Biology subjects

Johannesson, K.

Publications and source records attributed to Johannesson, K..

18 recordsLinked to original sources

bioRxiv2026

The role of chromosomal inversions in local adaptation and ecotype formation across a variable landscape in an intertidal snail

Adaption to environmental variation can be discrete or continuous, responding to sharp or gradual habitat transitions. Chromosomal inversions accentuate these adaptive responses as multiple loci respond in tandem across a habitat transition. Earlier studies of Littorina saxatilis (Olivi, 1792) have shown that three ecotypes segregate in different habitats supported by polymorphisms in a few inversions. However, many more large inversions are polymorphic in this species and potentially have adaptive effects in response to uncharacterised environmental gradients. We sampled 200 random shores representing all kinds of shore habitats present in a 12x12 km area of a Swedish archipelago, with L. saxatilis found at 196 sites. Environment and shell morphology were summarised using dimension reduction analyses, and Bayesian regression models were used to analyse the relationships between phenotype, environment and inversions. Phenotypic variation was a continuum with previously described ecotypes positioned in different parts. 18 inversions responded to at least one dimension of environmental variation, and over (12) half influenced the measured phenotypes. Overall, inversion arrangements explained 15% of phenotypic variation, with limited direct contributions from the environment (<1%). Chromosomal inversions thus are a major factor for local adaptation in L. saxatilis, supporting adaptation across a landscape more complex than the previously described ecotypes.

evolutionary biology↗

bioRxiv2026

Establishing a baseline for standardised genetic monitoring of Atlantic cod (Gadus morhua) in Sweden

Protecting populations and genetic diversity within them is critical to conserving the resilience and adaptive potential of species. Fisheries management has long had the ambition of managing species at the population level, but mainly define "fish stocks" based on geographical limits, which can lead to overfishing of sensitive populations in areas where many different populations coexist. Modern genetic methods are now sufficiently cost-effective, fast, and accurate to be integrated into fisheries management, enabling genetic identification and monitoring of fish populations. Here, we establish a genetic baseline for the commercially important fish Atlantic cod (Gadus morhua) in the waters surrounding Sweden, by using standardised sampling procedures and developing a genetic panel of 4000 single nucleotide polymorphisms (SNPs) for cost-effective assignment of population-of-origin and inversion genotypes. Using the SNP panel, we resolve the geographical distribution of three genetically distinct cod populations in the region: offshore, coastal/Western Baltic, and Eastern Baltic cod. While there is considerable spatial overlap between the three populations, they are genetically differentiated across the entire genome, as well as in genomic regions associated with chromosomal inversions. In addition, heterozygosity and effective population size estimates suggest differences in genetic diversity and rates of genetic erosion, underscoring the need to monitor the genetic diversity within each population separately. Repeating this methodology across years provides a first suggestion for establishing spatiotemporally resolved genetic monitoring of Atlantic cod in Sweden - simultaneously accounting for both population structure within the species and the genetic diversity within populations.

genomics↗

bioRxiv2026

Inversions support both parallel and location-specific adaptations in snail ecotypes

Replicated hybrid zones between ecotypes established over within shore environmental gradients provide an opportunity to study the genomic architecture of barriers to gene flow. The marine snail Littorina fabalis segregates locally into dwarf and large ecotypes over wave-exposure gradients on northwestern European shores. Previous work focusing on a hybrid zone in Sweden revealed strong genetic differentiation between the ecotypes, concentrated in 12 putative chromosomal inversions. Here we compare the Swedish hybrid zone with samples from France distributed across a similar wave-exposed gradient. Our aims were to test if similar exposure gradients promote parallel ecotype distributions and hybrid zones, and if similar genomic architectures contribute to divergence and adaptation across the gradients. Unpredictably, we found that the shell size cline was reversed in France compared to Sweden, with small individuals occupying the more-sheltered end of the environmental gradient in Sweden but the more-exposed end in France. We also observed a cline in shell colour in France, whereas nearly all Swedish snails were yellow. Using whole-genome sequencing, we found similar levels of genetic differentiation between ecotypes in both places. Most of the differences were accounted for by the same 15 inversions, and the arrangement clines showed similar associations to the wave-exposure gradient in both hybrid zones. These inversions were enriched in SNPs differentiating the ecotypes that were either specific to one hybrid zone or showed reversed cline patterns between zones. Genome-wide association studies (GWAS) detected significant associations between genomic regions within inversions and shell size in Sweden, while one inversion was associated with colour in France. Our results show that the same inversions play a dual role: they support ecotype differences across similar environmental gradients in distant locations, while also contribute site-specific variation contributing to local adaptation.

evolutionary biology↗

bioRxiv2024

Chromosome-scale genome assembly of the rough periwinkle Littorina saxatilis

The intertidal gastropod Littorina saxatilis is a model system to study speciation and local adaptation. The repeated occurrence of distinct ecotypes showing different levels of genetic divergence makes L. saxatilis particularly suited to study different stages of the speciation continuum in the same lineage. A major finding is the presence of several large chromosomal inversions associated with the divergence of ecotypes and, specifically, the species offers a system to study the role of inversions in this divergence. The genome of L. saxatilis is 1.35Gb and composed of 17 chromosomes. The first reference genome of the species was assembled using Illumina data, was highly fragmented (N50 of 44kb) and was quite incomplete, with a BUSCO completeness of 80.1% on the Metazoan dataset. A linkage map of one full-sibling family enabled the placement of 587 Mbp of the genome into 17 linkage groups corresponding to the haploid number of chromosomes, but the fragmented nature of this reference genome limited the understanding of the interplay between divergent selection and gene flow during ecotype formation. Here we present a newly generated reference genome that is highly contiguous, with a N50 of 67 Mb and 90.4% of the total assembly length placed in 17 super-scaffolds. It is also highly complete with a BUSCO completeness of 94.1 % of the Metazoa dataset. This new reference will allow for investigations into the genomic regions implicated in ecotype formation as well as better characterization of the inversions and their role in speciation. SignificanceThe rough periwinkle, L. saxatilis has become a model to study adaptation, evolutionary innovation and speciation, including the role of chromosomal inversions in these processes. Chromosomal inversions have also been identified in other species of Littorina providing a valuable opportunity for investigating their origin and evolution. Here, we present a new chromosome-scale reference genome of L. saxatilis generated from long reads and HiC chromatin proximity mapping replacing an earlier highly fragmented genome. This will enable detailed investigations of how inversions contribute to adaptation and reproductive isolation in L. saxatilis and related taxa, including studies of the effects of individual loci within and outside inversions.

genomics↗

bioRxiv2023

The brittle star genome illuminates the genetic basis of animal appendage regeneration

Species within nearly all extant animal lineages are capable of regenerating body parts. However, it remains unclear whether the gene expression programme controlling regeneration is evolutionarily conserved. Brittle stars are a species-rich class of echinoderms with outstanding regenerative abilities, but investigations into the genetic bases of regeneration in this group have been hindered by the limited genomic resources. Here, we report a chromosome-scale genome assembly for the brittle star Amphiura filiformis. We show that the brittle star genome is the most rearranged amongst echinoderms sequenced to date, featuring a reorganised Hox cluster reminiscent of the rearrangements observed in sea urchins. In addition, we performed an extensive profiling of gene expression during brittle star adult arm regeneration and identified sequential waves of gene expression governing wound healing, proliferation and differentiation. We conducted comparative transcriptomic analyses with other invertebrate and vertebrate models for appendage regeneration and uncovered hundreds of genes with conserved expression dynamics, particularly during the proliferative phase of regeneration. Our findings emphasise the crucial importance of echinoderms to detect long-range expression conservation between vertebrates and classical invertebrate regeneration model systems.

evolutionary biology↗

bioRxiv2023

Predicting rapid adaptation in time from adaptation in space: a 30-year field experiment in marine snails

Predicting the outcomes of adaptation is a major goal of evolutionary biology. When temporal changes in the environment mirror spatial gradients, it opens up the potential for predicting the course of adaptive evolution over time based on patterns of spatial genetic and phenotypic variation. We assessed this approach in a 30-year transplant experiment in the marine snail Littorina saxatilis. In 1992, snails were transplanted from a predation-dominated environment to one dominated by wave action. Based on spatial patterns, we predicted transitions in shell size and morphology, allele frequencies at positions throughout the genome, and chromosomal rearrangement frequencies. Observed changes closely agreed with predictions. Hence, transformation can be both dramatic and rapid, and predicted from knowledge of the phenotypic and genetic variation among populations.

evolutionary biology↗

bioRxiv2023

Phenotypic divergence and genomic architecture at two different stages of speciation in a marine snail

Speciation typically occurs over too long a time frame to be observed directly. A way forward is to compare pairs of ecotypes that evolved in parallel in similar contexts but have reached different degrees of reproductive isolation. Such comparisons are possible in the marine snail Littorina saxatilis by contrasting barriers to gene flow between parallel ecotypes in Spain and Sweden. In both countries, divergent ecotypes have evolved to withstand either crab predation or wave action. Here, we explore transects spanning contact zones between the Crab and the Wave ecotypes using low-coverage whole-genome sequencing, morphological and behavioural traits. Despite parallel phenotypic divergence, distinct patterns of differentiation between the ecotypes emerged: a continuous cline in Sweden indicating a weak barrier to gene flow, but two highly genetically and phenotypically divergent, and partly spatially-overlapping clusters in Spain suggesting a much stronger barrier to gene flow. Absence of Spanish early-generation hybrids supported strong isolation, but a low level of gene flow is evident from molecular data. In both countries, highly differentiated loci were located in both shared and private chromosomal inversions but were also present in collinear regions. Despite being considered the same species and showing similar levels of phenotypic divergence, the Spanish ecotypes are much closer to full reproductive isolation than the Swedish ones. Barriers to gene flow of very different strengths between ecotypes within the same species might be explained by dissimilarities in the spatial arrangement of habitats, the selection gradients or the ages of the systems. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=158 SRC="FIGDIR/small/558824v2_ufig2.gif" ALT="Figure 2"> View larger version (38K): org.highwire.dtl.DTLVardef@c72ac4org.highwire.dtl.DTLVardef@1c8cd22org.highwire.dtl.DTLVardef@13ac83org.highwire.dtl.DTLVardef@1a301d6_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical abstract.C_FLOATNO Distinct patterns of divergence between parallel ecotypes in Sweden and Spain. C_FIG

evolutionary biology↗

bioRxiv2023

Coupling of 12 chromosomal inversions maintains a strong barrier to gene flow between ecotypes

Chromosomal rearrangements lead to the coupling of reproductive barriers, but whether and how they contribute to completion of speciation remains unclear. Marine snails of the genus Littorina repeatedly form hybrid zones between taxa segregating for inversion arrangements, providing opportunities to study this question. Here, we analysed two adjacent transects across hybrid zones between large and dwarf ecotypes of Littorina fabalis covering wave exposure gradients in a Swedish island. Applying whole-genome sequences we found 12 putative inversions reaching near differential fixation between the opposite ends of each transect, and being in strong linkage disequilibrium. These inversions cover 20% of the genome and carry 93% of divergent SNPs. Bimodal hybrid zones in both transects indicate that the two ecotypes of Littorina fabalis maintain their genetic and phenotypic integrity following contact due to strong coupling between inversion clines that strengthened the reproductive barrier. The bimodality resulting from the linked inversions extends into collinear parts of the genome, suggesting a genome-wide coupling. Demographic inference suggests that the coupling built up during a period of allopatry, and has been maintained for more than 1K generations after secondary contact. Overall, this study shows that the coupling of multiple chromosomal inversions contributes to strong reproductive isolation. Importantly, two of the inversions overlap with inverted genomic regions associated with ecotype differences in a closely-related species (L. saxatilis), suggesting the same regions, with similar structural variants, repeatedly contribute to ecotype evolution in distinct species.

evolutionary biology↗

bioRxiv2023

Understanding the adaptive role of chromosomal inversions across large geographical scales: The potential of pool-seq data

A growing body of research shows that chromosomal inversions, where each arrangement is associated with a certain environment and maintains a set of adaptive alleles, make an important contribution to local adaptation. However, inversions often remain unexplored across large geographical scales. It is unclear whether inversions contribute to adaptation across species ranges, which environmental factors affect arrangement frequencies, and whether the adaptive content of the same arrangement varies between locations. Here, we discuss ideas of how allele frequency data (e.g. pool-sequencing data) can be used to learn about inversions in a simple and cost-effective way. If populations connected by migration differ in arrangement frequency, plotting their SNP allele frequencies against each other will reveal a parallelogram whose corners reflect arrangement frequencies. We demonstrate the usefulness of this approach in locally-adapted populations of the intertidal snail Littorina saxatilis (Olivi). For twelve inversions, we estimate arrangement frequencies in 20 populations across the European species range. While roughly half of the inversions contribute to adaptation to the well-studied contrast between wave-exposed and crab-infested habitats, the other half likely contribute to adaptation to shore height. We also find evidence for geographical variation in arrangement content, suggesting variation in adaptive role.

evolutionary biology↗

bioRxiv2023

Selection on many loci drove the origin and spread of a key innovation

Key innovations are fundamental to biological diversification, but their genetic architecture is poorly understood. A recent transition from egg-laying to live-bearing in Littorina snails provides the opportunity to study the architecture of an innovation that has evolved repeatedly in animals. Samples do not cluster by reproductive mode in a genome-wide phylogeny, but local genealogical analysis revealed numerous genomic regions where all live-bearers carry the same core haplotype. Associated regions show evidence for live-bearer-specific positive selection, and are enriched for genes that are differentially expressed between egg-laying and live-bearing reproductive systems. Ages of selective sweeps suggest live-bearing alleles accumulated gradually, involving selection at different times in the past. Our results suggest that innovation can have a polygenic basis, and that novel functions can evolve gradually, rather than in a single step.

evolutionary biology↗

bioRxiv2022

Clones on the run - the genomics of a recently expanded facultative asexual species

Why, in facultative asexual species, marginal populations are often richer in clones than are core populations, remains unclear. Cloning freezes genotypes but hampers recombination and local adaptation. During expansion, clones are favoured over non-selfing sexuals by uniparental reproduction. To better understand the dynamics of clones and sexual lineage, we used genome-wide sequencing to analyse a recently expanded seaweed. We found large clones and sexual populations mixed close to range margins. Clones had evolved repeatedly from sexual populations but were unexpectedly low in genetic variation. Modelling suggested clones form from sexual populations after repeated bottlenecks at the expansion front. A clonal wave of depauperate genotypes thereafter spread ahead of the sexual population. As we observed, these early formed clones may survive side-by-side sexual individuals, which suggests they lost their sexual capacity. Our study illustrates how range expansion can result in complex and dynamic patterns of genetic variation in facultative asexual species. TeaserWe use genome data and modelling to find out why large clones are only found at range margins in a recently expanded seaweed

evolutionary biology↗

bioRxiv2022

Species' ranges and the steepening-gradient hypothesis

One hypothesis invoked to explain limits to species ranges is a mismatch in environmental conditions between the central and marginal areas of species ranges. Low population size at the margins causes genetic drift to outplay selection locally, and limits the accumulation of genetic variance, so that adaptation is hindered locally. Earlier theoretical work shows that, for a population expanding over a spatially heterogeneous environment without any geographical barriers, adaptation will fail abruptly and sharp range margins will establish only when the underlying environmental conditions change more and more severely across space, whereas an environment changing constantly will result either in infinite expansion or rapid global extinction. Here, we extend this "steepening-gradient hypothesis" to encompass situations when multiple (up to three) environmental factors impose selection on separate adaptive traits. We show that multiple selection gradients steepen each other and that it is sufficient that just one of the gradients steepen in space for sharp range margins to form. This is true even if this gradient is shallow throughout the realised range. Thus, despite its detrimental role in forming range margins, it could be overlooked in field studies. Finally, by decomposing an environmental gradient to selection on two (or three) adaptive traits, we show that a population can withstand harsher environmental conditions than when selection acts on one adaptive trait alone. This finding argues for the evolution of novel traits in harsh environments.

evolutionary biology↗

bioRxiv2021

A metagenomic analysis of the wrackbed microbiome indicates a phylogeographic break along the North Sea - Baltic Sea transition zone

Sandy beaches are biogeochemical hotspots that bridge marine and terrestrial ecosystems via the transfer of marine organic matter, such as seaweed (termed wrack). A keystone of this unique ecosystem is the microbial community, which helps to degrade wrack and re-mineralize nutrients. However, little is known about the wrackbed microbiome, its composition, trophic ecology, or how it varies over time and space. Here we characterize the wrackbed microbiome as well as the microbiome of a primary consumer, the seaweed fly Coelopa frigida, and examine how they change along one of the most studied ecological gradients in the world, the transition from the marine North Sea to the brackish Baltic Sea. We found that polysaccharide degraders dominated both the wrackbed and seaweed fly microbiomes but there were still consistent differences between wrackbed and fly samples. Furthermore, we observed a shift in both microbial communities and functionality between the North and Baltic Sea. These shifts were mostly due to changes in the frequency of different groups of known polysaccharide degraders (Proteobacteria and Bacteroidota). We hypothesize that microbes were selected for their abilities to degrade different polysaccharides corresponding to a shift in polysaccharide content in the seaweed communities of the North vs. Baltic Sea. Our results reveal the complexities of both the wracked microbial community, with different groups specialized to different roles, and the cascading trophic consequences of shifts in the near shore algal community.

genomics↗

bioRxiv2021

A large chromosomal inversion shapes gene expression in seaweed flies (Coelopa frigida)

Inversions often underlie complex adaptive traits, but the genic targets inside them are largely unknown. Gene expression profiling provides a powerful way to link inversions with their phenotypic consequences. We examined the effects of the Cf-Inv(1) inversion in the seaweed fly Coelopa frigida on gene expression variation across sexes and life stages. Our analyses revealed that Cf-Inv(1) shapes global expression patterns but the extent of this effect is variable with much stronger effects in adults than larvae. Furthermore, within adults, both common as well as sex specific patterns were found. The vast majority of these differentially expressed genes mapped to Cf-Inv(1). However, genes that were differentially expressed in a single context (i.e. in males, females or larvae) were more likely to be located outside of Cf-Inv(1). By combining our findings with genomic scans for environmentally associated SNPs, we were able to pinpoint candidate variants in the inversion that may underlie mechanistic pathways that determine phenotypes. Together the results in this study, combined with previous findings, support the notion that the polymorphic Cf-Inv(1) inversion in this species is a major factor shaping both coding and regulatory variation resulting in highly complex adaptive effects.

evolutionary biology↗

bioRxiv2020

Ecological load and balancing selection in circumboreal barnacles

Acorn barnacle adults experience environmental heterogeneity at various spatial scales of their circumboreal habitat, raising the question of how adaptation to high environmental variability is maintained in the face of strong juvenile dispersal and mortality. Here we show that 4% of genes in the barnacle genome experience balancing selection across the entire range of the species. Many of these genes harbor mutations maintained across 2 million years of evolution between the Pacific and Atlantic oceans. These genes are involved in ion regulation, pain reception, and heat tolerance, functions which are essential in highly variable ecosystems. The data also reveal complex population structure within and between basins, driven by the trans-Arctic interchange and the last glaciation. Divergence between Atlantic and Pacific populations is high, foreshadowing the onset of allopatric speciation, and suggesting that balancing selection is strong enough to maintain functional variation for millions of years in the face of complex demography.

evolutionary biology↗

bioRxiv2020

Assortative mating, sexual selection and their consequences for gene flow in Littorina

When divergent populations are connected by gene flow, the establishment of complete reproductive isolation usually requires the joint action of multiple barrier effects. One example where multiple barrier effects are coupled consists of a single trait that is under divergent natural selection and also mediates assortative mating. Such multiple-effect traits can strongly reduce gene flow. However, there are few cases where patterns of assortative mating have been described quantitatively and their impact on gene flow has been determined. Two ecotypes of the coastal marine snail, Littorina saxatilis, occur in North Atlantic rocky-shore habitats dominated by either crab predation or wave action. There is evidence for divergent natural selection acting on size, and size-assortative mating has previously been documented. Here, we analyze the mating pattern in L. saxatilis with respect to size in intensively-sampled transects across boundaries between the habitats. We show that the mating pattern is mostly conserved between ecotypes and that it generates both assortment and directional sexual selection for small male size. Using simulations, we show that the mating pattern can contribute to reproductive isolation between ecotypes but the barrier to gene flow is likely strengthened more by sexual selection than by assortment.

evolutionary biology↗

bioRxiv2019

Strong spatial genetic structure in a Baltic Sea herbivore due to recent range expansion, multiple bottlenecks and low connectivity

In the Baltic Sea, recent range expansions following the opening of the Danish straits have resulted in a low-diversity ecosystem, both among and within species. However, relatively little is known about population genetic patterns within the basin, except for in a few commercially caught species and some primary producers thought to be ecosystem engineers. Here, we investigate the population genetic structure of the ecologically important crustacean Idotea balthica throughout the Baltic Sea using an array of 33,774 genome-wide SNP markers derived from 2b-RAD sequencing. We also generate a biophysical connectivity matrix, with which we compare the genomic data. We find strong population structure on small scales across the Baltic Sea, and that genomic patterns in most cases closely match biophysical connectivity, suggesting that current patterns are important for dispersal of this species. We also find a strong signal of multiple bottlenecks during the initial range expansion, in the form of reduced heterozygosity along the historical expansion front. The lack of gene flow among sampling sites in the Baltic Sea environmental gradient potentiates local adaptation, while at the same time also increasing genetic drift in low-diversity areas.

evolutionary biology↗

bioRxiv2018

Genomic architecture of parallel ecological divergence: beyond a single environmental contrast

The genetic basis of parallel ecological divergence provides important clues to the operation of natural selection and the predictability of evolution. Many examples exist where binary environmental contrasts seem to drive parallel divergence. However, this simplified view can conceal important components of parallel divergence because environmental variation is often more complex. Here, we disentangle the genetic basis of parallel divergence across two axes of environmental differentiation (crab-predation vs. wave-action and low-shore vs. high-shore habitat contrasts) in the marine snail Littorina saxatilis, a well established natural system of parallel ecological divergence. We used whole-genome resequencing across multiple instances of these two environmental axes, at local and regional scales from Spain to Sweden. Overall, sharing of genetic differentiation is generally low but it is highly heterogeneous across the genome and increases at smaller spatial scales. We identified genomic regions, both overlapping and non-overlapping with recently described candidate chromosomal inversions, that are differentially involved in adaptation to each of the environmental axis. Thus, the evolution of parallel divergence in L. saxatilis is largely determined by the joint action of geography, history, genomic architecture and congruence between environmental axes. We argue that the maintenance of standing variation, perhaps as balanced polymorphism, and/or the re-distribution of adaptive variants via gene flow can facilitate parallel divergence in multiple directions as an adaptive response to heterogeneous environments.

evolutionary biology↗