Chromosomal inversions are often implicated in divergence between distinct ecotypes, but their role in maintaining continuous adaptive divergence in complex traits remains poorly understood. Using quantitative and population genetics, transcriptomics, and artificial selection experiments, we demonstrate how inversions enable clinal adaptive divergence along a steep environmental gradient despite extensive gene flow in a widely distributed marine fish. We show that three inversions are associated with multiple adaptive traits and harbor the strongest signatures of divergent selection in the genome, implying a crucial adaptive role. These inversions exhibit contrasting selection signatures across latitudes, suggesting that they control distinct aspects of the same complex traits and facilitate adaptation in a modular way to different environmental pressures despite gene flow.

Anthropogenic pressures can have detrimental impacts on fish populations, with their effective management and conservation requiring accurate monitoring tools. Yet, this is not straightforward for closely-related, co-existing species that are difficult to distinguish using simple phenotypic or genetic approaches. Coregonids are of cultural and economic importance across Europe but have faced a multitude of pressures over the last century. Yet genomic management tools are lacking. In Lake Constance, a large pre-alpine lake, stocks have drastically collapsed due to a multitude of pressures, leading to a fishery closure. Here, we adopt a cost-effective, whole genome sequencing approach for lake-wide assessment of stock composition, spatial distribution and genetic diversity of highly admixed Lake Constance whitefish (Coregonus spp.). By sequencing 983 adult and larval genomes, we show that nearly 90% of the stock is made up by one of three species, the Gangfisch (C. macrophthalmus), and define the genetic relationship between Upper and Lower Lake Constance whitefish stocks. We also identified strong mixing between Gangfisch and Blaufelchen (C. wartmanni) on traditionally specific-specific spawning grounds, and detected strong admixture in larvae, with potentially drastic impacts on the effectiveness of hatchery supplementation and stocking. Despite the collapse and admixture, species still exhibit low to moderate levels of genetic diversity, maintain ecologically-relevant genetic differences, and seem to show differences in habitat use. Overall, we present a cost-effective, translatable tool for stock-wide sequencing and genetically-informed fisheries management, with our results calling for the re-evaluation of current management practices to avoid the potential genetic mixing between species. ### Competing Interest Statement The authors have declared no competing interest.

ABSTRACT Introduced in the late 19th Century, Oncorhynchus mykiss (rainbow trout) has been stocked historically in streams throughout Baden‐Württemberg, Germany, and some populations have become self‐sustaining with unclear impact on native salmonid populations. We sampled 223 rainbow trout from 14 streams and 3 hatcheries, each with different levels of domestication, from which the streams are known to have been stocked. We conducted genomic analyses to uncover evidence confirming self‐sustaining populations, to deduce potential sources of these populations, to compare the genetic diversity of hatchery versus stream populations and to discover genetic differences between stream and hatchery populations. We found genetic population structuring amongst the stream populations, consistent with natural reproduction over several generations, and we inferred multiple genetic origins, potentially including source populations beyond the three hatcheries considered, indicating that naturalisation occurs independently of domestication level and that all lineages pose similar likelihoods of establishing in the wild. We found no significant difference in genetic diversity between stream and hatchery populations, but there were nine loci across four genomic regions associated with naturalisation within or adjacent to immunity, growth and development genes. Whether such genes are under selection in wild stream environments needs still to be determined to inform fisheries and conservation management.

Abstract Lampreys are the only ancestrally parasitic vertebrate lineage, yet parasitism has been repeatedly lost alongside a suite of life-history changes, such as loss of migration and juvenile feeding and accelerated maturation. Combining whole-genome resequencing, haplotype-resolved assemblies, hybrid-zone genotyping, multi-tissue transcriptomics, and sperm phenotyping, we map this life-history syndrome in European Lampetra to six chromosomes spanning a mosaic of genomic architectures: a ∼20 Mb low-recombination region on chromosome 1 lacking chromosomal rearrangements within Lampetra but involving inter-specific rearrangements across deep lamprey lineages; a translocated inversion with ecotype-dependent sperm-velocity effects; and ecotype-divergent deletions overlapping genes crucial for nervous system ( CNTNAP2 ) and reproductive development ( FSHR ). However, this genomic basis is not shared with a convergent sister lineage, pointing to independent routes to a recurring life-history transition in lampreys.

The impact of genome structure on adaptation is a growing focus in evolutionary biology, revealing an important role for structural variation and recombination landscapes in shaping genetic diversity across genomes and among populations. This is particularly relevant when local adaptation occurs despite gene flow, where clustering of differentiated loci can maintain locally adapted variants by reducing recombination between them. However, the limited genomic resources for nonmodel species, including reference genomes and recombination maps, have constrained our understanding of these patterns. In this study, we leverage the Atlantic silverside-a nonmodel fish with extensive local adaptation across a steep latitudinal gradient-as an ideal system to explore how genome structure influences adaptation under varying levels of gene flow, using a newly available reference genome and multiple recombination maps. Analyzing 168 genomes from four populations, we found a continuum of genome-wide differentiation increasing from south to north, reflecting higher connectivity among southern populations and reduced gene flow at northern latitudes. With increasing gene flow, the number and clustering of FST outlier loci also increased, with differentiated loci found exclusively within large haploblocks harboring inversions and smaller peaks overlapping putative centromeric regions. Notably, sequence divergence was only evident in inversions, supporting their role in adaptive divergence with gene flow, whereas centromeric regions appeared differentiated because of low recombination and diversity, with no indication of elevated divergence. Our results support the hypothesis that clustered genomic architectures evolve with high gene flow and enhance our understanding of how inversions and centromeres are linked to different evolutionary processes.

The role played by omega-3 long-chain polyunsaturated fatty acids (n-3 LC-PUFA) in life-history polymorphisms in partially migratory species remains poorly understood. Yet, brain development is highly dependent upon nutrition, particularly the supply of n-3 LC-PUFA, derived from diet or internally converted from their shorter-chain precursors, and the fitness of animals may be shaped by cognitive performance, including effective spatial navigation required by migration. We investigated juveniles of a wild polymorphic population of brown trout, Salmo trutta , with three distinct migratory ecotypes, at the point of first outward migration. Using a combination of fatty acid contents, compound-specific stable isotope analysis, and liver transcriptomics, we found that non-migrants compensated for dietary deficiency by biosynthesising n-3 LC-PUFA from precursor molecules and routing them to cell membranes to a greater extent than did migrants. These findings highlight contrasting intake and processing between migratory and non-migratory life histories of nutrients associated with brain development. ### Competing Interest Statement The authors have declared no competing interest. Natural Environment Research Council, https://ror.org/02b5d8509, NR/W008963/1 Leverhulme Trust, https://ror.org/012mzw131, ECF-2020-509 FWF Austrian Science Fund, https://ror.org/013tf3c58, 10.55776/P35515 Fisheries Society of the British Isles, https://ror.org/00q2kx914

Adaptive divergence and increased genetic differentiation among populations can lead to reproductive isolation. In Lake Constance, Germany, a population of invasive three-spined stickleback (Gasterosteus aculeatus) is currently diverging into littoral and pelagic ecotypes, which both nest in the littoral zone. We hypothesized that assortative mating behaviour contributes to reproductive isolation between these ecotypes and performed a behavioural experiment in which females could choose between two nest-guarding males. Behaviour was recorded, and data on traits relevant to mate choice were collected. Both females of the same and different ecotypes were courted with equal vigour. However, there was a significant interaction effect of male and female ecotypes on the level of aggression in females. Littoral females were more aggressive towards pelagic males, and pelagic females were more aggressive towards littoral males. This indicates rejection of males of different ecotypes in spite of the fact that littoral males were larger, more intensely red-coloured and more aggressive than the pelagic males—all mating traits female sticklebacks generally select for. This study documents the emergence of behavioural barriers during early divergence in an invasive and rapidly diversifying stickleback population and discusses their putative role in facilitating reproductive isolation and adaptive radiation within this species.

Gene regulatory divergence is thought to play an important role in adaptation, yet its extent and underlying mechanisms remain largely elusive for local adaptation with gene flow. Local adaptation is widespread in marine species despite generally high connectivity and is often associated with tightly linked genomic architectures, such as chromosomal inversions. To investigate gene regulatory evolution under gene flow and the role of inversions associated with local adaptation to a steep thermal gradient, we generated RNA-seq data from Atlantic silversides (Menidia menidia) from two locally adapted populations and their F1 hybrids, reared under two temperatures. We found substantial divergence in gene expression and thermal plasticity between populations, with up to 31% of genes being differentially expressed. Reduced thermal plasticity, temperature-dependent gene misexpression, and the disruption of coexpression networks in hybrids point toward a role of regulatory incompatibilities in local adaptation, particularly under colder temperatures. Chromosomal inversions show an accumulation of regulatory incompatibilities but are not consistently enriched for differentially expressed genes. Together, these results suggest that gene regulation can diverge substantially among populations despite gene flow, partly due to the accumulation of temperature-dependent regulatory incompatibilities within inversions.

The rapid expansion of three-spined stickleback (Gasterosteus aculeatus Linnaeus, 1758 (Perciformes, Gasterosteida)) in the pelagic zone of Lake Constance, Central Europe, since 2012 contributed to stark ecosystem-wide effects, such as food-web shifts and declines in native biodiversity, including commercially important fish species. Yet, the origin of this invasive pelagic population remains unclear. Using RAD-sequencing of Lake Constance sticklebacks, we show that the pelagic Lake Constance population likely arose recently within the lake, potentially from the littoral population. We did not detect any substantial genome-wide genetic differentiation between individuals from different habitats, supporting a recent origin of the pelagic population and/or ongoing gene flow. This is further supported by minimal differences in meristic and morphometric traits. However, we also identified multiple outlier loci between littoral and pelagic individuals across the genome, potentially suggesting early signs of adaptation despite high connectivity. In this study, we provide an important example of rapid within-lake ecological diversification of an invasive species from standing genetic variation. Ultimately, our findings will have major implications for the management of invasive pelagic stickleback, as they indicate that the stickleback population has to be managed as a whole and that management efforts cannot only focus on the hyper-abundant pelagic population.

Across its Holarctic range, Arctic charr (Salvelinus alpinus) populations have diverged into distinct trophic specialists across independent replicate lakes. The major aspect of divergence between ecomorphs is in head shape and body shape, which are ecomorphological traits reflecting niche use. However, whether the genomic underpinnings of these parallel divergences are consistent across replicates was unknown but key for resolving the substrate of parallel evolution. We investigated the genomic basis of head shape and body shape morphology across four benthivore-planktivore ecomorph pairs of Arctic charr in Scotland. Through genome-wide association analyses, we found genomic regions associated with head shape (89 SNPs) or body shape (180 SNPs) separately and 50 of these SNPs were strongly associated with both body and head shape morphology. For each trait separately, only a small number of SNPs were shared across all ecomorph pairs (3 SNPs for head shape and 10 SNPs for body shape). Signs of selection on the associated genomic regions varied across pairs, consistent with evolutionary demography differing considerably across lakes. Using a comprehensive database of salmonid QTLs newly augmented and mapped to a charr genome, we found several of the head and body shape associated SNPs were within or near morphology QTLs from other salmonid species, reflecting a shared genetic basis for these phenotypes across species. Overall, our results demonstrate how parallel ecotype divergences can have both population-specific and deeply shared genomic underpinnings across replicates, influenced by differences in their environments and demographic histories.

Animals plastically adjust their physiological and behavioural phenotypes to conform to their social environment—social niche conformance. The degree of sexual competition is a critical part of the social environment to which animals adjust their phenotypes, but the underlying genetic mechanisms are poorly understood. We conducted a study to investigate how differences in sperm competition risk affect the gene expression profiles of the testes and two brain areas (posterior pallium and optic tectum) in breeding male zebra finches (Taeniopygia castanotis). In this pre-registered study, we investigated a large sample of 59 individual transcriptomes. We compared two experimental groups: males held in single breeding pairs (low sexual competition) versus those held in two pairs (elevated sexual competition) per breeding cage. Using weighted gene co-expression network analysis (WGCNA), we observed significant effects of the social treatment in all three tissues. However, only the treatment effects found in the pallium were confirmed by an additional randomisation test for statistical robustness. Likewise, the differential gene expression analysis revealed treatment effects only in the posterior pallium (ten genes) and optic tectum (six genes). No treatment effects were found in the testis at the single gene level. Thus, our experiments do not provide strong evidence for transcriptomic adjustment specific to manipulated sperm competition risk. However, we did observe transcriptomic adjustments to the manipulated social environment in the posterior pallium. These effects were polygenic rather than based on few individual genes with strong effects. Our findings are discussed in relation to an accompanying paper using the same animals, which reports behavioural results consistent with the results presented here.

We investigated how phenotypic plasticity induced by experimentally manipulated sperm competition risk is reflected in transcriptomic profiles of testes and two brain areas (posterior pallium and optic tectum) in breeding male zebra finches ( Taeniopygia guttata ). Based on an exceptionally large sample of 59 individual transcriptomes, we compared two experimental groups: males held in single pairs versus two pairs per breeding cage. We found tissue-specific differential gene expression in all three tissues at the level of gene co-expression network modules. The treatment affected multiple cellular functions in the testes, which can be associated with germ cell production and modification. Moreover, neural and glial brain cell changes indicate phenotypic adjustment of male zebra finch behaviour to the social environment. Finally, individual co-expression modules correlated with individual behavioural phenotypes and hormonal profiles. Our pre-registered study shows the importance of transcriptomic plasticity for phenotypic adjustment to male-male competition in zebra finches. Peter Korsten, Uwe Mayer and Tim Schmoll share the last authorship.

The rapid invasion of the pelagic zone in Lake Constance by three-spined sticklebacks ( Gasterosteus aculeatus ) since 2012 and their subsequent drastic population growth has had stark ecosystem-wide effects, such as food-web shifts and declines in native biodiversity, including commercially important fish species. Yet, the origin of this invasive pelagic ecotype remains unclear. This study aims to determine if the pelagic ecotype arose in situ from the existing littoral population or following external colonisation, identify potential phenotypic differences between individuals from different habitats, and assess genomic signals of selection. Integrating RAD-sequencing of Lake Constance individuals and whole-genome sequence data for European outgroup populations, this study shows that the pelagic Lake Constance population likely arose recently within the lake from the littoral population, with only weak genome-wide differentiation between individuals from different habitats. This is further supported by minimal differences in meristic and morphometric traits, with shape differences only found between pelagic/inflow sticklebacks and littoral sticklebacks. Using genome scans, we identified multiple outlier loci between littoral and pelagic ecotypes across the genome, potentially suggesting early signs of sympatric speciation despite high connectivity. Furthermore, increased differentiation between pelagic and littoral sticklebacks for body shape-associated loci and the overlap of outlier loci with quantitative trait loci for ecologically relevant traits points toward a driving role of selection in this pelagic invasion. This study provides an important example of rapid ecological diversification from standing genetic variation and a rare case of littoral-pelagic ecotype divergence under high gene flow in a large oligotrophic lake. Ultimately, the results of this study will have major implications for the management of the invasive pelagic ecotype, and the entire stickleback population as a whole.

Accurate prediction of vectors dispersal, as well as identification of adaptations that allow blood-feeding vectors to thrive in built environments, are a basis for effective disease control. Here we adopted a landscape genomics approach to assay gene flow, possible local adaptation, and drivers of population structure in Rhodnius ecuadoriensis, an important vector of Chagas disease. We used a reduced-representation sequencing technique (2b-RADseq) to obtain 2,552 SNP markers across 272 R. ecuadoriensis samples from 25 collection sites in southern Ecuador. Evidence of high and directional gene flow between seven wild and domestic population pairs across our study site indicates insecticide-based control will be hindered by repeated re-infestation of houses from the forest. Preliminary genome scans across multiple population pairs revealed shared outlier loci potentially consistent with local adaptation to the domestic setting, which we mapped to genes involved with embryogenesis and saliva production. Landscape genomic models showed elevation is a key barrier to R. ecuadoriensis dispersal. Together our results shed early light on the genomic adaptation in triatomine vectors and facilitate vector control by predicting that spatially-targeted, proactive interventions would be more efficacious than current, reactive approaches.

The levels and distribution of standing genetic variation in a genome can provide a wealth of insights about the adaptive potential, demographic history, and genome structure of a population or species. As structural variants are increasingly associated with traits important for adaptation and speciation, investigating both sequence and structural variation is essential for wholly tapping this potential. Using a combination of shotgun sequencing, 10X Genomics linked reads and proximity-ligation data (Chicago and Hi-C), we produced and annotated a chromosome-level genome assembly for the Atlantic silverside ( Menidia menidia ) - an established ecological model for studying the phenotypic effects of natural and artificial selection - and examined patterns of genomic variation across two individuals sampled from different populations with divergent local adaptations. Levels of diversity varied substantially across each chromosome, consistently being highly elevated near the ends (presumably near telomeric regions) and dipping to near zero around putative centromeres. Overall, our estimate of the genome-wide average heterozygosity in the Atlantic silverside is the highest reported for a fish, or any vertebrate, to date (1.32-1.76% depending on inference method and sample). Furthermore, we also found extreme levels of structural variation, affecting ~23% of the total genome sequence, including multiple large inversions (> 1 Mb and up to 12.6 Mb) associated with previously identified haploblocks showing strong differentiation between locally adapted populations. These extreme levels of standing genetic variation are likely associated with large effective population sizes and may help explain the remarkable adaptive divergence among populations of the Atlantic silverside.

Understanding the contribution of different molecular processes to evolution and development is crucial for identifying the mechanisms of adaptation. Here, we used RNA-sequencing data to test the importance of alternative splicing and differential gene expression in a case of parallel adaptive evolution, the replicated postglacial divergence of the salmonid fish Arctic charr (Salvelinus alpinus) into sympatric benthic and pelagic ecotypes across multiple independent lakes. We found that genes differentially spliced between ecotypes were mostly not differentially expressed (<6% overlap) and were involved in different biological processes. Differentially spliced genes were primarily enriched for muscle development and functioning, while differentially expressed genes were involved in metabolism, immunity and growth. Furthermore, alternative splicing and gene expression were mostly controlled by independent cis-regulatory quantitative trait loci (<3.4% overlap). Cis-regulatory regions were associated with the parallel divergence in splicing (16.5% of intron clusters) and expression (6.7%-10.1% of differentially expressed genes), indicating shared regulatory variation across ecotype pairs. Contrary to theoretical expectation, we found that differentially spliced genes tended to be highly central in regulatory networks ("hub genes") and were annotated to significantly more gene ontology terms compared to nondifferentially spliced genes, consistent with a higher level of pleiotropy. Together, our results suggest that the concerted regulation of alternative splicing and differential gene expression through different regulatory regions leads to the divergence of complementary processes important for local adaptation. This provides novel insights into the importance of contrasting but putatively complementary molecular processes in rapid parallel adaptive evolution.