Molecular Ecology

Evolutionary and demographic processes such as selection, drift and migration shape the genetic variation of populations. Genetic diversity is often lower in populations toward higher latitudes. This decrease potentially threatens their survival as several factors are putting more pressure on the populations, including the spread of infectious diseases. In this study, we combined whole-genome re-sequencing with MHC class II genotyping and skin microbiome profiling in Bufo bufo and B. spinosus, two closely related European toad species. We investigated the underlying immunogenetic and microbial variation resulting from different demographic histories and environmental conditions to identify their potential impact on infection outcomes in these two species. We found lower immunogenetic diversity in B. bufo compared to B. spinosus, with highly significant differences in genes related to adaptive and innate immunity. We found lower overall MHC class II diversity and skin microbiome diversity at the species level in B. bufo, compared with B. spinosus. In contrast, at the individual level, B. bufo showed higher MHC allelic diversity and greater diversity in the core skin microbiota than B. spinosus. Together, our findings suggest that divergence in immunogenetic background and host-associated microbial communities may underlie differences in susceptibility to emerging infectious diseases. This integrative framework provides new insight into how host genetics and microbial communities jointly influence disease outcomes across environmental gradients.

Infection can substantially reduce host fitness and influence population dynamics, yet it is often difficult to detect and quantify in wild animal populations. Molecular tools offer a valuable means of identifying cryptic infection in natural systems. Using whole-genome bisulfite sequencing, we examined whether infection with the parasitic leech Ozobranchus margoi is associated with DNA methylation variation in loggerhead sea turtles (Caretta caretta), while also assessing the potential value of this variation as a biomarker of parasite infection. In nesting females, we identified infection-associated differentially methylated CpG sites associated with genes implicated in immune signalling and cellular regulation. Offspring of infected females also showed infection-associated methylation patterns, despite not being directly exposed to the parasite themselves. Differential methylation analyses identified genes involved in immunity, neurodevelopment and metabolic activity, with limited overlap in associated genes and no overlap in differentially methylated sites between generations. Maternal and offspring genome-wide methylation levels showed a non-linear association that differed subtly with maternal infection status, indicating that infection modifies intergenerational methylation associations. Finally, methylation profiles showed strong discriminatory power for maternal infection status in both maternal and hatchling samples using machine learning models, supporting their potential as candidate biomarkers of cryptic infection. Together, these results show that parasite infection is associated with distinct, generation-specific DNA methylation signatures, and highlight the potential value of epigenetic data for monitoring cryptic infection states in conservation-relevant systems.

The coast redwood (Sequoia sempervirens) is a long-lived, hexaploid conifer of high ecological, cultural, and economic value whose range has been greatly reduced by historical logging. Effective restoration and conservation depend on understanding patterns of genetic differentiation across the redwood range to delineate populations for management prioritization. Yet, past range-wide studies provided only a partial picture of population structure in coast redwood as they relied on a limited set of genetic markers or limited sampling, as sequencing was done on the same range-wide provenance collection. Here, we analyze 334,029 SNPs from a new range-wide set of 224 individuals using a dosage-based approach that accounts for polyploidy. Principal coordinates and neighbor-joining analyses reveal clear latitudinal genetic differentiation, with a distinct break south of San Francisco Bay. Outlier SNP analysis indicates new candidate loci involved in salinity tolerance, climate stress response, and nutrient uptake, suggesting potential local adaptation. These results point to the central role of geography in shaping genetic variation in coast redwood and give scientific basis for designing new conservation strategies and future experiments, including assisted migration, provenance trials, and restoration planning aimed at preserving the species into the future.

The unprecedented rate of climate warming threatens many species, and assessing their vulnerability to climate change represents a critical challenge in conservation biology. The Apollo butterfly, an emblematic mountain species, is expected to be impacted by climate change. Here, we analysed thousands of SNPs from 101 localities across Apollo French distribution. We identified 93 SNPs strongly associated with climate variation using five genotype-environment association analyses. We forecasted future climate maladaptation of French Apollo populations using four genomic offset methods and integrated these results with neutral and adaptive genetic diversity, genetic structure and adaptive climatic niches to infer their vulnerability to climate change. Jura and Alps populations exhibited the lowest risk of vulnerability to climate change, with low genomic offsets, high genetic diversity and connectivity, whereas Auvergne populations showed the highest genomic offsets and lowest neutral and adaptive genetic diversity. Only a reduced percentage (<1%) of the current distribution is predicted to face climatic conditions outside the current range, suggesting that adaptive variability required to adapt to future climates may already be present, and that assisted gene flow could represent an effective conservation strategy. Finally, we discuss some of the main challenges of genomic forecasts, particularly for declining non-model species.

The potential for environmental change to compound the detrimental effects of inbreeding depression in small and isolated populations is a significant concern in conservation biology. Previous evidence syntheses suggested that environmental stress exacerbates inbreeding depression, but were based on limited data. Here, we comprehensively test the relationship between inbreeding depression and environmental stress in natural populations using Bayesian mixed-effects meta-analysis on a large, high-quality data set of 2127 inbreeding depression effect sizes from animals and plants. Our results show that inbreeding depression is significantly higher in benign than in stressful environments. Analyses of both inbreeding depression and stress-induced changes in genetic load supported a unimodal (humped) relationship between the costs of inbreeding and stress intensity, with a peak at intermediate stress. At the highest levels of stress there was, on average, a significantly greater inbreeding load in benign than in stressful environments. We suggest that the lower cost of inbreeding associated with extreme stress results from constraints on the expression of inbreeding depression as fitness and phenotypes decline towards zero. Our findings help to resolve long-standing uncertainty around how inbreeding and environmental change interact, revealing that inbreeding responses vary non-linearly with environmental stress intensity, but showing that stress does not generally amplify inbreeding depression. As such, they will inform both the management of populations of conservation concern and predictions of species responses to global environmental change.

Understanding spatial and temporal connectivity among individuals with different migration strategies is essential for migratory ecology and effective conservation, yet it often requires integrating multiple data sources. In Northeast Atlantic European sea bass (Dicentrarchus labrax), electronic tagging has revealed partial migration, with both resident and long-distance migrants showing fidelity to summer feeding and winter spawning areas. However, the role of regional spawning-site philopatry in shaping migration patterns and stock connectivity remains unclear. Here, we combine reconstructed migration trajectories with genome-wide analyses of gene flow and recent relatedness in 708 individuals sampled from 10 French Atlantic locations. We identify a seasonally shifting genetic discontinuity between the Bay of Biscay (BOB) and Northern (NS) stocks, located off western Brittany during winter spawning and displaced northeastward into the central English Channel during summer feeding. Despite seasonal mixing in the English Channel, an association between individual genetic composition and spawning-site selection supports regional spawning-site philopatry. Analyses of long genomic segments shared identical-by-descent reveal substantially greater connectivity within stocks than between stocks, indicating that philopatry constrains effective gene flow despite seasonal mixing. Reanalysis of independent genomic data further shows that sea bass from the northern Atlantic range predominantly belong to the Northern stock. Together, these results show how seasonal movements reshape spatial genetic structure while maintaining demographic subdivision, with direct implications for fisheries management.

Thermal history provenancing can guide the choice of parental broodstock for selective breeding of corals from distinct reefs and has been proposed as an intervention for enhancing climate resilience. However, the genetic and molecular mechanisms underlying resultant offspring responses to heat stress, particularly during early life stages, remain poorly understood. Here, we generated Acropora tersa larvae and recruits by crossing parental colonies from the historically warmer Martin Reef and cooler Davies Reef and assessed the effects of within- and between-reef crosses on genetic diversity and transcriptional responses to heat stress. Genome-wide single nucleotide polymorphism analyses showed that broodstock from Martin and Davies Reefs were weakly differentiated (FST = 0.008) and exhibited comparable heterozygosity, as did all larval offspring groups. Transcriptomic analyses of recruits exposed to heat stress (32 {degrees}C for 36 days) revealed that both within- and between-reef offspring groups activated conserved stress-response pathways, with seven genotype-independent heat-responsive genes detected across all offspring groups. Differential expression and enrichment analyses showed induction of defence, protein homeostasis, intracellular transport, and metabolic processes alongside repression of growth- and signalling-related functions, consistent with the Type A General Coral Stress Response. Taken together, these findings suggest that the benefits of thermal history provenancing-informed selective breeding may be limited in low-differentiation systems and that targeted pre-screening of broodstock may help capture functional genetic variation relevant to restoration applications.

Bees and wasps are ecologically vital, but many species are declining due to anthropogenic stressors. Social bees harbour host-specific and dense gut microbiomes that affect their resilience to stress. However, there are tens of thousands of other bee and wasp species that vary in sociality and diet (including pollen-feeding and predatory guilds), traits known to influence host-microbe symbioses. The role of gut microbes in the biology of these species is largely unknown. Here, we measured the composition and absolute abundance of bacterial communities in adult abdomens across 61 genera and 14 families of field-collected bees, predatory wasps, and pollen wasps. We found that solitary bees and both wasp guilds harbor distinct bacterial taxa and lower bacterial abundances as compared with social bees. Bacterial abundances also varied extensively among and within genera of solitary bees, with little variation explained by body size, diet breadth, or nesting ecology. Further, microbiome composition was only weakly differentiated among solitary bees and the two wasp groups, even comparing herbivorous (pollen-feeding) and carnivorous taxa. We suggest that the sparse and somewhat stochastic microbiomes of solitary bees and wasps reflect weak host dependence on microbially mediated functions, a trait that may influence their responses to environmental change.

Bird migration evolved as an adaptation to seasonally changing habitats. Migratory behaviour can vary within the same species in case of partial migratory behaviour, i.e. one population (or individual) is migratory and another one is resident. Species that exhibit a wide variety of migratory phenotypes provide valuable systems to understand the evolutionary drivers behind different phenotypes and how populations adapt to habitats with distinct seasonality. The European robin (Erithacus rubecula) expresses migratory behaviour in central and northern areas of the species distribution range, whereas populations in the South and on the Macaronesian islands are predominantly resident, providing a suitable system to investigate these questions. We use high coverage whole genome re-sequencing data of 125 European robins to investigate how migration behaviour affects population structure and demography, and how it affects the selection landscape in the genome. Genetic structure in European robins coincides with migratory phenotype and geography and populations are characterised by distinct demographic histories. Our results suggest that both the continental resident population as well as the Macaronesian island populations have derived independently from an ancestral migratory population. Unexpectedly, tests for differential selection revealed extensive positive selection pressure acting across all chromosomes in the resident populations, while selective sweeps are largely absent from migrants. We speculate that this might be an analytical artifact due to mismatching timescales between what population genomics methods can detect and the scale on which migration behaviour likely evolved in the robin. We suggest that future studies on the genomics of migration should more focally account for different time scales on which these processes happen, such as including the wider phylogenomic background of the target species, to capture the full evolutionary history of migratory traits.

O_LISpawning salmon transport marine-derived nutrients (MDN) into riparian forests, influencing soil, plant, and animal communities, yet their effects on fungal communities remain poorly understood. C_LIO_LIWe used DNA metabarcoding to examine fungal responses to three spatial patterns of salmon-derived nitrogen (N) in southwest Alaska: (i) patchy inputs from wildlife-deposited carcasses, (ii) a 21-year carcass relocation experiment, and (iii) natural N gradients with distance from streams. C_LIO_LIDecomposing carcasses increased saprotrophic fungal diversity, identifying taxa responsible for salmon carcass decomposition. Long-term carcass relocation reduced diversity of medium-distance fringe ectomycorrhizal fungi (EMF), whereas recent, patchy carcass inputs increased diversity of both medium-distance fringe and long-distance EMF--guilds often associated with low-nutrient environments. Along natural stream N gradients, EMF responses varied markedly within functional guilds and genera, revealing unexpected variation in N sensitivity among closely related taxa. C_LIO_LIPulsed, spatially heterogeneous nutrient inputs enhanced diversity of typically nitrophobic EMF, likely reflecting their capacity to maintain extensive mycelial networks, exploit nutrient hotspots, and mobilize organic N and phosphorus. The diversity of responses along natural N gradients suggests that mechanisms linking EMF traits to nutrient acquisition and tolerance remain unresolved. Our findings emphasize the importance of linking fungal community composition with functional attributes and nutrient dynamics. C_LI

The evolutionary transition to terrestrial life required overcoming several physiological hurdles; however, such challenges were amplified in desert environments. While several xeric-adapted arachnids utilize permanent burrows or "sit-and-wait" foraging strategies as possible energy conservation adaptations in harsh habitats, camel spiders exhibit a counterintuitive, high-energy lifestyle. To investigate the molecular underpinnings distinguishing Solifugae within Chelicerata, we utilized a comparative genomics framework that incorporates a newly sequenced, previously unpublished solifuge genome. We identified lineage-specific expanded orthogroups and evaluated selective pressures acting upon paralogous sequences within our ingroup solifuge species. Additionally, we also focused on fatty acid-associated proteins and heat shock proteins to elucidate how Solifugae may have evolved such anomalous behaviors compared to their arachnid relatives. Our analyses revealed significant signatures of positive selection within key gene families across the solifuge lineage. Notably, paralogs within the cytochrome P450 and biotinidase families showed consistent evidence of selection across all three taxa, suggesting specialized metabolic or detoxification requirements. Furthermore, we identified candidate loci implicated in axonal guidance and lipid metabolism, and a specialized fatty acid enzyme repertoire. While subsequent research is required to determine whether some of the genomic signatures unveiled here are shared across a broader phylogenetic distribution within Solifugae, we establish a critical baseline for future functional validation.

Adult mosquitoes rely on plant-derived sugars for survival, reproduction, and flight, yet the plant taxa that mosquitoes encounter in nature and the odors that make those plants attractive remain poorly understood. Most studies of mosquito attraction to plant odors have focused on candidate plants selected a priori, rather than plants linked to field-collected mosquitoes. Here, we combined plant DNA barcoding, semi-field behavioral assays, and volatile profiling to identify field-associated plant resources relevant to Aedes aegypti. Plant DNA recovered from mosquitoes collected across three Florida counties revealed broad plant associations, including 90 genera spanning 37 families, with several taxa recurring across counties or appearing prominently within particular localities. Behavioral experiments in semi-field sticky-trap assays found that five field-associated plant taxa were significantly attractive relative to blank controls, indicating that taxa associated with mosquitoes in nature can also function as attractive cues under semi-field conditions. GC-MS analyses of headspace collections from 42 plant taxa detected 211 volatile compounds and revealed substantial variation in both total emission rate and odor composition among taxa. Although several compounds, including -pinene, limonene, 4-ethylacetophenone, 2-ethyl-1-hexanol, 4-ethylbenzaldehyde, and caryophyllene, were broadly distributed across plant groups, volatile profiles differed significantly among taxa and shared compounds often occurred at markedly different proportional abundances. The five behaviorally tested taxa likewise showed both overlap and divergence, sharing 17 compounds across all five taxa while differing in dominant constituents and total emissions. Together, these results show that Ae. aegypti interacts with a diverse set of plants in the field, and suggests nectar-seeking is shaped not simply by plant identity or total odor abundance, but by the composition and proportional structure of plant odors.

Chemosensory systems play a central role in host detection, feeding behavior, and habitat selection in hematophagous insects. Here, we performed a comparative evolutionary analysis of chemosensory gene repertoires across 13 species of the Chagas disease vector genus Rhodnius. While gustatory receptors (GRs), ionotropic receptors (IRs), odorant-binding proteins (OBPs), and chemosensory proteins (CSPs) remained globally conserved, odorant receptors (ORs) displayed extensive lineage-specific expansions, tandem duplications, dynamic transcriptomic regulation, and recurrent signatures of positive selection. Major OR expansions were observed in Rhodnius robustus and Rhodnius colombiensis, suggesting increased sensory diversification in ecologically heterogeneous lineages. In contrast, conserved GR1 expression supports the maintenance of ancestral sugar-detection pathways despite hematophagy lifestyle. We further found no evidence of the canonical insect CO2-associated GRs, suggesting alternative molecular mechanisms for CO2 perception in Triatominae. Several receptors, including Orco, also displayed shifts in selective constraints between sylvatic and domiciliary species, consistent with sensory remodeling associated with adaptation to domestic habitats. Together, our results identify ORs as the most evolutionarily dynamic component of the Rhodnius chemosensory repertoire and highlight contrasting evolutionary trajectories among chemosensory gene families during ecological diversification and vector adaptation.

Genomic offset (GO) is increasingly used to predict population maladaptation risk under climate change, with larger offsets assumed to indicate greater vulnerability. Despite rapid adoption in conservation planning, it remains unclear how sensitive GO estimates are to key methodological choices, including SNP set composition, genotype-environment association (GEA) methods, and the specific GO metric used. Empirical validation against observed population dynamics also remains limited. Here, we evaluate the methodological robustness and predictive performance of GO using multidecadal demographic monitoring data from Lycaeides butterflies, a system with short generation times and high fecundity that may facilitate rapid adaptive responses. GO estimates were broadly consistent across SNP sets, regardless of composition or size, with climate-associated and randomly selected SNPs yielding largely concordant values. Consistency across GEA methods was moderate and depended on the SNP set used. In contrast, GO metrics differed substantially in the magnitude of maladaptation estimated, suggesting they capture distinct biological signals and should not be treated as interchangeable. Crucially, GO was a poor predictor of observed population trends, regardless of SNP set composition, GO metric, or GEA method, both at sites used to fit GEA models and when extrapolated to independent demographic sites. These findings suggest that, while GO provides a valuable conceptual framework for assessing potential maladaptation, its quantitative estimates and predictive power are sensitive to methodological choices and species-specific biological context. We therefore urge careful alignment of GO metric assumptions with conservation objectives, along with rigorous empirical validation, before GO estimates are used to inform management decisions.

Biodiversity is predicted to stabilize ecosystems if species have different environmental responses. How this response diversity is shaped by ecological and evolutionary processes remains poorly understood. We determine the drivers of thermal response diversity of 16 Swiss peri-alpine lake-fish communities. We report the first evidence that evolutionary diversification of lineages through adaptive radiation can increase the response diversity of an ecosystem. In-situ diversification increases response diversity in the cold-deep lake environment, but non-endemic and non-native species contributed only weakly to response diversity. The loss of endemic species during historical anthropogenic eutrophication led to a negative legacy on present thermal response diversity in cold and deep lake strata. Overall, the interplay of evolutionary diversification, ecological assembly and anthropogenic impacts drives variation in response diversity. Conserving and restoring processes that generate diversity may help maintain ecosystem stability beyond the Anthropocene.

Introgression following hybridization is increasingly recognized as a major driver of evolution. However, its importance depends on its frequency in nature, which remains to be quantified. To address this, we provide a snapshot of ongoing introgression in a whole species assemblage (4126 ant colonies). 23% of all 82 local species show signs of introgression, which is more than twice previous estimates. Introgression is typically subtle, yet we find that it contributes measurably to genetic diversity. Species divergence, rather than classical prezygotic reproductive barriers (mating phenology, ecological niche, fine-scale habitat use) constrains introgression, suggesting that the main reproductive barriers are postzygotic at this stage of divergence. Our results indicate that introgression may be a common but often overlooked feature of natural communities.

Late Pleistocene sea-level fluctuations and glacial corridors intermittently connected the island of Ireland to Britain and continental Eurasia, shaping patterns of megafaunal dispersal and occupation. However, the scarcity of genetic data from ancient Irish fauna has limited our understanding of their demographic histories and relationships to continental populations. To address this, we generated sedimentary ancient DNA sequences from Castlepook Cave in southwest Ireland, detecting twelve ancient taxa, including two without zooarchaeological records at the site. We recovered the first mitochondrial sequences from Irish cave hyenas and woolly mammoths, providing new insights into their maternal population history: cave hyenas carried mtDNA haplogroup A1, previously identified in Late Pleistocene European populations, while woolly mammoths belonged to clade III/B2, which was replaced in Europe at approximately the same time. We also identify two mitochondrial clades (1b and 2), consistent with pre-Last Glacial Maximum mitochondrial lineage turnover in Ireland. Together, these results indicate that Irish megafauna formed a biogeographical continuum with their conspecifics in Europe, extend the known geographical range of several mtDNA lineages, and support faunal connectivity at the northwestern edge of Europe prior to the Last Glacial Maximum.

Although the roles of host-associated microbiomes in animal health are increasingly recognised, the factors influencing their variation remain understudied. The relatively simple microbiome of honey bees is a relevant system to address this gap. In particular, the relationship between variations in microbiome composition and the ectoparasite Varroa destructor, the main threat to honey bee health worldwide, is poorly established. In this study, we used metagenomic and statistical analyses of 1442 European honey bee colonies to investigate the relationships between the honey bee microbiome, temporality, location, V. destructor load, and behavioural response to its infestation by the host. While season, year, and location were identified as the main drivers of microbiome variation, V. destructor load emerged as a significant factor associated with microbiome variation. Notably, we identify several pathogens and opportunists that correlated positively with V. destructor load, while the core symbiont Bombilactobacillus correlated negatively. This is compatible with a shift in the microbiome toward dysbiosis, which may be driven by or promote V. destructor parasitism. By contrast, we found only limited evidence of an association between the microbiome and resistance behaviours of the host against this parasite. While the study cannot establish causal relationships, we present the largest metagenomic analysis of honey bee microbiomes to date, providing robust, generalisable evidence about the factors driving variation in the microbiome composition of this ecologically and economically important pollinator. These findings may serve as additional markers in selective breeding programs targeting V. destructor resistance, which could ultimately improve honey bee health.

Japanese chum salmon supported by one of the world largest hatchery programs have experienced severe declines in marine survival and egg size. To investigate the underlying mechanisms, we analyzed a 21-year time series (1999-2019) of reproductive traits of age-4 chum salmon from 13 rivers together with climate and salmon abundance data using a bootstrap-supported Bayesian network. Here, we assumed that environmental variables can affect the chum salmon populations, but not vice versa, and that there could be maternal effect on reproductive traits, but not the other way around. These constraints enabled us to infer the causal links that shaped the biogeography of North Pacific chum salmon. Global warming caused a decline in Japanese chum salmon abundance, resulting in the increase of the competing Russian chum, which in turn decreased the female body size, fecundity, and egg size of Japanese chum. These findings suggest that climate-driven warming may have exposed genetic effects of hatchery practices, contributing to fitness decline in Japanese chum salmon and the ecological reorganization of chum salmon populations in the North Pacific.

The global study of freshwater clams in the genus Corbicula is frequently confounded by invasive androgenetic lineages that experience mitochondrial DNA capture and clonal propagation. In contrast, the endemic Corbicula of Sulawesi's ancient lakes reproduce sexually, offering a uniquely reliable system for mitochondrial population genetics. This study provides the first population-genetic framework for two endemic species, Corbicula possoensis (Lake Poso) and C. linduensis (Lake Lindu), using the cytochrome c oxidase subunit I (COI) marker. We analysed 90 newly generated COI sequences from C. possoensis (six stations) and C. linduensis (three stations), integrated with reference sequences from GenBank, to assess genetic diversity, population structure, and phylogeographic patterns. Hierarchical AMOVA revealed deep divergence between the two lakes ({Phi}_CT = 0.607), consistent with prolonged independent isolation rather than a single shared vicariance event, as the two species do not form a sister pair in the phylogeny. Within Lake Poso, C. possoensis exhibited exceptionally high genetic diversity (24 haplotypes; h = 0.876; {pi} = 0.016) and pronounced micro-geographic structuring into three phylogeographic zones (North: Tentena and Siuri; East: Tando Nceppo and Busogo Beach; Southwest: Bancea and Pendolo), each characterised by distinct haplogroups. Remarkably, the maximum divergence between zones (K2P = 2.33%) approached the interspecific distance between C. possoensis and C. linduensis (K2P = 2.42%), indicating that within-lake mitochondrial divergence has reached near-interspecific levels. Conversely, C. linduensis displayed near-panmixia and extreme genetic depauperation (3 haplotypes; h = 0.246; {pi} = 0.0004), indicating long-term demographic stasis within a restricted habitat. The deep phylogeographic zonation in C. possoensis suggests that its discrete populations should be treated as separate Management Units (MUs) in conservation planning to preserve locally adapted gene complexes, whereas the severely depauperate gene pool of C. linduensis renders it critically vulnerable to environmental disturbance and invasive species, warranting urgent IUCN Red List assessment. To validate these mitochondrial boundaries and inform future conservation strategies, multi-marker and genome-wide reassessments are strongly recommended.