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Adaptation to ocean climate is increasingly recognized as an important driver of diversity in marine species despite the lack of physical barriers to dispersal and the presence of pelagic stages in many taxa. A robust understanding of the genomic and ecological processes involved in structuring populations is lacking for most marine species, often hindering management and conservation action. Cunner (Tautogolabrus adspersus), is a temperate reef fish that displays both pelagic early life history stages and strong site-associated homing as adults; the species is also presently of interest for use as a cleaner fish in salmonid aquaculture in Atlantic Canada. Here we produce a chromosome-level genome assembly for cunner and characterize spatial population structure throughout Atlantic Canada using whole genome resequencing. The genome assembly spanned 0.72 Gbp and resolved 24 chromosomes; whole genome resequencing of 803 individuals from 20 locations spanning from Newfoundland to New Jersey identified approximately 11 million genetic variants. Principal component analysis revealed four distinct regional groups in Atlantic Canada, including three near the range edge in Newfoundland. PairwiseFSTand selection scans revealed consistent signals of differentiation and selection at discrete genomic regions including adjacent peaks on chromosome 10 recurring across multiple pairwise comparisons (i.e.,FST0.5-0.75). Redundancy analysis suggested significant association of environmental variables related to benthic temperature and oxygen range with genomic structure, again highlighting the previously identified region on chromosome 10. Our results suggest that climate associated adaptation in this temperate reef fish drives regional diversity despite high early life history dispersal potential.

The negative genetic impacts of gene flow from domestic to wild populations can be dependent on the degree of domestication and exacerbated by the magnitude of pre-existing genetic differences between wild populations and the domestication source. Recent evidence of European ancestry within North American aquaculture Atlantic salmon (Salmo salar) has elevated the potential impact of escaped farmed salmon on often at-risk wild North American salmon populations. Here we compare the ability of single nucleotide polymorphism (SNP) and microsatellite (SSR) marker panels of different sizes (7-SSR, 100-SSR, and 220K-SNP) to detect introgression of European genetic information into North American wild and aquaculture populations. Linear regression comparing admixture predictions for a set of individuals common to the three data sets showed that the 100-SSR panel and 7-SSR panels replicated the full 220K-SNP-based admixture estimates with low accuracy (r2of 0.64 and 0.49 respectively). Additional tests explored the effects of individual sample size and marker number, which revealed that ~300 randomly selected SNPs could replicate the 220K-SNP admixture predictions with greater than 95% fidelity. We designed a custom SNP panel (301-SNP) for European admixture detection in future monitoring work and then developed and tested a Python package, SalmonEuAdmix (https://github.com/CNuge/SalmonEuAdmix), that uses a deep neural network to makede novoestimates of individuals’ European admixture proportion without the need to conduct complete admixture analysis utilizing baseline samples. The results demonstrate the mobilization of targeted SNP panels and machine learning in support of at-risk species conservation and management.

Teleosts exhibit extensive diversity of sex determination (SD) systems and mechanisms, providing the opportunity to study the evolution of SD and sex chromosomes. Here we sequenced the genome of the common lumpfish (Cyclopterus lumpus Linnaeus), a species of increasing importance to aquaculture, and identified the SD region and master SD locus using a 70 K single nucleotide polymorphism array and tissue-specific expression data. The chromosome-level assembly identified 25 diploid chromosomes with a total size of 572.89 Mb, a scaffold N50 of 23.86 Mb and genome annotation-predicted 21,480 protein-coding genes. Genome-wide association analysis located a highly sex-associated region on chromosome 13, suggesting that anti-Müllerian hormone (AMH) is the putative SD factor. Linkage disequilibrium and heterozygosity across chromosome 13 support a proto-XX/XY system, with an absence of widespread chromosome divergence between sexes. We identified three copies of AMH in the lumpfish primary and alternate haplotype assemblies localized in the SD region. Comparison to sequences from other teleosts suggested a monophyletic relationship and conservation within the Cottioidei. One AMH copy showed similarity to AMH/AMHY in a related species and was also the only copy with expression in testis tissue, suggesting this copy may be the functional copy of AMH in lumpfish. The two other copies arranged in tandem inverted duplication were highly similar, suggesting a recent duplication event. This study provides a resource for the study of early sex chromosome evolution and novel genomic resources that benefits lumpfish conservation management and aquaculture.