Reference genome of Lumpfish Cyclopterus lumpus Linnaeus provides evidence of male heterogametic sex determination through the AMH pathway

acceptedVersio

Genome-wide association identifies genomic regions influencing fillet color in Northwest Atlantic salmon (Salmo salar Linnaeus 1758)

Atlantic salmon (Salmo salar) is an important source of food globally; however, fillet color can significantly affect consumer purchasing, leading to potential food waste. Fish diets can be supplemented with astaxanthin to increase the organic pigment, carotenoid, responsible for flesh coloration; however, there is variation in the amount of overall fillet coloration in response to feeding astaxanthin. The uptake of this pigment is influenced by the environment and genetics and has been shown to be heritable. Therefore, we set out to determine the genomic associations of two separate year classes of farmed North American Atlantic salmon with measured Minolta Chroma Meter (lightness, redness, and yellowness) and SalmoFan phenotypic traits. Using ASReml-R genome-wide association, two genetic markers on chromosome 26 were significantly associated with almost all color traits, and these two markers explained between 6.0% and 12.5% of the variances. The genomic region on chromosome 26 was importantly found to be associated with the beta-carotene oxygenase 1 (bco1) gene, which is essential in the conversion of beta-carotenoids to vitamin A, implying that this gene may also play an important role in flesh coloration in North American Atlantic salmon. Additionally, there were several genomic regions significantly associated with color traits, in which the accompanying genes had functions in line with thermogenesis, immune function, and pathogenic responses. Understanding how environmental and genetic factors work together to affect fillet quality traits will help inform genetic improvement

How blind are they? : phototactic responses in stygobiont diving beetles (Coleoptera: Dytiscidae) from calcrete aquifers of Western Australia

Subterranean water beetles endemic to groundwater calcretes of Western Australia exhibit convergent traits typical of troglomorphic arthropods, including loss of eyes, pigmentation and wings. As these dytiscid species are estimated to have been isolated underground in permanent darkness for over three million years, it is predicted that they will completely lack phototactic responses. We tested this hypothesis by analysing the behaviour of six subterranean beetle species within an observational arena with dark and light hemispheres. Scan samples at 1 min intervals and total time spent on each hemisphere were recorded over a 20 min period, testing at least 15 individuals per species. We quantified behaviour as an index (dark ratio) so that individual species in this, and future, studies can be consistently compared. Results analysed as both categorical and absolute proportion of time spent in each hemisphere suggest negative phototaxis in Paroster macrosturtensis. The remaining five species did not display any preference for either light or dark hemispheres. These results raise the possibility that some ancestral Paroster species may have exhibited negative phototactic behaviour prior to subterranean colonization. The retention of such a behavioural trait in lightless environments could represent the maintenance for some unknown pleiotropic function. Alternatively, it is possible that insufficient time has passed for neutral processes to render photoreception genes and phototactic behaviours non-functional. Our study adds to a growing body of evidence that implies highly troglomorphic animals may have evolved from ancestral species that exhibited negative phototaxis as a preadaptation to living in permanent darkness

Massive parallel regression : a précis of genetic mechanisms for vision loss in diving beetles

Two tribes of subterranean dytiscid diving beetles independently colonized groundwater systems of the Western Australian arid zone, a habitat transition that was most likely driven by the contraction of surface water bodies following late Neogene aridification of the Australian continent. These “stygofauna” are now trapped within discrete calcrete aquifers that have formed in paleodrainage valleys, resulting in the world’s most diverse radiations of subterranean dytiscid beetles. Approximately 100 species from three genera exhibit partial or fully regressed visual systems and are essentially blind. This unique study system, with multiple independent transitions to subterranean life enables regressive and adaptive evolutionary processes to be studied in parallel at an unheralded comparative scale. Here we provide an overview of the progression of dytiscid beetle research and undertake a literature survey of published research within the field of regressive evolution as it applies to eye loss. We detail our exploration of insect vision genes for signatures of adaptive and neutral evolutionary mechanisms related to eye regression, largely within photoreceptor and eye pigment genes. Our project makes use of transcriptome data from five representative dytiscid beetle species (two surface and three subterranean) in order to design a customized set of RNA baits for use in a hybrid-capture method to target a pool of vision genes sequenced using high-throughput Illumina platforms. This methodological design permits the assessment of modifications in the genomic sequence of beetle vision genes at a much broader scale than Sanger sequencing, enabling a higher number of both target species and genes to be simultaneously assessed relative to research time-investments. Based on our literature search criteria of the research field (“regressive evolution”þ“eyes”), 81 papers have been published since the late 1980s accruing an h-index of 27 and a mean citation rate of 24.57. Collective annual citations for this field of research have surged over the past 5 years, an indication that broader scientific community interest is gaining momentum. The majority of publications (75%) have focused on the chordate clade Actinopterygii. Historically, research on variant subterranean taxa has faced difficulties inferring the evolutionary mechanisms of eye regression (and vision loss) using molecular approaches because only a handful of target genes could be feasibly addressed within grant funding cycles. From a comparative phylogenetic perspective, next-generation sequencing approaches applied to stygobiontic dytiscid beetles hold the potential to greatly improve our understanding of the genetic mechanisms underlying regressive evolution generally

Evidence for speciation underground in diving beetles (Dytiscidae) from a subterranean archipelago

Most subterranean animals are assumed to have evolved from surface ancestors following colonisation of a cave system, however very few studies have raised the possibility of „subterranean speciation‟ in underground habitats (i.e. obligate cave-dwelling organisms (troglobionts) descended from troglobiotic ancestors). Numerous endemic subterranean diving beetle species from spatially-discrete calcrete aquifers in Western Australia (stygobionts) have evolved independently from surface ancestors; however, several cases of sympatric sister species raises the possibility of subterranean speciation. We tested this hypothesis using vision (phototransduction) genes that are evolving under neutral processes in subterranean species and purifying selection in surface species. Using sequence data from 32 subterranean and five surface species in the genus Paroster (Dytiscidae), we identified deleterious mutations in: long wavelength opsin (lwop), arrestin 1 (arr1), and arrestin 2 (arr2) shared by a sympatric sister-species triplet, arr1 shared by a sympatric sister-species pair, and lwop and arr2 shared among closely related species in adjacent calcrete aquifers. In all cases, a common ancestor possessed the function-altering mutations, implying they were already adapted to aphotic environments. Our study represents one of the first confirmed cases of subterranean speciation in cave insects. The assessment of genes undergoing pseudogenisation provides a novel way of testing modes of speciation and the history of diversification in blind cave animals

Fine‐scale environmentally associated spatial structure of lumpfish (Cyclopterus lumpus) across the Northwest Atlantic

Abstract Lumpfish, Cyclopterus lumpus, have historically been harvested throughout Atlantic Canada and are increasingly in demand as a solution to controlling sea lice in Atlantic salmon farms—a process which involves both the domestication and the transfer of lumpfish between geographic regions. At present, little is known regarding population structure and diversity of wild lumpfish in Atlantic Canada, limiting attempts to assess the potential impacts of escaped lumpfish individuals from salmon pens on currently at‐risk wild populations. Here, we characterize the spatial population structure and genomic‐environmental associations of wild populations of lumpfish throughout the Northwest Atlantic using both 70K SNP array data and whole‐genome re‐sequencing data (WGS). At broad spatial scales, our results reveal a large environmentally associated genetic break between the southern populations (Gulf of Maine and Bay of Fundy) and northern populations (Newfoundland and the Gulf of St. Lawrence), linked to variation in ocean temperature and ice cover. At finer spatial scales, evidence of population structure was also evident in a distinct coastal group in Newfoundland and significant isolation by distance across the northern region. Both evidence of consistent environmental associations and elevated genome‐wide variation in FST values among these three regional groups supports their biological relevance. This study represents the first extensive description of population structure of lumpfish in Atlantic Canada, revealing evidence of broad and fine geographic scale environmentally associated genomic diversity. Our results will facilitate the commercial use of lumpfish as a cleaner fish in Atlantic salmon aquaculture, the identification of lumpfish escapees, and the delineation of conservation units of this at‐risk species throughout Atlantic Canada