Julian G. Pepperell

Global overview of the major constituent-based billfish tagging programs and their results since 1954

Release and recovery files from the worlds five major constituent-based billfish (Istiophoridae) tagging programs were assembled into a single composite database. Data sources included the National Marine Fisheries Services (NMFS) Cooperative Tagging Center (MIA) in the Atlantic Ocean, the NMFSs Cooperative Billfish Tag- ging Program (LJA) in the Pacific and Indian Oceans, the Australian Cooperative Tagging Program in the Pacific and Indian Oceans, the New Zealand Cooperative Game Fish Tagging Program in the Pacific Ocean, and The Billfish Foundations (TBF) tagging program in the Atlantic, Pacific and Indian Oceans. Results for the main target species, including black marlin (Makaira indica), blue marlin (Makaira nigricans), white marlin (Tetrapturus albidus), striped marlin (Tetrapturus audax) and sailfish (Istiophorus platypterus) were compared and contrasted based on species, ocean body and tagging program. A total of over 317 000 billfish have been tagged and released, and 4122 have been recovered since 1954. Tag recovery percentages were generally higher for a recently developed double- barb nylon anchor tag compared with the typically used stainless steel dart tag. Greatest distances moved were largest for blue marlin and black marlin, followed by striped marlin, white marlin and sailfish. The TBF program had the highest tag recovery percentages for white marlin (2.4%) and blue marlin (1.7%), whereas the MIA program had the highest percentage recovery for sailfish (1.8%). The LJA program had the highest recovery percentages for black marlin (1.9%) and striped marlin (1.4%). The annual number of releases and recoveries for each tar- get species tended to increase over the time series, particularly during the last decade. Cyclic annual movement patterns and/or seasonal site fidelity were evident for black marlin and white marlin. The data suggest that tag recovery percentages can be affected by tag type, reporting rate, localized fishing activities, outreach activities, and a variety of logistical issues indirectly related to size of ocean body. The efficiencies of the tagging programs are compared and recommendations are made to improve the programs. The composite tagging database provides the opportunity for a more comprehensive evaluation of the data and tagging programs than has previously been pos- sible by examining the individual programs in isolation. The main advantage of constituent-based tagging programs is that large numbers of billfish can be tagged at a minimum cost. The main drawbacks are a lack of control over the tagging event and return of recovery data. Constituent-based tagging programs provide essential data on billfish movement and biology, and should be expanded and improved to meet the increasing need for this information.

Short-term movement and behaviour of black marlin Makaira indica in the Coral Sea as determined through a pop-up satellite archival tagging experiment

Pop-up satellite tags were deployed on seven black marlin, Makaira indica,in the north-western Coral Sea, to examine movement, post-capture mortality and habitat preferences. Five of these tags popped up and transmitted positions, and detailed data on diving behaviour, ambient water temperature and daily movement were received via ARGOS transmission from two tags. One tag was later found on a beach, allowing a complete archival data set to be downloaded and geolocation estimates provided by software on-board the pop-up tags and those based on the complete archival tag data sets to be compared. The tags indicated rapid movement away from release sites; three south-easterly displacements (222 km (120 nm), 222 km (120 nm), and 1185.3 km (640 nm) net) appeared to be associated with the East Australian Current, one moved 555.6 km (300 nm) directly east, and the last tag moved offshore and then back towards the coast over a 2-month period for a net displacement of 384 km (207 nm). Based on displacement speeds and diving behaviour, it was concluded that five of the seven fish survived capture and handling for periods ranging from 3 to 64 days. The fate of the other two is unknown. Estimates of longitude made on board the pop-up tag were very similar to the best estimates that could be made using the complete archival data set; however, pop-up tag latitude estimates were significantly more variable than those using the archival data. In the two cases in which pop-up tags were scheduled to stay on the marlin for more than 3 months, the tags detached prematurely, after 39 and 64 days. Temperature and depth data indicated a preference for waters of the mixed layer (20–120 m) and temperatures warmer than 24°C.

Spatial genetic subdivision among populations of the highly migratory black marlin Istiompax indica within the central Indo-Pacific

The black marlin Istiompax indica is a highly migratory species and as a result is expected to show little genetic population structure throughout its broad geographic range. Tissue samples from 183 I. indica were collected from three geographic regions within the central Indo-Pacific and analysed using mitochondrial and nuclear DNA markers. Nuclear genetic heterogeneity was found among populations in the south-western Pacific Ocean, eastern Indian Ocean and South China Sea (significant FST values of 0.013–0.037). Combining information from nuclear markers with published movement and reproductive data suggests that reproductive philopatry plays a role in maintaining contemporary I. indica population structure. Analyses of the mitochondrial control region did not reflect this pattern; however, it identified historical population structure. Differing patterns of genetic population structure revealed by mitochondrial and nuclear markers demonstrated that a transition must have occurred between historical and contemporary population structures. This restructuring presumably reflects a species whose populations have become genetically isolated before experiencing a period of secondary contact. The spatial subdivision evident among populations indicates that I. indica in this central Indo-Pacific region should be managed as three independent stocks, to guide the sustainability of this fisheries resource.

Use of charter boat data to infer the annual availability of black marlin, Makaira indica, to the recreational fishery off Cairns, Australia

Catch data, recorded in daily diaries kept by the captains of charter boats in the recreational fishery that targets black marlin (Makaira indica) in the Cairns/Lizard Island region off north-eastern Australia, were used to calculate annual indices of fishing success (catch per day). Generalized Linear Models were used to investigate factors likely to influence catch rates, such as captain, area fished, water temperature, moon phase and the strength and direction of prevailing currents. Despite a high degree of inter-annual variability in the catch, results indicate that there has been a long-term decline of between 20-30% in estimated availability between 1970 and 1997. Models fitted to the data for the period 1987-1996 indicate that several environmental factors can have a significant influence on availability in any given year, with higher catch rates occurring close to a half moon and associated with water temperatures around 26.0-26.5 ◦ C. Catch rates for the period 1980-1997 were also found to be negatively correlated with longline effort levels within the inshore region close to the recreational fishery, though this correlation was not found to be significant.

Extracting DNA from ‘jaws’: high yield and quality from archived tiger shark (Galeocerdo cuvier) skeletal material

Archived specimens are highly valuable sources of DNA for retrospective genetic/genomic analysis. However, often limited effort has been made to evaluate and optimize extraction methods, which may be crucial for downstream applications. Here, we assessed and optimized the usefulness of abundant archived skeletal material from sharks as a source of DNA for temporal genomic studies. Six different methods for DNA extraction, encompassing two different commercial kits and three different protocols, were applied to material, so‐called bio‐swarf, from contemporary and archived jaws and vertebrae of tiger sharks (Galeocerdo cuvier). Protocols were compared for DNA yield and quality using a qPCR approach. For jaw swarf, all methods provided relatively high DNA yield and quality, while large differences in yield between protocols were observed for vertebrae. Similar results were obtained from samples of white shark (Carcharodon carcharias). Application of the optimized methods to 38 museum and private angler trophy specimens dating back to 1912 yielded sufficient DNA for downstream genomic analysis for 68% of the samples. No clear relationships between age of samples, DNA quality and quantity were observed, likely reflecting different preparation and storage methods for the trophies. Trial sequencing of DNA capture genomic libraries using 20 000 baits revealed that a significant proportion of captured sequences were derived from tiger sharks. This study demonstrates that archived shark jaws and vertebrae are potential high‐yield sources of DNA for genomic‐scale analysis. It also highlights that even for similar tissue types, a careful evaluation of extraction protocols can vastly improve DNA yield.

The Novel Application of Non-Lethal Citizen Science Tissue Sampling in Recreational Fisheries

Increasing fishing pressure and uncertainty surrounding recreational fishing catch and effort data promoted the development of alternative methods for conducting fisheries research. A pilot investigation was undertaken to engage the Australian game fishing community and promote the non-lethal collection of tissue samples from the black marlin Istiompax indica, a valuable recreational-only species in Australian waters, for the purpose of future genetic research. Recruitment of recreational anglers was achieved by publicizing the project in magazines, local newspapers, social media, blogs, websites and direct communication workshops at game fishing tournaments. The Game Fishing Association of Australia and the Queensland Game Fishing Association were also engaged to advertise the project and recruit participants with a focus on those anglers already involved in the tag-and-release of marlin. Participants of the program took small tissue samples using non-lethal methods which were stored for future genetic analysis. The program resulted in 165 samples from 49 participants across the known distribution of I. indica within Australian waters which was a sufficient number to facilitate a downstream population genetic analysis. The project demonstrated the potential for the development of citizen science sampling programs to collect tissue samples using non-lethal methods in order to achieve targeted research objects in recreationally caught species.

Misidentification of istiophorid billfishes by fisheries observers raises uncertainty over stock status

We investigated whether commercially landed black marlin Istiompax indica were being misidentified by fisheries observers operating throughout the Pacific Ocean. Of 83 samples reported by observers as I. indica, 77% were genetically identified to be blue marlin Makaira nigricans and 2% to be striped marlin Kajikia audax. The high rate of misidentification by observers places considerable uncertainty over historic catch ratios of Indo-Pacific marlin and stock assessments relying on the validity of these data.

The trophic role of a large marine predator, the tiger shark Galeocerdo cuvier

Tiger sharks were sampled off the western (Ningaloo Reef, Shark Bay) and eastern (the Great Barrier Reef; GBR, Queensland and New South Wales; NSW) coastlines of Australia. Multiple tissues were collected from each shark to investigate the effects of location, size and sex of sharks on δ13C and δ15N stable isotopes among these locations. Isotopic composition of sharks sampled in reef and seagrass habitats (Shark Bay, GBR) reflected seagrass-based food-webs, whereas at Ningaloo Reef analysis revealed a dietary transition between pelagic and seagrass food-webs. In temperate habitats off southern Queensland and NSW coasts, shark diets relied on pelagic food-webs. Tiger sharks occupied roles at the top of food-webs at Shark Bay and on the GBR, but not at Ningaloo Reef or off the coast of NSW. Composition of δ13C in tissues was influenced by body size and sex of sharks, in addition to residency and diet stability. This variability in stable isotopic composition of tissues is likely to be a result of adaptive foraging strategies that allow these sharks to exploit multiple shelf and offshore habitats. The trophic role of tiger sharks is therefore both context- and habitat-dependent, consistent with a generalist, opportunistic diet at the population level.

Environmental influences and ontogenetic differences in vertical habitat use of black marlin (Istiompax indica) in the southwestern Pacific

The black marlin (Istiompax indica) is a highly migratory billfish that occupies waters throughout the tropical and subtropical Indo-Pacific. To characterize the vertical habitat use of I. indica, we examined the temperature-depth profiles collected using 102 pop-up satellite archival tags deployed off the east coast of Australia. 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. Distinct differences in diel movements were observed between the size classes, with larger size classes of marlin (greater than 50 kg) undertaking predictable bounce-diving activity during daylight hours, while diving behaviour of the smallest size class occurred randomly during both day and night. Overall, larger size classes of I. indica were found to use an increased thermal range and spend more time in waters below 150 m than fish of smaller size classes. The differences in the diving behaviour among size classes were suggested to reflect ontogenetic differences in foraging behaviour or physiology. The findings of this study demonstrate, for the first time to our knowledge, ontogenetic differences in vertical habitat in a species of billfish, and further the understanding of pelagic fish ecophysiology in the presence of global environmental change.