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The Global Biology, Ecology and Phylogenetic Status of Black Marlin (Istiompax Indica)

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The Global Biology, Ecology and Phylogenetic Status of Black Marlin (Istiompax Indica) The global biology, ecology and phylogenetic status of black marlin (Istiompax indica) Samuel Mackey Williams BSc (Hons) A thesis submitted for the degree of Doctor of Philosophy at The University of Queensland in 2018 Faculty of Medicine 1 ABSTRACT The black marlin [Istiompax indica (Morrow, 1968)] is one of the largest teleost fish and has a continuous distribution throughout tropical waters of the Indo-Pacific. Throughout its range, I. indica has been documented to undertake wide-ranging, transoceanic and trans- equatorial movements. In coastal waters and on the high seas I. indica may be targeted by commercial and artisanal fisheries, but the majority of the world’s landings are as a by-product species of tuna longline and purse seine fisheries. Due to its large size and ‘fighting qualities’, I. indica is also valued as a prized sport or game fish in recreational fisheries. While considerable effort to understand the level of exploitation of high value species such as the tunas has occurred, the stock status for many other species caught on the high seas such as many sharks, dolphinfish and istiophorid billfishes remain unassessed. This lack of attention is reflected by I. indica being listed as ‘Data Deficient’ on the International Union for Conservation of Nature Red List. The lack of attention and data available on I. indica extends to biological, ecological, taxonomic and fisheries catch records, which in turn hinders stock assessments and management. This thesis aims to improve the biological and ecological knowledge of I. indica, thereby providing a stronger foundation for assessments and management of stocks globally. Since the original taxonomic classification of billfishes (suborder Xiphioidei) using morphological data, the systematics of billfishes have been reshaped using genetic markers. The results of phylogenetic analysis recommended the expansion of Istiophoidae from three genera to five; Makaira, Istiophorus, Kajikia, Istiompax and Tetrapturus. Despite the taxonomic revision, several aspects of the Istiophoridae phylogeny remained unresolved, including the position of the genus Istiompax. To address the outstanding issues within Istiophoridae, a phylogenetic analysis was undertaken using whole mitogenomes for all billfish species. Phylogenetic analyses supported the presence of five genera within Istiophoridae and resolved the placement of Istiompax as the sister taxon to Kajikia + Tetrapturus. The investigation also provided new insights into the close genetic relatedness between a number of morphologically similar species within Tetrapturus and Kajikia. This study increased the phylogenetic resolution of istiophorid billfishes and highlighted the need for further work to resolve the genetic relationships among closely related billfish. II Increases in landings of billfishes has highlighted the need for accurate reporting and identification of morphologically similar species by boats operating in multi-species tuna fisheries. In the Atlantic Ocean, high rates of misidentification and misreporting between species of billfish have been identified, confounding our understanding of the stock status of Atlantic billfishes. Genetic analysis was undertaken to investigate whether misidentification of Pacific billfishes by fisheries observers was occurring in multi-species tuna fisheries. Tissue samples were collected from billfish that fisheries observers morphologically identified as I. indica. Genetic analysis of 83 samples using a suite of microsatellite markers revealed that 77.1% of the putative I. indica were in fact blue marlin (Makaira nigricans) and 2.4% were striped marlin (Kajikia audax). The high rate of misidentification (~80%) by observers places considerable uncertainty over historic catch ratios of Indo-Pacific marlin species and stock assessments relying on the validity of these data. Increasing fishing pressure and uncertainty surrounding the valid identification of I. indica landed by commercial operators provided the impetus for development of methods for collecting tissue samples for population genetics research from recreational fisheries. A pilot investigation was undertaken to engage the Australian game fishing community and promote the non-lethal collection of tissue samples from I. indica. After validating the success of a pilot minimally invasive, non-lethal sampling program, the program was extended throughout the range of I. indica. Through a combination of non-lethal recreational sampling and tissue collected from commercially landed I. indica at fish markets, a total of 465 samples were collected from 13 locations throughout the species’ range. A suite of 17 microsatellite markers and 1557 nuclear single nucleotide polymorphisms was used to investigate genetic stock structure throughout the Indo-Pacific. The results indicated the presence of three genetic stocks 1) Indian Ocean, 2) South Pacific Ocean and 3) North-west Pacific Ocean. Resolution of the genetic stock structure of I. indica provides a basis for implementing biologically meaningful assessments and management of the species throughout its range. The development of additional biological and ecological information will continue to reduce uncertainty around the status of black marlin stocks, and provide decision makers with capacity to drive the enforcement of other fishery-specific management controls. Understanding how environmental factors influence the distribution and abundance of billfishes provides insights into how environmental change may alter migration phenology, spawning, vertical distribution and survival rate of larvae. To characterise the vertical habitat III use of I. indica, temperature-depth profiles from 102 pop-up satellite archival tags deployed on I. indica off the east coast of Australia were examined in this study. Modelling of environmental variables revealed location, sea surface height deviation, mixed layer depth, and dissolved oxygen to all be significant predictors of vertical habitat use. This investigation also demonstrates, for the first-time, ontogenetic differences in vertical habitat in a species of billfish. Distinct differences in diel movements, diving behaviour and thermal range were observed among different size classes of I. indica. The differences in the diving behaviour among size classes were suggested to reflect ontogenetic differences in foraging behaviour and/or physiology. The outcomes from this study characterise the vertical habitat use of I. indica and further the understanding of pelagic fish ecophysiology in the presence of global environmental change. Furthermore, the vertical distribution of I. indica identified herein provides information that could be used by policy makers to reduce bycatch mortality rates in fisheries where they are not targeted. It is anticipated that the outcomes of this research will provide fisheries managers with an enhanced understanding of population biology and ecology that can be used to inform management decisions and future research priorities of billfish. Knowledge gained by this thesis also add new insights into phylogeny and physiology of large pelagic fishes to benefit the disciplines of conservation and systematics. IV 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, financial support 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 higher degree by research 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 and have sought permission from co-authors for any jointly authored works included in the thesis. V PUBLICATIONS DURING CANDIDATURE Peer-reviewed papers and book chapters A Cohen, D. Spooner and SM. Williams (In Press). Examining the importance of marine transport and transport infrastructure and the initiatives adopted for managing potential impacts whilst enhancing transport services. Moreton Bay and Catchment. SM. Williams, JG Pepperell, MB. Bennett, & JR. Ovenden (2018). Misidentification of Pacific Ocean billfishes by fisheries observers raises uncertainty over stock status. Journal of Fish Biology. DOI: 10.1111/jfb.13738 BJ. Holmes, L. Pope, SM. Williams, I. Tibbetts, MB. Bennett & JR. Ovenden (2018). Lack of multiple paternity in the oceanodromous
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