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Distinct genetic architectures underlie divergent thorax, leg, and wing pigmentation between Drosophila elegans and D. gunungcola

Understanding the genetic basis of species differences is a major goal in evolutionary biology. Pigmentation divergence between Drosophila species often involves genetic changes in pigmentation candidate genes that pattern the body and wings, but it remains unclear how these changes affect pigmentation evolution in multiple body parts between the same diverging species. Drosophila elegans and D. gunungcola show pigmentation differences in the thorax, legs, and wings, with D. elegans exhibiting male-specific wing spots and D. gunungcola lacking wing spots with intensely dark thoraces and legs. Here, we performed QTL mapping to identify the genetic architecture of these differences. We find a large effect QTL on the X chromosome for all three body parts. QTL on Muller Element E were found for thorax pigmentation in both backcrosses but were only marginally significant in one backcross for the legs and wings. Consistent with this observation, we isolated the effects of the Muller Element E QTL by introgressing D. gunungcola alleles into a D. elegans genetic background and found that D. gunungcola alleles linked near the pigmentation candidate gene ebony caused intense darkening of the thorax, minimal darkening of legs, and minimal shrinking of wing spots. D. elegans ebony mutants showed changes in pigmentation consistent with Ebony having different effects on pigmentation in different tissues. Our results suggest that multiple genes have evolved differential effects on pigmentation levels in different body regions.

evolutionary biology↗

Eocene origin, Miocene diversification and intercontinental dispersal of the genus Drosera (Droseraceae)

Resolving the evolutionary history of plant carnivory is of great interest to biologists throughout the world. Among the carnivorous plants, Genus Drosera (Droseraceae) is highly diverse with a wide pantropical distribution. Despite being a group of interest for evolutionary biology studies since the time of Charles Darwin, the historical biogeography of this group remains poorly understood. In this study, with an improved species sampling from Genbank, we present a reanalyzed phylogenetic hypothesis of the genus Drosera. We developed a dated molecular phylogeny of Drosera from DNA sequences of nuclear ITS and chloroplast rbcL genes. Divergence times were estimated on the combined dataset using an uncorrelated lognormal relaxed clock model and a known fossil calibration implemented in BEAST. The maximum clade credibility tree was then used for ancestral range estimations using DEC+J model implemented in BioGeoBEARS. Our analysis suggests that Drosera evolved during the Mid Eocene 36 Ma [95% HPD: 49.5-26] and have diversified and dispersed from the late Miocene onwards. Ancestral areas estimated using the DEC+J models suggest an African origin followed major radiation within Australia. Diversification in Drosera is temporally congruent with the prevailing drier conditions during the Miocene. From Miocene, grasslands and open habitats dominated across continents and might have provided ecological opportunities for their dispersal and diversification. Several long-distance dispersals and range extensions and in situ radiations coinciding with the evolution of drier conditions can explain their extant distribution across continents. Overall our data set provides fresh insights into the biogeographic factors that shaped the origin and evolution of the genus Drosera.

evolutionary biology↗

Non-linear phenotypic variation uncovers the emergence of heterosis in Arabidopsis thaliana

Heterosis describes the phenotypic superiority of hybrids over their parents in traits related to fitness. Understanding and predicting non-additive inheritance such as heterosis is crucial for evolutionary biology, as well as for plant and animal breeding. However, the physiological bases of heterosis remain debated. Moreover, empirical data in various species have shown that diverse genetic and molecular mechanisms are likely to explain heterosis, making it difficult to predict its emergence and amplitude from parental genotypes alone. In this study, we evaluated a model of physiological dominance proposed by Sewall Wright to explain the non-additive inheritance of metabolic fluxes at the cellular level. We used 450 hybrids derived from crosses among natural inbred accessions of Arabidopsis thaliana to test Wrights model for two fitness-related traits at the whole-plant level: growth rate and fruit number. We found that allometric relationships between traits constrain phenotypic variation in hybrids and inbreds to a similar extent. These allometric relationships behave predictably, in a non-linear manner, explaining up to 75% of heterosis amplitude, while genetic distance among parents at best explains 7%. Thus, our findings are consistent with Wrights model of physiological dominance on plant performance, and suggest that the emergence of heterosis is an intrinsic property of non-linear relationships between traits. Furthermore, our study highlights the potential of a geometric approach of phenotypic relationships for predicting heterosis of two major components of crop productivity and yield.

evolutionary biology↗

Adaptive Evolution Of Transcription Factor Binding Affinities

Understanding the molecular basis of gene expression evolution is a central problem in evolutionary biology. However, connecting changes in gene expression to increased fitness, and identifying the functional basis of those changes, remains challenging. To study adaptive evolution of gene expression in real time, we performed long term experimental evolution (LTEE) of Saccharomyces cerevisiae (budding yeast) in ammonium-limited chemostats. Following several hundred generations of continuous selection we found significant divergence of nitrogen-responsive gene expression in lineages with increased fitness. In multiple independent lineages we found repeated selection for non-synonymous mutations in the zinc finger DNA binding domain of the activating transcription factor (TF), GAT1, that operates within incoherent feedforward loops to control expression of the nitrogen catabolite repression (NCR) regulon. Missense mutations in the DNA binding domain of GAT1 reduce its binding affinity for the GATAA consensus sequence in a promoter-specific manner, resulting in increased expression of ammonium permease genes via both direct and indirect effects, thereby conferring increased fitness. We find that altered transcriptional output of the NCR regulon results in antagonistic pleiotropy in alternate environments and that the DNA binding domain of GAT1 is subject to purifying selection in natural populations. Our study shows that adaptive evolution of gene expression can entail tuning expression output by quantitative changes in TF binding affinities while maintaining the overall topology of a gene regulatory network.

evolutionary biology↗

The interplay between developmental stage and environment determines the adaptive effect of a natural transposable element insertion

Establishing causal links between adaptive mutations and their ecologically relevant phenotypes is key to understanding the process of adaptation, a central goal in evolutionary biology that is also relevant for conservation biology, medicine and agriculture. Although progress has been made, the number of causal adaptive mutations identified so far is still limited as gene by gene, and gene by environment interactions, among others, complicates linking genetic variation with its fitness-related effects. Transposable elements, often ignored in the quest for the genetic basis of adaptive evolution, are known to be a genome-wide source of regulatory elements across organisms that at times can lead to adaptive phenotypes. In this work, we combine gene expression, in vivo reporter assays, CRISPR/Cas9 genome editing, and survival experiments to characterize in detail the molecular and phenotypic consequences of a natural Drosophila melanogaster transposable element insertion: the roo solo-LTR FBti0019985. This transposable element provides an alternative promoter to the transcription factor Lime, involved in cold- and immune-stress responses. We found that the effect of FBti0019985 on Lime expression depends on the interplay between the developmental stage and the environmental conditions. We further establish a causal link between the presence of FBti0019985 and increased survival to cold- and immune-stress. Our results exemplify how several developmental stages and environmental conditions need to be considered to characterize the molecular and functional effects of a genetic variant, and add to the growing body of evidence that transposable elements can induce complex mutations with ecologically relevant effects.

evolutionary biology↗

Mosaic of Somatic Mutations in the Ancient and Still-Living Aspen Clone, Pando

While evolutionary biology traditionally focuses on the spread of mutations within populations, the dynamics of mutational spread within individuals, particularly in long-lived clonally-spreading organisms, remain poorly understood. Here we examine the genetic structure of Pando, Earths largest known quaking aspen (Populus tremuloides) clone. We sequenced over 500 samples across Pando and neighboring clones, including multiple tissue types. At fine spatial scales, we detected significant genetic structure, particularly in leaf tissue, but this signal weakened across larger distances, suggesting either rapid root growth homogenizes the system over time or mechanisms exist that prevent widespread mutation transmission. Phylogenetic analyses date Pando between [~]12,000 and 37,000 years old, supported by continuous aspen pollen presence in nearby lake sediments. Tissues accumulated mutations at different rates, with leaves showing significantly higher mutation loads than roots or branches. This work provides the first quantitative age estimate for this remarkable organism and offers initial insights into the spatial dynamics of somatic mutation in a massive clonal plant. While our reduced-representation sequencing approach limits detection of rare variants, these findings establish a foundation for understanding how long-lived modular organisms accumulate and distribute genetic variation, questions that will benefit from future high-coverage whole-genome sequencing across tissues.

evolutionary biology↗

Gene conversion facilitates the adaptive evolution of self-resistance in highly toxic newts

Reconstructing the histories of complex adaptations and identifying the evolutionary mechanisms underlying their origins are two of the primary goals of evolutionary biology. Taricha newts, which contain high concentrations of the deadly toxin tetrodotoxin (TTX) as an antipredator defense, have evolved resistance to self-intoxication, which is a complex adaptation requiring changes in six paralogs of the voltage-gated sodium channel (Nav) gene family, the physiological target of TTX. Here, we reconstruct the origins of TTX self-resistance by sequencing the entire Nav gene family in newts and related salamanders. We show that moderate TTX resistance evolved early in the salamander lineage in three of the six Nav paralogs, preceding the proposed appearance of tetrodotoxic newts by [~]100 million years. TTX-bearing newts possess additional unique substitutions across the entire Nav gene family that provide physiological TTX resistance. These substitutions coincide with signatures of positive selection and relaxed purifying selection, as well as gene conversion events, that together likely facilitated their evolution. We also identify a novel exon duplication within Nav1.4 encoding an expressed TTX-binding site. Two resistance-conferring changes within newts appear to have spread via nonallelic gene conversion: in one case, one codon was copied between paralogs, and in the second, multiple substitutions were homogenized between the duplicate exons of Nav1.4. Our results demonstrate that gene conversion can accelerate the coordinated evolution of gene families in response to a common selection pressure.

evolutionary biology↗

Testing Wright's Intermediate Population Size Hypothesis - When Genetic Drift is a Good Thing

In his 1931 monograph, Sewall Wright predicted genetic drift would overwhelm selection in very small populations, and selection would dominate in large ones, but also concluded drift could facilitate selection in populations of intermediate size. The idea that drift and selection would act together in smaller populations has not been evaluated using analytical or numerical approaches even as empirical evidence of rapid evolution associated with population bottlenecks has continued to accumulate. I used forward-time simulations with random mating and discrete generations to test the hypothesis that drift can facilitate selection in small populations. I find evidence of drift facilitation of selection as increases in levels of{Delta} q in small populations (N<100) when selection is weak (s<0.2) and when allele frequencies are low (q<0.5). Fixation of beneficial mutations is accelerated by drift facilitation in small populations for recessive and codominant alleles, and less so for dominant alleles. Drift facilitation accelerated fixation of beneficial mutations in small populations compared to predictions from diffusion equations, while fixation time was longer than predicted in large populations. Drift facilitation increases the probability of fixation of new mutations in small populations. Accumulation of beneficial mutations (fixation flux) over several thousand generations was high in small populations and declined rapidly for large populations, which accumulated large amounts of standing genetic variation. Even though selection is more efficient in large populations, the increased time for allele replacement and lack of drift facilitation can result in substantially slower rates of adaptive evolution. Small populations were more susceptible to the accumulation of drift load, while larger populations maintained higher levels of segregation load. These results indicate that drift facilitation in small populations promotes purging of genetic load and accelerated fixation of beneficial mutations, and may account for the large number of observations of rapid adaptation during population bottlenecks. Impact Summary - After the recognition of Gregor Mendels contributions to our understanding of the inheritance of genetically-determined traits around 1900, there was confusion as to whether the type of variation Mendel studied could account for evolution by natural selection, as described by Charles Darwin. This controversy was resolved when three theoreticians (Ronald Fisher, Sewell Wright, and J.B.S. Haldane) published books that integrated Mendelian genetics with evolution. Their contributions (referred to as the Modern Synthesis), focused on evolutionary processes occurring within and among populations of a species, and established a mathematical foundation for our understanding of evolutionary biology. The mathematical models developed by the three architects of the modern synthesis, and those who followed, predicted that the effects of natural selection would be overwhelmed by random genetic changes (referred to as Genetic Drift) in small populations, and that genetic drift would be minimal, while selection would be most effective in large populations. Even though one of Wrights major conclusions was that genetic drift and selection would work together (Drift Facilitation) to promote adaptive evolution in intermediate-sized populations, this idea has been almost completely ignored since it was first introduced in 1931. In this study, I use simulations of evolution in natural populations to evaluate the potential for drift facilitation to promote evolution in small populations. My work largely confirms Wrights predictions; the removal of deleterious mutations and promotion of adaptive evolution are enhanced in population sizes ranging from about 10 to 100. These results indicate that our paradigm for our understanding of evolution within populations needs refinement to emphasize the importance of drift facilitation in small populations, and to recognize that periods of reduced population size are opportunities for enhanced levels of adaptive evolution. "In a population of intermediate size ... there is continual random shifting of gene frequencies ... which leads to a relatively rapid, continuing, irreversible, and largely fortuitous, but not degenerative series of changes, even under static conditions." Wright 1931, Page 157.

evolutionary biology↗

Low-dimensional genotype-fitness mapping across divergent environments suggests a limiting functions model of fitness

A central goal in evolutionary biology is to be able to predict the effect of a genetic mutation on fitness. This is a major challenge because fitness depends both on phenotypic changes due to the mutation, and how these phenotypes map onto fitness in a particular environment. Genotype, phenotype, and environment spaces are extremely large and complex, rendering bottom-up prediction difficult. Here we show, using a large collection of adaptive yeast mutants, that fitness across a set of lab environments can be well-captured by low-dimensional linear models of abstract genotype-phenotype-fitness maps. We find that these maps are low-dimensional not only in the environment where the adaptive mutants evolved, but also in divergent environments. We further find that the genotype-phenotype-fitness spaces implied by these maps overlap only partially across environments. We argue that these patterns are consistent with a "limiting functions" model of fitness, whereby only a small number of limiting functions can be modified to affect fitness in any given environment. The pleiotropic side-effects on non-limiting functions are effectively hidden from natural selection locally, but can be revealed globally. These results combine to emphasize the importance of environmental context in genotype-phenotype-fitness mapping, and have implications for the predictability and trajectory of evolution in complex environments.

evolutionary biology↗

Analysis of multi-trait evolution across independently evolved cavefish populations reveals shared and independent evolution of suites of cave-associated traits

Environmental perturbations often lead to the evolution of multiple traits. Determining whether shared genetic factors underlie multi-trait evolution is a central question in evolutionary biology. In the Mexican tetra, Astyanax mexicanus, cave-dwelling populations have repeatedly evolved multiple traits. The repeated evolution of these traits, paired the robust environmental differences between the surface and cave habitats, provide an opportunity to investigate the genetic basis of multi-trait evolution. Here, we investigate the extent to which shared genetic mechanisms underlie the repeated evolution of multiple traits in cavefish. Across cave populations, we find evidence for shared and distinct genetic mechanisms contributing to the evolution of individual traits. Further, multiple traits covary in cave-surface F2 hybrids and many of the same trait correlations are found across independently evolved cave populations. Finally, we assessed traits that differ between pigmented and albino F2 fish in surface fish with mutations in the albinism gene oculocutaneous albinism 2 (oca2). This revealed that mutations in oca2 reduce bottom-dwelling behavior in A. mexicanus. Together, these findings suggest that multi-trait evolution occurs repeatedly through shared genetic factors across A. mexicanus cave populations. These results are consistent with pleiotropy or linkage playing a large role in multi-trait evolution in this species.

evolutionary biology↗

Independent genetic mapping experiments identify diverse molecular determinants of host adaptation in a generalist herbivore

Interactions between plants and herbivores promote evolutionary change. Studying the evolution of herbivore mechanisms aimed to cope with diUerent host plant species is a critical intersection between evolutionary biology and sustainable pest management. Generalist herbivores are of particular interest, as hybridization between genetically distinct populations can increase the standing genetic variation and therefore the adaptive potential of the species. Tetranychus urticae is a generalist arthropod known for its adaptive potential, evidenced in its immense host range and ability to develop metabolic resistance to xenobiotics. However, the molecular underpinnings associated with the potential of host adaptation and the consequences of host adaptation in this and many other pests remain elusive. Here, we use two independent, empirical approaches to identify and map the genetic basis of host plant performance and adaptation in genetically distinct populations of T. urticae. In the first approach, we subject a genetically diverse mite population to tomato selection and map genomic regions linked to the phenotypic evolution of increased reproductive performance. In the second approach, we map genomic regions responsible for performance on tomato by comparing the genomes of pooled individuals from a F2 backcross between populations with high and low reproductive performance. Both approaches revealed specific and shared genomic regions associated with host plant performance and adaptation and key candidate genes were identified. Our findings highlight the power of spider mite genetic approaches to identify the complex genetic basis of host adaptation in a generalist herbivore.

evolutionary biology↗

Multiple genetic changes underlie the evolution of long-tailed forest deer mice

Understanding both the role of selection in driving phenotypic change and its underlying genetic basis remain major challenges in evolutionary biology. Here we focus on a classic system of local adaptation in the North American deer mouse, Peromyscus maniculatus, which occupies two main habitat types, prairie and forest. Using historical collections we demonstrate that forest-dwelling mice have longer tails than those from non-forested habitats, even when we account for individual and population relatedness. Based on genome-wide SNP capture data, we find that mice from forested habitats in the eastern and western parts of their range form separate clades, suggesting that increased tail length evolved independently from a short-tailed ancestor. Two major changes in skeletal morphology can give rise to longer tails--increased number and increased length of vertebrae--and we find that forest mice in the east and west have both more and longer caudal vertebrae, but not trunk vertebrae, than nearby prairie forms. Using a second-generation intercross between a prairie and forest pair, we show that the number and length of caudal vertebrae are not correlated in this recombinant population, suggesting that variation in these traits is controlled by separate genetic loci. Together, these results demonstrate convergent evolution of the long-tailed forest phenotype through multiple, distinct genetic mechanisms (controlling vertebral length and vertebral number), thus suggesting that these morphological changes--either independently or together--are adaptive.

Evolutionary Biology↗

Genomic tree scans identify loci underlying adaptive peaks in Antirrhinum

A key question in evolutionary biology is how barriers to gene flow operate and arise between populations, leading to speciation. Barriers are typically identified by comparing populations distinguished by phenotype, geographical location and/or environment. However, such prior classifications may bias recovery towards features obvious to the human eye, influencing mechanistic interpretations. Here we develop a method blind to prior classifications. We apply it to 18 Antirrhinum populations occupying habitats from coastal to alpine. By scanning the genome for regions with deeply rooted similar trees, we identify a single multi-locus partition, comprising less than 0.5% of the genome. It derives from eight genes, three newly identified here, which interact to generate complementary pollinator guides, likely corresponding to two adaptive peaks in a fitness landscape. Hybrid genotypes fall in a fitness valley, allowing the partition to be maintained through hybrid incompatibility and creating steep clines in allele frequency at a hybrid zone. Another partition derives from a single locus linked to a gene controlling plant height. The locus exhibits a shallow cline in allele frequency across an eco-geographic barrier and may be eco-adaptive. Our results suggest that two ancestral subspecies underwent extensive gene flow except at a few barrier loci, showing how both hybrid incompatibility and eco-adaptation can operate to maintain diversity.

evolutionary biology↗

Admixture influences the genetic architecture of DNA methylation in a wild primate hybrid zone

BackgroundHybrid zones play a central role in evolutionary biology because they serve as natural laboratories for studying how traits and taxa diverge. Changes in gene regulation make important contributions to this process. However, the degree to which admixture shapes gene regulatory variation in hybrid populations remains poorly understood. Here, we combine genome-wide resequencing and DNA methylation data from 295 hybrid baboons--members of a single, intensively studied natural population--to investigate how admixture affects the genetic architecture of this important epigenetic mark. ResultsWe find that local genetic ancestry frequently predicts DNA methylation levels and recapitulates differences between the parent species. By performing methylation quantitative trait locus (meQTL) mapping, we show that these differences predominantly arise due to evolved differences in allele frequencies. Thus, admixture in the hybrid population increases variance in DNA methylation, including by introducing meQTL that would otherwise be invariant. Finally, we integrate massively parallel reporter assay data to show that admixture-derived variation in DNA methylation alters enhancer activity and gene expression. ConclusionsTogether, these results demonstrate how admixture can meaningfully alter the genetic architecture of gene regulatory traits in natural hybrid zones. They also suggest that the genetic architecture of DNA methylation is conserved across closely related primates, suggesting that genetic effects on gene regulation may remain stable over timescales that range into the millions of years.

evolutionary biology↗

DGEN: A Test Statistic for Detection of General Introgression Scenarios

When two species hybridize, one outcome is the integration of genetic material from one species into the genome of the other, a process known as introgression. Detecting introgression in genomic data is a very important question in evolutionary biology. However, given that hybridization occurs between closely related species, a compli-cating factor for introgression detection is the presence of incomplete lineage sorting, or ILS. The D-statistic, famously referred to as the \"ABBA-BABA\" test, was pro-posed for introgression detection in the presence of ILS in data sets that consist of four genomes. More recently, DFOIL--a set of statistics--was introduced to extend the D-statistic to data sets of five genomes.\n\nThe major contribution of this paper is demonstrating that the invariants underly-ing both the D-statistic and DFOIL can be derived automatically from the probability mass functions of gene tree topologies under the null species tree model and alterna-tive phylogenetic network model. Computational requirements aside, this automatic derivation provides a way to generalize these statistics to data sets of any size and with any scenarios of introgression. We demonstrate the accuracy of the general statistic, which we call DGEN, on simulated data sets with varying rates of introgression, and apply it to an empirical data set of mosquito genomes.\n\nWe have implemented DGEN and made it available, both as a graphical user interface tool and as a command-line tool, as part of the freely available, open-source software package ALPHA (https://github.com/chilleo/ALPHA).

evolutionary biology↗

Sex differentiation and a chromosomal inversion lead to cryptic diversity in Lake Tanganyika sardines

Identifying patterns in genetic structure and the genetic basis of ecological adaptation is a core goal of evolutionary biology and can inform the management and conservation of species that are vulnerable to population declines exacerbated by climate change. We used reduced representation genomic sequencing methods to gain a better understanding of genetic structure among and within populations of Lake Tanganyikas two sardine species, Limnothrissa miodon and Stolothrissa tanganicae. Samples of these ecologically and economically important species were collected across the length of Lake Tanganyika, as well as from nearby Lake Kivu, where L. miodon was introduced in 1959. Our results reveal unexpected differentiation within both S. tanganicae and L. miodon that is not explained by geography. Instead, this genetic differentiation is due to the presence of large sex-specific regions in the genomes of both species, but involving different polymorphic sites in each species. Our results therefore indicate rapidly evolving XY sex determination in the two species. Additionally, we found evidence of a large segregating inversion in L. miodon. We found all inversion karyotypes throughout Lake Tanganyika, but the frequencies vary along a north-south gradient, and differ substantially in the introduced Lake Kivu population. We do not find evidence for significant isolation-by-distance, even over the hundreds of kilometers covered by our sampling, but we do find shallow population structure.

evolutionary biology↗

Comparison of the full distribution of fitness effects of new amino acid mutations across great apes

The distribution of fitness effects (DFE) is central to many questions in evolutionary biology. However, little is known about the differences in DFEs between closely related species. We use more than 9,000 coding genes orthologous one-to-one across great apes, gibbons, and macaques to assess the stability of the DFE across great apes. We use the unfolded site frequency spectrum of polymorphic mutations (n = 8 haploid chromosomes per population) to estimate the DFE. We find that the shape of the deleterious DFE is strikingly similar across great apes. We confirm that effective population size (Ne) is a strong predictor of the strength of negative selection, consistent with the Nearly Neutral Theory. However, we also find that the strength of negative selection varies more than expected given the differences in Ne between species. Across species, mean fitness effects of new deleterious mutations co-varies with Ne, consistent with positive epistasis among deleterious mutations. We find that the strength of negative selection for the smallest populations: bonobos and western chimpanzees, is higher than expected given their Ne. This may result from a more efficient purging of strongly deleterious recessive variants in these populations. Forward simulations confirm that these findings are not artifacts of the way we are inferring Ne and DFE parameters. All findings are replicated using only GC-conservative mutations, thereby confirming that GC-biased gene conversion is not affecting our conclusions.

evolutionary biology↗

The epigenomic landscape of deep lineage divergence: The case of the European sea bass

BackgroundUnderstanding the role of non-coding genomic variation in speciation remains a major challenge in evolutionary biology. Here, we investigated whether regulatory elements contribute to this process between Atlantic and Mediterranean lineages of European sea bass (Dicentrarchus labrax), a well-characterized case-study near speciation where barriers to introgression exist in the presence of connectivity between diverging populations. ResultsWe generated a novel, highly contiguous genome assembly, which was annotated at the epigenomic level using ATAC-seq and ChIP-seq with six embryonic developmental stages and five tissue types in adult fish, identifying thousands of promoters, enhancers, and open chromatin regions. Integrating this annotation with whole-genome sequence data from 65 individuals across three geographically distinct populations, we identified 57,505 outlier SNPs and 332 structural variants (SVs) showing elevated differentiation between Atlantic and East Mediterranean lineages. Outlier SVs affected key regulatory elements and coding genes, while outlier SNPs were enriched in regulatory elements, particularly enhancers active in adult tissues. Local genomic divergence correlated positively with regulatory element density, especially on chromosomes 1, 9, and 18, which are enriched in genes related to osmoregulation, immune response, and oxidative stress -- processes relevant to adaptation across contrasting marine environments. ConclusionsThese findings support a major role for regulatory variation in driving deep lineage divergence through local adaptation.

evolutionary biology↗