Population genomics of a critically endangered data-deficient elasmobranch, the blue skate Dipturus batis

Doctoral thesis (PhD) - Nord University, 2021publishedVersio

Genetic structure of Sufflogobius bibarbatus in the Benguela upwelling ecosystem using microsatellite markers

The bearded goby Sufflogobius bibarbatus is an abundant endemic small fish species on the continental shelf of the northern Benguela. The goby habitat is characterised by generally low bottom oxygen concentrations that vary spatially and seasonally. In the present study of population structure, 13 samples of S. bibarbatus from inner and outer shelf areas between 19°S and 32°S were screened using ten microsatellite loci. The genetic data were analysed in relation to isolation by distance and depth. Furthermore, for the first time, this study examined genetic data in relation to bottom oxygen concentration at the sampling locations. The data show low but significant genetic heterogeneity (G‐test; FST = 0.007, p < .05). There was weak but significant genetic differentiation along a latitudinal gradient across all sampling sites from 19.50°S to 32.37°S (Mantel test; r = .464, p = .001), but this disappeared when the southernmost sample was removed. On the other hand, a positive correlation of bottom oxygen concentration with pairwise FST (r = .336; p = .017) was observed among the sampling sites from the Northern Benguela shelf area. Overall, the data are complex but suggest that isolation by distance and bottom oxygen concentration may play a role in the genetic structuring of S. bibarbatus. The findings are discussed in relation to the species’ life history features and oceanographic characteristics of the Benguela upwelling ecosystem.publishedVersio

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 (Ne), 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.publishedVersio

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

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.publishedVersio

Population genomics of a critically endangered data-deficient elasmobranch, the blue skate Dipturus batis

Doctoral thesis (PhD) - Nord University, 2021publishedVersio

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

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