Evolutionary Applications

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.

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.

In Germany, insecticide use is recommended during mosquito-borne disease outbreaks, yet nationwide data on insecticide resistance in key vector species are scarce. This is particularly relevant for Culex pipiens s.l., a vector of West Nile virus. Here, we provide the first broad-scale assessment of molecular insecticide resistance (kdr and ace-1 mutations) in Cx. pipiens f. pipiens across Germany. We associated insecticide resistances with environmental conditions, potential links with mitochondrial variation of the cytochrome c oxidase I (COI) gene as well as phenotypic resistance (CDC bottle assay with permethrin) of the Frankfurt population with elevated kdr frequencies. Kdr resistance alleles were detected in German Cx. pipiens f. pipiens reaching frequencies of up to 50% in the metropolitan areas of Berlin and Frankfurt am Main. Annual precipitation was negatively associated with kdr allele frequency. Interestingly, ace-1 resistance mutations were only present in the metropolitan area of Frankfurt am Main and in Muggensturm (Rhine valley, southwestern Germany). COI haplotype analyses revealed low genetic variability within German Cx. pipiens f. pipiens populations with no association to the insecticide resistance genotype. Phenotypic assays of the Frankfurt population showed early signs of permethrin resistance, but unmatched genotypic and phenotypic resistance state. This study provides the first broad-scale assessment of molecular insecticide resistance in Cx. pipiens f. pipiens across Germany, establishing a baseline for resistance surveillance and vector control. Further research is needed to identify factors shaping phenotypic resistance, as molecular markers alone may not reliably predict resistance. Since sampling was restricted to urban green spaces, broader sampling across environmental gradients is needed to identify additional environmental effectors.

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.

Populations that have detectable additive genetic variance for fitness (VA(W)) have the capacity for increase in their mean fitness through natural selection. The extent to which the magnitude of VA(W) in wild populations is predictive of the rate of adaptation is not well known, because few empirical field-based studies have been designed to address this question. Here, we report a two-year field experiment with pedigreed seeds embedded in four natural populations of the annual wildflower Baby Blue Eyes (Nemophila menziesii H. & A.), a species native to western North America. We first estimated VA(W) in a parental generation and then evaluated whether that estimate accurately predicted the adaptive response observed in the subsequent offspring generation grown under natural field conditions. We achieved this by directly comparing the mean fitnesses of the parental generation and their progeny grown under the same environmental conditions. We detected VA(W) and evidence of adaptation in all populations despite inter-annual differences in environmental conditions that directly affected fitness. Genotype-by-year interactions in fitness indicate that the fitness ranking of families differed between years, implying that the selective environment shifted over time. Additionally, although the environment in the second year reduced population mean fitness in three sites, the offspring generation maintained mean fitness at or above replacement, suggesting that adaptive evolution may have buffered the effects of environmental change. Overall, our results suggest that the four populations harbored sufficient VA(W) for adaptation through natural selection to the environmental conditions observed during the two years of this study.

Rubber vines (Cryptostegia madagascariensis and C. grandiflora) are highly invasive weeds in the semi-arid landscapes of many tropical regions. The rust fungus Maravalia cryptostegiae has provided a spetatular and sustainable control of invasive C. grandiflora populations in Australia, after its scientific and quarantine-authorized release in the context of a classical biological control program. The Caatinga biome of Northeastern Brazil is under a devastating invasion by C. madagascariensis. This species is also susceptible to M. cryptostegia but its epidemic potential towards C. madagascariensis in Brazil remains unknown. We developed a weather-driven epidemiological model integrating experimentally derived relationships for infection as a function of temperature and wetness duration and for temperature-dependent latent development. Three infection-response models were fitted to 20 experimental temperature x wetness combinations from the literature and compared using information criteria, grouped cross-validation and a parametric bootstrap. The selected model, in which thermal breadth increases with wetness duration, was best supported (R2 = 0.931; {Delta}AICc [≥] 3.3 relative to the alternatives), and prolonged wetness significantly broadened the thermal range favorable for infection ({gamma} = 0.30 oC h-1; bootstrap P = 0.002). The infection and latent-development models were coupled with 25 years (2001-2025) of hourly NASA POWER data for 65 grid cells representing rubber-vine-infested locations in Northeastern Brazil, with wetness defined as hours with relative humidity equal or greater than 90%. Infection potential was concentrated in March-June (73% of the annual total, peaking in April), coinciding with the regional rainy season, and was highest in the interior of northern and central Ceara. Predicted potential varied more than a hundredfold among grid cells and was lowest along parts of the Ceara coast and the lower Jaguaribe valley, which include some of the largest infestations; the magnitude of these contrasts depended on the humidity threshold used to define wetness. Applied with identical rules to 13 historical release sites in Queensland, Australia, the model reproduced the documented wet-season timing of rust activity, and predicted potential was on average higher at sites with reported high rust impact, although the difference was not statistically significant. These results indicate strong seasonal and geographic structuring of weather-driven epidemic potential and provide testable hypotheses for selecting release periods and locations for M. cryptostegiae in Brazil.

Pterocarpus erinaceus Poir. (Fabaceae), the barwood or vene, is at the heart of one of the most severe conservation crises currently affecting tropical timber species. It has become the most heavily traded timber species in the world by volume, at the centre of an illegal rosewood trade to Asia that has driven the species to near-total disappearance in several countries despite its listing on CITES Appendix II since 2016. Faced with this urgency, ex situ conservation and restoration programmes often rest on the untested assumption that selecting seed trees by size improves the quality of the offspring produced in the nursery. This study rigorously tests this hypothesis against the competing one of a determinism dominated by the planting site, using six complementary analytical approaches (continuous regression, linear mixed models with a site x seed-tree interaction, seed-mass mediation analysis, non-linear growth modelling of height and diameter, between-site phenotypic plasticity, and multi-predictor allometric equations), across two contrasting bioclimatic sites in COte d'Ivoire (Korhogo: dry zone; Daloa: humid zone) and six seed-tree categories. Site exerts a decisive influence on growth at all ages (ANOVA, p<0.001 for height, diameter and biomass), whereas germination does not differ significantly between sites (70.3% at Daloa versus 61.6% at Korhogo; X2=1.95; p=0.162). Seed-tree DBH does not affect growth in any of the tests (continuous regression, p>0.30; mixed model, p>0.07), and the seed-mass mediation analysis remains inconclusive, seed mass varying only slightly among seed trees in this species (0.07-0.08 g). The exponential growth model provides the best fit for height and diameter at both sites, and two-predictor allometric equations explain 96.2% of biomass variance compared with 89.9% for the single-predictor model. These results indicate that ex situ conservation and compensatory reforestation programmes for this endangered species would benefit from prioritising the choice of planting site over the dendrometric selection of seed trees. A recommendation directly applicable to conservation nurseries established in response to the rosewood crisis.

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.

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.

Extreme climatic events (ECEs) could potentially induce episodes of rapid adaptive evolution, altering the evolutionary trajectories and viability of wild populations experiencing increasingly stochastic environments. Adaptive potential stems substantially from additive genetic variance (V) in survival. However, the degree to which ECEs impact this variance, and the resulting evolutionary implications, have not been fully conceptualised or quantified in nature. These aims are highly challenging because underlying genetic and environmental variances have fundamentally non-linear effects on the dichotomous phenotypic outcome of survival versus death, while substantial data are required for estimation. We present a conceptual and analytical framework that formalises biological hypotheses for how V depends on environmental severity, how such dependences are reshaped by non-linear genotype-environment-phenotype relationships and demographic structure, and the implications for evolutionary responses. We then use 25 years of survival and pedigree data from European shags (Gulosus aristotelis) to decompose variance in adult survival across diverse environmental conditions including ECEs. Using a capture-recapture animal model, we demonstrate non-negligible V underlying adult survival across all years combined, implying notable adaptive potential. Yet, partitioning by environmental severity revealed substantial V in good years with high survival but negligible V in bad years with ECE-induced low survival, implying a genotype-by-environment interaction that constrains adaptive potential under severe conditions. However, scale transformations showed how the non-linear genotype-environment-phenotype relationship can distort or even reverse such patterns, by reducing the extent to which V is phenotypically expressed in good conditions with high mean survival and amplifying it in more severe conditions with lower mean survival. Evolutionary responses to severe conditions could consequently be non-negligible even given small underlying V. We thereby demonstrate how ECEs can reshape adaptive potential, highlighting the need to integrate impacts of environmental severity on genetic variation in fitness components into predictions of population resilience under climate change.

Urbanization is an accelerating evolutionary force, yet the patterns and drivers of urban gene flow remain largely obscured. This leaves a critical gap in testing the interplay between demographic and genetic models of urban connectivity. Specifically: the urban fragmentation model, where structural barriers restrict gene flow and drive genetic drift; the urban facilitation model, where permeable matrices enhance functional connectivity; and the urban sink hypothesis, a demographic model where high mortality creates unsustainable population sinks. We used high-resolution RAD-capture data to conduct landscape genomics and gene flow analyses to resolve these models and investigate contemporary evolution in urban coyotes (Canis latrans) across the greater Los Angeles, CA, USA metropolitan area. By incorporating fine-scale environmental, social-ecological, and historical variables of the built environment, we rigorously assessed how urban heterogeneity shapes intra-city evolutionary dynamics. We found weak population structure, heavily influenced by family groups. There was extensive landscape permeability and gene flow across the study area including across four major highways. We also identified heavily asymmetric gene flow from exurban source populations into the urban core, supporting the urban sink paradigm. However, rather than acting as a genetic dead-end, the urban matrix showed striking functional heterogeneity: one urban core functioned as a 'genetic sponge,' absorbing unique transient alleles from multiple surrounding sources, and both urban cores operated as permeable 'leaky sinks,' exporting critical gene flow to other populations. Consequently, urban demographic sinks can simultaneously act as vital genetic bridges. Our findings reject a pure urban fragmentation model while demonstrating that demographic sink dynamics and genetic facilitation are not mutually exclusive. This demonstrates that high-turnover urban sinks can buffer regional biodiversity against genetic erosion, highlighting the need to prioritize matrix permeability and inter-patch connectivity in urban conservation strategies.

Megadiverse countries concentrate most of the World's biodiversity. These countries encompass different levels of research infrastructure, and nearly all of them have been historically committed to the Convention of Biological Diversity, often setting precedents and leading new approaches. Here, we ask whether the assessment of genetic diversity indicators provide novel insights for biodiversity management and conservation in one of those countries, Mexico. We evaluated the first national application of the Kunming-Montreal Global Biodiversity Framework (GBF), genetic diversity indicators in Mexico. The data covered 97 taxa across diverse ecosystem types and taxonomic groups, including crop wild relatives, to assess the capacity of genetic diversity indicators to provide novel insights, as well as their relevance for strengthening national conservation strategies. We calculated two indicators: the proportion of populations with an effective population size greater than 500 (Ne 500) and the proportion of populations maintained (PM). Data were sufficient to estimate the Ne 500 indicator for 47 taxa and the PM for 28 taxa, with mean indicator values of 0.217 and 0.936, respectively. Species' geographic range was positively associated with Ne 500, whereas national endemicity had no significant effect. Comparisons with the IUCN Red List and Mexico's national extinction-risk legislation revealed that genetic vulnerability occurs even among taxa not currently recognized as threatened. Our findings highlight a gap in legal recognition of genetic diversity protection that could be strengthened by incorporating population-level assessments focused on maintaining adaptive potential in the long-term. Additionally, the indicators allowed to highlight conservation concerns within crop wild relatives, though fully realizing their potential requires integrating the entire wild-to-domesticated complex. The Mexican experience highlights that the main challenge for scaling the monitoring of genetic diversity is not only generating new data, but integrating existing information into systems that strengthen collaboration and communication among researchers, local communities, and government institutions.

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.

The southern house mosquito Culex quinquefasciatus is a major disease vector for multiple arboviruses, including West Nile virus and St. Louis encephalitis virus. Insecticides are widely used to control Cx. quinquefasciatus populations, but resistant mosquitoes have emerged in numerous locations across the globe, including the United States. Much progress has been made in recent years in identifying insecticide resistance (IR) mutations in various pest species. In most species, these studies have focused primarily on SNPs as they are readily detectable. However, several genomic structural variants (SVs) have been experimentally shown to impact IR in Drosophila melanogaster, and structural variation has been observed in natural populations of vector species at a few genes that may be relevant to IR (e.g., cytochrome P450s). Because most population genomic data are derived from short sequencing reads, which fail to detect a large fraction of SVs, the contribution of structural variants to the evolution of IR and other adaptations in vector species is likely to be underestimated in the absence of long-read sequencing data. Here, we present the first genome-wide assessment of structural variants in Cx. quinquefasciatus from wild populations in Puerto Rico and Zambia using PacBio long-read sequencing. We constructed high-quality genome assemblies for each and found a total of 259,046 SVs which consisted predominantly of insertions and deletions. We found that 154,071 of these variants contained or overlapped genes. Of these SVs, 5,225 intersected IR genes and 56 of these were predicted to result in changes to downstream protein function. Several SVs predicted to severely impact protein-coding genes also coincided with signatures of selective sweeps, highlighting their possible role as targets of selection. Many of these variants would have gone undetected using short-read approaches, underscoring the importance of long-read sequencing for comprehensive population genetic analyses of adaptation to pesticides and other strong selective pressures, not only in insects but across the tree of life.

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.

Understanding the demographic processes shaping population connectivity is essential for conservation. Yet disentangling the effects of dispersal and local effective density remains challenging because traditional genetic approaches integrate signals over evolutionary timescales. Identity-by-descent (IBD) segments provide opportunities to reconstruct recent demographic connectivity over timescales relevant to contemporary conservation challenges, but their reliability under realistic ecological conditions remains poorly evaluated. Here, we assess the ability of two promising spatiall IBD-based methods, IBD-Analysis and MAPS, to estimate effective density and dispersal variance. Using a simulation-inference framework combining spatially explicit simulations, IBD segment extraction, and demographic inference, we evaluated both methods across a wide range of demographic, ecological and methodological scenarios. Both approaches reliably recovered demographic parameters under homogeneous landscapes, with IBD-Analysis providing accurate estimates of global effective density and dispersal across a broad range of conditions. Spatial heterogeneity emerged as the main driver of inference performance. When demographic parameters varied across space, IBD-Analysis integrated local variation into biased global estimates, whereas MAPS captured spatial patterns but showed substantial variability and generated spurious spatial structure in homogeneous landscapes. Methodological factors had comparatively weaker effects than ecological complexity, highlighting the importance of accounting for landscape structure when applying IBD-based demographic inference. These results highlight the potential of IBD-based approaches to move beyond descriptive patterns of genetic connectivity toward mechanistic inference of demographic processes. By distinguishing the contributions of dispersal and density, these methods can improve conservation decisions by linking genomic patterns to key demographic parameters relevant for conservation.

Self-fertilization results in reduction of heterozygosity over time, accelerated by small population sizes, restricted ranges, and fragmented habitats. Yet some species maintain heterozygosity despite these factors. One is Corallorhiza bentleyi, a threatened, mycoheterotrophic, self-pollinating orchid restricted to Virginia and West Virginia, USA. Reduced representation sequencing was employed across five of the ~12 known localities of C. bentleyi, including representatives of sister species C. involuta from Mexico, to quantify patterns of population structure and genomic diversity. Surveys of C. bentleyi revealed a predominance of the cleistogamous (closed-flowered) growth form. Differentiation was observed between the two species but with weak population structure in C. bentleyi. Surprisingly, excess heterozygosity and negative inbreeding were recovered in both species, counter to expectations. Analyses provided evidence against bioinformatic artifacts (collapsed paralogs), small-sample bias (Robertson effect), and accumulation of mutations along chromosomes due to low recombination associated with selfing (Meselson effect) as explanations for excess heterozygosity. Demographic analyses favored a model of post-glacial divergence among C. bentleyi and C. involuta lacking bottlenecks. Finally, simulations under alternative selection scenarios favored models of overdominance vs. those of negative frequency dependent selection. It was concluded that overdominance, namely selection against selfed homozygotes, is the most likely explanation for elevated heterozygosity in C. bentleyi. Conservation concerns are discussed in light of these findings and the threats of extinction for one of the most vulnerable orchid species in North America.

Following a severe 2018 drought affecting much of Europe, European beech (Fagus sylvatica) exhibited patchy canopy dieback. To investigate the drivers of this mortality, we used a paired case-control design across Swiss forests, integrating phenotypic assessments and genomic analyses. Phenotypically, crown transparency and discoloration were used to classify tree damage state, while several other characteristics were measured to evaluate whether paired, neighboring damaged and undamaged trees were otherwise comparable, and to identify physiological stress signatures. Elevated leaf calcium content and red edge reflectance in dried leaves emerged as robust indicators of physiological stress. Genomic association models using reference-based SNP markers and reference-free k-mers were heavily confounded by micro-environmental variance and local population stratification even within our geographically limited study region. Our cross-validated genomic outliers showed no spatial overlap with predictive drought-associated loci previously identified in an independent German cohort. These findings indicate that drought survival in European beech is not governed by a universal set of major-effect alleles. Instead, tree performance appears highly context-dependent, likely shaped by micro-environmental heterogeneity and phenotypic condition. However, our results do not exclude polygenic drought responses involving multiple small-effect loci.

Detecting dugongs at low densities remains a major challenge for conservation monitoring, particularly in remote or turbid coastal habitats where conventional surveys are difficult. Environmental DNA (eDNA) offers a complementary approach, but robust species-specific tools are needed before it can be confidently applied to dugong surveillance. We developed and analytically validated a quantitative PCR TaqMan assay for detecting dugong (Dugong dugon) eDNA and evaluated its performance across controlled aquarium conditions in Australia and Abu Dhabi, and wild populations in northern Australia and the Arabian/Persian Gulf. The assay detected dugong eDNA in aquarium and field samples, with Sanger sequencing confirming amplification of dugong mitochondrial DNA from positive field detections. Our assay provides a robust and geographically transferable tool for targeted dugong eDNA detection, performing reliably across contrasting coastal environments and widely separated populations. This approach can strengthen local-scale surveillance of low-density or difficult-to-detect dugong populations.

Okanagan sockeye salmon have shown a strong recovery over the past three decades, but the contribution of environmental conditions and management actions to this recovery has not been determined. We developed a hierarchical Bayesian model linking spawner abundances to fry emergence observations to evaluate how flow and water temperature during adult upstream migration and incubation periods influence spawner-to-fry production. Production declined by 62% in years with earlier onset and longer duration of periods when warm river temperatures created barriers to adult migration, indicating that migration conditions can have carry-over effects on reproductive success even when spawners successfully reach the spawning grounds. Additionally, production was 46% lower when flows fell above or below the management target range designed to minimize scour and desiccation during egg incubation. In contrast, we found little support for effects of pre-spawning flows or incubation temperature on production. These findings provide quantitative evidence that current flow management is increasing freshwater spawner-to-fry production and has likely contributed to the Okanagan sockeye recovery. Effective flow management may therefore help offset climate-driven impacts that increasingly threaten this population.