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.

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.

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.