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From 2005 to 2022, the main node of the ARC Centre of Excellence for Coral Reef Studies was headquartered at James Cook University in Townsville, Queensland (Australia)

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Using whole genome sequencing to identify signatures of recent selection, divergence and demographic change in populations of Acropora digitifera from North Western Australia


Thursday July 29th 01:00 pm (AEST)

https://jcu.zoom.us/j/81661844049 Password: 792728
Ira Cooke
Ira Cooke

Abstract: Coral assemblages from the remote Kimberley coast in North Western Australia thrive despite experiencing extreme heat, aerial exposure and fluctuating turbidity.  These corals present an opportunity to learn about the mechanisms underpinning tolerance to heat and other stressors, but perhaps due to their extreme remoteness they remain little studied compared other extremophilic assemblages.  In this talk I will present results from population whole genome sequencing of Acropora digitifera across multiple inshore and offshore sites in North Western Australia. A unique aspect of this study is the relatively deep (>15x) sequencing per-individual which allowed us to phase haplotypes and employ a range of powerful new techniques to infer demographic history and identify sites under selection.  Although there are many benefits to this approach, one of the most compelling is the ability to probe recent evolutionary history, potentially allowing genomic signatures to be linked with specific events such as the end of the last glacial maximum. As sequencing costs continue to fall whole genome sequencing is becoming an attractive alternative to reduced representation approaches in corals.  It is hoped that this talk will shed light on some of the opportunities afforded by this technique.

Biography: Ira Cooke received his PhD in soft-matter physics from ANU in 2004 and did his first post-doc at the Max-Planck Institute for Polymer Physics in Germany from 2005-2006.  He then moved to the University of Cambridge, UK where he attempted to apply his computational skills to building socio-ecological models of farmed landscapes.  In 2010 he moved back to Australia where he worked as a bioinformatician in the La Trobe University proteomics facility and had the opportunity to work on a variety of DNA, RNA and Protein sequencing projects.  From 2012-2016 he was a significant contributor to the Galaxy bioinformatics framework, adding its first suite of tools for Proteomics.  Since 2016 he has been employed as a senior lecturer in bioinformatics at James Cook University where he teaches a full semester course in bioinformatics. His research is now focused on understanding population genetics and genome evolution of marine taxa, especially corals.  To achieve these goals he often adapts cutting-edge methods from human genomics to non-model organisms and occasionally develops new bioinformatic tools.


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