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Two hundred and seven species of fish, mostly Australian marine fish, were sequenced (barcoded) for a 655 bp region of the mitochondrial cytochrome oxidase subunit I gene (cox1). Most species were represented by multiple specimens, and 754 sequences were generated. The GC content of the 143 species of teleosts was higher than the 61 species of sharks and rays (47.1% versus 42.2%), largely due to a higher GC content of codon position 3 in the former (41.1% versus 29.9%). Rays had higher GC than sharks (44.7% versus 41.0%), again largely due to higher GC in the 3rd codon position in the former (36.3% versus 26.8%). Average within-species, genus, family, order and class Kimura two parameter (K2P) distances were 0.39%, 9.93%, 15.46%, 22.18% and 23.27%, respectively. All species could be differentiated by their cox1 sequence, although single individuals of each of two species had haplotypes characteristic of a congener. Although DNA barcoding aims to develop species identification systems, some phylogenetic signal was apparent in the data. In the neighbour-joining tree for all 754 sequences, four major clusters were apparent: chimaerids, rays, sharks and teleosts. Species within genera invariably clustered, and generally so did genera within families. Three taxonomic groups-dogfishes of the genus Squalus, flatheads of the family Platycephalidae, and tunas of the genus Thunnus-were examined more closely. The clades revealed after bootstrapping generally corresponded well with expectations. Individuals from operational taxonomic units designated as Squalus species B through F formed individual clades, supporting morphological evidence for each of these being separate species. We conclude that cox1 sequencing, or 'barcoding', can be used to identify fish species.

Members of the genus Brevitrygon are small, locally abundant tropical stingrays (family Dasyatidae) occurring in soft sedimentary habitats of inner continental shelves of the Indo-West Pacific from the Red Sea to Indonesia. Formerly members of the genus Himantura, whose members lack dorsal and ventral skin folds on the tail (typical of most dasyatid genera), folds are present or rudimentary in some Brevitrygon. Important to artisanal fisheries and known to consist of at least five species, these fishes are possibly the most frequently misidentified of all stingrays. Most were inadequately described in the 19th century, and they are often taxonomically confused due to morphological similarity, ontogenetic variability, and sexual dimorphism. Their nomenclatural history is complex with four of the known species represented within the type series of one species, B. walga (Müller & Henle). Also, the type of the species with which B. walga is most often confused, B. imbricata (Bloch & Schneider) from off southern India and Sri Lanka, is in very poor condition. A lectotype has been designated for B. walga (confined to the Bay of Bengal). The genus also contains B. heterura (Bleeker) from the Indo-Malay Archipelago, B. javaensis (Last & White) from off southern Indonesia, and a new species, B. manjajiae sp. nov., from the western Indian Ocean. The former species are redescribed and redefined based largely on a combination of morphometrics, tail morphology, squamation, and molecular data. Molecular divergences were detected within lineages of B. heterura, B. walga and B. manjajiae sp. nov., requiring further investigation.

Over 15 000 species of fishes are found globally in the marine environment and DNA barcodes are used extensively to describe, catalogue, understand and manage this diversity. The dataset outlined here represents a DNA barcode reference library of the mitochondrial cytochrome c oxidase subunit 1 gene (COI) from 9767 voucher specimens (representing at least 2220 species and 288 families) of marine fishes. This publicly available dataset in the Barcode of Life Data System (BOLD) represents 17 years (2005–2022) of barcoding of marine fishes identified from Australian territorial waters. Tissues targeted for sequencing with their matching physical specimens (and extracted DNA), obtained via a multi-agency sampling effort, are mostly maintained and curated by the CSIRO Australian National Fish Collection (ANFC) in Hobart, Australia. Species-level integrated taxonomy (assigned after combined morphological and genetic assessment) has been determined for 91% of the dataset. The library represents the most complete COI barcode reference dataset for marine fishes from Australian waters and is currently utilised for integrated taxonomy, (meta)barcoding and eDNA studies.

Maskrays of the genus Neotrygon (Dasyatidae) have dispersed widely in the Indo‐West Pacific being represented largely by an assemblage of narrow‐ranging coastal endemics. Phylogenetic reconstruction methods reproduced nearly identical and statistically robust topologies supporting the monophyly of the genus Neotrygon within the family Dasyatidae, the genus Taeniura being consistently basal to Neotrygon, and Dasyatis being polyphyletic to the genera Taeniurops and Pteroplatytrygon. The Neotrygon kuhlii complex, once considered to be an assemblage of color variants of the same biological species, is the most derived and widely dispersed subgroup of the genus. Mitochondrial (COI, 16S) and nuclear (RAG1) phylogenies used in synergy with molecular dating identified paleoclimatic fluctuations responsible for periods of vicariance and dispersal promoting population fragmentation and speciation in Neotrygon. Signatures of population differentiation exist in N. ningalooensis and N. annotata, yet a large‐scale geological event, such as the collision between the Australian and Eurasian Plates, coupled with subsequent sea‐level falls, appears to have separated a once homogeneous population of the ancestral form of N. kuhlii into southern Indian Ocean and northern Pacific taxa some 4–16 million years ago. Repeated climatic oscillations, and the subsequent establishment of land and shallow sea connections within and between Australia and parts of the Indo‐Malay Archipelago, have both promoted speciation and established zones of secondary contact within the Indian and Pacific Ocean basins. We used molecular phylogenetics and phylogeography to assess the evolutionary history of Neotrygon Maskrays (Dasyatidae) across the geologically and climatically dynamic tropical Indo‐West Pacific. Molecular clock approximations suggest that the group may have arrived in the region via tectonic rafting and dispersed across the tropics. Sharp genetic breaks recovered within Neotrygon kuhlii, N.  annotata, and, to a lesser extent, N. ningalooensis are indicative of multiple cryptic speciation events likely due to glacio‐eustatic sea‐level oscillations responsible for vicariant divergences.

Aim: South-eastern Australia is a climate change hotspot with well-documented recent changes in its physical marine environment. The impact on and temporal responses of the biota to change are less well understood, but appear to be due to influences of climate, as well as the non-climate related past and continuing human impacts. We attempt to resolve the agents of change by examining major temporal and distributional shifts in the fish fauna and making a tentative attribution of causal factors. Location: Temperate seas of south-eastern Australia. Methods: Mixed data sources synthesized from published accounts, scientific surveys, spearfishing and angling competitions, commercial catches and underwater photographic records, from the 'late 1800s' to the ' present', were examined to determine shifts in coastal fish distributions. Results: Forty-five species, representing 27 families (about 30% of the inshore fish families occurring in the region), exhibited major distributional shifts thought to be climate related. These are distributed across the following categories: species previously rare or unlisted (12), with expanded ranges (23) and/or abundance increases (30), expanded populations in south-eastern Tasmania (16) and extralimital vagrants (4). Another 9 species, representing 7 families, experienced longerterm changes (since the 1800s) probably due to anthropogenic factors, such as habitat alteration and fishing pressure: species now extinct locally (3), recovering (3), threatened (2) or with remnant populations (1). One species is a temporary resident periodically recruited from New Zealand. Of fishes exhibiting an obvious poleward movement, most are reef dwellers from three Australian biogeographic categories: widespread southern, western warm temperate (Flindersian) or eastern warm temperate (Peronian) species. Main conclusions: Some of the region's largest predatory reef fishes have become extinct in Tasmanian seas since the ' late 1800s', most likely as a result of poor fishing practices. In more recent times, there have been major changes in the distribution patterns of Tasmanian fishes that correspond to dramatic warming observed in the local marine environment.

A new species of eagle ray, Aetomylaeus caeruleofasciatus sp. nov., is described based on specimens collected in northern Australia and southern Papua New Guinea. The new species is very closely related to Aetomylaeus nichofii and was previously considered to be conspecific with this species. The new species and A. nichofii differ from their congeners in having a dorsal pattern of seven or eight transverse pale blue bands. As with other eagle ray species, morphological characteristics which distinguish the closely related species were largely obscured by intraspecific variation. The clearest morphological differences were apparent when comparing adult males to adult males and adult females to adult females, e.g. disc longer in adult female A. caeruleofasciatus compared to adult female A. nichofii. The two species also differ in the number of pelvic radials in both females and males and show subtle colour differences. A neotype is also allocated for A. nichofii.

The complex multi-gear, multi-species tropical fisheries in developing countries are poorly understood and characterising the landings from these fisheries is often impossible using conventional approaches. A rapid assessment method for characterising landings at fish markets, using an index of abundance and estimated weight within taxonomic groups, is described. This approach was developed for contexts where there are no detailed data collection protocols, and where consistent data collection across a wide range of fisheries types and geographic areas is required, regardless of the size of the site and scale of the landings. This methodology, which was demonstrated at seven fish landing sites/fish markets in southern Indonesia between July 2008 and January 2011, provides a rapid assessment of the abundance and diversity in the wild catch over a wide variety of taxonomic groups. The approach has wider application for species-rich fisheries in developing countries where there is an urgent need for better data collection protocols, monitoring future changes in market demographics, and evaluating health of fisheries.

Aim To develop a comparative phylogeographic framework to understand the origins, evolution, taxonomic richness, and distribution of Australian demersal fish endemics in the context of the Indo‐West Pacific (IWP). Location Southern Australia and the IWP. Taxon Platycephalidae (flathead fishes). Methods Nuclear and mitochondrial phylogenies of flathead fishes were inferred from 46 of 85 nominal species, and 14 additional cryptic species‐level lineages, representing 17 of the 18 genera. Molecular clocks and habitat trait reconstructions were used to infer the palaeoclimatic and geological events responsible for shaping the evolution and diversification of the group. Results The family Platycephalidae comprises two sister subfamilies; Platycephalinae and Onigociinae, which diverged in the Eocene into predominantly temperate and tropical assemblages respectively. The basal platycephalin taxa are confined to southern Australia with the most derived groups in the tropics, following a high‐ to low‐latitudinal evolutionary trajectory. In contrast, the onigociins are predominantly associated with the tropics, and have diversified across the region since the early Miocene with very few introductions into temperate Australia. Main conclusions Platycephalinae and Onigociinae show contrasting evolutionary scenarios. Platycephalins have a temperate to tropical evolutionary trajectory consistent with their arrival into the region via tectonic rafting and subsequent dispersal. This dispersal was likely facilitated by formation of shallow‐water environments along the Sunda Arc margin following collision of the Australian and Eurasian Plates. In contrast, the Onigociinae has likely maintained a tropical presence across the IWP since the Eocene and has experienced higher diversification rates leading to circa three times the species diversity found in the Platycephalinae. Rounds of dispersal and allopatric speciation have subsequently played out across both low and high latitudes with both subfamilies harbouring cryptic species‐level lineages. This work provides an explicit working hypothesis for exploring origins and diversification in other demersal fishes endemic to the Australian continent.

Aim To investigate distributional patterns and derivation of skates in the Australasian realm. Location Australasia. Methods Genus-group skate taxa were defined for this region for the first time and new systematic information, as well as bathymetric and geographical data, used to identify distribution patterns. Results The extant skate fauna of Australasia (Australia, New Zealand, New Caledonia and adjacent subAntarctic dependencies) is highly diverse and endemic with sixty-two species from twelve currently recognized, nominal genus-group taxa. These include the hardnose skate (rajin) groups Anacanthobatis, Amblyraja, Dipturus, Okamejei, Rajella and Leucoraja, and softnose skate (arhynchobatin) genera Arhynchobatis, Bathyraja, Insentiraja, Irolita, Pavoraja and Notoraja. Additional new and currently unrecognized nominal taxa of both specific and supraspecific ranks also occur in the region. The subfamily Arhynchobatinae is particularly speciose in Australasia, and the New Zealand/New Caledonian fauna is dominated by undescribed supraspecific taxa and species. The Australian fauna, although well represented by arhynchobatins, is dominated by Dipturus-like skates and shows little overlap in species composition with the fauna of New Zealand and New Caledonia. Similarly, these faunas exhibit no overlap with the polar faunas of the Australian subAntarctic dependencies (Heard and Macdonald Islands) to the south. Skates appear to be absent from the Macquarie Ridge at the southern margin of the New Zealand Plateau. Their absence off New Guinea probably reflects inadequate sampling and the subsequent poor knowledge of that region's deepwater fish fauna. Main conclusions Skates appear to have existed in the eastern, Australasian sector of Gondwana before fragmentation in the late Cretaceous. The extant fauna appears to be derived from elements of Gondwanan origin, dispersal from the eastern and western Tethys Sea, and intraregional vicariance speciation.

Aim To investigate the biogeographical structure and affinities of the Australian marine demersal ichthyofauna at the scale of provinces and bathomes for the purposes of regional marine planning. Location Australia. Methods Patterns of distribution in the Australian fish fauna, at both intra-regional and global scales, were examined using a science-based, management framework dividing Australia's marine biodiversity into 16 province-level biogeographical units. Occurrences of 3734 species in eight depth-stratified bathomes (from the coast to the mid-continental slope) within each province were analysed to determine the structure and local affinities of their assemblages and their association with faunas of nearby regions and oceans basins. Results Strong geographic and depth-related structure was evident. Fish assemblages in each province, and in each bathome of each province, were distinct, with the shelf-break bathome more similar to the adjacent continental shelf bathome than to the upper slope bathome. Data based only on endemic species performed well as a surrogate of the entire dataset, yielding comparable patterns of similarity between provinces and bathomes. Tropical and temperate elements were better discriminated than elements of the Pacific and Indian oceans, with the central western province more similar to the tropical provinces (including those in the east), and the eastern province closer to southern temperate provinces. The fauna shares the closest regional affinities with those of the adjacent south-west Pacific, western Pacific Rim, and elements of wide-ranging Indo-Pacific components. Elements unique to the Pacific and Indian oceans are poorly represented. Main conclusions The complex nature of Australia's marine ichthyofauna is confirmed. A hierarchy of provinces and bathomes, used to ensure that Australia's developing marine reserve network is both representative and comprehensive, is equally robust when based on all known Australian fish species or on only those species endemic to this continent. Latitude and depth are more important than oceanic influences on the composition of this fauna at these scales.