A new paper by Jia in Molecular Biology and Evolution showcases the power of whole genome sequencing to understand adaptive evolution in corals. Thanks to our collaborators in Western Australia we were able to obtain samples for deep WGS on 75 corals, including samples from the inshore Kimberley reefs and two offshore atolls. The results revealed very recent divergence driven by founder effects and strong selection, especially in the inshore reefs.

Paper: https://doi.org/10.1093/molbev/msac201

Press Release: https://www.coralcoe.org.au/media-releases/dna-reveals-the-past-and-future-of-coral-reefs

New paper by Sally, Catarina and Jan in Ecology & Evolution, uses COI sequences to investigate the population genetic patterns of the Antarctic brittle stars Ophionotus victoriae and O. hexactis with contrasting life histories (broadcasting vs brooding) and morphology (5 vs 6 arms). They found that, throughout the Pleistocene glacial maxima, O. victoriae likely persisted in deep sea refugia; whereas O. hexactis likely persisted in Antarctic island refugia. This work proposes the evolutionary innovations in O. hexactis (increase in arm number and a switch from broadcast spawning to brooding) could be linked to survival within island refugia, which open up new avenues for future genomic research!   

New paper by Ira, Jan and Jia in Science Advances (full article here), uses shallow whole genome sequencing to look at demographic history and selection for Acropora tenuis. The main findings are outlined in this tweet thread. Maria Nayfa also made this nice video of Ira explaining why genomes are so useful for understanding the history of the GBR.

Antimicrobial peptides are part of the innate immune system and help defend the host against pathogens and regulate the microbiome. Antimicrobial peptides occur in all life, are incredibly diverse, mostly quite small (< 200 amino acids), and only comprise of a small proportion in a genome (~ 1%). This makes them very difficult to find. We created a classification model implemented in an R package, ampir, to predict antimicrobial peptides from protein sequences on a genome-wide scale. ampir was tested on multiple test sets (including complete proteomes) and performed with high accuracy. ampir can be used to narrow down the search space for novel antimicrobial peptides in genomes.

ampir was recently published in Bioinformatics and is available on CRAN and github . Legana has also created a companion repository to accompany the paper and document the thinking behind ampir’s model building process.