Molecular Ecology

Closely related sympatric species are hypothesized to face strong selection against hybridization, favoring species-specific signals that maintain reproductive isolation. Within species, olfaction may also mediate social interactions and facilitate social cohesion. Here, we investigated the potential for microbiome-derived scent signals to contribute to inter- and intra-species communication in two sympatric wild tamarins (Leontocebus weddelli and Tamarinus subgrisescens). We analyzed scent gland samples to characterize odor profiles (volatile organic compounds, VOCs) and microbiome taxonomic composition and putative functions from metagenomic shotgun sequences. Species membership was predicted accurately from microbiome profiles, whereas VOCs alone discriminated poorly between species. We found high abundance of Corynebacterium in L. weddelli, a genus associated with fatty acid metabolism, alongside the exclusive detection of acetic acid, highlighting microbially derived fatty acids as candidates for further investigation in this species. In T. subgrisescens, we found a more diverse microbiota, with fewer taxa known to be related to odor production, while VOC profiles appeared less variable among individuals. In contrast, group-level signatures were weak, suggesting that intra-specific odor may not strongly contribute to signaling group membership. We highlight the challenge of linking high-dimensional microbial communities, which include taxa not necessarily involved in odor production, to the smaller dataset of detectable VOCs. Although scent gland microbiota differed between tamarin species, whether these differences translate into species-specific odor cues remains to be tested. Future research involving behavioural assays and targeted experimental approaches that focus on key microbes and metabolites may shed further insight into roles and mechanisms of olfactory communication.

Endangered species often suffer from genetic threats such as inbreeding depression, the accumulation of mutation load and the general loss of genetic diversity, which may deprive them from future adaptation. Since the genetic make-up of a species is strongly affected by its evolutionary past, however, interspecific comparisons are difficult and absolute levels of genetic diversity may be a relatively poor predictor of extinction risk. To better interpret current levels of genetic diversity of actively managed species, the comparison of present-day genomic data to that of ancient material pre-dating recent anthropogenic population declines has been advocated, but remains rarely done at the evolutionary time scales necessary to understand past population dynamics. Here we demonstrate the usefulness of deep genomic time series through 40 high quality ancient genomes of the Alpine ibex, which faced near-extinction in the 19th century but has since been reintroduced across the Alps and recovered remarkably. The samples, which span the last 14,000 years, evidence strong and stable population structure at the continental scale, paired with frequent extinction and recolonization events at the local scale. These metapopulation dynamics resulted in small and largely isolated populations, with present-day, reintroduced populations only having 20% to 40% less neutral genetic diversity and 3% higher mutation load, likely due to efficient purging in the past. At the species level, however, the loss of genetic diversity was dramatic and reduced to the small fraction that segregated within the only surviving population in the Gran Paradiso area. Our analyses of ancient metapopulation dynamics in Alpine ibex underscore the importance of a healthy genetic pool for successful recolonization and long-term survival, as well as the real possibility of regional extinctions.

Gene flow between diverging species can reshuffle genomic variation and greatly influence the speciation process, sometimes reinforcing, sometimes eroding species boundaries. However, the effect of ecological and historical processes on the patterns of introgression remains poorly understood. Here, we focus on the evolutionary history of Heliconius besckei, a geographically restricted butterfly endemic to the Brazilian Atlantic Forest, together with the mimetic H. melpomene nanna, the sympatric non-mimetic H. ethilla narcaea, and its closely related H. numata robigus. Using whole-genome sequencing, genome-wide tests of introgression, demographic modelling and palaeoclimatic species distribution models, we tested the extent and timing of interspecific gene flow in relation to mimicry, ecological context, and changes in geographic overlap. Despite strong genomic differentiation among the four focal Heliconius species, we detected widespread signatures of interspecific gene flow, greatly influenced by geographical overlap. Demographic models including post-divergence gene flow were better supported than strict-isolation models. In addition, genome-wide introgression analyses showed more numerous and larger candidate introgressed regions between H. besckei and H. ethilla narcaea, consistent with recurrent opportunities for exchange between these currently sympatric species. Species distribution models further recovered repeated expansions of suitable habitat for H. besckei during cold periods, providing a potential geographic context for secondary contact within the Atlantic Forest. Together, our results reveal recurrent gene flow occurring under different temporal, geographic, and potentially selective contexts, and show that the evolutionary history of a geographically restricted lineage can be shaped by repeated genetic exchange while substantial species differentiation is maintained.

DNA methylation, an epigenetic mechanism, has been proposed as a basis for Lamarckian inheritance of acquired characteristics. This hypothesis raises questions about environmental induction of DNA methylation, its persistence across generations, and associations with gene expression. We investigated these processes in the California oak, Quercus lobata. Based on 40 range-wide adult trees and their progeny grown in two common gardens, we tested four predictions: (i) DNA methylation is environmentally induced; (ii) methylation shows parent-offspring correspondence; (iii) environmentally induced patterns remain stable after transmission; and (iv) DNA methylation is associated with gene expression, varying by sequence context and TE proximity. Using methylomes and transcriptomes, we found support for all predictions except the third: CHH methylation was environmentally induced, but rarely showed parent/offspring correspondence, whereas CG methylation showed the opposite pattern. DNA methylation was associated with gene expression, depending on the sequence context and proximity to TEs. We identified one stress-associated gene with environmentally responsive CHH methylation that showed parent offspring correspondence in two common gardens in both gardens. Still, overall evidence for Lamarckian like evolution is not compelling. Nevertheless, DNA methylation was environmentally responsive, showed parent offspring correspondence, and was associated with gene expression, highlighting its potential importance for the ecological and evolutionary responses of long-lived trees to environmental change.

Chromosomal inversions are proposed to aid local adaptation to divergent habitats when there is gene flow by creating regions of low recombination that can maintain tight linkage between multiple locally adaptive alleles. However, key theoretical predictions about the role of chromosomal inversions in local adaptation remain largely untested in empirical systems. Here, we test the prediction that inversions will concentrate relatively small genetic effects across multiple ecologically relevant traits by exploring inversion-phenotype associations of three inversions in threespine stickleback (Gasterosteus aculeatus). Using complementary approaches of association mapping in wild-caught individuals and genetic mapping in lab-raised individuals from two divergent genomic backgrounds, we found that an inversion on chromosome XXI influences multiple ecologically relevant traits. The inversion has small-to-moderate effects on these traits, as expected for inversions involved in polygenic adaptation. Further consistent with theoretical predictions, inversion heterozygotes show intermediate phenotypes. While most inversion-phenotype associations are consistent across different genomic backgrounds and experimental approaches, some inversion-phenotype associations were specific to a single dataset. These results indicate that the phenotypic effects of inversions are shaped by both genomic and environmental context, which could facilitate population-specific adaptation. Together, these results support the role of the chromosome XXI inversion in ecological divergence in threespine stickleback. More broadly, our results suggest that inversions can contribute to local adaptation by preserving linkage between small-effect adaptive alleles despite extensive gene flow.

While studies of molecular convergence typically focus on species that independently evolved similar phenotypes, similar questions can be asked among populations of different species adapting to the same environment. Here, we study the Baltic Sea environmental gradient and two co-distributed, ecologically similar, but distantly related pipefish species, the broadnosed pipefish (Syngnathus typhle) and the straightnose pipefish (Nerophis ophidion), to test whether independent colonization of the Baltic Sea led to similar population structure and caused convergence at different genomic levels. Using a new diploid genome for S. typhle and whole-genome resequencing data (N=99 for S. typhle; N=81 for N. ophidion) across seven locations from France to Finland, we identified stronger population structure in S. typhle than in N. ophidion, while both species showed differentiation between North Atlantic, Danish Straits, and Baltic Sea populations. Genetic diversity was lower in Baltic populations, particularly in S. typhle. Cross-species comparisons of Baltic populations revealed contrasting chromosome-level patterns of genomic differentiation, with differentiation spread across the genome in S. typhle but concentrated in specific chromosomal regions in N. ophidion. Nonetheless, we identified multiple orthologous genes and SNPs showing convergent differentiation in the Baltic populations of both species, including genes related to metabolism, immunity, and regulatory functions. Overall, we identified molecular convergence at the gene and nucleotide level between Baltic populations of distantly related pipefish species, while convergence was limited at broader genomic scales. These findings suggest that similar environmental pressures can repeatedly target specific genetic elements even when genomic backgrounds and population structures differ.

Marine species with broad distributions often exhibit complex patterns of genetic connectivity, shaped by historical and contemporary processes. Understanding these patterns is critical for conserving taxa threatened by ongoing and future environmental change. Here, we use reduced-representation and whole-genome sequencing to investigate population genetic patterns in three co-occurring sea snake species (Hydrophis stokesii, Hydrophis major, and Aipysurus laevis) across northern Australia and New Caledonia. Broadscale analyses revealed major genetic breaks across all species between: (1) Australia and New Caledonia, (2) northwestern and northeastern Australia, and (3) the offshore Timor Sea reefs and adjacent northwestern continental shelf of Australia. More subtle genetic differentiation was observed between Shark Bay in Western Australia and northern localities. All species showed relatively large effective population sizes and broadscale connectivity across ~1,300 km of Australia's northwestern continental shelf. This likely reflects substantial historical range expansion over late Quaternary timescales, which may have contributed to the observed genetic connectivity across the region. However, subtle patterns of isolation by distance emphasised the contribution of species-specific traits in shaping connectivity. The isolated offshore reef populations are genetically distinct and potentially threatened by environmental change. Disjunct populations in Shark Bay and the Timor Sea maintain similar levels of genetic diversity to the extensive continental shelf populations, while New Caledonian populations exhibit reduced diversity. Our results support the delineation of spatial units for sea snake conservation based on shared phylogeographic structure, while also finding important population- and species-specific differences in connectivity at finer spatial and temporal scales.

Intraspecific variation in microbial symbioses is shaped by a variety of ecological and evolutionary processes. In geographically separated populations, divergence in genomic traits is expected due to dispersal barriers and habitat differentiation, whereas sympatric populations might exhibit functional convergence to the characteristics of a shared environment. While these two processes have been well documented in many animal and plant species, they remain understudied in symbiotic systems. Here, we examined these processes in Atlantic cold seep mussel species that associate with environmentally acquired methane and/or sulfur-oxidizing bacteria. Using genomic methods, we reveal an eco-geographical barrier between the Western Atlantic and Gulf of Mexico that influences the distribution of symbiont species and the level of divergence between holobiont populations. While host populations were only slightly differentiated across this divide, symbiont populations were structured both between and within regions. The sulfur-oxidizing symbionts contained different regional types of dissimilatory nitrate reductase, possibly due to variation in oxygen availability. The methane-oxidizing symbionts showed evidence for convergent evolution, such as retention of a secondary, iron-dependent methane monooxygenase in Western Atlantic populations, driven by local copper limitation. These findings advance our understanding of divergent and convergent adaptive mechanisms underlying intraspecific host-symbiont variation in horizontally transmitted symbioses.

Hybridization between invasive and native species can generate novel genetic variation with ecological and evolutionary consequences, yet introgression often remains cryptic. We investigated natural hybridization between the invasive pinewood nematode Bursaphelenchus xylophilus, the causal agent of pine wilt disease, and native Bursaphelenchus mucronatus in Japan. Using multiplexed inter-simple sequence repeat genotyping by sequencing, we genotyped 342 field-collected nematodes and then conducted pedigree-calibrated analysis using HIest v2.0, based on 48 highly informative diagnostic single-nucleotide polymorphisms (SNPs), followed by ADMIXTURE, complementary NeighborNet and principal component analyses of a broader 2,756-SNP dataset. The results identified nine high-confidence hybrids (2.6%) across two consecutive years (2023-2024), including relatively balanced F1-like individuals and strongly parentally biased advanced backcross-like individuals, demonstrating recurrent, multigenerational introgression. Four hybrids (44.4%) were undetectable using a single-locus diagnostic marker, showing that advanced introgression can escape conventional surveillance. Chemotaxis assays detected no volatile-mediated pre-mating discrimination, whereas post-mating barriers were incomplete and asymmetric. Crosses with B. xylophilus as the maternal parent showed reduced hatchability, particularly with B. mucronatus mucronatus, while reciprocal crosses generally retained higher hatchability, although some showed reduced fecundity. These results provide a mechanistic basis for natural gene flow in a recent secondary contact zone. Because B. mucronatus kolymensis is widespread in Europe and produces viable hybrid offspring with B. xylophilus in both directions, pathogen establishment could create new opportunities for introgression. Our findings reveal cryptic, multigenerational introgression between an invasive forest pathogen and its native congener, highlighting the importance of genomic surveillance for forest disease management and invasion-risk assessment under climate change.

Arctic ecosystems are undergoing rapid climate warming, providing an opportunity to examine molecular evolution under environmental stress. Here, we used whole-genome resequencing to assess population structure, genetic diversity, and recent demographic history in the snowy owl (Bubo scandiacus), a highly mobile Arctic apex predator classified as Vulnerable by the IUCN. We analysed genome-wide data from individuals sampled across the species' circumpolar range using a chromosome-level reference genome. Population genomic analyses revealed an absence of detectable population structure, indicating extensive gene flow and near-panmixia across continents. Genome-wide nucleotide diversity was low ({pi}= 2.47 x 10^(-4)), while runs of homozygosity were dominated by short tracts, indicating limited standing genetic variation despite little evidence for recent close inbreeding. Our demographic inference revealed a sustained decline in effective population size over the past ~1,600 years, a pronounced reduction coinciding with the Medieval Warm Period followed by a partial recovery during the subsequent cooler interval. This direct, measurable effect of past climate warming on effective population size raises concerns for the long-term survival of the snowy owl. Our results demonstrate that high connectivity and low levels of recent inbreeding have not necessarily buffered this species against climate-driven demographic erosion of genetic diversity. This study highlights the value of using whole-genome population genomics to inform genomic monitoring and conservation decision-making in rapidly changing environments.

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.

Habitat fragmentation and destruction in old-growth forests represents a primary threat to specialist species, frequently resulting in the erosion of genetic diversity. The Hermit Beetle, Osmoderma barnabita, is a protected relic of primeval forests and an obligate saproxylic specialist whose larval development depends exclusively on the wood-mould of hollow trees. This study provides the first high-resolution, genome-wide assessment of O. barnabita across seven Polish forest complexes using double-digestion Restriction-site Associated DNA sequencing data from 49 individuals. Following rigorous quality control and reference bias assessment, we evaluate contemporary population structure. To distinguish between evolutionary processes, we isolated 2,920 putatively adaptive outliers from the neutral background, evaluating both neutral and adaptive genomic signals. The analyses revealed four distinct genetic clusters, confirming that the Polish metapopulation is severely subdivided. Crucially, the westernmost population in the Lower Silesian Forest emerged as the most divergent evolutionary unit (FST up to 0.360), suggesting potential hybrid origin or long-term isolation. We observed a striking linear correlation (R2=0.986) between neutral diversity and adaptive potential, indicating that genetic drift in small and isolated forest fragments is actively depleting the variation required for long-term persistence of this species. Our findings demonstrate significant gene flow restriction across all sites, suggesting that current conservation frameworks fail to encompass these highly differentiated lineages. To mitigate this genetic vulnerability, we recommend reclassifying these clusters as independent Management Units and Evolutionary Significant Units. Maintaining forest continuity and protecting local micro-habitats are essential to prevent further isolation and preserve the genomic integrity of this saproxylic flagship species.

Floodplains are highly dynamic ecotones where species persistence depends on synchrony between natural flow regimes and life-history. Artificial river engineering has profoundly altered these systems by reducing the frequency and magnitude of spring floods while increasing the unpredictability of flood timing and intensity during summer. These hydrological changes have disrupted historical patterns of dispersal, growth, reproduction, and competitive success among floodplain specialists. Effective conservation in these ecosystems therefore requires understanding how human-altered flow regimes have reshaped floodplain specialists' demography, genetic diversity, genetic connectivity, functional variation, and adaptive potential. Here, we address this challenge in Boltonia decurrens, a federally threatened floodplain plant endemic to the Illinois River Valley, by integrating a chromosome-scale reference genome, whole-genome resequencing, and common-garden adaptive trait measurements from 424 individuals across 17 populations. Demographic analyses revealed a severe recent bottleneck and a subsequent rebound. Population structure was clinal with downstream-dominant gene flow, indicating that regional population connectivity predominates over longer-distance gene flow. A subset of populations showed elevated genetic isolation with increased inbreeding and homozygous deleterious burden, revealing a genomic cost of disrupted floodplain connectivity. Common-garden observations and GWAS showed extensive within-population phenotypic and genetic variation in flowering time, flowering stem height, and year of first flowering (1st vs. 2nd year), which are hypothesized to buffer populations and to be selectively maintained under human-altered flow regimes. Finally, landscape-genomic approaches detected a divergent haplotype block separating northern and southern populations, suggesting that adaptive divergence can persist even in a system shaped by recurrent disturbance and ongoing gene flow.

Whole genome analysis of spittlebug populations, an Aphrophora species (Hemiptera: Aphrophoridae) known to spread Pierce's disease, from various vineyards in Napa and Sonoma Counties demonstrates that these insects are conspecific with Aphrophora permutata found in quasi-natural populations. The genomes analyzed fall in three autosomal clusters with two sympatric populations (based on admixture) that diverged around 40,000-90,000 years before present according to demographic models. We also recover three related but distinct mitochondrial clusters. There is no genetic differentiation between Napa and Sonoma County vineyard populations and very modest differentiation among vineyards and quasi-natural Berkeley/Oakland Hills population. These vineyard and quasi-natural populations have distinct life histories, including divergent oviposition hosts (understory herbs versus pines) and different patterns of adult seasonal migration (out-migration and return versus simple movement from the understory to the pine canopy). Analysis of the mitochondrial gene COI indicates that A. permutata, Aphrophora fulva and Aphrophora maculosa are intermingled in the same mitochondrial clade, along with the more distantly related species Aphrophora gelida. Further, all three autosomal genetic clusters show evidence of selection for insecticide resistance. We also find that endosymbionts Wolbachia and Rickettsia were both present in a substantial fraction of specimens analyzed, but neither appears to influence population structure. Overall, our findings elucidate an intriguing degree of life history divergence between geographically proximate, conspecific populations linked by gene flow and may have implications for the continued management of vineyard populations.

Coastal organisms experience natural and anthropogenic stressors simultaneously, yet the interactive effects of multiple stressors are largely unknown. In urbanized estuaries, coastal acidification (CA) is coupled to sewage effluent (SE): nutrient loading from SE stimulates microbial CO2 production, and this lowers the pH. The genomic targets of selection of CA and SE have been characterized separately but never together in early life stages of marine organisms. Here, we exposed eastern oyster (Crassostrea virginica) larvae to control, CA (~2800 atm pCO2), SE (5% by volume), and the combination (CASE) for 24 h across independent spawns, and used expressed exome capture sequencing to measure allele-frequency change before and after exposure, removing loci that also shifted in controls. CASE generally produced the lowest survival, although mortality was driven primarily by effluent and did not exceed the additive expectation. The size of allele-frequency change under CASE stayed close to the additive sum of the single stressors, but it showed compositional synergy: CASE had more outlier loci than CA and SE combined with 1,941 loci (747 genes) detected only under the combined treatment. CASE outliers were enriched for proteostasis, ciliary function, mitochondrial calcium handling, and a steroid-metabolizing (CYP17) module consistent with effluent endocrine disruptors. Selection acted repeatedly on standing variation across spawns and genetic backgrounds, with the largest allele-frequency shifts at rare, spawn-private loci. Enriched biological functions recurred across spawns more often than expected, while most outlier loci were specific to one or two spawns, consistent with genotypic redundancy. Our results show that combined stressors can recruit a compositionally synergistic genomic response, at loci and functions not detected under either stressor alone, even when survival and the size of allele-frequency change are additive.

Domestication is an evolutionary process that can begin before deliberate breeding, when association with humans reshapes gene flow and selection. The yellow mealworm, Tenebrio molitor, is undergoing this transition from a synanthropic pest of stored grain to farmed species. We asked whether gene flow between farmed populations contributes to adaptation to captivity and whether selection extends to production traits. We combined population genomics of 320 beetles from eight farmed and wild populations with genetic mapping of 15 production traits from 3,575 individuals. Farm stocks retained high diversity and weak differentiation, with Netherlands-related ancestry connecting populations across Europe and Canada. Farm-restricted sweep-like signatures were 2.06-fold enriched within regions of excess allele sharing, suggesting local selection on introgressed variation. Across 305 production-trait QTLs, overlaps with selection and introgression signals showed no significant enrichment or depletion, suggesting that adaptive gene flow may primarily contribute to adaptation to captivity rather than broadly shaping growth, development and fertility. Nevertheless, egg-hatching-rate and development-time QTLs overlapped regions of reduced nucleotide diversity and low Tajima's D. These findings support a model in which gene flow supplies variation for unintended selection under intensive rearing. Crowding and physiological stress may favour adaptation to captive environments before sustained breeding establishes a broad genomic response at production loci.

As ecosystems face rapid environmental change, understanding the interplay between landscape structure, genetic diversity, and adaptive potential is critical for predicting resilience. We investigated how biome-specific connectivity and environmental heterogeneity mediate adaptive strategies and resilience in the tropical rainbowfish (Melanotaenia splendida splendida) across contrasting rainforest and savannah ecosystems in tropical Australia. Using an integrative framework combining genomic, morphological, and environmental analyses, we inferred that hydroclimatic variation has been a key driver of genetic and phenotypic divergence. Rainforest populations exhibited strong local adaptation to fragmented, stable environments, while savannah populations showed less genomic differentiation and morphological divergence, patterns consistent with weaker local adaptation. We hypothesise that greater reliance on phenotypic plasticity may facilitate adaptive responses in savannah populations, reflecting their exposure to more connected and variable environments. Variance partitioning highlighted the contrasting roles of neutral and adaptive processes across biomes, with implications for managing resilience in freshwater systems under climate change. Our findings underscore the trade-offs between connectivity, local adaptation, and plasticity, providing a model for understanding adaptation and resilience across diverse ecosystems.

Rapid diversification can generate regional biodiversity through ancestral polymorphism, admixture, and ecological differentiation, while leaving complex genomic signals. We analysed whole-genome variation in 325 butterflies, including 166 individuals of the Papilio bianor species complex and six outgroup species, to reconstruct lineage relationships and demographic history. Nuclear genomic analyses recovered three major clades corresponding to the recognized species and placed the island lineage as sister to continental P. bianor. Analyses of 18,635 autosomal window trees revealed extensive genealogical discordance, with incomplete lineage sorting predominating among continental lineages and the strongest introgression signals involving island related ancestry. Demographic modelling supported early island continental divergence followed by continental diversification and ancient admixture. The best fitting fastsimcoal2 model inferred an admixed origin of the Eastern China lineage, while BPP analyses supported ancient island-related introgression into the Eastern China ancestor, Western Himalaya and southwestern Thailand. Peripheral populations exhibited pronounced genetic differentiation and distinct demographic histories; Western Himalaya additionally showed mitochondrial affinity with Yaeyama despite its placement within the Himalayan nuclear lineage. Together, these findings suggest that introgression among deeply differentiated ancestral populations and incomplete lineage sorting during rapid divergence jointly shaped lineage diversity in the P. bianor complex. This study provides an empirical framework for investigating how lineage diversity emerges rapidly during the early stages of speciation, particularly in groups with deep ancestral population structure.

While the influence of microorganisms in the thermal physiology of animals is increasingly recognised, the role of the gut microbiome in enhancing phenotypic plasticity remains underexplored, particularly in ectotherms. Here, we tested the effect of gut microbiomes in modulating the physiological response of lizards to sudden temperature fluctuations. In captivity, we conducted an experiment with wild-caught Podarcis lizards: Mediterranean Podarcis liolepis (n=9) adapted to warm and dry environments, and Atlantic P. muralis (n=18) adapted to cooler and wetter conditions. Animals were assigned to three groups (intervention, control-cold and control-warm) and subjected to microbiota manipulations using antibiotics and faecal microbiota transplants (FMT). In the intervention group, cold-adapted P. muralis received faecal suspension from warm-adapted P. liolepis, while control-cold and control-warm groups received intraspecific transplants. Microbiome variation was analysed through genome-resolved metagenomics of 162 faecal samples, yielding 313 MAGs across 15 phyla, containing almost 1M annotated genes. One week after transplantation, microbiomes of control animals differed from their original state, whereas those of the intervention group (P. muralis), transitioned to a state resembling P. liolepis. After two weeks, both control groups showed trends of reversing their microbiomes to their original states. However, the intervention group displayed a distinct trajectory, resembling the microbial donors'. Although potentially relevant trends were observed, these microbiome alterations did not translate into detectable significant differences in their thermal physiology. Nevertheless, our results provide proof of concept for microbial transplants in lizards, and opportunities to further explore the link between gut microbes and host physiological responses in ectotherms.

Heterogeneous genomic landscapes of differentiation can reveal evolutionary processes acting over different timescales. Whereas genetic structure in the European flat oyster, Ostrea edulis, is mainly shaped by geography, previous work suggested parallel differentiation between western and eastern Mediterranean populations and between Atlantic and North Sea populations, resulting in genetic convergence between range margin populations in some genomic regions. Here, we analyzed 27 oysters from four locations using moderate-coverage (~20X) short-read whole-genome sequencing. We first examined three known chromosomal inversions and found evidence that they predate divergence with the sister species O. chilensis. We then scanned the genome for parallel differentiation at the individual-SNP rather than sliding-window scale using the product of allele-frequency differences across the two geographic contrasts. Two of the three inversions were detected, but we also identified 12 small non-inverted genomic regions showing even stronger signals of parallel differentiation. These 'islands of parallelism' typically overlap one or a few genes, and most showed elevated dXY consistent with long-term barriers to gene flow. Two islands overlap nuclear ATP synthase subunits, while mitochondrial ATP8 shows a convergent amino-acid change, suggesting possible nuclear-nuclear and mitonuclear incompatibilities. Finally, demographic inference with heterogeneous gene flow supported post-glacial secondary contact and a lineage-based rather than geography-based population topology. Our results suggest that the genomes of O. edulis lineages have been largely porous to gene flow upon secondary contact, except for chromosomal inversions and small genomic islands. These regions likely act as barrier loci, preserving a signal of a shared evolutionary history among marginal populations that has otherwise been erased by rampant gene flow.