A new paper led by Jia shows that there are at least five large, highly polymorphic chromosomal inversions in Acropora kenti, a widespread coral on the Great Barrier Reef. This paper highlights the potential importance of structural variation in corals, and the need for new approaches to characterise it. Published in Molecular Ecology.
by Jesselyn Brown
Often in science, it is assumed most of the big discoveries happen out in the field, on glorious expeditions into the unknown. While this is an essential step in research, most of the discoveries are made afterwards, where researchers spend months to years compiling their collected data into a coherent, well curated paper for the scientific community. Such is the case for the Antarctic marine invertebrate samples collected for the Marine Omics’ group! Rosie and Jesselyn have been sampling tissue for genomic analyses and preserving specimens for the Museum of Tropical Queensland in JCU’s own Townsville (Bebegu Yumba) Campus; a far stretch in distance and weather from Antarctica!
Rosie (left) and Jesselyn (right) dissecting tissue from echinoderms collected from Heard and McDonald Islands
Each specimen has to be appropriately sampled for genomic analysis and preserved for the museum’s collection. Some of the jarred specimens will eventually be on display for the public, allowing visualization of the creatures living below the ice. However, the most critical part of the project comes from the tiny tissue samples collected before the specimens are preserved.
These echinoderms hold secrets about their evolutionary history and how it has been impacted by past climate and tectonic change.
For example, these echinoderms, as seen on Jesselyn’s dissection board, have tissue samples taken from their arms and from their tube feet. Although infinitesimally small, such DNA houses a wealth of information! This may reveal anything from population dynamics, evolutionary tracks and divergence records, survival rates over time, and occasionally, enable the prediction of species survival through a rapidly changing climate via paleorecords. These samples will play a vital role in piecing together genetic databases and allowing scientists to develop a deeper understanding of Antarctic fauna!
Ben Rennie led a great study as part of his Masters project to investigate filtration rates and the bioremediation potential of the tropical blacklip rock oyster, Saccostrea lineage J, which was published in Aquaculture Environment Interactions. The study found that the Blacklip Rock Oysters significantly reduced total nitrogen, total phosphorous, total suspended solids and chlorophyll a from prawn pond effluent. In addition the oysters have a filtration rate three to five times higher than other frequently cultured oyster species suggesting that they may be well suited to biofiltration roles.
JCU highlighted the story in a media release and a feature article the paper has led to interest in the oysters ability to provide reef credits.
Jan with a Tropical Blacklip Rock Oyster at Bowen Fresh Oysters.
Sally Lau led a fantastic study published in Science which used octopus DNA to discover that the West Antarctic Ice Sheet (WAIS) likely collapsed during the Last Interglacial period around 125,000 years ago – when global temperatures were similar to today. This provides the first empirical evidence that the tipping point of this ice sheet could be reached even under the Paris Agreement targets of limiting warming to 1.5 – 2 degrees C.
This research solves a long-running mystery regarding whether or not the WAIS collapsed during the Last Interglacial. This was a period when global average temperatures were 0.5 – 1.5 oC warmer than preindustrial levels, but global sea level was 5 – 10 metres higher than today. What makes the WAIS important is that it’s also Antarctica’s current biggest contributor to global sea level rise. A complete collapse could raise global sea levels by somewhere between 3 and 5 metres.
In the study we employed a novel population genomic approach to answer this question. By employing demographic modelling and comparing the genetic profiles of Turquet’s octopus found in the Weddell, Amundsen, and Ross seas enabled detection of genetic connectivity dating back to the Last Interglacial. This would only be possible if a complete collapse of the WAIS occurred during the Last Interglacial, opening seaways linking the present-day Weddell, Amundsen and Ross seas. This would have allowed octopus to travel across the opened straits and exchange genetic material, which we can detect in the DNA of today’s populations.
This research was interdisciplinary, bringing together geneticists, physical scientists and geologists and was only possible through international collaboration and the use of samples collected over a 30 year time period. Our work was supported by the Australian Research Council, the Australian Academy of Science, an Antarctic Science International Bursary, the SCAR INSTANT programme, Ministry of Business Innovation & Employment, NZ, the Antarctic Science Foundation, Australasian eResearch Organisations and Suomen Akatemia.
Interdisciplinary team work makes the dream work! From L to R: Nick Golledge (Victoria University of Wellington), Nerida Wilson (University of Western Australia), Sally Lau (James Cook University), Tim Naish (Victoria University of Wellington) and Jan Strugnell (James Cook University).
We are delighted with the media attention our paper has received! Some of our favourites include First Dog on the Moon, The New York Times, The Washington Post and CNN. You can also read more about our research in an article we wrote for The Conversation.
Brooke Whitelaw led a fantastic study investigating species diversity in the iconic blue-ringed octopus genus, Hapalochlaena. Using genome-wide SNP data and mitochondrial loci, Brooke found 11 relevant taxonomic units – likely all species, suggesting MUCH greater diversity than is currently described! The origin of the genus Hapalochlaena was predicted to be in the Indo-Australian Archipelago and is older than you might thing ~30 mya.
The paper is published in Molecular Phylogenetics and Evolution and you can access it here.
Fig. 2. Delineation of Hapalochlanea species boundaries and genetic structure throughout the Indo Pacific using 10,346 SNPs: (a) SVDQuartet phylogeny of Hapalochlaena throughout the Indo Pacific generated using 10,346 SNPs, coloured branches represent putative taxonomic units A-K: brown (A/Southern coast of Australia), lilac (B/NSW), apple green (C/Taiwan lined), pink (D/Taiwan ringed), light orange (E/Darwin, NT & Kimberly & Exmouth, WA), red (F/Timor Leste), dark orange (G/G* Great Barrier Reef, QLD), purple (H/Cape York, QLD & Shark Bay, QLD) light blue (I/Deep water Yeppoon, QLD & North West, WA), dark blue (J/North West Shelf, WA) and light green (K/Ningaloo, WA). Posterior support values > 0.90 present on nodes. Bars at terminal branches indicate admixture of OTUs inferred using STRUCTURE, colours approximately correspond to OTUs. Lined box adjacent to OTU indicated lined markings while, OTUs without a box exhibit ringed markings. (b) Species delineation using the mitochondrial COI gene. Bayesian phylogeny (MrBayes) of Hapalochlaena throughout the Indo Pacific is coloured according to OTU with black used to represent taxa included from NCBI. Boxes represent putative species in accordance to sPTP, GYMC SC (strict clock) and GYMC RC (relaxed clock) methods. Boxes with diagonal lines represent specimens with lined markings as opposed to rings present in all other specimens. (c) Arrangement of samples according to the first two principal components of a PCoA based on SNP data generated using the dartR package. (d) Map of sample locations coloured by organisational taxonomic units A-K. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)
Nikki, Sally, and Jan had a blast at the SAEF conference in Adelaide. Held at the National Library, it was the first time that many of the participants in SAEF had the opportunity to meet one another!
The ‘Connect’ dream team – from L to R, Sally, Jan, Nikki, and Nerida Wilson.
Biggest congratulations to Sally Lau, who together with Rachael Lappan, was the inaugural recipient of the SAEF biddable Research funding. Aimed at ECRs, it’s an initiative designed to support innovative, high-risk science. Go Sally!
Jan was delighted to meet Alun Thomas, Mawson’s grandson, who gave an inspiring speech about his Grandad. Alun now volunteers at the South Australian Museum where he works on accessioning his grandad’s valuable collections.
Nikki, Sally, Nerida, and Jan sampled Antarctic marine invertebrates at the Australian Antarctic Division (AAD). We collected tissue samples to investigate evolutionary processes in the Southern Ocean, and also prepared the samples to be accessioned at the Tasmanian Museum and Art Gallery (TMAG).
At the Australian Antarctic Division. Sunny, but nippy for Townsvillians!
Check out those invertebrates! (and our PPE).
Big thanks for all your work helping us accession these valuable samples Kirrily Moore at the Tasmanian Museum and Art Gallery (TMAG).
Big thanks to Glenn Johnstone, Jonny Stark and Kirrily Moore for all their help!
All the hard work and dedication that comes with being a student was celebrated yesterday at the JCU graduate ceremony. Congratulations to all the graduates! As they say, the world is your oyster and we can’t wait to see where you end up next!
The latest in Antarctic research from the Marine Omics lab, Sally, Ira and Jan used a novel genomic approach to answer if the West Antarctic Ice Sheet (WAIS) had collapsed during the Last Interglacial period, and they did so by looking into the genomic loci of an Antarctic octopus (Pareledone turqueti). They found a clear, distinct connectivity between Ross Sea and Weddell Sea, dating it back to the last interglacial period, that is different from the signal of the octopus’s general circumpolar movement around the continent. By comparing the genomic data against contrasting hypothesised scenarios via demographic modelling, including no, partial or complete WAIS collapse in the past, their findings suggest the Ross and Weddell connectivity was only possible if the WAIS completely collapsed and opened the seaway connecting the two basins.
A focus of Sally’s PhD research this paper is available as a pre-print on bioRxiv and has certainly made waves, with an interview in The Guardian, IFLScience and has been re-imaged by the creator First Dog on the Moon! Their research is a successful transdisciplinary example demonstrating that only by bringing different disciplines together, we can have the best shot to help solving the current climate change.
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
