where no variation in topology was observed. This is the first large-scale study to address the impact of orthology detection using transcriptomic data and emphasizes the importance of quality over quantity particularly for understanding relationships of poorly sampled taxa. Karen was a Marie Curie Postdoctoral Fellow between our group and Prof Creevey when she carried out this work and she is now based at Queen’s University in Belfast. Congratulations to Karen on a lovely piece of work.

Return to the sea, get huge, beat cancer: an analysis of cetacean genomes including an assembly for the humpback whale…

In the May issue of MBE we have published the outcome of a collaboration with Dr Marc Tollis, Prof Carlo Maley, Prof Per Palsbol and others where we sequenced and analysed the genome of the humpback whale. The paper aimed to Peto’s Paradox – where large-bodied and long-lived animals do not suffer higher risks of cancer mortality than humans and more generally to understand other cetacean adaptations. We compared the genomes of 10 cetacea and dated the rorqual radiation to the Miocene or earlier. We could also infer that perturbations in abundance and/or the inter-ocean connectivity of North Atlantic humpback whale populations likely occurred throughout the Pleistocene. Our comparative genomic results suggest that the evolution of cetacean gigantism was accompanied by strong selection on pathways that are directly linked to cancer. Large segmental duplications in whale genomes contained genes controlling the apoptotic pathway, and genes inferred to be under accelerated evolution and positive selection in cetaceans were enriched for biological processes such as cell cycle checkpoint, cell signaling, and proliferation. We also inferred positive selection on genes controlling the mammalian appendicular and cranial skeletal elements in the cetacean lineage, which are relevant to extensive anatomical changes during cetacean evolution. We hope you enjoy the paper – it has been a real pleasure working together on it.

Paternally Expressed Imprinted Genes under Positive Darwinian Selection in Arabidopsis thaliana.

In this paper in MBE we examined the selective pressure variation across genomically imprinted genes in the inbreeding species Arabidopsis thaliana. Genomic imprinting is an epigenetic phenomenon where autosomal genes display uniparental expression depending on whether they are maternally or paternally inherited. Genomic imprinting can arise from parental conflicts over resource allocation to the offspring, which could drive imprinted loci to evolve by positive selection. Strikingly, we find a statistically significant enrichment of imprinted paternally expressed genes (iPEGs) evolving under positive selection, 50.6% of the total, but no such enrichment for positive selection among imprinted maternally expressed genes (iMEGs). This suggests that maternally- and paternally expressed imprinted genes are subject to different selective pressures. Almost all positively selected amino acids were fixed across 80 sequenced A. thaliana accessions, suggestive of selective sweeps in the A. thaliana lineage. The imprinted genes under positive selection are involved in processes important for seed development including auxin biosynthesis and epigenetic regulation. Our findings support a genomic imprinting model for plants where positive selection can affect paternally expressed genes due to continued conflict with maternal sporophyte tissues, even when parental conflict is reduced in predominantly inbreeding species.

Cover of Structure (Cell Press)

In a recent collaboration with Joe Cockburn et al published in Structure – we reveal the structure of the cargo binding TPR domain of kinesin light chain bound to the cargo molecule JIP3. Along with solving the crystal structure – the biophysical and evolutionary analysis we carried out have revealed the kinesin-1 cargo binding site is conserved right across the metazoa from sponges to humans. We propose a mechanism by which multiple, unrelated cellular cargo molecules can “hotwire” the kinesin-1 molecule into motility.

Link to the paper here: https://www.sciencedirect.com/science/article/pii/S0969212618302570?via%3Dihub

Citation: Cockburn JJB, Hesketh, SJ, Mulhair PJ, O’Connell MJ, and Way M. “Insights into Kinesin-1 activation from the crystal structure of KLC2 bound to JIP3.” Structure (Cell Press) 2018 Nov 6;26(11):1486-1498.e6. doi: 10.1016/j.str.2018.07.011.

 

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.

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.

Elected as Fellow of the Linnean Society

On May 21st 2017 I was officially elected as Fellow of the Linnean Society. I am very excited to receive this honour and look forward to the ceremony.

“Founded in 1788, the Society takes its name from the Swedish naturalist Carl Linnaeus… It is the oldest active biological society… As it moves into its third century the Society continues to play a central role in the documentation of the world’s flora and fauna – as Linnaeus himself did – recognising the continuing importance of such work to biodiversity conservation.”

“The Fellowship is international and includes world leaders in each branch of biology who use the Society’s premises and publications to communicate new advances in their fields.”

https://www.linnean.org/

 

 

“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).

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:

http://leedsomicslaunch.eventbrite.co.uk

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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 (www.leedsomics.org). 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:

http://lists.leeds.ac.uk/mailman/listinfo/leedsomics

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 (J.Aspden@leeds.ac.uk:M.OConnell@leeds.ac.uk: N.Forde@leeds.ac.uk) and we will give you the information that we need.

Looking forward to seeing you there!

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