Biology subjects

Knutsen, H.

Publications and source records attributed to Knutsen, H..

8 recordsLinked to original sources

bioRxiv2026

Female-biased sex ratios despite stable genetic sex determination across a climatic gradient in a marine fish

Adult sex ratio (ASR) is a fundamental parameter shaping population dynamics and evolutionary trajectories. In theory, ASR is governed by the sex determination (SD) system and sex-specific mortality. Yet, ASR is often hard to predict in natural populations because of ecological effects on its determinants. We address this ecological complexity by investigating the drivers of ASR across a steep climatic gradient in Scandinavian populations of the two-spotted goby Pomatoschistus flavescens. Demographic surveys accounting for over 25000 fish in 30 locations, spanning 10{degrees} of latitude, revealed a general female-bias of the ASR, ca. 75%. To assess the contribution of SD, we combined reduced representation sequencing of 180 adults with our novel long-read male genome assembly. We characterised the genetic architecture of an XX/XY SD system, and identified a male-specific duplicate from the TGF-{beta} signaling pathway, amhr2y, as a candidate sex-determining gene. Subsequent genotyping of eggs and juveniles showed consistently unbiased sex ratios across latitudes, implying that the female-biased arises at later life stages. Interpreted in the light of historical data, our findings allow us to reject environmental sex determination and sex-biased mortality as important drivers of ASR bias in this species. We propose instead that the female bias originates from sex-specific patterns of habitat distribution, which could result from ecological conditions interacting with the distinct reproductive strategies of females and males. Our results underscore the need to go beyond primary theoretical expectations to understand fundamental demographic parameters within their relevant ecological context.

evolutionary biology↗

bioRxiv2025

Atlantic cod (Gadus morhua) ecotypes, not inversion frequencies, underlie divergence in egg buoyancy distribution

Life-history divergence between Atlantic cod (Gadus morhua) ecotypes in Skagerrak is maintained despite gene flow. Fjord and North Sea ecotypes differ in growth, body size, and reproductive ecology. One environmental heterogeneity in Skagerrak is salinity, as coastal habitats experience substantially lower and more variable salinities than offshore waters. Egg buoyancy is highly sensitive to salinity and represents a critical life-history trait shaping survival and recruitment. Inversions on chromosomes 2, 7, and 12 in cod are linked to salinity adaptation and might be important for egg buoyancy and survival. Here, we conducted a buoyancy test on Atlantic cod eggs, spawned from North Sea and Fjord ecotypes, using Coombs apparatus. Genotypes for the inversions on chromosomes 2, 7, and 12 and ecotype were determined in all individuals (N=242). We hypothesized that individuals with different inversion genotypes and ecotypes would have divergent buoyancies. We found that buoyancy was variable and followed a bimodal distribution sorted by ecotype, with Fjord and North Sea individuals having mean buoyancies at neutral salinity (at 7{degrees}C) of 27 and 31 ppt, respectively. Therefore, individuals with intermediate buoyancies might be selected against. This finding is consistent with our expectations, as Fjord ecotypes experience lower salinities compared to North Sea ecotypes. Interestingly, there was little evidence that the inversions on chromosomes 2, 7, and 12 impacted buoyancy. Overall, we provide experimental evidence of the relative contributions of ecotypic background and inversions on a key life history trait, which helps to explain the maintained divergence among ecotypes.

evolutionary biology↗

bioRxiv2025

Chromosomal inversions assist acute salinity and temperature adaptation in Atlantic cod (Gadus Morhua) eggs

Chromosomal inversions, on chromosomes 2, 7, and 12 in Atlantic cod (Gadus morhua), have been consistently associated with environmental gradients, particularly salinity and temperature, across the species natural range. While these correlations suggest a role for local adaptation, the underlying selective mechanisms remain unresolved. Critically, few experiments have yet tested the fitness consequences of these inversions under controlled environmental conditions. Such work is essential to establish causality. Here, we conducted an acute stressor experiment with ten treatments of combined temperature and low salinity stress. Cod eggs (N = 1265) were placed into each treatment for 24 hours, and the number of individuals that floated initially and finally was counted. The ability of an egg to float is directly related to its survival, as sunk individuals cannot survive, and individuals lose buoyancy after they die. Inversion genotypes for the inversions on chromosomes 2, 7, and 12 were determined for individuals from the T03-S25, T07-S25, T16-S25, and T16-S35 treatments. We found that sinking increased with temperature and that more individuals sank in 25 ppt than in 35 ppt after 24 hours. Interestingly, some individuals in the 25 ppt treatments recovered (sank initially but floated finally) after 24 hours. We found evidence that the inversions on chromosomes 2 and 12 might assist with temperature and salinity adaptation, respectively, in cod eggs, while the inversion on chromosome 7 did not affect floating. Our results can inform the management and conservation of this endangered species. Summary statementWe show that chromosomal inversions found in Atlantic cod help with adaptation to short-term temperature and salinity stress at the egg stage.

evolutionary biology↗

bioRxiv2024

Connectivity and population structure in a marginal sea - a review

The current biodiversity crisis calls for conservation measures that limit the negative human impact on important habitats and sensitive wild populations. To effectively protect biodiversity at all levels, including intraspecific diversity, conservation measures should be aligned with the connectivity and genetic structure of wild populations. In this review, we synthesise scientific literature on the connectivity and population structure of marine species in the Skagerrak - a marginal sea in the northeast Atlantic Ocean. We discuss the results in relation to the current management practices in the region, as well as the general transferability of our findings. The Skagerrak is one of the most intensively studied regions within this research field, and our findings show that the overall connectivity with adjacent seas is high, but asymmetric, for most species. Simultaneously, most species have populations in the Skagerrak distinct from both each other, and those in adjacent seas. Most of this population structure is associated with the convoluted Skagerrak coastline - population structure is common both among coastal populations and between coastal and offshore populations. In many mobile species, multiple populations are temporally sympatric in certain areas, but retain their genetic divergence through natal homing or other barriers to gene flow. The presence of population structure despite high connectivity is a challenge for area-based protection measures, and calls for temporally flexible management that also monitors intraspecific genetic diversity on multiple timescales.

ecology↗

bioRxiv2022

Comparison of de novo and reference genome-based transcriptome assembly pipelines for differential expression analysis of RNA sequencing data

ObjectiveAs sequencing technologies become more accessible and bioinformatic tools improve, genomic resources are increasingly available for non-model species. Using a draft genome to guide transcriptome assembly from RNA sequencing data, rather than performing assembly de novo, affects downstream analyses. Yet, direct comparisons of these approaches are rare. Here, we compare the results of the standard de novo assembly pipeline ( Trinity) and two reference genome-based pipelines ( Tuxedo and the new Tuxedo) for differential expression and gene ontology enrichment analysis of a companion study on Atlantic cod (Gadus morhua). ResultsThe new Tuxedo pipeline produced a higher quality assembly than the Tuxedo suite. However, greater enrichment of Trinity-identified differentially expressed genes suggests that a higher proportion of them represent biologically meaningful differences in transcription, as opposed to transcriptional noise or false positives. Coupled with the ability to annotate novel loci, the increased sensitivity of the Trinity pipeline might make it preferable over the reference genome-based approaches for studies aimed at broadly characterizing variation in the magnitude of expression differences and biological processes. However, the new Tuxedo pipeline might be appropriate when a more conservative approach is warranted, such as for the identification of candidate genes.

bioinformatics↗

bioRxiv2022

Mixed origin of juvenile Atlantic cod (Gadus morhua) along the Swedish west coast

Cryptic population structure in exploited fish species poses a major challenge for fisheries management. Atlantic cod (Gadus morhua) is a species in which the presence of sympatric ecotypes has been known for a long time, for instance off the coast of Northern Norway. More recently, two sympatric ecotypes of cod have also been documented in the Skagerrak and Kattegat; one ecotype is of an apparent offshore origin and undertakes spawning migrations to the North Sea, and the other is resident at the coast throughout its life. However, their relative contributions of juveniles to the Swedish west coast remain poorly understood. The lack of adult cod along the Skagerrak and Kattegat coasts in recent years has led to the hypothesis that the offshore ecotype is the main source of juveniles to the area, but recent studies have shown large proportions of coastal cod inside Norwegian Skagerrak fjords. In this study, juvenile cod were collected at a high spatial resolution along the Swedish west coast, and genetically assigned to each of the two ecotypes. The results reveal that there is a considerable proportion of juvenile coastal cod in the southern Kattegat, Oresund, and in inshore Swedish Skagerrak, but that the offshore ecotype dominates in offshore areas. Model selection suggests that differences in bottom depth, rather than distance from the open sea, may explain the heterogenous spatial distribution of the two ecotypes. In addition, the two ecotypes displayed differences at loci known to be associated with environmental adaptation, suggesting that their spatial distribution is maintained by natural selection in response to specific environmental conditions.

genomics↗

bioRxiv2022

Finding coarse and fine scale population structure in a coastal species: population demographics meets genomics

Population genetic studies often focus on patterns at a regional scale and use spatially aggregated samples to draw inferences about population structure and drivers, potentially masking ecologically relevant population sub-structure and dynamics. In this study we use a multidisciplinary approach combining genomic, demographic, and habitat data with an oceanographic particle drift model, to unravel the patterns of genetic structure at different scales in the black goby (Gobius niger) along the Norwegian coast. Using a high-density sampling protocol, we observed restricted gene flow both at a surprisingly fine (kms) and large (100s km) scale. Our results showed a pattern of isolation by distance related to the level of exposure along the Skagerrak coast, where sheltered sampling stations had an overall level of genetic divergence about three times higher (FST =0.0046) than levels observed among exposed samples (FST =0.0015). These results were corroborated by demographic analyses which showed that population-fluctuations decrease in synchrony with distance at much smaller scales for sheltered samples (20 km) than for exposed sites (80 km), suggesting higher population connectivity among exposed sites. We also found a pronounced genetic discontinuity between populations along the Norwegian west and east coasts, with a sharp "break" around the southern tip of Norway, likely driven both by lack of habitat and by oceanographic features.

genomics↗

bioRxiv2021

Cryptic microgeographic variation in responses of larval Atlantic cod to warmer temperatures

Although temperature is known to drive species dynamics and distributions, our understanding of the extent to which thermal plasticity varies within species is poor. Differences in plasticity can arise through local adaptation to heterogeneous environments, hybridization, and the release of cryptic genetic variation in novel environments. Here, wild Atlantic cod (Gadus morhua) from contrasting environments inside and outside of a fjord system in southern Norway spawned freely in a semi-natural laboratory environment, generating pure crosses and reciprocal hybrids. A common-garden rearing experiment of the larvae at 6{degrees}C, 9.5{degrees}C, and 13{degrees}C revealed cryptic genetic variation in thermal responses of growth and survival at warmer temperatures. Variation in growth plasticity was greatest from 9.5{degrees}C to 13{degrees}C, the latter of which exceeds temperatures currently typical of larvae in their native environments. In contrast to our prediction of intermediate hybrid responses consistent with additive genetic effects, one reciprocal hybrid cross showed a 4% increase in size at the highest temperature, whereas most crosses exhibited 4-12% reductions in size. All crosses experienced severe (76-93%) reductions in survival from 9.5{degrees}C to 13{degrees}C. Variation in survival plasticity suggests a genetically variable basis for the severity with which survival declines with increasing temperature and the potential for an adaptive response to warming. Notably, we demonstrate the potential for hybridization between coexisting fjord and North Sea ecotypes that naturally inhabit the inner and outer fjord environments at contrasting frequencies. Yet, ecotype explained a minor (3-10%) component of growth reaction norm variation, suggesting it is insufficient for describing important biological variation. Current broad-scale management and lack of coastal monitoring impede the development of strategies to maintain the potential for adaptation to warming temperatures in systems with such phenotypic complexity resulting from cryptic genetic variation, coexisting ecotypes, and gene flow.

evolutionary biology↗