Biology subjects

Kess, T.

Publications and source records attributed to Kess, T..

9 recordsLinked to original sources

bioRxiv2025

Large haplotypes linked to climate and life history variation in divergent lineages of Atlantic salmon (Salmo salar)

Advances in sequencing are revealing that linked genomic architectures, enabling the evolution of co-adapted alleles at multiple loci, often shape complex phenotypes. Several recent studies have identified such architectures (e.g., chromosomal rearrangements and supergenes) contributing to adaptation or divergence across diverse species, from plants to mammals. Specifically, within Atlantic salmon (Salmo salar), genomic studies are revealing large haplotypes and structural variants that may underpin local adaptation in the species. Using data from >4000 individuals from 134 locations spanning the North Atlantic Ocean, we identify a large ([~]3-Mbp) genomic region on Ssa18 showing patterns of differentiation and linkage disequilibrium indicative of a large haplotype block containing three divergent haplotypes (herein A, B, and C haplotypes). In Europe, haplotypes A and B were common, whereas A and C were more common within North America, suggesting a shared ancestral A haplotype, with different continent-specific alternative haplotypes. Data support independent origins of divergent haplotypes in each continent, as well as signals of trans-oceanic introgression of haplotypes. Haplotype frequency is strongly associated with latitude, climate, and life history (smolt age); however, the strength and direction of these relationships vary across continents. Overall analyses were consistent with other studies that identify chromosomal rearrangements; however, long read sequence data could not confirm evidence of a structural variant, although an ancestral fusion polymorphism may explain the formation and maintenance of the observed haplotypes. Our study contributes to ongoing efforts to understand the evolutionary role of linked genomic architecture in Atlantic salmon and its significance in salmonid diversification.

genomics↗

bioRxiv2025

eDNA metabarcoding and whole genome sequencing detect European-American Eel hybrids in northeastern Canada

American and European Eels (Anguilla rostrata and Anguilla anguilla, respectively) are sister species of conservation concern, as they have declined in abundance in recent decades. Although there is evidence of gene flow between the two species, most previous hybrid detections have been found in Iceland. Here we expand upon existing reports of interspecific hybrids using a combination of an environmental DNA (eDNA) survey and whole genome sequencing of 347 eels from Newfoundland and Labrador. Metabarcoding of eDNA samples at multiple loci detected the presence of European Eel mitochondrial DNA (mtDNA) at eight locations primarily along the south coast of Newfoundland. Genome sequencing of eels collected in the region revealed three hybrid individuals with levels of European admixture consistent with one first generation hybrid and two North American backcrosses, all with European mtDNA. This work supports the presence of a previously unknown, seemingly localized region of hybrid occurrence in southern Newfoundland and expands our understanding of the relationship between these species across the North Atlantic.

genomics↗

bioRxiv2024

Maloja: simple and scalable Snakemake workflow orchestration in the cloud

As sequencing technologies have matured, bioinformatics tasks have become more complex, computationally demanding, and data intensive. Workflow management software has been developed to aid in simplifying the replicable chaining of complex bioinformatics jobs, and cloud computing has emerged as a potential solution to the computational demands of this work. However, the capacity to effectively deploy these resources is limited by the expertise required to implement these solutions. Here, we develop Maloja, an easily deployed cloud workflow orchestrator. This tool interprets existing scientific workflows written in Snakemake and deploys them in appropriately scaled AWS cloud resources. We test the utility of this new toolset using previously published and custom built Snakemake workflows for ecological genomics tasks, revealing how this tool can facilitate the use of cloud resources without prior cloud architecture expertise.

bioinformatics↗

bioRxiv2023

Post-glacial recolonization and multiple scales of secondary contact contribute to contemporary Atlantic salmon (Salmo salar) genomic variation in North America.

AimIn northern environments, periods of isolation during Pleistocene glaciations and subsequent recolonization and secondary contact have had a significant influence on contemporary diversity of many species. The recent advent of high-resolution genomic analyses allows unprecedented power to resolve genomic signatures of such events in northern species. Here, we provide the highest resolution genomic characterization of Atlantic salmon in North America to infer glacial refugia and the geographic scales of postglacial secondary contact. LocationNorth America. TaxonAtlantic salmon, Salmo salar. MethodsSamples were collected for 5455 individuals from 148 populations encompassing the majority of Atlantic salmons native range in North America, from Labrador to Maine. Individuals were genotyped using a 220K SNP array aligned to the Atlantic salmon (Salmo salar) genome. Spatial genetic structure (PCA, k-means clustering, admixture) was evaluated in conjunction with genomic comparisons of identified lineages to infer the refugia during the last glacial maximum and regions of secondary contact following recolonization. ResultsSpatial genomic analyses identified three phylogeographic groups, consistent with the northward recolonization from two southern glacial refugia in North America (a western Maritime lineage and an eastern Newfoundland and Labrador lineage), with subsequent differentiation of the eastern lineage into two separate groups. Secondary contact among these North American groups was present within the northern Gulf of St. Lawrence and evidence of trans-Atlantic secondary contact was detected within the eastern Newfoundland and Labrador lineage. Comparison of groups from insular Newfoundland with those from mainland Labrador suggests genomic regions displaying high differentiation were characterized by elevated European admixture, suggesting a possible role of European secondary contact in population divergence. Main ConclusionsThese findings present the first evidence suggesting that genomic diversity in extant North American Atlantic salmon populations has resulted from allopatric isolation in two glacial refugia followed by both regional and trans-Atlantic recolonization and secondary contact and demonstrate the power of genomic tools to resolve historical drivers of diversity in wild populations.

evolutionary biology↗

bioRxiv2022

Whole genome sequencing reveals fine-scale climate associated adaptive divergence near the range limits of a temperate reef fish.

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. Pairwise FST and 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., FST 0.5-0.75). 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.

genomics↗

bioRxiv2022

Genomic and machine learning-based screening of aquaculture associated introgression into at-risk wild North American Atlantic salmon (Salmo salar) populations.

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 (r2 of 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 make de novo estimates 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.

genomics↗

bioRxiv2022

Parallel genomic basis of age at maturity across spatial scales in Atlantic Salmon

Complex traits often exhibit complex underlying genetic architectures resulting from a combination of evolution from standing variation, hard and soft sweeps, and alleles of varying effect size. Increasingly, studies implicate both large-effect loci and polygenic patterns underpinning adaptation, but the extent that common genetic architectures are utilized during repeated adaptation is not well understood. Sea age or age at maturation represents a significant life history trait in Atlantic Salmon (Salmo salar), the genetic basis of which has been studied extensively in European Atlantic populations, with repeated identification of large-effect loci. However, the genetic basis of sea age within North American Atlantic Salmon populations remains unclear, as does the potential for a parallel trans-Atlantic genomic basis to sea age. Here, we used a large SNP array and low coverage whole genome re-sequencing to explore the genomic basis of sea age variation in North American Atlantic Salmon. We found significant associations at the gene and SNP level with large-effect loci (vgll3, six6) previously identified in European populations, indicating genetic parallelism, but found that this pattern varied based on both sex and geographic region. We also identified largely non-repeated sweep signatures and sets of highly predictive loci associated with sea age among populations and sexes within North America, indicating polygenicity and low rates of repeated genomic parallelism. Despite low genome-wide parallelism, we uncovered a set of conserved molecular pathways associated with sea age that were consistently enriched among comparisons. Together, our results indicate parallelism of the molecular basis of sea age in North American Atlantic Salmon across large-effect genes and molecular pathways despite population-specific patterns of polygenicity. These findings reveal roles for both contingency and repeated adaptation at the molecular level in the evolution of life history variation.

evolutionary biology↗

bioRxiv2018

A migration-associated supergene reveals loss of biocomplexity in Atlantic cod

Intraspecific phenotypic diversity is integral to ecological resilience and the provision of ecosystem services1. Chromosome structural variation may underpin intraspecific diversity and complex phenotypes2 by reducing recombination within supergenes containing linked, co-adapted alleles. Connecting ecologically-relevant phenotypes to genomic variation can enable more precise conservation of exploited marine species by protecting important genetic diversity3,4. Here, using genome-wide association analysis of a 12K single nucleotide polymorphism (SNP) array we confirm that an ancient, derived chromosomal rearrangement consisting of two adjacent inversions is strongly associated with migratory phenotype and individual-level genetic structure in Atlantic cod (Gadus morhua) across the Northwest Atlantic. The presence of all identified migration-associated loci within this rearrangement indicates that pervasive variation in migration phenotype is in part controlled by a recombination-resistant supergene, facilitating fine-scale individual phenotypic variation within Northern cod. Furthermore, we reconstruct trends in effective population size over the last century, and find genomic signatures of population collapse, and different patterns of population expansion and decline among individuals based on supergene alleles. We demonstrate declines in effective population size consistent with the onset of industrialized harvest (post 1950) and substantially reduced effective size of individuals homozygous for the derived chromosomal rearrangement relative to heterozygous individuals or those homozygous for the ancestral version of this chromosomal region. These results illustrate how chromosomal structural diversity can mediate fine-scale genetic and phenotypic variation in a highly connected marine species, and suggest a loss of biocomplexity from a migration-associated supergene within Northern cod by overfishing.

genomics↗

bioRxiv2018

Chromosome polymorphisms track trans-Atlantic divergence, admixture and adaptive evolution in salmon

Pleistocene glaciations drove repeated range contractions and expansions shaping contemporary intraspecific diversity. Atlantic salmon (Salmo salar) from the western and eastern Atlantic range diverged >600K YBP, with each clade isolated in independent southern refugia during glacial maxima, driving trans-Atlantic genomic and karyotypic differences. Here, we investigate genomic consequences of glacial isolation and transAtlantic secondary contact using a 220K single nucleotide polymorphism (SNP) array genotyped in 80 North American and European populations. Throughout North America, we identified large inter-individual variation and discrete linkage blocks within and between chromosomes with known rearrangements: Ssa01/Ssa23 translocation and Ssa08/Ssa29 fusion. Spatial genetic analyses suggest independence of rearrangements, with Ssa01/Ssa23 showing high European introgression (>50%) in northern populations indicative of post-glacial trans-Atlantic secondary contact, contrasting low European ancestry genome-wide (3%). Ssa08/Ssa29 showed greater intra-population diversity suggesting a derived chromosome fusion polymorphism within North America. Evidence of selection on both regions suggests adaptive variation associated with karyotypes. Our study highlights how Pleistocene glaciations can drive large-scale intraspecific variation in genomic architecture of northern species.

genomics↗