The genome of the Balearic shearwater (Puffinus mauretanicus), a Critically Endangered seabird: a valuable resource for evolutionary and conservation genomics

The Balearic shearwater (Puffinus mauretanicus) is the most threatened seabird in Europe. The fossil record suggests that human colonisation of the Balearic Islands resulted in a sharp decrease of the population size. Currently, populations continue to be decimated mainly due to predation by introduced mammals and bycatch in longline fisheries, and some studies predict their extinction by 2070. We present the first high-quality reference genome for the species which was obtained by a combination of short and long-read sequencing. Our hybrid assembly includes 4,169 scaffolds, with a scaffold N50 of 2.1 Mbp, a genome length of 1.2 Gbp, and BUSCO completeness of 96%, which is amongst the highest across sequenced avian species. This reference genome allowed us to study critical aspects relevant to the conservation status of the species, such as an evaluation of overall heterozygosity levels and the reconstruction of its historical demography. Our phylogenetic analysis using whole-genome information resolves current uncertainties in the order Procellariiformes systematics. Comparative genomics analyses uncover a set of candidate genes that may have played an important role into the adaptation to a pelagic lifestyle of Procellariiformes, including those for the enhancement of fishing capabilities, night vision and the development of natriuresis. This reference genome will be the keystone for future developments of genetic tools in conservation efforts for this Critically Endangered species.

Evaluation of the Impacts of Climate Change on Albacore Distribution in the South Pacific Ocean by Using Ensemble Forecast

South Pacific albacore (Thunnus alalunga) is a highly migratory tuna species widely distributed throughout 0°–50°S in the South Pacific Ocean. Climate-driven changes in the oceanographic condition largely influence the albacore distribution, relative abundance, and the consequent availability by the longline fisheries. In this study, we examined the habitat preference and spatial distribution of south Pacific albacore using a generalized additive model fitted to the longline fisheries data from the Western and Central Pacific Fisheries Commission (WCPFC) and Inter-American Tropical Tuna Commission (IATTC). Future projections of albacore distributions (2020, 2050, and 2080) were predicted by using an ensemble modeling approach produced from various atmosphere-ocean general circulation models and anthropogenic emission scenarios (i.e., RCP 4.5 and RCP 8.5) to reduce the uncertainty in the projected changes. The dissolved oxygen concentration at 100 meters (DO100) and sea surface temperature (SST) were found to have the most substantial effects on the potential albacore distribution that the albacore preferred in the habitat with DO100 of 0.2–0.25 mmol L–1 and SST of 13–22°C. This study suggested that the northern boundary of albacore preferred habitat is expected to shift southward by about 5° latitudes, and the relative abundance is expected to gradually increase in the area south of 30°S from 2020 to 2080 for both RCP scenarios, especially with a higher degree of change for the RCP 8.5. Moreover, the albacore relative abundance is projected to decrease in the most exclusive economic zones (EEZs) of countries and territories in the South Pacific Ocean by 2080. These findings could lend important implications on the availability of tuna resources to the fisheries and subsequent evaluation of tuna conservation and management under climate change.

Fishing trip cost modeling using generalized linear model and machine learning methods – A case study with longline fisheries in the Pacific and an application in Regulatory Impact Analysis

Fishing trip cost is an important element in evaluating economic performance of fisheries, assessing economic effects from fisheries management alternatives, and serving as input for ecosystem and bioeconomic modeling. However, many fisheries have limited trip-level data due to low observer coverage. This article introduces a generalized linear model (GLM) utilizing machine learning (ML) techniques to develop a modeling approach to estimate the functional forms and predict the fishing trip costs of unsampled trips. GLM with Lasso regularization and ML cross-validation of model are done simultaneously for predictor selection and evaluation of the predictive power of a model. This modeling approach is applied to estimate the trip-level fishing costs using the empirical sampled trip costs and the associated trip-level fishing operational data and vessel characteristics in the Hawaii and American Samoa longline fisheries. Using this approach to build models is particularly important when there is no strong theoretical guideline on predictor selection. Also, the modeling approach addresses the issue of skewed trip cost data and provides predictive power measurement, compared with the previous modeling efforts in trip cost estimation for the Hawaii longline fishery. As a result, fishing trip costs for all trips in the fishery can be estimated. Lastly, this study applies the estimated trip cost model to conduct an empirical analysis to evaluate the impacts on trip costs due to spatial regulations in the Hawaii longline fishery. The results show that closing the Western and Central Pacific Ocean (WCPO) could induce an average 14% increase in fishing trip costs, while the trip cost impacts of the Eastern Pacific Ocean (EPO) closures could be lower.

Horizontal and vertical movements of immature dusky sharks Carcharhinus obscurus in relation to commercial longline fisheries in the western North Atlantic Ocean

Background Many species of sharks, including the dusky shark Carcharhinus obscurus, are often incidentally captured in commercial pelagic and bottom longline fisheries. Incidental capture can lead to at-vessel or post-release mortality and can be detrimental to populations of threatened, endangered, or prohibited species. The estimated at-vessel mortality for dusky sharks can be high in longline fisheries and, to minimize mortality, time–area closures have been designated in the western North Atlantic Ocean to mitigate interactions with longline fisheries, yet incidental capture of dusky sharks is still common. We compared the vertical and horizontal movements of dusky sharks to the overall fishing effort and depth fished of commercial pelagic and bottom longline fisheries to determine when and where overlap is present that could lead to incidental capture. Results Twenty-one (n = 21) dusky sharks were tagged with pop-up archival transmitting satellite tags and all were immature animals (123–200 cm FL) apart from two individuals (230 and 300 cm FL). Sharks were tagged off the coasts of North Carolina (71%) and Florida (29%). Twenty tags (95%) reported and provided tracks between 1 and 107 days (median 15 days) and 10 tags (50%) remained on sharks for > 4 days. Most individuals remained within the bottom longline closed area off the coast of North Carolina during their time at liberty. Dusky sharks primarily occupied the 20–40 m depth range 26% of the time, and overlapped with bottom and pelagic longline gears 41% and 59% of the time, respectively. Overlap was highest in the winter and spring for both commercial fisheries. Conclusions The use of archival satellite telemetry in this study has provided valuable preliminary information on vertical and horizontal movements of immature dusky sharks in western North Atlantic Ocean. Dusky sharks may be more vulnerable to incidental capture in the pelagic longline fishery due to the high fishing effort, larger areas of horizontal overlap, and greater percentage of vertical overlap. This information will inform mitigation measures of commercial longline fisheries, which can work toward population rebuilding of the species.

Life history parameters of the crocodile shark, Pseudocarcharias kamoharai, in the tropical Atlantic Ocean

The crocodile shark (Pseudocarcharias kamoharai) is a small lamniform shark that is occasionally by-caught in pelagic longline fisheries targeting tunas and swordfish. Due to its biological features, this species is highly vulnerable to overexploitation. However, at present, the crocodile shark is not evaluated for its stock status by any of the Regional Fisheries Management Organizations. In this study, the biology of 391 specimens (220 females and 171 males), ranging from 44.2 cm to 101.5 cm fork length (FL), collected from the tropical region of the Atlantic Ocean, was examined. Ages were assigned from growth band counts in vertebral sections, with the modified von Bertalanffy growth model, using a fixed size at birth (L0) at 32 cm FL, producing the best fit: Linf = 105.6 cm FL and k = 0.14 y−1 for females; Linf = 94.6 cm FL and k = 0.18 y−1 for males. Maturity ogives were fitted to both length- and age-based data. The size (L50) and age (A50) at 50% maturity was estimated at 67.2 cm FL (5 years) and 81.6 cm FL (8 years) for males and females, respectively. Mean uterine fecundity was 3.7 pups per litter with a 1:1 embryonic sex ratio. Further work is needed regarding crocodile shark life-history characteristics, especially because there are no age validation studies of the band pair deposition periodicity. However, the parameters now presented can contribute to future evaluations of this species, which is especially important given its potentially vulnerable life history.

Seabird bycatch vulnerability in pelagic longline fisheries based on modelling of a long-term dataset

Summary The incidental mortality of seabirds in fisheries remains a serious global concern. Obtaining unbiased and accurate estimates of bycatch rates is a priority for seabird bycatch mitigation and demographic research. For measuring the capture risk of seabird interactions in fisheries, the rate of carcass retrieval from hauled gear is commonly used. However, reliability can be limited by a lack of direct capture observations and the substantial pre-haul bycatch losses known to occur, meaning incidence of seabird bycatch is underestimated. To solve this problem, a new measure (bycatch vulnerability) that links an observed interaction directly to the underlying capture event is proposed to represent the capture risk of fishery interactions by seabirds. The new measure is not affected by subsequent bycatch loss. To illustrate how to estimate and analyse bycatch vulnerability, a case study based on a long-term dataset of seabird interactions and capture confirmation is provided. Bayesian modelling and hypothesis testing were conducted to identify important bycatch risk factors. Competition was found to play a central role in determining seabird bycatch vulnerability. More competitive environments were riskier for seabirds, and larger and thus more competitive species were more at risk than smaller sized and less competitive species. Species foraging behaviour also played a role. On the other hand, no additional effect of physical oceanic condition and spatio-temporal factors on bycatch vulnerability was detected. Bycatch vulnerability is recommended as a replacement for the commonly used bycatch rate or carcass retrieval rate to measure the capture risk of an interaction. Combined with a normalized contact rate, bycatch vulnerability offers an unbiased estimate of seabird bycatch rate in pelagic longline fisheries.

The Challenges of Managing Depredation and Bycatch of Toothed Whales in Pelagic Longline Fisheries: Two U.S. Case Studies

Direct interactions with fisheries are broadly recognized as the leading conservation threat to small cetaceans. In open-ocean environments, one of the primary gear types implicated in these interactions is the pelagic longline. Unlike accidental entanglement in driftnets or deliberate entrapment by purse-seines, interactions between cetaceans and longlines are often driven by attraction of the animals to feed on bait or fish secured on the gear, a behavior known as depredation. Many small and medium-sized delphinid species have learned to exploit such opportunities, leading to economic costs to fisheries and a risk of mortality to the animals from either retaliation by fishermen or hooking or entanglement in fishing gear. Two pelagic longline fisheries in the United States experience depredation and bycatch by odontocete depredators: the Hawai‘i deep-set longline fishery, which is depredated primarily by false killer whales (Pseudorca crassidens), and the Atlantic pelagic longline fishery depredated primarily by short-finned pilot whales (Globicephala macrorhynchus). These fisheries are among the most intensively documented and managed pelagic longline fisheries in the world, with high levels of observer coverage, and bycatch mitigation measures required to reduce the mortality of seabirds, sea turtles and cetaceans. Both fisheries have active, multi-stakeholder “Take Reduction Teams,” enacted under the U.S. Marine Mammal Protection Act (MMPA), that are tasked to develop measures to reduce the bycatch of cetaceans below statutory reference points. Consequently, these two Teams represent model processes within which to address depredation and bycatch, having access to detailed, high-quality data on the nature and frequency of interactions with cetaceans, meaningful stakeholder involvement, resources to test potential solutions, and the institutional will to improve outcomes. We review how mitigation strategies have been considered, developed, and implemented by both Teams and provide a critical analysis of their effectiveness in addressing these problems. Notably, in the absence of straightforward avoidance or deterrence strategies, both Teams have developed gear and handling strategies that depend critically on comprehensive observer coverage. Lessons offered from these Teams, which have implemented consensus-driven management measures under a statutory framework, provide important insights to managers and scientists addressing other depredation problems.