As a commercially valuable crustacean species in mariculture systems, mud crab (Scylla paramamosain) has a broad geographical distribution across intertidal zones of the Indo-Pacific region, particularly in Southeast Asian. Mud crab reovirus (MCRV) is a double-stranded RNA virus that causes severe disease in cultured mud crabs, leading to serious economic loss for the mud crab aquaculture. In this study, the dynamic distribution and tropism of MCRV in the tissues of S. paramamosain was investigated, also, transcriptome differences of hemocytes between MCRV-infected and control group were compared. Results demonstrated a significant reduction of the cumulative survival rate in the MCRV-infected group compared to the PBS-injected control group at 96 h post-infection (45.83 % vs.100.00 %), with the highest mortality at the initial 24 h post-infection (hpi). A remarkable increase of MCRV could be detected in hepatopancreas, hemocytes, muscles and gills, with hemocytes exhibited the highest viral load from 6 to 96 hpi. Transcriptome analysis of hemocytes identified 196 differentially expressed genes (147 up-regulated and 49 down-regulated genes), including eukaryotic elongation factor 1-alpha (EEF1A), interferon gamma inducible protein 30 (IFI30) and myoferlin (MYOF). GO enriched pathways linked to plasma membrane and neural regulation were identified, KEGG pathway analysis indicated that differentially expressed genes were obviously enriched in the pathways related to vascular smooth muscle contraction, which contribute to the molecular mechanisms underlying the response to MCRV infection. These results will be helpful to future research on the pathogenicity of MCRV and the development of effective control strategies against this pathogen in S. paramamosain.

Thermal condition has profound influence on physiology and behaviour of ballan wrasse (Labrus bergylta), a cleaner fish commonly deployed in salmon cages to control sea lice infection. To address knowledge gaps on the species thermal biology, critical thermal limits were determined by acclimating fish (21.5 ± 3.1 g, 10.5 ± 0.4 cm) at a range of temperatures (6, 10, or 14°C) found in its natural habitat on the west coast of Scotland for one week and subjecting them to ramping temperature (~0.3°C/min) until loss of equilibrium. Critical thermal maxima (CTmax), minima (CTmin), and thermal breadth values increased with acclimation temperature. Thermal tolerance polygon was constructed and showed the intrinsic (7.9 to 16.8°C) and acquired (3.4°C and 22.8°C) thermal tolerance zones, supporting the seasonal differences in behaviour and delousing efficacy of ballan wrasse deployed in salmon farms. Gill transcriptomic profiles of ballan wrasse were performed following thermal acclimation and subsequent exposure to CTmax and CTmin. Initial acclimation resulted in unique differentially expressed genes (DEGs) and enrichment of GO terms that were almost exclusively found in each acclimation group. Transcriptome response to CTmax and CTmin also varied between acclimation groups. CTmax and CTmin shared 0% DEGs at 6°C, 43% at 10°C, and 7% at 14°C, but some overlapping GO terms. This study is the first to investigate the thermal tolerance limits of ballan wrasse and provides new data into the plasticity of thermal tolerance limits and molecular response to thermal stimuli in fish.

Atlantic salmon, Salmo salar, have traditionally been reared in net-pens in freshwater (FW) lochs up to smoltification, with subsequent transfer to saltwater (SW) cages for grow-out. Recently, interest in recirculating aquaculture systems (RAS) has grown due to environmental and husbandry benefits. To investigate the impact of RAS on their production cycle, we conducted an experiment under commercial conditions, raising a group of salmon in either a FW-RAS or -loch system. The study evaluated the effects of FW-rearing on SW performance by investigating phenotypic performance, genetic architecture, and genotype-environment interactions (GxE), which describe how the effects of different genotypes on traits change with environmental variation, potentially impacting performance across systems. We co-reared salmon for approximately nine-months before splitting them: half remained in FW-RAS and half transferred to FW-loch, where they were separated for about eight weeks. Both groups were then transferred to a SW cage-site. We sampled fish at the end of FW-rearing as smolts and three-months post-SW transfer as post-smolts, taking fin clips for genotyping. Results indicate that RAS-reared smolts were smaller in FW but demonstrated enhanced growth and lower trait variance post-transfer. Sexually dimorphic growth was observed in the loch population. Heritability of morphological traits increased post-SW transfer in the loch population but decreased in RAS. GxE for SW morphological traits were minimal, though significant genotype re-ranking was observed for SW growth. Genetic correlations between FW and SW morphological traits were high, except for whole-body weight in the loch population. These findings indicate that RAS-origin post-smolts, despite smaller FW size, showed faster growth and reduced phenotypic variance in SW compared to loch-origin fish. Differences in heritability estimates and genotype re-ranking for SW growth suggest that breeding programs may need to refine selection strategies for varied rearing environments.

The interest in recirculating aquaculture systems (RAS) is growing due to their benefits such as increased productivity, better control over animal care, reduced environmental effects, and less water consumption. However, in some regions of the world, traditional aquaculture methods remain prevalent, and selective breeding has often been designed for performance within these systems. Therefore, it is important to evaluate how current fish populations fare in RAS to guide future breeding choices. In a commercial setting, we explore the genetic structure of growth characteristics, measure genotype-environment interactions (GxE) in salmon smolts, and examine genetic markers related to growth in freshwater lochs and RAS. Young salmon were raised together until they reached the parr stage, after which they were divided equally between freshwater net-pens and RAS. After an 8-week period, we sampled fish from each environment and genotyped them. Our findings revealed that fish reared in RAS were generally smaller in weight and length but exhibited a higher condition factor and uniformity. We found a notably smaller component of unexplained variance in the RAS, leading to higher heritability estimates. We observed a low GxE effect for length and condition factor, but significant re-ranking for whole-body weight, as well as noticeable differences in trait associations across environments. Specifically, a segment of chromosome 22 was found to be linked with the condition factor in the RAS population only. Results suggests that if the use of RAS continues to expand, the efficiency of existing commercial populations may not reach its full potential unless breeding programs specific to RAS are implemented.

Scylla paramamosain is an euryhaline species that is extensively distributed in coastal regions along the Indian and Pacific Oceans. Recently, S. paramamosain are considered as species that can be cultured in low-salinity areas to improve the local economy. However, the long-term effects and mechanisms of low salinity on its physiology remain unclear. In this study, S. paramamosain were reared in low-salinity (5 ppt) and normal sea-water environment (25 ppt) for 30 days. We compared haemolymph osmolality, gill structure, and transcriptome changes between the two groups. Results indicated that S. paramamosain subjected to a low-salinity environment showed gill damage such as broken lamellar and reduced haemocytes, some adaptive responses as increased mitochondria in chloride cells were also observed. Even with decreased water ion concentration in lower salinity, the concentrations of Na+, K+, and Cl- in the haemolymph of crab were remained higher than the surrounding water. Transcriptomic analysis revealed 2086 differentially expressed genes, including significant alterations in genes like hexosaminidase and neprilysin. Enriched pathways linked to ion transport were identified, highlighting the main adaptive mechanisms in long-term hypotonic environments. Our findings elucidated the effects and mechanism of long-term low salinity on gill structure and osmoregulation in S. paramamosain, providing theoretical basis for the development of low salinity aquaculture technology of this species.

Abstract Background The salmon louse (Lepeophtheirus salmonis) is a parasite of wild and farmed salmonid fish, causing huge economic damage to the commercial farming of Atlantic salmon (Salmo salar) in the northern hemisphere. The avermectin emamectin benzoate (EMB) is widely used for salmon delousing. While resistance to EMB is widespread in Atlantic populations of L. salmonis, the molecular mechanisms of resistance remain to be elucidated. The aim of the present work was to obtain insights into potential EMB resistance mechanisms by identifying genetic and transcriptomic markers associated with EMB resistance. Results Crosses were performed between EMB-susceptible and -resistant L. salmonis, sourced from two parental strains isolated in Scotland, producing fully pedigreed families. The EMB susceptibility of individual parasites was characterised using time-to-response bioassays. Parasites of two families were subjected to double digest restriction site-associated DNA sequencing (ddRAD-seq) for simultaneous discovery of single nucleotide polymorphisms (SNPs) and genotyping. Data analysis revealed that EMB resistance is associated with one quantitative trait locus (QTL) region on L. salmonis chromosome 5. Marker-trait association was confirmed by genotyping assays for 7 SNPs in two additional families. Furthermore, the transcriptome of male parasites of the EMB-susceptible and -resistant L. salmonis parental strains was assessed. Among eighteen sequences showing higher transcript expression in EMB-resistant as compared to drug-susceptible lice, the most strongly up-regulated gene is located in the above QTL region and shows high homology to β spectrin, a cytoskeleton protein that has roles in neuron architecture and function. Further genes differentially regulated in EMB-resistant lice include a glutathione S-transferase (GST), and genes coding for proteins with predicted roles in mitochondrial function, intracellular signalling or transcription. Conclusions Major determinants of EMB resistance in L. salmonis are located on Chromosome 5. Resistance can be predicted using a limited number of genetic markers. Genes transcriptionally up-regulated in EMB resistant parasites include a β spectrin, a cytoskeletal protein with still incompletely understood roles in neuron structure and function, as well as glutathione S-transferase, an enzyme with potential roles in the biochemical defence against toxicants.

Anthropogenically driven environmental changes over recent centuries have led to severe declines of wildlife populations. Better tools are needed to assess the magnitude and consequences of these declines. Anecdotal evidence suggests European bat populations have suffered substantial declines in the past centuries. However, there is little empirical evidence of these declines that can be used to put more recent population trends into historic context.This study is a collaboration between academics and conservation practitioners to develop molecular approaches capable of providing evidence of historic population changes that can inform conservation status assessments and management. We generated a genomic dataset of 46,872 SNPs for the Western barbastelle, Barbastella barbastellus, a regionally Vulnerable bat species, including colonies from across the species' British and Iberian ranges. We used a combination of landscape genetics and model-based inference of demographic history to identify both evidence of population size changes and possible drivers of these changes.Levels of genetic diversity increased and inbreeding decreased with increasing broadleaf woodland cover around the colony. Genetic connectivity was impeded by artificial lights and facilitated by rivers and broadleaf woodland cover.The demographic history analysis showed that both the northern and southern British barbastelle populations have declined by 99% over the past 330-548 years. These declines may be linked to the loss of large oak trees and native woodlands due to shipbuilding during the early colonial period.Synthesis and applications. Genomic approaches can provide a better understanding of the conservation status of threatened species, within historic and contemporary contexts, and inform their conservation management. Our findings of will directly influence the definition of the Favourable Conservation Status of the barbastelle, in turn influencing considerations of the conservation of the species in development plans. Knowledge gained will also help set species recovery targets. Policymakers are interested in using our approach for other species. This study shows how we can bridge the implementation gap between genomic research and direct conservation applications. There is an urgent need to carry out such collaborative studies for other priority species to enable informed species recovery interventions via policy mechanisms and project delivery. Los cambios ambientales impulsados por el hombre en los ultimos siglos han provocado una grave perdida de biodiversidad, sobre todo de poblaciones e individuos. Se necesitan mejores herramientas para evaluar la magnitud de este declive de las poblaciones naturales. Evidencias anecdoticas sugieren que las poblaciones de murcielagos europeos han sufrido una disminucion sustancial en los ultimos siglos. Sin embargo, hay poca evidencia empirica de esta disminucion que pueda usarse para poner las tendencias demograficas mas recientes en su contexto historico.Este estudio es una colaboracion entre cientificos y voluntarios conservacionistas para desarrollar enfoques moleculares capaces de proporcionar estimas cuantitativas de cambios historicos de las poblaciones y sus impulsores y que puedan usarse para evaluarla gestionar el estado de conservacion de las especies. Para ello, hemos generado un conjunto de datos genomicos de 46,872 SNPs (usando secuenciacion ddRAD) para el murcielago de bosque occidental, Barbastella barbastellus, una especie de murcielago considerada casi amenazada a nivel global, y a nivel regional como vulnerable. Se han incluido colonias situadas a lo largo de toda el area de distribucion britanica e iberica de la especie. Utilizamos una combinacion de genetica del paisaje y tecnicas de inferencia bayesiana de la historia demografica para identificar evidencia tanto de cambios en el tamano de la poblacion como los posibles impulsores de estos cambios.Encontramos que Los niveles de diversidad genetica aumentan y el nivel de endogamia disminuye a medida que aumento la cobertura de bosques de hoja caduca alrededor de la ubicacion de la colonia. La conectividad genetica se vio afectada negativamente por la luz artificial y es facilitada por la presencia de rios y la cubierta vegetal de bosques de hoja caduca.El analisis de la historia demografica mostro que las poblaciones de B. barbastellus britanicas tanto del norte como del sur han disminuido en un 99% durante los ultimos 330 a 548 anos. Esta disminucion puede estar relacionada con la perdida de arboles viejos de robles y bosques nativos debido a la construccion naval durante el periodo colonial temprano.Sintesis y aplicaciones. Los enfoques genomicos pueden proporcionar una comprension mas completa del estado de conservacion de las especies amenazadas, dentro del contexto historico y contemporaneo, y proporcionar informacion para su gestion de conservacion. Los hallazgos de este articulo influiran directamente en la definicion del estado de conservacion del murcielago de bosque y de hecho, responsables politicos para la conservacion han mostrado interes en el uso del mismo enfoque para otras especies de murcielagos. Esto a su vez influye en las consideraciones para la conservacion de las especies reflejadas en los planes y proyectos de desarrollo correspondientes. El conocimiento adquirido tambien puede ayudar a identificar las especies objetivo para la conservacion. Los elementos paisajisticos identificados asociados a la diversidad genetica pueden contribuir al desarrollo de estrategias de gestion adecuadas. Este estudio muestra como podemos cerrar la brecha de implementacion entre la investigacion genomica y las aplicaciones directas de conservacion. Existe una necesidad urgente de llevar a cabo mas estudios colaborativos de este tipo para otras especies prioritarias que proporcionen la informacion necesaria para intervenciones de recuperacion de especies a traves del establecimiento de politicas adecuadas y la ejecucion de proyectos. Nestes ultimos seculos as mudancas ambientais de origem humana levaram a graves declinios nas populacoes de vida selvagem. Porem, sao necessarias melhores ferramentas de analise para avaliar a magnitude e as consequencias desses declinios. Ha evidencias anedoticas indicando que as populacoes de morcegos europeus sofreram declinios substanciais nos ultimos seculos. Contudo, ha pouca evidencia empirica desses declinios que possa ser utilizada para interpretar as tendencias populacionais mais recentes num contexto historico.Este estudo e o resultado duma colaboracao entre academicos e profissionais da conservacao com o objetivo de desenvolver abordagens com analises moleculares capazes de fornecer evidencias acerca das mudancas historicas numa populacao natural e que essa informacao possa ser utilizada na gestao e avaliacao do estado de conservacao duma especie. Para o morcego-negro, Barbastella barbastellus, uma especie regionalmente Vulneravel, foram analisados um conjunto de dados genomicos de 46.872 SNPs obtidos de colonias englobando toda a distribuicao britanica e iberica da especie. Foram ainda integradas as metodologias de analise de genetica da paisagem e inferencia baseada em modelos de historia demografica para identificar evidencias de mudancas no tamanho da populacao e possiveis impulsionadores dessas mudancas.Foi verificado que os niveis de diversidade genetica aumentaram e a endogamia diminuiu com o aumento da cobertura de floresta de folhosas em torno duma colonia. Verificou-se ainda que a conectividade genetica foi limitada pela presenca de luzes artificiais e promovida pelos rios e pela cobertura da floresta de folhosas.A analise da historia demografica mostrou que as populacoes do morcego-negro existentes no norte e no sul da Gra-Bretanha diminuiram 99% nos ultimos 330-548 anos. Estes declinios podem estar ligados a perda de grandes carvalhos e area de florestas nativas devido a construcao naval durante o inicio do periodo colonial.Sintese e aplicacoes. As abordagens genomicas podem proporcionar uma melhor compreensao do estado de conservacao das especies ameacadas, no contexto historico e contemporaneo, e deste modo melhor gerir a sua conservacao. As nossas descobertas podem influenciar diretamente a definicao do Estatuto de Conservacao Favoravel do morcego-negro, podendo tambem contribuir para o delineamento de planos de conservacao para a especie. Consequentemente, este conhecimento adquirido tambem podera apoiar na definicao de metas de recuperacao para esta especie. Alem disso, os decisores politicos poderao tambem utilizar a nossa abordagem em outras especies. Este estudo mostra como poderemos colmatar as falhas na implementacao da investigacao genomica nas acoes diretas de conservacao. Ainda assim, ha uma necessidade urgente de realizar este tipo de estudos colaborativos em outras especies prioritarias, atraves de mecanismos politicos e entrega de projetos, com o intuito de se fazer uma gestao informada na recuperacao de especies. Genomic approaches can provide a better understanding of the conservation status of threatened species, within historic and contemporary contexts, and inform their conservation management. Our findings of will directly influence the definition of the Favourable Conservation Status of the barbastelle, in turn influencing considerations of the conservation of the species in development plans. Knowledge gained will also help set species recovery targets. Policymakers are interested in using our approach for other species. This study shows how we can bridge the implementation gap between genomic research and direct conservation applications. There is an urgent need to carry out such collaborative studies for other priority species to enable informed species recovery interventions via policy mechanisms and project delivery.image

The mussel industry faces challenges such as low and inconsistent levels of larvae settlement and poor-quality spat, leading to variable production. However, mussel farming remains a vital sustainable and environmentally responsible method for producing protein, fostering ecological responsibility in the aquaculture sector. We investigate the population connectivity and larval dispersion of blue mussels ( Mytilus edulis ) in Scottish waters, as a case study, using a multidisciplinary approach that combined genetic data and particle modelling. This research allows us to develop a thorough understanding of blue mussel population dynamics in mid-latitude fjord regions, to infer gene-flow patterns, and to estimate population divergence. Our findings reveal a primary south-to-north particle transport direction and the presence of five genetic clusters. We discover a significant and continuous genetic material exchange among populations within the study area, with our biophysical model’s outcomes aligning with our genetic observations. Additionally, our model reveals a robust connection between the southwest coast and the rest of the west coast. This study will guide the preservation of mussel farming regions, ensuring sustainable populations that contribute to marine ecosystem health and resilience.

Diploid and triploid Atlantic salmon show distinct physiological differences including heart, brain, and digestive system morphology, propensity for certain deformities, temperature tolerance as eggs and once hatched, and different nutritional requirements. Whilst several studies have looked in detail at the rate of embryogenesis in diploid salmon, no study has compared the rate of embryogenesis between ploidies from fertilisation to hatch. This study based its assessment on a seminal paper by Gorodilov (1996) and used the same techniques to compare the rate at which triploid and diploid embryos developed morphological characteristics. Whilst no significant difference was found, this study provides well-needed justification for the assumption that both ploidies develop at the same rate and gives scientific weight to studies which involve manipulation at these stages of development. Two factors that did differ, however, were the timing of hatch, and mortality. Triploids hatched more quickly than diploids and reached 50% hatch at a significantly earlier point. Triploids also suffered from a significantly higher rate of mortality.

IntroductionAeromonads are ubiquitous in aquatic environments and several species are opportunistic pathogens of fish. Disease losses caused by motile Aeromonas species, particularly Aeromonas hydrophila, can be challenging in intensive aquaculture, such as at striped catfish (Pangasianodon hypophthalmus) farms in Vietnam. Outbreaks require antibiotic treatments, but their application is undesirable due to risks posed by resistance. Vaccines are an attractive prophylactic and they must protect against the prevalent strains responsible for ongoing outbreaks.MethodsThis present study aimed to characterize A. hydrophila strains associated with mortalities in striped catfish culture in the Mekong Delta by a polyphasic genotyping approach, with a view to developing more effective vaccines.ResultsDuring 2013–2019, 345 presumptive Aeromonas spp. isolates were collected at farms in eight provinces. Repetitive element sequence-based PCR, multi-locus sequence typing and whole-genome sequencing revealed most of the suspected 202 A. hydrophila isolates to belong to ST656 (n = 151), which corresponds to the closely-related species Aeromonas dhakensis, with a lesser proportion belonging to ST251 (n = 51), a hypervirulent lineage (vAh) of A. hydrophila already causing concern in global aquaculture. The A. dhakensis ST656 and vAh ST251 isolates from outbreaks possessed unique gene sets compared to published A. dhakensis and vAh ST251 genomes, including antibiotic-resistance genes. The sharing of resistance determinants to sulphonamides (sul1) and trimethoprim (dfrA1) suggests similar selection pressures acting on A. dhakensis ST656 and vAh ST251 lineages. The earliest isolate (a vAh ST251 from 2013) lacked most resistance genes, suggesting relatively recent acquisition and selection, and this underscores the need to reduce antibiotics use where possible to prolong their effectiveness. A novel PCR assay was designed and validated to distinguish A. dhakensis and vAh ST251 strains.DiscussionThis present study highlights for the first time A. dhakensis, a zoonotic species that can cause fatal human infection, to be an emerging pathogen in aquaculture in Vietnam, with widespread distribution in recent outbreaks of motile Aeromonas septicaemia in striped catfish. It also confirms vAh ST251 to have been present in the Mekong Delta since at least 2013. Appropriate isolates of A. dhakensis and vAh should be included in vaccines to prevent outbreaks and reduce the threat posed by antibiotic resistance.

We report the first genetic linkage map of the catfish Lophiosilurus alexandri, a South American threatened and promising aquaculture catfish species. Using the progeny of three full-sib families, with 141, 74, and 49 offspring, respectively, we could genotype 2351 SNP markers using the ddRAD technology, shared by the male and the female maps constructed. The averaged, female and male maps spanned a total length of 2201.3 cM, 2481.9 cM, and 1872.8 cM, respectively, and comprehended the expected 27 linkage groups according to the karyotype information of the species (2n = 54). The recombination rate was nearly twice higher in the female than in the male map. The average map was used to estimate the historical effective population size (Ne) of the species from linkage disequilibrium between pairs of SNPs using parental individuals and revealed a remarkable drop in Ne about 20–25 generations in the past. The construction of the biggest artificial reservoir in Latin America and associated nutrient retention is pointed as a possible reason for such a reduction and suggests a reevaluation of the conservation status of the species. The current map lays the groundwork for understanding the genetic basis of economically important traits in breeding programs and will be useful for the genome assembly of this important commercial species.

The current methods used for producing triploid Atlantic salmon are generally reliable but not infallible, and each batch of triploids must be validated to ensure consumer trust and licensing compliance. Microsatellites have recently been shown to offer a cheaper and more convenient alternative to traditional flow cytometry for triploidy validation in a commercial setting. However, incubating eggs to at least the eyed stage for microsatellite validation poses challenges, such as reduced quality and performance of triploids produced from later eggs in the stripping season. To address these issues, we propose another option: extracting DNA from recently fertilised eggs for use in conjunction with microsatellite validation. To achieve this, we have developed an optimized protocol for HotSHOT extraction that can rapidly and cheaply extract DNA from Atlantic salmon eggs, which can then be used for triploidy validation through microsatellites. Our approach offers a simpler and more cost-effective way to validate triploidy, without the need for skilled dissection or expensive kits.

Cleaner fish species have gained great importance in the control of sea lice, among them, lumpfish (Cyclopterus lumpus) has become one of the most popular. Lumpfish life cycle has been closed, and hatchery reproduction is now possible, however, current production is reliant on wild caught broodstock to meet the increasing demand. Selective breeding practices are called to play an important role in the successful breeding of most aquaculture species, including lumpfish. In this study we analysed a lumpfish population for the identification of genomic markers linked to production traits. Sequencing of RAD libraries allowed us to identify, 7193 informative markers within the sampled individuals. Genome wide association analysis for sex, weight, condition factor and standard length was performed. One single major QTL region was identified for sex, while nine QTL regions were detected for weight, and three QTL regions for standard length. A total of 177 SNP markers of interest (from QTL regions) and 399 high Fst SNP markers were combined in a low-density panel, useful to obtain relevant genetic information from lumpfish populations. Moreover, a robust combined subset of 29 SNP markers (10 associated to sex, 14 to weight and 18 to standard length) provided over 90% accuracy in predicting the animal's phenotype by machine learning. Overall, our findings provide significant insights into the genetic control of important traits in lumpfish and deliver important genomic resources that will facilitate the establishment of selective breeding programmes in lumpfish.

ABSTRACT Cleaner fish species have gained great importance in the control of sea lice, among them, lumpfish ( Cyclopterus lumpus ) has become one of the most popular. Lumpfish life cycle has been closed, and hatchery reproduction is now possible, however, current production is reliant on wild caught broodstock to meet the increasing demand. Selective breeding practices are called to play an important role in the successful breeding of most aquaculture species, including lumpfish. In this study we analysed a lumpfish population for the identification of genomic markers linked to production traits. Sequencing of RAD libraries allowed us to identify, 7,193 informative markers within the sampled individuals. Genome wide association analysis for sex, weight, condition factor and standard length was performed. One single major QTL region was identified for sex determination, while nine QTL regions were detected for weight, and three QTL regions for standard length. A total of 177 SNP markers of interest (from QTL regions) and 399 top F st SNP markers were combined in a low-density panel, useful to obtain relevant genetic information from lumpfish populations. Moreover, a robust combined subset of 29 SNP markers (10 associated to sex, 14 to weight and 18 to standard length) provided over 90% accuracy in predicting the animal’s phenotype. Overall, our findings provide significant insights into the genetic control of important traits in lumpfish and deliver important genomic resources that will facilitate the establishment of selective breeding programs in lumpfish.

Anthropogenically-driven environmental changes over the past two centuries have led to severe biodiversity loss, most prominently in the form of loss of populations and individuals. Better tools are needed to assess the magnitude of these wildlife population declines. Anecdotal evidence suggests European bat populations have suffered substantial declines in the past few centuries. However, there is little empirical evidence of these declines that can be used to put more recent population changes into historic context and set appropriate targets for species recovery. This study is a collaboration between academics and conservation practitioners to develop molecular approaches capable of providing quantitative evidence of historic population changes and their drivers that can inform the assessment of conservation status and conservation management. We generated a genomic dataset for the Western barbastelle, Barbastella barbastellus, a globally Near Threatened and regionally Vulnerable bat species, including colonies from across the species’ British and Iberian ranges. We used a combination of landscape genetics and approximate Bayesian computation model-based inference of demographic history to identify both evidence of population size changes and possible drivers of these changes. We found that levels of genetic diversity increased and inbreeding decreased with increasing broadleaf woodland cover around the colony location. Genetic connectivity was impeded by artificial lights and facilitated by the combination of rivers and broadleaf woodland cover. The demographic history analysis showed that both the northern and southern British barbastelle populations have declined by 99% over the past 330-548 years. These declines may have been triggered by loss of large oak trees and native woodlands due to shipbuilding during the early colonial period. Synthesis and applications. Genomic approaches can be applied to provide a better understanding of the conservation status of threatened species, within historic and contemporary context, and inform their conservation management. This study shows how we can bridge the implementation gap and promote the application of genomics in conservation management through co-designing studies with conservation practitioners and co-developing applied management targets and recommendations.

Mycobacterium avium subsp. paratuberculosis (MAP) causes Johne's disease in animals with zoonotic potential; it has been linked to many chronic diseases in humans, especially gastrointestinal diseases (GID). MAP has been extensively studied in Europe and America, but little reports were published from Africa. Sudan is a unique country with close contact between humans and livestock. Despite such interaction, the one health concept is neglected in dealing with cases of humans with GID. In this study, patients admitted to the reference GID hospital in the Sudan over a period of 8 months were screened for presence of MAP in their faeces or colonic biopsies. A total of 86 patients were recruited for this study, but only 67 were screened for MAP, as 19 did not provide the necessary samples for analysis. Both real-time PCR and culture were used to detect MAP in the collected samples and the microbial diversity in patients´ faecal samples was investigated using 16S rDNA nanopore sequencing. In total, 27 (40.3%) patients were MAP positive: they were 15 males and 12 females, of ages between 21 and 80 years. Logistic regression analysis revealed no statistical significance for all tested variables in MAP positive patients (occupation, gender, contact with animal, milk consumption, chronic disease, etc.). A unique microbiome profile of MAP-positive patients in comparison to MAP-negative was found. These findings suggest that a considerable proportion of the population could be MAP infected or carriers. Therefore, increase awareness at community level is urgently needed to decrease the risk of MAP at human/animal interface. This study represents the first report of MAP in humans in the Sudan; nevertheless, a better view of the situation of MAP in humans in the country requires a larger study including patients with other conditions.

The pyrethroid deltamethrin (DTM) is used to treat Atlantic salmon ( Salmo salar ) against salmon louse ( Lepeophtheirus salmonis ) infestations. However, DTM resistance has evolved in L. salmonis and is currently common in the North Atlantic. This study aimed to re-assess the association between DTM resistance and mitochondrial (mtDNA) mutations demonstrated in previous reports. Among 218 L. salmonis collected in Scotland in 2018–2019, 89.4% showed DTM resistance in bioassays, while 93.6% expressed at least one of four mtDNA single nucleotide polymorphisms (SNPs) previously shown to be resistance associated. Genotyping at further 14 SNP loci allowed to define three resistance-associated mtDNA haplotypes, named 2, 3 and 4, occurring in 72.0%, 14.2% and 7.3% of samples, respectively. L. salmonis strains IoA-02 (haplotype 2) and IoA-10 (haplotype 3) both showed high levels (~ 100-fold) of DTM resistance, which was inherited maternally in crossing experiments. MtDNA haplotypes 2 and 3 differed in genotype for 17 of 18 studied SNPs, but shared one mutation that causes an amino acid change (Leu107Ser) in the cytochrome c oxidase subunit 1 (COX1) and was present in all DTM resistant while lacking in all susceptible parasites. We conclude that Leu107Ser (COX1) is a main genetic determinant of DTM resistance in L. salmonis.

In Scotland, bivalves are widely distributed. However, their larvae dispersion is still largely unknown and difficult to assess in situ . And, while Mytilus spp. dominate shellfish production, it is mostly dependent on natural spat recruitment from wild populations. Understanding the larval distribution pattern would safeguard natural resources while also ensuring sustainable farming practises. The feasibility of a model that simulates biophysical interactions between larval behaviour and ocean motions was investigated. We employed an unstructured tri-dimensional hydrodynamic model (finite volume coastal ocean model) to drive a particle tracking model, where prediction of larval movement and dispersal at defined locations might aid in population monitoring and spat recruitment. Our findings reveal a strong link between larval distribution and meteorological factors such as wind forces and currents velocity. The model, also, depicts a fast and considerable larval movement, resulting in a substantial mix of plankton and bivalve larvae, forming a large connection between the southern and northern regions of Scotland’s West coast. This enables us to forecast the breeding grounds of any area of interest, potentially charting connectivity between cultivated and wild populations. These results have significant implications for the dynamics of ecologically and economically important species, such as population growth and loss, harvesting and agricultural management in the context of climate change, and sustainable shellfish fisheries management. Furthermore, the observations on Scottish water flow suggest that tracking particles with similar behaviour to bivalve larvae, such as other pelagic larval stages of keystone species and potential pathogens such as sea lice, may have policy and farming implications, as well as disease control amid global warming issues.

A non-synonymous single nucleotide polymorphism (SNP) underlies a diallelic allozyme polymorphism at the mitochondrial NADP-dependent mMEP-2* locus in Atlantic salmon (Salmo salar L.). The resultant amino acid substitution, which alters the charge of the allelic products, matches the differential mobility of the two allozyme alleles, whereas allozyme and SNP assays revealed genotyping concordance in 257 of 258 individuals. A single mismatch, homozygous allozyme vs. heterozygote SNP, suggests the presence of a second, less common null allele.

Background Molluscs remain one significantly under-represented taxa amongst available genomic resources, despite being the second-largest animal phylum and the recent advances in genomes sequencing technologies and genome assembly techniques. With the present work, we want to contribute to the growing efforts by filling this gap, presenting a new high-quality reference genome for Mytilus edulis and investigating the evolutionary history within the Mytilidae family, in relation to other species in the class Bivalvia. Results Here we present, for the first time, the discovery of multiple whole genome duplication events in the Mytilidae family and, more generally, in the class Bivalvia. In addition, the calculation of evolution rates for three species of the Mytilinae subfamily sheds new light onto the taxa evolution and highlights key orthologs of interest for the study of Mytilus species divergences. Conclusions The reference genome presented here will enable the correct identification of molecular markers for evolutionary, population genetics, and conservation studies. Mytilidae have the capability to become a model shellfish for climate change adaptation using genome-enabled systems biology and multi-disciplinary studies of interactions between abiotic stressors, pathogen attacks, and aquaculture practises.