DNA reveals the past and future of coral reefs

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

Emerging biological archives can reveal ecological and climatic change in Antarctica

Jan led a paper with co-authors from Securing Antarctica’s Environmental Future (SAEF) to highlight the utility and power of biological archives to understand past ecological and climatic change in Antarctica. Biological archives included extant moss beds and peat profiles, biological proxies in lake and marine sediments, vertebrate animal colonies, and extant terrestrial and benthic marine invertebrates. The paper highlights how emerging biological archives complement other Antarctic paleoclimate archives (e.g. ice cores) by recording the nature and rate of past ecological change, the paleoenvironmental drivers of that change, and constrain current ecosystem and climate models. Significant advances in analytical techniques (e.g., genomics, biogeochemical analyses) have led to new applications and greater power in elucidating the environmental records contained within biological archives. The paper highlights how these emerging biological archives will significantly expand our understanding of past, present, and future ecological change, alongside climate change in Antarctica and at the Southern Ocean.

A video about the article made by GCB: https://twitter.com/GlobalChangeBio/status/1561850857334923269

Link to SAEF article about the paper: https://arcsaef.com/story/accessing-earths-memories/

Link to paper: https://onlinelibrary.wiley.com/doi/10.1111/gcb.16356

Is the Southern Ocean ecosystem primed for change or at the cliff edge?

New editorial by Sally and Jan in Global Change Biology (full article here), explores the unprecedented environmental risks and consequences that the Southern Ocean is experiencing from current climate change. They also outlined that knowing how benthic fauna persisted through environmental extremes in the past may inform future predictions. Right now, understanding and preserving current genetic diversity and connectivity between populations will give species the best chance to adapt.

Townsville bulletin news story: Study needs DNA of deer

Matt was recently interviewed by the local newspaper about his PhD project on chital deer. Did you know that the Australian chital deer population, currently in the tens of thousands, was originated from only four introduced individuals?! He is looking for leads that can help him collect tissue samples to understand their movement patterns from a genomic perspective!  

Evolutionary innovations in Antarctic brittle stars linked to glacial refugia

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!   

Global drivers of recent diversification in a marine species complex

New paper by Catarina and Jan in Molecular Ecology, (full article here), investigates genome-wide divergence, introgression patterns and inferred demographic history between species pairs of all six extant rock lobster species within the genus Jasus – species with a larval duration of up to two years. Funded by the Australian Research Council, this work shows the important effect of habitat and demographic processes on the recent divergence of species in the genus.

Reference Genome and Population Genomics of coral (Acropora tenuis) on the inshore Great Barrier Reef

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.

ampir a new R package from the group

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.