A revision of the gudgeon genus Hypseleotris (Gobiiformes: Gobioidei: Eleotridae) of northwest Australia, describing three new species and synonymizing the genus Kimberleyeleotris.

Species within the northwest Australian clade of Hypseleotris (six species) and the genus Kimberleyeleotris (two species) are reviewed following the recording of new populations in the region and a molecular study of the group that identified three undescribed candidate species. Based on the analysis of extensive morphological and nuclear and mitochondrial molecular datasets, Kimberleyeleotris is here formally synonymised with Hypseleotris. Furthermore, three species from the Kimberley region, Western Australia, are described to science: Hypseleotris maranda sp. nov., Hypseleotris wunduwala sp. nov., and Hypseleotris garawudjirri sp. nov. The presence of, or number of scales across the head and body, the pattern of sensory papillae on the head, fin ray counts, dorsal and anal fin colouration (particularly in breeding males), and body depth, can be used to distinguish the members of the northwest Australia lineage. Furthermore, the newly described species were genetically separated from all northwest Australian congeners by K2P distances ranging from 7.8-11.3% based on the CO1 gene, and 7.7-16.3 % based on the entire mitochondrial genome. Two of the new species, H. maranda sp. nov. and H. wunduwala sp. nov., have extremely narrow ranges being found in single sub-catchments of the Roe and King Edward Rivers respectively. On the other hand, H. garawudjirri sp. nov. is moderately widespread, being found across the Charnley, Calder, and Sale rivers. While the conservation risk to H. maranda sp. nov. and H. wunduwala sp. nov. is inherently high due to their small range, there are currently no obvious local threatening processes to either of these species given their remote locations that are little impacted by human activities.

Evaluating the suitability of close-kin mark-recapture as a demographic modelling tool for a critically endangered elasmobranch population.

Estimating the demographic parameters of contemporary populations is essential to the success of elasmobranch conservation programmes, and to understanding their recent evolutionary history. For benthic elasmobranchs such as skates, traditional fisheries-independent approaches are often unsuitable as the data may be subject to various sources of bias, whilst low recapture rates can render mark-recapture programmes ineffectual. Close-kin mark-recapture (CKMR), a novel demographic modelling approach based on the genetic identification of close relatives within a sample, represents a promising alternative approach as it does not require physical recaptures. We evaluated the suitability of CKMR as a demographic modelling tool for the critically endangered blue skate (Dipturus batis) in the Celtic Sea using samples collected during fisheries-dependent trammel-net surveys that ran from 2011 to 2017. We identified three full-sibling and 16 half-sibling pairs among 662 skates, which were genotyped across 6291 genome-wide single nucleotide polymorphisms, 15 of which were cross-cohort half-sibling pairs that were included in a CKMR model. Despite limitations owing to a lack of validated life-history trait parameters for the species, we produced the first estimates of adult breeding abundance, population growth rate, and annual adult survival rate for D. batis in the Celtic Sea. The results were compared to estimates of genetic diversity, effective population size (N e ), and to catch per unit effort estimates from the trammel-net survey. Although each method was characterized by wide uncertainty bounds, together they suggested a stable population size across the time-series. Recommendations for the implementation of CKMR as a conservation tool for data-limited elasmobranchs are discussed. In addition, the spatio-temporal distribution of the 19 sibling pairs revealed a pattern of site fidelity in D. batis, and supported field observations suggesting an area of critical habitat that could qualify for protection might occur near the Isles of Scilly.

The complete mitochondrial genomes of the flapper skate Dipturus intermedius and the longnose skate Dipturus oxyrinchus.

We describe the complete mitochondrial genomes of the flapper skate Dipturus intermedius (Parnell 1837) and the longnose skate Dipturus oxyrinchus (Linnaeus 1758), which have been obtained by Sanger sequencing. We report the length of the sequences to be 16,906 and 16,911 bp, respectively. The length and structure of gene regions, containing 13 protein-coding regions, 22 tRNA genes, two rRNA genes, and two non-coding areas, resemble those of related skate species. Despite D. intermedius being considered a cryptic species with D. batis, the full mitogenomes confirm that D. intermedius and D. oxyrinchus are more genetically similar. In comparison to other Dipturus species, D. intermedius is missing a whole codon in its cytochrome oxidase subunit 2 gene. These mitogenomes will be a useful resource furthering investigation of the population genetic differences and evolutionary history of skate species.

Population and seascape genomics of a critically endangered benthic elasmobranch, the blue skate Dipturus batis.

The blue skate (Dipturus batis) has a patchy distribution across the North-East Atlantic Ocean, largely restricted to occidental seas around the British Isles following fisheries-induced population declines and extirpations. The viability of remnant populations remains uncertain and could be impacted by continued fishing and by-catch pressure, and the projected impacts of climate change. We genotyped 503 samples of D. batis, obtained opportunistically from the widest available geographic range, across 6 350 single nucleotide polymorphisms (SNPs) using a reduced-representation sequencing approach. Genotypes were used to assess the species' contemporary population structure, estimate effective population sizes and identify putative signals of selection in relation to environmental variables using a seascape genomics approach. We identified genetic discontinuities between inshore (British Isles) and offshore (Rockall and Faroe Island) populations, with differentiation most pronounced across the deep waters of the Rockall Trough. Effective population sizes were largest in the Celtic Sea and Rockall, but low enough to be of potential conservation concern among Scottish and Faroese sites. Among the 21 candidate SNPs under positive selection was one significantly correlated with environmental variables predicted to be affected by climate change, including bottom temperature, salinity and pH. The paucity of well-annotated elasmobranch genomes precluded us from identifying a putative function for this SNP. Nevertheless, our findings suggest that climate change could inflict a strong selective force upon remnant populations of D. batis, further constraining its already-restricted habitat. Furthermore, the results provide fundamental insights on the distribution, behaviour and evolutionary biology of D. batis in the North-East Atlantic that will be useful for the establishment of conservation actions for this and other critically endangered elasmobranchs.

Does Vaterite Otolith Deformation Affect Post-Release Survival and Predation Susceptibility of Hatchery-Reared Juvenile Atlantic Salmon?

Sagittal otoliths are calcareous structures in the inner ear of fishes involved in hearing and balance. They are usually composed of aragonite; however, aragonite can be replaced by vaterite, a deformity which is more common in hatchery-reared than in wild fish. Vaterite growth may impair hearing and balance and affect important fitness-related behaviours such as predator avoidance. Captive rearing techniques that prevent hearing loss may have the potential to improve fish welfare and the success of restocking programmes. The aim of this study was to test the effect of structural tank enrichment on vaterite development in the otoliths of hatchery-reared juvenile Atlantic salmon Salmo salar, and to assess the effects of vaterite on immediate predation mortality and long-term survival after release into the wild. Fry were reared in a structurally enriched or in a conventional rearing environment and given otolith marks using alizarin during the egg stage to distinguish between the treatment groups. Otoliths were scrutinised for the presence and coverage of vaterite at 6, 13, and 16 weeks after start feeding, and the growth traits were measured for enriched and control fry when housed in tanks. In a subsequent field experiment, juveniles were released in the Rasdalen river (western Norway), and otoliths of enriched reared and control reared fry were scrutinised from samples collected immediately prior to release, from predator (trout Salmo trutta) stomachs 48 h after release and from recaptures from the river 2-3 months after release. Vaterite otoliths occurred as early as 6 weeks after start feeding in hatchery-reared S. salar. Vaterite occurrence and coverage increased with fish length. Enriched rearing had no direct effect on vaterite formation, but enriched reared fry grew slower than control fry. After release into the wild, fewer salmon fry with vaterite otoliths had been eaten by predators, and a higher proportion of fry with vaterite otoliths than those lacking vaterite were recaptured in the river 2-3 months after release. Contrary to expectations, this suggests that vaterite does not increase predation mortality nor reduce survival rates in the wild during the early life stages.

Long-term monitoring of a brown trout (Salmo trutta) population reveals kin-associated migration patterns and contributions by resident trout to the anadromous run.

BACKGROUND: In species showing partial migration, as is the case for many salmonid fishes, it is important to assess how anthropogenic pressure experienced by migrating individuals affects the total population. We focused on brown trout (Salmo trutta) from the Guddal River in the Norwegian Hardanger Fjord system, which encompasses both resident and anadromous individuals. Aquaculture has led to increased anthropogenic pressure on brown trout during the marine phase in this region. Fish traps in the Guddal River allow for sampling all ascending anadromous spawners and descending smolts. We analyzed microsatellite DNA markers from all individuals ascending in 2006-2016, along with all emigrating smolts in 2017. We investigated (1) if there was evidence for declines in census numbers and effective population size during that period, (2) if there was association between kinship and migration timing in smolts and anadromous adults, and (3) to what extent resident trout were parents of outmigrating smolts. RESULTS: Census counts of anadromous spawners showed no evidence for a decline from 2006 to 2016, but were lower than in 2000-2005. Estimates of effective population size also showed no trends of declines during the study period. Sibship reconstruction of the 2017 smolt run showed significant association between kinship and migration timing, and a similar association was indicated in anadromous spawners. Parentage assignment of 2017 smolts with ascending anadromous trout as candidate parents, and assuming that unknown parents represented resident trout, showed that 70% of smolts had at least one resident parent and 24% had two resident parents. CONCLUSIONS: The results bear evidence of a population that after an initial decline has stabilized at a lower number of anadromous spawners. The significant association between kinship and migration timing in smolts suggests that specific episodes of elevated mortality in the sea could disproportionally affect some families and reduce overall effective population size. Finally, the results based on parentage assignment demonstrate a strong buffering effect of resident trout in case of elevated marine mortality affecting anadromous trout, but also highlight that increased mortality of anadromous trout, most of which are females, may lower overall production in the system.

Revision of the genus Hannia (Teleostei, Terapontidae), with description of a new species, Hannia wintoni, from the Kimberley, Western Australia.

The systematics of the genus Hannia Vari 1978, endemic to freshwater habitats of remote north-western Australia, is revised in light of recent collections in the region and a molecular study of the group that identified an undescribed candidate species. A new freshwater fish species (Hannia wintoni sp. nov) is described based on analysis of multiple nuclear genetic markers (53 allozyme loci), mitochondrial DNA sequence data (601 bp cytochrome b) and morphology (examination of a suite of 66 morphometric and meristic characters). Head profile, postorbital length, maximum length, preopercular spines and pectoral-fin rays are characters that best distinguish H. wintoni sp. nov from its only congener, H. greewayi. While the existing description of H. greenwayi is robust and accurate, we present a number of additional characters that enhance to the original description, based on type and fresh material. Information on the known distribution, habitats and conservation status of the two species is summarised. The new species is a narrow-range endemic.

The complete mitochondrial genome of the blue skate Dipturus batis.

The complete mitochondrial genome of the blue skate Dipturus batis is described from shotgun sequencing on an Illumina next-generation sequencing platform. We report a 16,911 bp long sequence similar in size to other members of the genus, containing 13 protein-coding regions, 22 tRNA genes, 2 rRNA genes, and 2 non-coding areas. Phylogenetic analysis was performed using the complete mitochondrial genomes of 17 related species, placing D. batis within the Rajini tribe of the Rajidae family, consistent with current taxonomy. The new resource adds to a growing database of rajid mitogenomes which will help resolve phylogenetic relationships within the family.

A revision of the grunter genus Syncomistes (Teleostei, Terapontidae, Syncomistes) with descriptions of seven new species from the Kimberley region, northwestern Australia.

The systematics of the genus Syncomistes Vari, 1978 endemic to freshwater habitats of remote northwestern Australia, is reviewed in light of recent collections in the region and a fine scale molecular study of the group that identified new taxa. Based primarily on external morphology, seven taxa are described as new: Syncomistes bonapartensis sp. nov., S. carcharus sp. nov., S. dilliensis sp. nov., S. holsworthi sp. nov., S. moranensis sp. nov., S. wunambal sp. nov. and S. versicolor sp. nov. The species complexes Syncomistes butleri Vari, 1978 and S. trigonicus Vari, 1978 are resolved and redescribed, and S. kimberleyensis Vari, 1978 and S. rastellus Vari Hutchins, 1978 are redescribed based on juvenile and adult specimens. Finally, a neotype is provided for S. trigonicus sensu stricto in place of the destroyed holotype. Meristic and morphometric data are collected and analysed for the entire genus. Syncomistes have a broad range of meristic and morphometric character differences between species, and juveniles and adults, as well as variations in colour. The head, particularly feeding structures such as the jaw and dentition, were found to be the most important morphological features in discriminating between taxa. Some characters undergo distinct ontogenetic shifts in form, which are discussed. Of note, four of the new species, and seven from the entire genus, are narrow-range endemics, each found in single river systems, and are thus of conservation concern.