A prickly problem: Genome skimming reveals varying levels of phylogenetic diversity in the freshwater crayfish Euastacus armatus complex (Parastacidae) with implications for taxonomy and conservation

A prickly problem: Genome skimming reveals varying levels of phylogenetic diversity in the freshwater crayfish Euastacus armatus complex (Parastacidae) with implications for taxonomy and conservation | Authorea try { document.documentElement.classList.add('js'); } catch (e) { } var _gaq = _gaq || []; _gaq.push(['_setAccount', 'G-8VDV14Y67G']); _gaq.push(['_trackPageview']); (function() { var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true; ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js'; var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s); })(); Skip to main content Preprints Collections Wiley Open Research IET Open Research Ecological Society of Japan All Collections About About Authorea FAQs Contact Us Quick Search anywhere Search for preprint articles, keywords, etc. Search Search ADVANCED SEARCH SCROLL Ecology and Evolution This is a preprint and has not been peer reviewed. Data may be preliminary. 17 September 2025 V1 Latest version Share on A prickly problem: Genome skimming reveals varying levels of phylogenetic diversity in the freshwater crayfish Euastacus armatus complex (Parastacidae) with implications for taxonomy and conservation Authors : Christopher M. Austin , Shane Ahyong , Adam Miller , Tarmo Raadik , Mark Lintermans , Rob McCormack , Sylvia Zukowski , Michael Hammer , Frederic Grandjean , Dean Gilligan , Matt Beitzel , and Nick Whiterod 0000-0002-7356-9834 [email protected] Authors Info & Affiliations https://doi.org/10.22541/au.175808912.20487302/v1 Published Ecology and Evolution Version of record Peer review timeline 261 views 235 downloads Contents Abstract Supplementary Material Information & Authors Metrics & Citations View Options References Figures Tables Media Share Abstract Aim The aim of this study is to explore the molecular taxonomy and phylogeography of the E. armatus complex to help overcome current knowledge gaps impacting the conservation of this group of species. Location Southeast Australia Methods We use genome skimming to successfully recover whole mitogenomes and nuclear markers to examine the molecular taxonomy, phylogeography and range uncertainty in a wide-ranging complex, which includes the nationally Vulnerable Murray crayfish Euastacus armatus; the nationally Endangered Glenelg spiny crayfish E. bispinosus, and the Southern Victorian spiny crayfish E. yarraensis. Results The analyses revealed high levels of genetic structure in both E. armatus and E. yarraensis, including sufficiently divergent lineages within E. yarraensis that potentially warrants independent taxonomic recognition. Furthermore, analyses resolved the status of E. armatus populations persisting outside known contemporary ranges as being relictual and of high conservation importance. Whilst one outlying population of E. bispinosus was confirmed as relictual, another was revealed as being translocated. Main conclusions This study demonstrates genome skimming as a powerful technique for generating molecular data to support key elements of conservation for freshwater crayfish and other species. A prickly problem: Genome skimming reveals varying levels of phylogenetic diversity in the freshwater crayfish Euastacus armatus complex (Parastacidae) with implications for taxonomy and conservation Chris Austin 1,2,3 , Shane T. Ahyong 4 , Adam Miller 5 , Tarmo A. Raadik 6, Mark Lintermans 7,8 , Rob McCormack 9 , Sylvia Zukowski 10 , Michael P. Hammer 3 , Frederic Grandjean 11 , Dean M. Gilligan 12 , Matt Beitzel 13 , and Nick S. Whiterod 10,14, 15 1 School of Life and Environmental Sciences, Deakin University, Geelong, 3220, Australia 2 Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, 0815, Australia 3 Museum and Art Gallery of the Northern Territory, Darwin, 0820, Northern Territory, Australia 4 Australian Museum Research Institute, Australian Museum, Sydney, 2010, New South Wales, Australia, and School of Biological, Earth & Environmental Sciences, UNSW, Kensington, New South Wales, 2052, Australia 5 Cesar Australia, Brunswick, Victoria, 3056, Australia 6 Arthur Rylah Institute for Environmental Research, Department of Energy, Environment and Climate Action, 123 Brown Street, Heidelberg, Victoria, 3084, Australia 7 Centre for Applied Water Science, University of Canberra, Canberra, Australian Capital Territory, 2601, Australia 8 Fish Fondler Pty Ltd, Bungendore, New South Wales, 2621 Australia 9 Australian Aquatic Biological Pty Ltd, Karuah, New South Wales, 2324, Australia 10 Nature Glenelg Trust, Victor Harbor, South Australia, 5211, Australia 11 Laboratoire Ecologie, Biologie des Interactions, équipe Ecologie, Evolution, Symbiose, Université de Poitiers, Poitiers, 86073, France 12 Bush Heritage Australia, Surfside, New South Wales, 2536, Australia 13 City and Environment Directorate, ACT Government, Dickson, Australian Capital Territory, 2602, Australia 14 Goyder Institute for Water Research CLLMM Research Centre, Goolwa, South Australia, 5214, Australia 15 College of Science and Engineering, Flinders University, Bedford Park, South Australia, 5042, Australia Running title: phylogenetic diversity of the Euastacus armatus complex Correspondence: [email protected] Funding and Acknowledgements This project was partially supported by the Threatened Species Initiative and the Australian Government’s Bushfire Recovery for Wildlife and their Habitats. Jared Tromp (Deakin University) assisted with the bioinformatic analyses. Keywords Euastacus bispinosus , Euastacus yarraensis , genome skimming, outlying populations, Parastacidae, phylogenetics, relictual, spiny crayfish Conflict of Interest The authors declare that there is no conflict of interest that could be perceived as prejudicing the impartiality of the research reported. Biosketch Chris Austin is an honorary professor who studies freshwater crayfish genomics, evolution, conservation and taxonomy. His research focuses on molecular genetic techniques to understand patterns of conservation biogeography and taxonomy in often highly threatened species. Supplementary Material File (figures (landscape) v2.pptx) Download 6.49 MB File (figures (portrait) v2.pptx) Download 584.53 KB File (figures captions v2.docx) Download 27.87 KB File (final ms v2.docx) Download 169.45 KB Information & Authors Information Version history V1 Version 1 17 September 2025 Peer review timeline Published Ecology and Evolution Version of Record 20 Apr 2026 Published Copyright This work is licensed under a Non Exclusive No Reuse License. Collection Ecology and Evolution Keywords freshwater genetics invertebrate molecular genetics Authors Affiliations Christopher M. Austin Deakin University School of Life and Environmental Sciences View all articles by this author Shane Ahyong Australian Museum Research Institute View all articles by this author Adam Miller Cesar Australia, Brunswick, Victoria, 3056, Australia View all articles by this author Tarmo Raadik Arthur Rylah Institute for Environmental Research View all articles by this author Mark Lintermans University of Canberra View all articles by this author Rob McCormack Australian Aquatic Biological Pty Ltd, Karuah, New South Wales, 2324, Australia View all articles by this author Sylvia Zukowski Nature Glenelg Trust, Victor Harbor, South Australia, 5211, Australia View all articles by this author Michael Hammer Museum and Art Gallery of the Northern Territory View all articles by this author Frederic Grandjean Ecologie et Biologie des Interactions View all articles by this author Dean Gilligan Bush Heritage Australia, Surfside, New South Wales, 2536, Australia View all articles by this author Matt Beitzel City and Environment Directorate, ACT Government, Dickson, Australian Capital Territory, 2602, Australia View all articles by this author Nick Whiterod 0000-0002-7356-9834 [email protected] Nature Glenelg Trust, Victor Harbor, South Australia, 5211, Australia View all articles by this author Metrics & Citations Metrics Article Usage 261 views 235 downloads .FvxKWukQNSOunydq8rnd { width: 100px; } Citations Download citation Christopher M. Austin, Shane Ahyong, Adam Miller, et al. A prickly problem: Genome skimming reveals varying levels of phylogenetic diversity in the freshwater crayfish Euastacus armatus complex (Parastacidae) with implications for taxonomy and conservation. Authorea . 17 September 2025. DOI: https://doi.org/10.22541/au.175808912.20487302/v1 If you have the appropriate software installed, you can download article citation data to the citation manager of your choice. Simply select your manager software from the list below and click Download. For more information or tips please see 'Downloading to a citation manager' in the Help menu . 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