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Svardal, H.

Publications and source records attributed to Svardal, H..

At least 19 recordsLinked to original sources

Elevated genetic load is associated with reduced bite force in insular lizard populations

Demographic history can profoundly shape genomic variation by altering levels of inbreeding, the strength of genetic drift, and the efficacy of purifying selection, thereby influencing both the accumulation and expression of deleterious variation. Yet the extent to which these genomic consequences translate into organismal performance remains poorly understood. Here, we investigated how contrasting demographic histories shape genomic diversity, inbreeding, genetic load, and performance across mainland and insular populations of the Italian wall lizard, Podarcis siculus. Using whole-genome sequence data from 263 wild-caught individuals and field-based performance measurements from 134 lizards, we characterised population structure and demographic history, quantified genomic diversity, runs of homozygosity, and deleterious variation, and tested associations between genomic inbreeding and performance traits. Island populations showed reduced genetic diversity, increased autozygosity, and elevated genetic load relative to mainland populations, consistent with stronger genetic drift and reduced efficacy of purifying selection. Patterns of deleterious variation were consistent with purging of strongly, but not mildly, deleterious variants. Greater genomic autozygosity was associated with reduced bite force in island lizards, a pattern consistent with inbreeding depression, whereas sprint speed, sperm quality, immunocompetence, and spatial cognition showed no significant association with inbreeding. Genome-wide mapping of runs of homozygosity further identified multiple genomic regions associated with reduced bite performance. Together, these results show how demographic history shapes genomic diversity, homozygosity, and deleterious variation in wild vertebrate populations, while revealing that phenotypic consequences can be trait-specific, a pattern that may reflect differences in genetic architecture and the extent of environmental influence on trait variation.

evolutionary biology↗

Sea stickleback genome reveals repeated chromosomal rearrangements in sticklebacks

Sticklebacks (Gasterosteidae) encompass model organisms which are of particular interest for evolutionary and ecological genomics. Within Gasterosteidae, chromosome number is variable (2n=40-46) and independent fusions of homologous chromosomes have been proposed. The sea stickleback (or fifteen-spined stickleback, Spinachia spinachia ) has the lowest known number of chromosomes (2n=40) and hence is crucial in understanding chromosome evolution among sticklebacks, but is so far missing in genomic datasets. Here, we present a high-quality diploid genome assembly of S. spinachia. PacBio HiFi and Hi-C reads were assembled into a genome of 407.5 Mb in size, consisting of 20 chromosomes, with an N50 of 6.6 Mb and 98.96% complete single-copy BUSCO genes. A phylogenetic tree inferred across five stickleback species and four outgroup genomes from 19,156 genes, alongside synteny analyses and ancestral chromosome reconstructions, confirms S. spinachia as the sister species to the four-spined stickleback (Apeltes quadracus) and not as the sister group to all other sticklebacks as once thought. It has one species-specific chromosome fusion and shares two fusions with the three-spined stickleback (Gasterosteus aculeatus), none of which are present in its sister species. One of these fusions is also present in Pungitius, leading to reinterpretion of this fusion as ancestral to Gasterosteidae, with subsequent fission in Apeltes. This implies a lower ancestral chromosome number in Gasterosteidae (2n=44) than previously thought. The other fusion shared with G. aculeatus presents a case of convergence. Our results suggest that karyotype evolution in Gasterosteidae has been shaped by ancestral chromosome fusion, convergent fusion, and secondary fission.

evolutionary biology↗

Parallel connectivity and genomic divergence but heterogeneous demographic history in sympatric Mediterranean clingfishes

Understanding the extent to which marine connectivity can be predicted from shared oceanographic and biogeographic conditions remains a central challenge in marine ecology and evolution. Comparative analyses of sympatric species provide a powerful framework for testing whether common environmental contexts generate repeatable patterns of population structure and connectivity and if this also unfolds on a genomic level. Here, we investigated this question in the endemic Mediterranean clingfish genus Gouania, a group of cryptobenthic gravel-beach specialists with limited adult mobility and a short pelagic larval phase. We combined whole-genome resequencing of two sympatric eastern Mediterranean species (G. orientalis and G. hofrichteri) around Crete and Kythira with Lagrangian particle drift simulations, mitochondrial phylogeography across all five Gouania species and demographic reconstructions using MSMC2. Passive drift simulations predicted strong isolation of Kythira and restricted exchange between northern and southern Crete. These predictions closely matched genome-wide population structure in both species, revealing highly concordant patterns of connectivity despite independent evolutionary histories. Shared population contrasts were furthermore associated with a significant excess of parallel genomic divergence, with both genomic windows and candidate genes overlapping more frequently than expected by chance. Nevertheless, most differentiated genomic regions remained species-specific and functional enrichment analyses identified no dominant shared pathways, suggesting a largely polygenic basis of divergence. In contrast to the strong concordance observed for contemporary connectivity and genomic divergence, mitochondrial phylogeographic patterns and species-level demographic histories were considerably more heterogeneous across the genus. Together, our results demonstrate that the predictability of marine population structure is scale-dependent: shared seascapes can generate repeatable patterns of connectivity and partially parallel genomic divergence, whereas deeper phylogeographic and demographic histories remain strongly influenced by species-specific historical processes.

evolutionary biology↗

Distinct genomic architectures but the same gene underlie the convergent evolution of a plant supergene

AO_SCPLOWBSTRACTC_SCPLOWEvolution reflects a balance between innovation and constraint, often repurposing existing components in new contexts. Convergent evolution exemplifies this interplay, with similar traits evolving independently in different species, yet the genomic mechanisms enabling such repeatability remain poorly understood. Here, by analyzing ten chromosome-scale genome assemblies, including seven newly generated, we discovered that the S-locus supergene (a cluster of tightly linked genes controlling a floral dimorphism called distyly) arose independently multiple times within the primrose family, Darwins iconic system for studying distyly. In each case, the same gene was independently duplicated and co-opted, yet the resulting genomic architectures differed, ranging from hemizygous (present on one chromosome copy) to heterozygous (on both copies). These diverse architectures shaped supergene evolution differently, with genetic degeneration occurring only in the heterozygous case. By uncovering multiple mechanisms for supergene origins, our work shows how convergent evolution can produce similar phenotypes by reusing the same genetic building blocks while exploring distinct genomic configurations.

evolutionary biology↗

Chromosomal Restructuring and Subgenome Divergence Drive Post-Polyploid Adaptive Diversification in Sinocyclocheilus Cavefish

Allopolyploidy generates extensive genomic potential, yet its role in adaptive diversification remains poorly understood. We assembled phased chromosome-level genomes of cave and surface ecotypes of Sinocyclocheilus, a rapidly diversifying cavefish lineage, the most species-rich in the world. Our analyses show that all species derive from the ancestral allotetraploidisation event common to all cyprinids without subsequent polyploidisation. Instead, diversification has been driven by chromosomal rearrangements and the emergence of subgenome asymmetry. The dominant D subgenome maintains more genes, exhibits higher expression, and is enriched for adaptive functions, while the submissive S subgenome is inclined towards housekeeping roles. This asymmetry is further reinforced by the accumulation of transposable elements near genes exhibiting expression biased toward the S-subgenome. We also identify a derived epigenetic mechanism in the cave ecotype, i.e., differential methylation of these elements, absent in the surface ecotype. These findings show how structural, regulatory, and epigenetic processes have interacted following allopolyploidy to produce ecological and phenotypic diversity in Sinocyclocheilus. Our findings also offer quantitative evidence that cave adaptation is a complex process characterised by an evolutionary trade-off - the regression of energetically expensive traits combined with the remodeling of neural and developmental pathways driven by natural selection.

evolutionary biology↗

The genomics of convergent adaptation to intertidal gravel beaches in Mediterranean clingfishes

IntroductionUnderstanding the genetic basis of widespread phenotypic convergence, particularly for complex morphological traits, remains a major challenge in evolutionary biology. The Mediterranean gravel beach clingfishes of the genus Gouania provide an excellent system to study this phenomenon. Within this genus, two distinct morphotypes, "slender" and "stout", have repeatedly evolved, adapting to different microhabitats. These morphotypes differ in multiple complex traits, including body elongation, head compression, vertebral number, eye size, and the structure of the adhesive disc. Materials and MethodsIn a first step, to scrutinize phylogenetic convergence, we combined 3D morphometrics of the pelvic girdle and skull, with molecular species delimitation based on >660 DNA barcodes, and a phylogenomic framework based on more than 3,400 single-copy orthologs. Secondly, by employing whole-genome resequencing and a novel "convergence score" statistic, we examined genomic convergence across multiple levels: nucleotides, sequences, genes, and functional pathways. Results and DiscussionWhile we found no evidence of large-scale genomic or protein-level convergence, we identified promising candidate regions at the level of single variants, genes, and biological pathways. Notably, a longer shared (but interrupted) haplotype around the morphogene adam12 was associated with convergent traits. The lack of simple genomic patterns may reflect the radiations age and the complex genetic basis of the underlying morphological traits (e.g., eye-size, neurocranium shape). Altogether, our findings highlight the importance of assessing genomic convergence at multiple molecular levels to uncover diagnostic signals across varying evolutionary processes and timescales. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=149 SRC="FIGDIR/small/675783v1_ufig1.gif" ALT="Figure 1"> View larger version (61K): org.highwire.dtl.DTLVardef@58265eorg.highwire.dtl.DTLVardef@13f1deaorg.highwire.dtl.DTLVardef@c51d79org.highwire.dtl.DTLVardef@112217d_HPS_FORMAT_FIGEXP M_FIG C_FIG

evolutionary biology↗

Multiple instances of river-lake introgression in the adaptive radiation of sailfin silversides in Wallace's Dreampond

While adaptive radiations significantly contribute to the worlds biodiversity, much is unknown about the genetic and ecological factors underlying these rapid successions of speciation. It has been suggested that hybridisation can facilitate the speciation process by generating genetic diversity on which diversifying selection can act. Sailfin silverside fishes (Telmatherinidae) in the Malili Lakes system in Sulawesi have diversified within the last 2 million years. We assembled and annotated a chromosome-scale reference genome of the riverine sailfin silverside Telmatherina bonti and generated whole genome sequences of all species of Telmatherina in Lake Matano, South Sulawesi, Indonesia, one of the worlds oldest and deepest lakes. We reconstructed the phylogenetic relationships within the adaptive radiation of sailfin silversides and inferred past and ongoing introgression patterns. Genome-wide tests confirmed two monophyletic clades, sharpfins and roundfins. However, within clades, we found mismatches between morphology-based taxonomic assignments and genome-wide genetic relationships. We found signs of both old and ongoing introgression between river-dwelling T. bonti and the lacustrine sharpfin group, as shown in elevated D-statistic, f4-ratio and f-branch statistic. Levels of excess allele sharing between riverine species and the three most common lacustrine species declined with increasing distance from the river-inlet, indicating ongoing introgression at the lake-river interface. This combination of past and ongoing hybridisation in a radiating species flock makes Lake Matano Telmatherina a particularly valuable system to study fundamental mechanisms driving rapid speciation under genomic exchange. The phylogenomic framework elaborated in this study provides the foundation for studies of the processes shaping this charismatic radiation.

evolutionary biology↗

Genomic diversity in felids correlates with range and density, not census size

As the world is hit by the sixth mass extinction, it becomes increasingly important to understand the factors relevant to the conservation of species, so that we may protect biodiversity to the best of our abilities. Although genetic diversity is known to reflect population demography and contribute to genetic health and adaptability, it is not explicitly used as a criterion in assessments by the International Union for the Conservation of Nature (IUCN). Additionally, studies comparing diversity estimates between species often rely on summarizing results across studies, which use different methodologies and may not be suited for direct comparison. Here we performed a family-wide assessment of genomic diversity in Felidae, covering most extant species. We tested for correlations between autosomal heterozygosity and ecological traits across (sub)species, and whether a subspecies genetic diversity was associated with its IUCN threat category. We found evidence for genetic diversity to be strongly positively correlated with both geographic range size and population density, but not with census size. Furthermore, although genetic diversity was not significantly correlated with IUCN status overall, threatened cat species had significantly lower levels of genetic diversity than non-threatened species. Our results confirm the association of population parameters and assessment of extinction risk with genetic diversity in one of the most iconic and threatened families of land carnivores. While mechanisms and causality behind these associations will need to be the subject of further investigation, our study adds further credence to the importance of incorporating genomic information in risk assessment and conservation efforts.

genomics↗

Whole genome sequencing reveals how plasticity and genetic differentiation underlie sympatric morphs of Arctic charr

Salmonids have a remarkable ability to form sympatric morphs after postglacial colonization of freshwater lakes. These morphs often exhibit differences in morphology, feeding, and spawning behaviour. Here we explore the genetics of morph differentiation by establishing a high-quality, annotated reference genome for the Arctic charr and use this as a resource for population genomic analysis of morphs from two Norwegian and two Icelandic lakes. The four lakes represent the spectrum of genetic differentiation between morphs from one lake with no genetic differentiation between morphs, implying phenotypic plasticity only, to two lakes with locus-specific genetic differentiation, implying incomplete reproductive isolation, and one lake with strong genome-wide divergence consistent with complete reproductive isolation. As many as 12 putative inversions ranging from 0.45 to 3.25 Mbp in size segregated among the four morphs present in one lake, Thingvallavatn, and these contributed significantly to the genetic differentiation among morphs. None of the putative inversions was found in any of the other lakes, but there were cases of partial haplotype sharing in similar morph contrasts in other lakes. The results are consistent with a highly polygenic basis of morph differentiation with limited genetic parallelism between lakes. The results support a model where morph differentiation is usually first established due to phenotypic plasticity that results in niche expansion and separation, followed by gradual development of reproductive isolation and locus-specific differentiation and eventually complete reproductive isolation and genome-wide divergence. A major explanation for salmonids ability to diversify into multiple sympatric morphs is likely the genome complexity caused by their ancient whole genome duplication that enhances evolvability.

evolutionary biology↗

Introgression dynamics of sex-linked chromosomal inversions shape the Malawi cichlid adaptive radiation

Chromosomal inversions contribute to adaptive speciation by linking co-adapted alleles. Querying 1,375 genomes of the species-rich Malawi cichlid fish radiation, we discovered five large inversions segregating in the benthic subradiation that each suppress recombination over more than half a chromosome. Two inversions were transferred from deepwater pelagic Diplotaxodon via admixture, while the others established early in the deep benthic clade. Introgression of haplotypes from lineages inside and outside the Malawi radiation coincided with bursts of species diversification. Inversions show evidence for transient sex linkage and a striking excess of protein changing substitutions points towards selection on neuro-sensory, physiological and reproductive genes. We conclude that repeated interplay between depth adaptation and sex-specific selection on large inversions has been central to the evolution of this iconic system.

evolutionary biology↗

Population genomic analysis reveals cryptic population structure in the commercially important Lake Malawi cichlid Copadichromis mloto

Fish is an important source of animal protein for many people living around Lake Malawi. The evaluation of population structure and genetic diversity can yield useful information for management and conservation of fish species but is complicated in Lake Malawi by the close genetic relatedness of species of the recent cichlid adaptive radiation. In this study, we analysed whole-genome sequencing data of "true utaka", a group of cichlids previously common in fisheries, but that has faced strong decline due to overfishing. Our analysis of 223 individuals collected from fishermens catches along the western shoreline of Lake Malawi confirmed that Copadichromis mloto (C. sp. "virginalis kajose") is the true utaka most targeted by fisheries. Genetic principal component analysis, phylogenetic inference, and admixture analysis revealed complex patterns of population structure. The presence of at least three geographically widespread genetic clades that have remained separate despite gene flow and partial sympatry hints at the presence of currently undescribed, cryptic species diversity in C. mloto. This result leads us to suggest that, despite the lack of obvious habitat barriers, benthic and pelagic species of Malawi cichlids might harbour unidentified species diversity and calls for further genetic and taxonomic research to define appropriate conservation units.

genomics↗

A pangenomic perspective of the Lake Malawi cichlid radiation reveals extensive structural variation driven by transposable elements

The East African Rift Lakes, namely Lake Malawi, Victoria, and Tanganyika, host a remarkable diversity of cichlid fishes, representing one of natures most striking vertebrate radiations. Despite rich phenotypic diversity, single nucleotide polymorphism (SNP)-based sequencing studies have revealed little sequence divergence between cichlids, with 0.1 to 0.25% pairwise divergence within Lake Malawi. These studies were based on aligning short reads to a single linear reference genome, which ignores the contribution of larger scale structural variants (SVs). To complement existing SNP-based studies, we adopted a pangenomic approach by constructing a multiassembly graph of haplochromine cichlids in Lake Malawi. We produced six new long read genome assemblies, alongside two publicly available ones, to span most of the major eco-morphological clades in the lake. This approach not only identifies longer SVs, but also visually represents complex and nested variation. Strikingly, the SV landscape is dominated by large insertions, many exclusive to individual assemblies. From a pangenomic perspective, we observed an exceptional amount of extra sequence, totaling up to 33.1% additional bases with respect to a single cichlid genome. Approximately 4.73 to 9.86% of the cichlid assemblies were estimated to be interspecies structural variation, suggesting substantial genomic diversity underappreciated in previous SNP-based studies. While coding regions remain highly conserved, our analysis uncovers a significant contribution of SVs from transposable element (TE) insertions, especially DNA, LINE, and LTR transposons. These findings underscore the intricate interplay of evolutionary forces shaping cichlid genome diversity, including both small nucleotide mutations and large TE-derived sequence alterations.

evolutionary biology↗

The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics

A global genome database of all of Earths species diversity could be a treasure trove of scientific discoveries. However, regardless of the major advances in genome sequencing technologies, only a tiny fraction of species have genomic information available. To contribute to a more complete planetary genomic database, scientists and institutions across the world have united under the Earth BioGenome Project (EBP), which plans to sequence and assemble high-quality reference genomes for all [~]1.5 million recognized eukaryotic species through a stepwise phased approach. As the initiative transitions into Phase II, where 150,000 species are to be sequenced in just four years, worldwide participation in the project will be fundamental to success. As the European node of the EBP, the European Reference Genome Atlas (ERGA) seeks to implement a new decentralised, accessible, equitable and inclusive model for producing high-quality reference genomes, which will inform EBP as it scales. To embark on this mission, ERGA launched a Pilot Project to establish a network across Europe to develop and test the first infrastructure of its kind for the coordinated and distributed reference genome production on 98 European eukaryotic species from sample providers across 33 European countries. Here we outline the process and challenges faced during the development of a pilot infrastructure for the production of reference genome resources, and explore the effectiveness of this approach in terms of high-quality reference genome production, considering also equity and inclusion. The outcomes and lessons learned during this pilot provide a solid foundation for ERGA while offering key learnings to other transnational and national genomic resource projects.

genomics↗

Evidence of selection in UCP1 gene region suggests local adaptation to irradiance rather than cold temperatures in savanna monkeys (Chlorocebus spp.)

The genus Chlorocebus is widely distributed throughout sub-Saharan Africa, and in the last 300 thousand years expanded from equatorial Africa into the southernmost latitudes of the continent. In these new environments, colder climate was a likely driver of natural selection. We investigated population-level genetic variation in the mitochondrial uncoupling protein 1 (UCP1) gene region - implicated in non-shivering thermogenesis within brown/beige adipocytes - in 73 wild savanna monkeys from three taxa representing this southern expansion (C. pygerythrus hilgerti, C. cynosuros, C. p. pygerythrus) ranging from Kenya to South Africa. We found 17 SNPs with extended haplotype homozygosity consistent with positive selective sweeps, 10 of which show no significant LD with each other. Phylogenetic generalized least squares modeling with ecological covariates suggest that most derived allele frequencies are significantly associated with solar irradiance and winter precipitation, rather than overall low temperatures. This selection and association with irradiance appears to be driven by a population isolate in the southern coastal belt of South Africa. We suggest that sunbathing behaviors common to savanna monkeys, in combination with strength of solar irradiance, may mediate adaptations to thermal stress via non-shivering thermogenesis among savanna monkeys. The variants we discovered all lie in non-coding regions, some with previously documented regulatory functions, calling for further validation and research.

genetics↗

Taxonomic investigation of the zooplanktivorous Lake Malawi cichlids Copadichromis mloto (Iles) and C. virginalis (Iles).

The taxonomic status of the zooplanktivorous cichlids Copadichromis mloto and C. virginalis has been confused since their original descriptions by lles in 1960. While two forms of C. virginalis, Kaduna and Kajose, were distinguished in the type material, C. mloto has not been positively identified since its original description. Here we re-examined the types as well as 54 recently collected specimens from multiple sampling locations. Genome sequencing of 51 recent specimens revealed two closely related but reciprocally monophyletic clades. Geometric morphological analysis indicated that one clade morphologically encompasses the type specimens of C. virginalis identified by Iles as the Kaduna form, including the holotype, while the other clade encompasses not only the paratypes identified as the Kajose form, but also the type series of C. mloto. Given that all three forms have the same type locality, that there are no meristic or character states to differentiate them and that there are no records of adult male C. mloto in breeding colours, we conclude that the Kajose form previously identified as C. virginalis represents relatively deeper bodied sexually active or maturing individuals of C. mloto.

zoology↗

Genomic consequences of domestication of the Siamese fighting fish

Siamese fighting fish, commonly known as betta, are among the worlds most popular and morphologically diverse pet fish, but the genetic processes leading to their domestication and phenotypic diversification are largely unknown. We assembled de novo the genome of a wild Betta splendens and whole-genome sequenced multiple individuals across five species within the B. splendens species complex, including wild populations and domesticated ornamental betta. Given our estimate of the mutation rate from pedigrees, our analyses suggest that betta were domesticated at least 1,000 years ago, centuries earlier than previously thought. Ornamental betta individuals have variable contributions from other Betta species and have also introgressed into wild populations of those species. We identify dmrt1 as the main sex determination gene in ornamental betta but not in wild B. splendens, and find evidence for recent directional selection at the X-allele of the locus. Furthermore, we find genes with signatures of recent, strong selection that have large effects on color in specific parts of the body, or the shape of individual fins, and are almost all unlinked. Our results demonstrate how simple genetic architectures paired with anatomical modularity can lead to vast phenotypic diversity generated during animal domestication, and set the stage for using betta as a modern system for evolutionary genetics. One-Sentence SummaryGenomic analyses reveal betta fish were domesticated more than 1,000 years ago and the genes that changed in the process.

evolutionary biology↗

The methylomes of Lake Malawi cichlids reveal epigenetic variation associated with phenotypic diversification

Epigenetic variation modulates gene expression and can be heritable. However, knowledge of the contribution of epigenetic divergence to adaptive diversification in nature remains limited. The massive evolutionary radiation of Lake Malawi cichlid fishes displaying extensive phenotypic diversity despite extremely low sequence divergence is an excellent system to study the epigenomic contribution to adaptation. Here, we present a comparative genome-wide methylome and transcriptome study, focussing on liver and muscle tissues in phenotypically divergent cichlid species. In both tissues we find substantial methylome divergence among species. Differentially methylated regions (DMR), enriched in evolutionary young transposons, are associated with transcription changes of ecologically-relevant genes related to energy expenditure and lipid metabolism, pointing to a link between dietary ecology and methylome divergence. Unexpectedly, half of all species-specific DMRs are shared across tissues and are enriched in developmental genes, likely reflecting distinct epigenetic developmental programmes. Our study reveals substantial methylome divergence in closely-related cichlid fishes and represents a resource to study the role of epigenetics in species diversification.

evolutionary biology↗

Towards complete and error-free genome assemblies of all vertebrate species

High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are only available for a few non-microbial species1-4. To address this issue, the international Genome 10K (G10K) consortium5,6 has worked over a five-year period to evaluate and develop cost-effective methods for assembling the most accurate and complete reference genomes to date. Here we summarize these developments, introduce a set of quality standards, and present lessons learned from sequencing and assembling 16 species representing major vertebrate lineages (mammals, birds, reptiles, amphibians, teleost fishes and cartilaginous fishes). We confirm that long-read sequencing technologies are essential for maximizing genome quality and that unresolved complex repeats and haplotype heterozygosity are major sources of error in assemblies. Our new assemblies identify and correct substantial errors in some of the best historical reference genomes. Adopting these lessons, we have embarked on the Vertebrate Genomes Project (VGP), an effort to generate high-quality, complete reference genomes for all ~70,000 extant vertebrate species and help enable a new era of discovery across the life sciences.

genomics↗