Skate-ing on thin ice: Molecular ecology of longnose skates in the Southeast Pacific Ocean Carolina Andrea Vargas Caro Bachelor of Science (Hon) A thesis submitted for the degree of Doctor of Philosophy at The University of Queensland in 2017 Faculty of Medicine Abstract Longnose skates may be one of the most vulnerable taxa of elasmobranch fishes, with documented local extinctions and population declines worldwide. Longnose skates are the main component of the commercial elasmobranch fisheries in the south-east Pacific Ocean, especially in Chilean waters where target and bycatch fisheries have led two species to the brink of collapse. The yellownose skate Zearaja chilensis and the roughskin skate Dipturus trachyderma are endemic of southern South America yet little is known about population ecology and stock structure. Additionally, the external morphology of longnose skates is remarkably similar, especially in early life stages, and a lack of accurate species identification has compromised official landings records which in turn has impacted fishery management. Overall abundance of longnose skates has declined substantially over the last decade due to intensive fishing pressure and the fishery is considered to be `fully exploited'. Based on all available information in peer-reviewed and grey literature, a comparative synthesis of the biology and ecology was conducted on Z. chilensis and D. trachyderma. A positive increase in relation to scientific knowledge over the past decade was noticeable, although several basic aspects of their biology and ecology are still missing. There is an urgent need to fill knowledge gaps on, for example, movement patterns, feeding ecology and habitat use, population size and structure, and levels of connectivity. In this study, taxonomic clarity was provided, and relevant information with regard to the biology, ecology and fisheries that interact with longnose skates was collated. Confusion of identity between longnose skates occurs to the present day. In order to address this issue, morphometric and genetic tools are provided to aid in species identification of early-life stage specimens. Thirty-seven morphometric measurements and three meristic characters were used to identify specimens. These results suggest that the number of midline, nuchal and inter-dorsal thorns could be used to discriminate between specimens of Z. chilensis and D. trachyderma. Previously, the presence of a single nuchal thorn was considered to be a feature that could be used to separate species, however, this morphological feature has proven to be variable in Z. chilensis. Additionally, partial sequences of the 16S, cox1, nadh2 and the control regions of the mitochondrial DNA were amplified and analysed for intraspecific and interspecific divergence. Amplified fragments of cox1 gene and the control region contained information to separate the target species; however, specimens of D. trachyderma and Z. chilensis were grouped indistinctly within a single clade using 16S and nadh2 fragments. –ii– The evolutionary history of Zearaja was also explored, in a broad taxonomic context by using whole mitochondrial genomes (mitogenomes) to understand higher-level phylogenetic relationships among batoids. A data set of 56 mitogenomes of 47 batoids and four outgroups was analysed. Overall, these results showed consensus phylogenomic trees that support previous phyletic reconstructions based on morphological characters, and consequently recovers all extant Orders within the Batoidea in two higher-level reciprocally monophyletic clades: Myliobatiformes + Rhinopristiformes, and Torpediniformes + Rajiformes. Intraspecific divergence is extremely low among the three Zearaja species and may suggest a radiation from a potential ancestral form (Z. chilensis) towards a derived species (Z. maugeana). The evolution of the genus Zearaja could be linked to major geological events, such as the terminal Eocene event and the sinking of Zealandia; which may explain the current restricted geographical distribution to the Southern Hemisphere. Longnose skates in Chilean waters are considered to be a single stock by the fishery management in Chile however, little is known about the level of demographic connectivity within the fishery. Here, population connectivity at five locations along the Chilean coast was explored by using the mitochondrial (control region) and nuclear (microsatellite loci) DNA. Analysis of Z. chilensis populations revealed significant genetic structure among off-shore locations (San Antonio, Valdivia), two locations in the Chiloe Interior Sea (Puerto Montt and Aysén), and Punta Arenas in southern Chile. An important research outcome was lack of connectivity among individuals from the Chiloe Interior Sea and the other two proposed management units. These results provide evidence for three management units for Z. chilensis, and recommendations of separate harvest strategies were made considering each of these units. However, there is no evidence to discriminate the extant population of D. trachyderma as separate management units. This thesis has expanded our general knowledge and has provided management guidelines for sustainable fishery practices in Chile; however, appropriate management and enforcement actions from the Chilean Government are urgently needed to avoid population collapse and extirpation of stocks. –iii– Declaration by author This thesis is composed of my original work, and contains no material previously published or written by another person except where due reference has been made in the text. I have clearly stated the contribution by others to jointly-authored works that I have included in my thesis. I have clearly stated the contribution of others to my thesis as a whole, including statistical assistance, survey design, data analysis, significant technical procedures, professional editorial advice, and any other original research work used or reported in my thesis. The content of my thesis is the result of work I have carried out since the commencement of my research higher degree candidature and does not include a substantial part of work that has been submitted to qualify for the award of any other degree or diploma in any university or other tertiary institution. I have clearly stated which parts of my thesis, if any, have been submitted to qualify for another award. I acknowledge that an electronic copy of my thesis must be lodged with the University Library and, subject to the policy and procedures of The University of Queensland, the thesis be made available for research and study in accordance with the Copyright Act 1968 unless a period of embargo has been approved by the Dean of the Graduate School. I acknowledge that copyright of all material contained in my thesis resides with the copyright holder(s) of that material. Where appropriate I have obtained copyright permission from the copyright holder to reproduce material in this thesis. –iv– Publications during candidature Conference abstracts Vargas-Caro, C., Bustamante, C., Bennett, M. B. & Ovenden, J. R. (2016). Population structure and genetic diversity of commercial skates in Chile: Tools towards sustainable fishery management. International Postgraduate Symposium in Biomedical Sciences, 31st October and 1st November 2016, The University of Queensland, Australia. Vargas-Caro, C., Bustamante, C., Bennett, M. B. & Ovenden, J. R. (2016). Estructura poblacional y diversidad genética de las rayas comerciales en chile: Herramientas para un manejo pesquero sustentable. XXXVI Congreso de Ciencias del Mar: Sustentabilidad y Multidisciplina en Ciencias del Mar, 23-27th of May 2016, Universidad de Concepción, Chile. Vargas-Caro, C., Bustamante, C. & Bennett, M. B. (2016). Fishing the twilight zone: Catch composition of the southeast Pacific Ocean demersal longline fishery. XXXVI Congreso de Ciencias del Mar: Sustentabilidad y Multidisciplina en Ciencias del Mar, 23-27th of May 2016, Universidad de Concepción, Chile. Bustamante, C., Vargas-Caro, C., Ovenden, J. R. & Bennett, M. B. (2016). Más allá de los genes: Aplicación de la filogenómica en la taxonomía de peces elasmobranquios. XXXVI Congreso de Ciencias del Mar: Sustentabilidad y Multidisciplina en Ciencias del Mar, 23-27th of May 2016, Universidad de Concepción, Chile. Vargas-Caro, C., Bustamante, C. & Bennett, M. B. (2015). Fishing the twilight zone: Catch composition of the southeast Pacific Ocean demersal longline fishery. International Postgraduate Symposium in Biomedical Sciences, 3-5th November 2015, The University of Queensland, Australia. Vargas-Caro, C., Bustamante, C., Bennett, M. B. & Ovenden, J. R. (2015). Phylogeny of longnose skates (genus Zearaja) inferred from complete mitochondrial genomes. 1st Meeting of Chilean scientists in Brisbane: Strengthening ties between Chile and Australia, 31st of July 2015, The University of Queensland, Australia. Vargas-Caro, C., Bustamante, C., Bennett, M. B. & Ovenden, J. R. (2015). Phylogeny of longnose skates (genus Zearaja) inferred from complete mitochondrial genomes. Conference of the New Zealand Marine Sciences Society & Oceania Chondrichthyan Society, 6-9th of July 2015, The University of Auckland, New Zealand. –v– Vargas-Caro, C., Bennett, M. B. & Ovenden, J. R. (2014). Skate-ing on thin ice: How to resolve identification issues for future management. Conference of the Shark International symposium, 2- 6th of June 2014, the Southern Sun Elangeni-Maharani Hotel, Durban, South Africa. Listed journals with editorial committee Vargas-Caro, C., Bustamante,