Evolutionary responses of a reef-building coral to climate change at the end of the last glacial maximum Jia Zhang 1,2,3 , Zoe T. Richards 4,5 , Arne A. S. Adam 4 , Cheong Xin Chan 6 , Chuya Shinzato 7 , James Gilmour 8 , Luke Thomas 8,9 , Jan M. Strugnell 10,11 , David J. Miller 1,2,3,12 , Ira Cooke 1,2 1. Department of Molecular and Cell Biology, James Cook University, Townsville, QLD, 4811, Australia 2. Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD, 4811, Australia 3. ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, 4811, Australia 4. Coral Conservation and Research Group, Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia 5. Collections and Research, Western Australian Museum, 49 Kew Street Welshpool, WA 6106 6. The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, Brisbane, QLD 4072, Australia 7. Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, Japan 8. Australia Institute of Marine Science, Indian Oceans Marine Research Centre, Crawley, WA, 6009, Australia 9. Oceans Graduate School, The UWA Oceans Institute, The University of Western Australia, Perth, WA, 6009, Australia 10. Department of Marine Biology and Aquaculture, James Cook University, Townsville, QLD, 4811, Australia 11. Centre for Sustainable Fisheries and Aquaculture, James Cook University, Townsville, QLD, 4811, Australia 12. Marine Climate Change Unit, Okinawa Institute of Science and Technology, Onna-son, Okinawa, Japan 904-0495 Abstract Climate change threatens the survival of coral reefs on a global scale, primarily through mass bleaching and mortality as a result of marine heatwaves. While these short-term effects are clear, predicting the fate of coral reefs over the coming century is a major challenge. One way to understand the longer-term effects of rapid climate change is to examine the response of coral populations to past climate shifts. Coastal and shallow-water marine ecosystems such as coral reefs have been reshaped many times by sea-level changes during the Pleistocene, yet, few studies have directly linked this with its consequences on population demographics, dispersal, and adaptation. Here we use powerful analytical techniques, afforded by haplotype phased whole-genomes, to establish such links for the reef-building coral, Acropora digitifera. We show that three genetically distinct populations are present in . CC-BY 4.0 International license made available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is The copyright holder for this preprint this version posted April 5, 2022. ; https://doi.org/10.1101/2022.04.02.486852 doi: bioRxiv preprint