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This study provides a comprehensive molecular phylogenetic analysis of Uroteuthis squid from the Indo-Pacific region. The main aim was to increase sample coverage from northern and eastern Australian waters to resolve the identity and distribution of Uroteuthis species taken by local fisheries. Two mitochondrial regions, cytochrome c oxidase subunit I (COI) and 16S ribosomal RNA (16S rRNA), were sequenced from 220 new specimens and analysed with a further 51 sequences from GenBank to create a combined phylogeny for the genus. Three nuclear regions, 18S ribosomal DNA (18S rDNA), 28S ribosomal DNA (28S rDNA) and rhodopsin, were also sequenced from representatives of each species. Based on the mitochondrial phylogeny plus distance and tree-based delimitation models, a COI species barcode gap of 4–5% is proposed for discriminating Uroteuthis species. Applying this gap partitioned many described species into species complexes; for example, U. duvaucelii, U. noctiluca and U. edulis resolved into 10 species. Although more conserved, mitochondrial 16S rRNA sequences differentiated all new species clades, whereas none of the nuclear markers resolved the closest species. Results confirm that neither U. chinensis nor U. edulis occurs in Australian waters. Five undescribed species are identified from northern and eastern Australia, of which four are consistent with earlier allozyme studies (and two align with existing DNA sequences). One is a new southeastern, deeper shelf species differentiated in this study, along with a sixth undescribed species from Indonesian waters. Results of the molecular analysis are now being used to inform complementary morphometric analyses for new species descriptions, and genetic stock structure assessments of these important fisheries resources.

Targeted sequencing is an increasingly popular Next Generation Sequencing (NGS) approach for studying populations that involves focusing sequencing efforts on specific parts of the genome of a species of interest. Methodologies and tools for designing targeted baits are scarce but in high demand. Here, we present specific guidelines and considerations for designing capture sequencing experiments for population genetics for both neutral genomic regions and regions subject to selection. We describe the bait design process for three diverse fish species: Atlantic salmon, Atlantic cod and tiger shark, which was carried out in our research group, and provide an evaluation of the performance of our approach across both historical and modern samples. The workflow used for designing these three bait sets has been implemented in the R-package supeRbaits, which encompasses our considerations and guidelines for bait design for the benefit of researchers and practitioners. The supeRbaits R-package is user-friendly and versatile. It is written in C++ and implemented in R. supeRbaits and its manual are available from Github: https://github.com/BelenJM/supeRbaits.

We evaluated the population structure of M. nigricans within the Pacific Ocean using 17 microsatellite loci and 6204 single nucleotide polymorphisms. Evidence from both types of genetic markers supported the null hypothesis of a single genetic population throughout the Pacific Ocean. This study provides insight into the current stock structure of M. nigricans and discusses the implications for fisheries management.

Snapper Chrysophrys auratus is a high-value food fish in Australia targeted by both commercial and recreational fisheries. Along the east coast of Australia, fisheries are managed under four state jurisdictions (Queensland, Qld; New South Wales, NSW; Victoria, Vic.; and Tasmania, Tas.), each applying different regulations, although it is thought that the fisheries target the same biological stock. An allozyme-based study in the mid-1990s identified a weak genetic disjunction north of Sydney (NSW) questioning the single-stock hypothesis. This study, focused on east-coast C. auratus, used nine microsatellite markers to assess the validity of the allozyme break and investigated whether genetic structure exists further south. Nine locations were sampled spanning four states and over 2000 km, including sites north and south of the proposed allozyme disjunction. Analyses confirmed the presence of two distinct biological stocks along the east coast, with a region of genetic overlap around Eden in southern NSW, ~400 km south of the allozyme disjunction. The findings indicate that C. auratus off Vic. and Tas. are distinct from those in Qld and NSW. For the purpose of stock assessment and management, the results indicate that Qld and NSW fisheries are targeting a single biological stock.A

Multiple paternity has been documented as a reproductive strategy in both viviparous and ovoviviparous elasmobranchs, leading to the assumption that multiple mating may be ubiquitous in these fishes. However, with the majority of studies conducted on coastal and nearshore elasmobranchs that often form mating aggregations, parallel studies on pelagic, semi-solitary species are lacking. The tiger shark (Galeocerdo cuvier) is a large pelagic shark that has an aplacental viviparous reproductive mode which is unique among the carcharhinids. A total of 112 pups from four pregnant sharks were genotyped at nine microsatellite loci to assess the possibility of multiple paternity or polyandrous behaviour by female tiger sharks. Only a single pup provided evidence of possible multiple paternity, but with only seven of the nine loci amplifying for this individual, results were inconclusive. In summary, it appears that the tiger sharks sampled in this study were genetically monogamous. These findings may have implications for the genetic diversity and future sustainability of this population.

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 billfishes are a group of highly migratory fishes comprising two extant families. The family Xiphiidae is monotypic and contains only the broadbill swordfish (Xiphias gladius Linnaeus, 1758), while the nine-other species of billfishes constitute the family Istiophoridae. The outcomes of past phylogenetic investigations using partial nuclear and mitochondrial (mtDNA) sequences recommended a restructuring of Istiophoridae, by expanding the three existing genera into five: Makaira, Istiophorus, Kajikia, Istiompax, and Tetrapturus. However, several aspects of the Istiophoridae phylogeny remain unresolved, including the position of the genus Istiompax. In this investigation, we sequenced the whole mitogenomes for all istiophorid 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. Genetic identity between the striped marlin [Kajikia audax (Philippi, 1887)] and the white marlin [Kajikia albida (Poey, 1860)] was found to be higher than between Indo-Pacific and Atlantic clades of both the blue marlin (Makaira nigricans Lacépède, 1802) and sailfish [Istiophorus platypterus (Shaw, 1792)], suggesting recent isolation or ongoing genetic connectivity between K. audax and K. albida. An assessment of mtDNA gene regions identified NADH dehydrogenase subunit 4 (ND4) as best reflecting the phylogenetic reconstruction using the whole mitogenomes, while cytochrome b (Cytb) was the only gene region able to separate all species of billfishes in the present study. Our investigation increased the phylogenetic resolution of istiophorid billfishes and underscores the need for further investigations to fully resolve the complex genetic relationships within Tetrapturus and Kajikia.

The objectives of this study were (1) to develop novel genome-wide nuclear markers using a Reduced Representation Genotyping by Sequencing approach (RRGS) to evaluate the level of admixture between the sympatric populations of C. tilstoni and C. limbatus of the eastern coast of Australia; (2) to identify a minimum number of diagnostic single nucleotide polymorphisms (SNPs) with maximum power to delineate the hybrid classes present between the two blacktip species for application in fisheries enforcement and forensic cases; (3) to compare the power and resolution that diagnostic markers provide for hybrid class delineation with previous results that used mtDNA, microsatellite markers and pre-caudal vertebrae count discordance.

As pressure on coastal marine resources is increasing globally, the need to quantitatively assess vulnerable fish stocks is crucial in order to avoid the ecological consequences of stock depletions. Species of Sciaenidae (croakers, drums) are important components of tropical and temperate fisheries and are especially vulnerable to exploitation. The black-spotted croaker, Protonibea diacanthus, is the only large sciaenid in coastal waters of northern Australia where it is targeted by commercial, recreational and indigenous fishers due to its food value and predictable aggregating behaviour. Localised declines in the abundance of this species have been observed, highlighting the urgent requirement by managers for information on fine and broad-scale population connectivity. This study examined the population structure of P. diacanthus across northwestern Australia using three complementary methods: genetic variation in microsatellite markers, otolith elemental composition and parasite assemblage composition. The genetic analyses demonstrated that there were at least five genetically distinct populations across the study region, with gene flow most likely restricted by inshore biogeographic barriers such as the Dampier Peninsula. The otolith chemistry and parasite analyses also revealed strong spatial variation among locations within broad-scale regions, suggesting fine-scale location fidelity within the lifetimes of individual fish. The complementarity of the three techniques elucidated patterns of connectivity over a range of spatial and temporal scales. We conclude that fisheries stock assessments and management are required at fine scales (100's km) to account for the restricted exchange among populations (stocks) and to prevent localised extirpations of this species. Realistic management arrangements may involve the successive closure and opening of fishing areas to reduce fishing pressure.

Population genetic structure using nine polymorphic nuclear microsatellite loci was assessed for the tiger shark (Galeocerdo cuvier) at seven locations across the Indo-Pacific, and one location in the southern Atlantic. Genetic analyses revealed considerable genetic structuring (FST > 0.14, p<0.001) between all Indo-Pacific locations and Brazil. By contrast, no significant genetic differences were observed between locations from within the Pacific or Indian Oceans, identifying an apparent large, single Indo-Pacific population. A lack of differentiation between tiger sharks sampled in Hawaii and other Indo-Pacific locations identified herein is in contrast to an earlier global tiger shark nDNA study. The results of our power analysis provide evidence to suggest that the larger sample sizes used here negated any weak population subdivision observed previously. These results further highlight the need for crossjurisdictional efforts to manage the sustainable exploitation of large migratory sharks like G. cuvier.