Evolutionary Applications

The fall armyworm (FAW) Spodoptera frugiperda is thought to have undergone a rapid west-to-east spread since 2016 when it was first identified in western Africa. Between 2018 and 2020, it was also recorded from South Asia (SA), Southeast Asia (SEA), East Asia (EA), and Pacific/Australia (PA). Population genomic analyses enabled the understanding of pathways, population sources, and gene flow in this notorious agricultural pest species. Using neutral single nucleotide polymorphic (SNP) DNA markers, we detected genome introgression that suggested most populations were overwhelmingly C- and R-strain hybrids. SNP and mitochondrial DNA markers identified multiple introductions that were most parsimoniously explained by anthropogenic-assisted spread, i.e., associated with international trade of live/fresh plants and plant products, and involved bridgehead populations in countries to enable successful pest establishment in neighbouring countries. Distinct population genomic signatures between Myanmar and China do not support the African origin spread nor the Myanmar source population to China hypotheses. Significant genetic differentiation between populations from different Australian states supported multiple pathways involving distinct SEA populations. Our study identified Asia as a biosecurity hotspot and a FAW genetic melting pot, and demonstrated the use of genome analysis to disentangle preventable human-assisted pest introductions from unpreventable natural pest spread.

Anthropogenic drivers are restricting many species to small, genetically isolated populations. These are prone to inbreeding depression and are at an increased risk of extinction. Genetic rescue, the controlled introduction of genetic variation from another population, can alleviate inbreeding effects. A major conservation concern, restricting the use of this technique, is that such augmented gene flow may disrupt local adaptation crucial to a populations persistence. Using populations of the red flour beetle (Tribolium castaneum) experimentally adapted to reproduce at higher temperatures, we assess whether genetic rescue attempts disrupt thermal adaptation. Rescuers, drawn from populations adapted to either 30{degrees}C or 38{degrees}C, were introduced into populations adapted to 38{degrees}C, which had been inbred for two generations. We recorded population productivity for three generations post-rescue, in the adapted 38{degrees}C environment. Rescuers with and without local adaptation significantly increased the productivity of recipient inbred populations but, importantly, those sharing local adaptation to reproduction at 38{degrees}C provided greater increases in productivity. For the first time, we show that co-adaptation between rescuing individuals and rescuee population maybe an essential aspect of achieving desired conservation outcomes.

Genetic management is a critical component of threatened species conservation. Understanding spatial patterns of genetic diversity is essential for evaluating the resilience of fragmented populations to accelerating anthropogenic threats. Nowhere is this more relevant than on the Australian continent, which is experiencing an ongoing loss of biodiversity that exceeds any other developed nation. Using a proprietary genome complexity reduction-based method (DArTSeq), we generated a data set of 3,239 high quality Single Nucleotide Polymorphisms (SNPs) to investigate spatial patterns and indices of genetic diversity in the koala (Phascolarctos cinereus), a highly specialised folivorous marsupial that is experiencing rapid and widespread population declines across much of its former range. Our findings demonstrate that current management divisions across the state of New South Wales (NSW) do not fully represent the distribution of genetic diversity among extant koala populations, and that care must be taken to ensure that translocation paradigms based on these frameworks do not inadvertently restrict gene flow between populations and regions that were historically interconnected. We also recommend that koala populations should be prioritised for conservation action based on the scale and severity of the threatening processes that they are currently faced with, rather than placing too much emphasis on their perceived value (e.g., as reservoirs of potentially adaptive alleles), as our data indicate that existing genetic variation in koalas is primarily partitioned amongst individual animals. As such, the extirpation of koalas from any part of their range represents a potentially critical reduction of genetic diversity for this iconic Australian species.

Clam fishery stocks have experienced a significant, albeit uneven, decline along the Spanish coast, with stock delineation frequently mirroring political boundaries rather than biological ones. Nevertheless, it is crucial to align management units with the biological realities of the species to ensure sustainable exploitation. In this context, understanding the spatio-temporal population structure, genetic diversity, and effective population size (Ne) of the wedge clam Donax trunculus populations along the Iberian Peninsula coast is vital for making informed management decisions. Thus far, high-resolution genomic data on these key parameters remain limited for this species. Our analysis utilised a substantial dataset of 8,479 single-nucleotide polymorphisms (SNPs) derived from 331 individuals collected over approximately 2,000 kilometres along the Iberian coast, confirming a genetic structure that classified the individuals into three distinct groups: the Atlantic Ocean, the Balearic Sea, and the Alboran Sea. For the first time, we revealed contrasting temporal changes in neutral and adaptive genetic diversity across different fishing areas, reflecting the varying effectiveness of certain management strategies implemented to date. Furthermore, to safeguard genetic diversity and preserve potential local adaptations, we recommend that these genetically distinct groups be managed separately in future conservation, potential translocation and fishing plans.

Biological control agents often experience demographic bottlenecks during introduction, which can reshape genetic diversity and inbreeding pattern influencing establishment and long-term ecological success in the introduced populations. The leaf-feeding beetle Calligrapha (Zygogramma) bicolorata, introduced in multiple countries across the globe to control the weed Parthenium hysterophorus, provides an opportunity to examine how introduction bottleneck and post-introduction breeding practices shape genomic variation and inbreeding patterns. We analyzed whole-genome variation in the introduced beetle population in India by sampling six regions encompassing its current distribution in the country. Using genome-wide variation data, we assessed population structure, genetic diversity, and inbreeding patterns across regions, and inferred historical changes in effective population size to reconstruct post-introduction demographic trajectories. The analyses reveal subtle genetic structure across regions, with overall genetic diversity relatively low compared to other invasive and biocontrol insects. Inbreeding patterns vary among populations, with some regions exhibiting higher cumulative runs of homozygosity than others. Notably, regions subjected to intensive propagation of beetle populations show elevated signature of inbreeding alongside reduced historical effective population size. These results underscore the dynamic genomic consequences of biocontrol introduction and subsequent breeding practices, providing insight into the evolutionary trajectories of introduced biocontrol agents.

The fall armyworm (FAW) Spodoptera frugiperda is present in over 70 countries in Africa, Asia, and Oceania. Its rapid dispersal since 2016 when it was first reported in western Africa, and associated devastation to agricultural productivity, highlight the challenges posed by this pest. Currently, its management largely relies on insecticide sprays and transgenic Bacillus thuringiensis toxins, therefore understanding their responses to these agents and characteristics of any resistance genes enables adaptive strategies. In Australia, S. frugiperda was reported at the end of January 2020 in northern Queensland and by March 2020, also in northern Western Australia. As an urgent first response we undertook bioassays on two Australian populations, one each from these initial points of establishment. To assist with preliminary sensitivity assessment, two endemic noctuid pest species, Helicoverpa armigera and Spodoptera litura, were concurrently screened to obtain larval LC50 estimates against various insecticides. We characterised known resistance alleles from the VGSC, ACE-1, RyR, and ABCC2 genes to compare with published allele frequencies and bioassay responses from native and invasive S. frugiperda populations. An approximately 10x LC50 difference for indoxacarb was detected between Australian populations, which was approximately 28x higher than that reported from an Indian population. Characterisation of ACE-1 and VGSC alleles provided further evidence of multiple introductions in Asia, and multiple pathways involving genetically distinct individuals into Australia. The preliminary bioassay results and resistance allele patterns from invasive S. frugiperda populations suggest multiple introductions have contributed to the pests spread and challenge the axiom of its rapid west-to-east spread.

The Pacific oyster, Crassostrea (Magallana) gigas, is an important species in aquaculture globally, but its production is threatened by pathogens including ostreid herpesvirus 1 (OsHV-1) and Vibrio aestuarianus. A genetic marker associated with resistance to OsHV-1 infection has been identified on chromosome 8 (Chr8) of the Pacific oyster genome. Marker-assisted selective breeding has used the Chr8 marker to produce oyster families with increased survivorship and resistance to OsHV-1 infection. The potential effect of the Chr8 marker on susceptibility to other pathogens remains largely unknown, but was recently associated with increased resistance of spat to Vibrio coralliilyticus. Here we assess the effect of the presence and allelic dosage of the Chr8 marker on the susceptibility of selectively bred juvenile Pacific oysters to V. aestuarianus infection. Sixteen families were produced with various Chr8 marker genotypes, and a V. aestuarianus disease challenge was conducted. Challenged oysters were individually genotyped at the Chr8 marker, and Vibrio susceptibility was evaluated among genotypes within and between families. Prior to the challenge trial, the Chr8 marker did not occur at the expected Mendelian ratios in families with heterozygous parents; in multiple families the homozygous alternate genotype occurred at a lower frequency than was expected. Mortality rates in the Vibrio challenge differed between families, ranging from 47.9% to 85.4%, but no association was observed between the Chr8 marker and survival to V. aestuarianus exposure. Therefore, we observed no pleiotropic effect (positive or negative) of the Chr8 marker on survivorship to V. aestuarianus at the evaluated life stage. Reduced-representation sequencing was used to genotype the challenged oysters and a genome-wide association study for V. aestuarianus survivorship was performed, but no significant associations were found, suggesting polygenic architecture for the trait.

Populations of Atlantic salmon continue to suffer marked declines in abundance due to stressors acting in both their freshwater and marine habitats. It is therefore an imperative to identify populations in need of increased conservation intervention, with the aim of preserving as much as possible the genetic diversity present within the species. Previous microsatellite-based analyses have shown the chalk rivers of southern England and northern France to hold genetically distinct populations of salmon. However, these salmon populations have never been investigated in the same study. Using a suite of 93 single nucleotide polymorphism loci and samples from 42 British Isles and French rivers, we demonstrate the French and English chalk salmon to be closely related and distinct from salmon inhabiting non-chalk rivers. The identification of a small number of significant FST outliers suggests that this distinction is driven by local adaptation. We propose that the chalk and non-chalk salmon be designated as two distinct Evolutionarily Significant Units that each contain multiple Management Units. The chalk river salmon, especially those from southern England, are identified as making a significant contribution to the overall diversity of the species within the English Channel region. As a consequence, we propose that the salmon populations of the chalk streams may meet the criteria for recognition as a distinct subspecies of salmon, Salmo salar calcariensis. Taken together, the results presented here highlight the urgent need for enhanced conservation and protection for the Atlantic salmon populations inhabiting the chalk rivers of southern England and northern France.

BACKGROUNDInvasive Australian populations of redlegged earth mite, Halotydeus destructor (Tucker), are evolving increasing organophosphate resistance. In addition to the canonical ace gene, the target gene of organophosphates, the H. destructor genome contains many radiated ace-like genes that vary in copy number and amino acid sequence. In this work, we characterise copy number and target-site mutation variation at the canonical ace and ace-like genes and test for potential associations with organophosphate insensitivity. This was achieved through comparisons of whole-genome pool-seq data from alive and dead mites following organophosphate exposure. RESULTSA combination of increased copy number and target-site mutations at the canonical ace was associated with organophosphate insensitivity in H. destructor. Resistant populations were segregating for G119S, A201S, F331Y at the canonical ace. A subset of populations also had copy numbers of canonical ace >2, which potentially helps over-express proteins carrying these target-site mutations. Haplotypes possessing different copy numbers and target-site mutations of the canonical ace gene may be under selection across H. destructor populations. We also detected some evidence that increases in copy number of radiated ace-like genes are associated with organophosphate insensitivity, which might suggest potential roles in sequestration or breakdown of organophosphates. CONCLUSIONDifferent combinations of target-site mutations and (or) copy number variation in the canonical ace and ace-like genes may provide non-convergent ways for H. destructor to respond to organophosphate selection. However, these changes may only play a partial role in organophosphate insensitivity, which appears to have a polygenic architecture.

Marine species often exhibit genetic discontinuities concordant with biogeographic boundaries, frequently occurring due to changes in ocean circulation, bathymetry, coastline topography and temperature. Here we used 10,916 single nucleotide polymorphisms (SNPs) to assess the concordance between population genomic differentiation and coastal biogeography in the fishery important snapper (Chrysophrys auratus) across southeastern Australia. Additionally, we investigated whether spatial scales of assessment and management of snapper align with evidence from population genomics. Across 488 snapper samples from 11 localities between the west coast of South Australia and the south coast of New South Wales, we detected genomic structure concordant with the regions three biogeographic provinces. We also detected fine-scale genetic structuring relating to spatial variation in spawning and recruitment dynamics, as well as temporal stability in the genomic signal associated with two important spawning grounds. The current management boundaries in the region coincided with either the genetic breaks at bioregional boundaries or with localscale variation. Our study highlights the value of population genomic surveys in species with high dispersal potential for uncovering stock boundaries and demographic variation related to spawning and recruitment. It also illustrates the importance of marine biogeography in shaping population structure in commercial species with high dispersal potential.

Introduced in the late 19th Century, Oncorhynchus mykiss (rainbow trout) have been stocked historically in streams throughout Baden-Wurttemberg, Germany, and some populations have become self-sustaining with unclear impact on native salmonid populations. We sampled 223 rainbow trout from 14 streams and 3 hatcheries, from which the streams are known to have been stocked. We conducted genomic analyses to uncover evidence confirming self-sustaining populations, to deduce potential sources of these populations, to compare the genetic diversity of hatchery vs stream populations, and to discover genetic differences between stream and hatchery populations. We found genetic population structuring amongst the stream populations, consistent with natural reproduction over several generations, and we inferred multiple genetic origins, potentially including source populations beyond the three hatcheries considered. We found no significant difference in genetic diversity between stream and hatchery populations, but there were specific positions in the genome associated with naturalisation within or adjacent to immunity, growth and development genes. Whether such genes are under selection in wild stream environments needs still to be determined to inform fisheries and conservation management.

Hymenoscyphus fraxineus is an invasive fungal pathogen responsible for the ash dieback epidemic, which continues to cause severe mortality of common ash (Fraxinus excelsior L.) across Europe. Following its likely introduction in northeastern Europe, the pathogen rapidly colonized most regions where common ash is present. As it spread southward, H. fraxineus encountered warmer climates and a higher occurrence of Fraxinus ornus L., a species largely resistant to the disease. Despite this environmental heterogeneity, which likely imposed adaptive challenges on H. fraxineus at the epidemic front, ash dieback continues to expand in southern Europe. Aggressiveness is a key life-history trait that is expected to evolve during epidemics and to exhibit plasticity in response to environmental variation. We investigated whether the plasticity of aggressiveness in response to temperature and ash species has evolved in H. fraxineus during its propagation towards southern Europe. Using a synchronic approach based on leaf inoculations, we characterized individual reaction norms for aggressiveness in a long-established Lithuanian population and a recently established Italian population of H. fraxineus. The Italian H. fraxineus population is exposed to warmer summers than the Lithuanian population, while F. ornus is present in Italy but absent in Lithuania. We observed no difference in the aggressiveness expressed on F. excelsior under moderate temperature between the two H. fraxineus populations. However, the ability of Italian isolates to cause severe leaf symptoms was less negatively affected by increasing temperature and host species change than that of Lithuanian isolates, suggesting local adaptation of H. fraxineus during its spread toward southern Europe. Our findings highlight the importance of considering the evolution of adaptive traits and their plasticity in fungal pathogens when anticipating disease risk. They also suggest that ash trees in southern Europe may be slightly more vulnerable to ash dieback than previously anticipated.

Malaria remains a major global health burden, with traditional control methods facing challenges such as insecticide resistance and high operational costs. Genetic biocontrol offers a promising alternative for mosquito population suppression, but its field efficacy would require assessment. This study evaluates the role that population genomic statistics can play in detecting decreases in population size in the context of a cluster randomized control trial (cRCT), investigating the response of nucleotide diversity ({pi}), Tajimas D, segregating sites, and linkage disequilibrium (LD) under both constant and seasonal demographic scenarios. We simulated 90% and 99% population declines with various degrees of between-cluster heterogeneity, and assessed the detection power of each statistic over time and number of clusters per arm. Results show that Tajimas D is highly sensitive and robust across crash severity, seasonality and heterogeneity scenarios. Segregating sites has similar power to Tajimas D when baseline data are available. We further estimated that cRCTs require approximately 3 to 5 villages per treatment arm to achieve adequate statistical power. These findings provide recommendations for genetic monitoring of vector control interventions in wild populations.

Restoration and management of natural populations often assume that local genotypes are best suited for transplantation to their local environment. Prioritizing a single local genotype, however, contrasts with the framework of maximizing intraspecific diversity to increase population resilience to environmental change. Local populations may also become maladapted to a rapidly changing environment, motivating alternative frameworks that instead minimize environmental distance between source and transplantation sites. Here, we tested the predictive power of the local is best, maximize intraspecific diversity, and minimize environmental distance frameworks on the survival and growth of Eastern oyster (Crassostrea virginica) genotypes in field common gardens that differed in salinity and disease pressure. Although a genome scan revealed patterns of adaptation to disease, heat stress, and salinity among source populations, we did not find strong support for the local is best framework: geographically distant southern genotypes performed comparably to local selection lines and a local wild population. Higher genetic diversity within monocultures was associated with higher survival, yet highly diverse polycultures survived at lower rates than the best-performing monocultures, providing mixed support for the maximize intraspecific diversity framework. Temperature and salinity of the environments-of-origin of parents predicted the survival of their offspring in common gardens, but the relationship between survival and environmental distance was context-dependent, leading to mixed support for the minimize environmental distance framework. Together, these results demonstrate that no single framework reliably predicted transplantation success, suggesting that effective management strategies may need to integrate genomic and environmental lines of evidence to guide genotype selection.

Assessing genetic diversity is essential for conserving endangered populations, yet comprehensive genomic evaluations remain limited for many declining species. Here, we investigated inbreeding levels and effective population sizes (Ne) of caribou (Rangifer tarandus) in western Canada, where populations have experienced pronounced declines over the past centuries due to anthropogenic pressures and climate change. We analyzed 33,346 Single Nucleotide Polymorphisms (SNPs) from 759 individuals representing 45 subpopulations within six metapopulations to: (1) assess inbreeding using runs of homozygosity (ROHs), (2) estimate contemporary and historical Ne, and (3) evaluate relationships between census size (Nc), inbreeding, and Ne. Small and endangered subpopulations, predominantly in southern regions, generally exhibited high inbreeding (FROH > 0.1), although some larger populations also showed elevated levels. Most subpopulations displayed a mixture of short and long ROHs, indicating both ancient shared ancestry and recent inbreeding. Twelve subpopulations had Ne <50, and 28 subpopulations and all metapopulations had Ne < 500, suggesting compromised short-term viability and long-term adaptive potential. Nc significantly predicted inbreeding (R{superscript 2} = 0.25), whereas contemporary Ne did not. Historical Ne reconstructions revealed a north-to-south gradient in bottleneck timing: northern populations declined in [~]1700-1780, central populations in [~]1780-1860, and southern populations in [~]1860-1940, likely driven by sequential impacts of climate shifts and anthropogenic disturbances. Our findings identify at-risk populations requiring urgent genetic intervention and demonstrate that integrating inbreeding and Ne estimates provides a robust framework for caribou recovery and the management of fragmented wildlife populations.

ContextWhile resistant cultivars are valuable in safeguarding crops against diseases, they can be rapidly overcome by pathogens. Numerous strategies have been proposed to delay pathogen adaptation (evolutionary control), while still ensuring effective protection (epidemiological control). Resistance genes can be deployed in 1) single-gene-resistant cultivars sown in the same field (mixture strategy) or in different fields (mosaic strategy), 2) a pyramided cultivar (pyramiding strategy) or 3) hybrid strategies that combine the three previous strategies. In addition, the spatial scale at which resistant cultivars are deployed can affect the plant-pathogens interaction: small fields are thought to reduce pest density and disease transmission. ObjectivesWe aim to compare these strategies, focusing on the effects of the simultaneous deployment of single-gene-resistant and pyramided cultivars sharing resistance genes in an agricultural landscape. We also investigate the impact of field size. MethodsWe used the spatially-explicit stochastic model landsepi to compare the evolutionary and epidemiological control across spatial scales and deployment strategies for two major resistance genes. ResultsThe evolutionary control provided by the pyramiding strategy is at risk when single-gene-resistant cultivars are concurrently planted in the landscape (hybrid strategies). The probabilities of pathogen mutation and the corresponding fitness costs play a crucial role in determining the feasibility of planting pyramided cultivars alongside single-gene-resistant ones. Instead, field size did not affect strategies recommendation. ConclusionsPlanting pyramided cultivars alongside single-gene-resistant ones should be avoided. Socio-economic perspectives for the adoption of resistance management strategies are discussed.

AimTo assess how biogeographic barriers and environmental heterogeneity shape connectivity and local adaptation in the striped Venus clam (Chamelea gallina), a commercially exploited bivalve in the Mediterranean Sea. LocationNortheast Atlantic (Gulf of Cadiz) and Mediterranean Sea (Alboran, Balearic, Tyrrhenian and Adriatic regions). TaxonChamelea gallina (Bivalvia: Veneridae). MethodsWe analysed genome-wide single nucleotide polymorphisms (SNPs) from 226 individuals sampled across six regions (Gulf of Cadiz, Alboran Sea, Balearic Sea, Ebro Delta, Tyrrhenian Sea and Adriatic Sea) using a seascape genomic framework. Population structure was inferred using both putatively neutral and adaptive loci. Genotype-environment associations were tested against key oceanographic variables, including sea surface temperature, salinity and nutrient availability. ResultsNeutral loci revealed weak genetic differentiation, consistent with substantial gene flow across most of the species range. In contrast, putatively adaptive loci uncovered pronounced genetic structure that corresponded closely to major Mediterranean biogeographic regions, particularly the Adriatic Sea, the Gulf of Cadiz and western-central Mediterranean basins. Significant associations were detected between genetic variation and environmental gardients, with several candidate adaptive SNPs located within coding regions, suggesting functional responses to spatially heterogeneous conditions. Main conclusionsOur results demonstrate that local adaptation can generate biologically meaningful population structure in C. gallina despite high levels of connectivity inferred from neutral markers. This decoupling between neutral and adaptive variation highlights the importance of integrating adaptive genomic information into biogeographic inference. Recognizing environmentally driven genetic differentiation is essential for defining robust management units and for improving the long-term sustainability and resilience of C. gallina fisheries under increasing anthropogenic pressure and climate change.

ObjectiveMaintaining genetic diversity in small, isolated populations is a key goal in conservation genetics. Genetic monitoring can guide management decisions, but comparisons across studies and time points are often complicated by differences in genetic markers and data sets. We aimed to develop a consistent, replicable set of genetic markers to support long-term monitoring of Paiute Cutthroat Trout (Oncorhynchus henshawi seleniris), a federally threatened subspecies persisting in a network of isolated refuge populations in California, USA. MethodsWe used RAD (Restriction site-associated DNA) sequencing to identify single nucleotide polymorphisms (SNPs) from 476 individuals representing eight extant refuge populations. Filtering steps included the removal of paralogous loci and exclusion of FST outliers associated with sequencing batch effects. We selected a panel of 1,114 SNPs that were shared across all populations and validated the panel in silico by comparing population structure and genetic diversity estimates to those derived from the full RAD sequencing dataset. ResultsThe candidate panel SNPs captured key patterns of genetic differentiation and diversity consistent with previous studies and the larger RAD dataset. We present updated baseline genetic metrics for each refuge population, providing a consistent reference point for future monitoring efforts. We also demonstrate the ability of our candidate panel SNPs to detect successful spawning after a translocation event. ConclusionThis study provides a set of SNPs tailored for monitoring genetic diversity and structure in Paiute Cutthroat Trout refuge populations. Future work should include development of a high-throughput genotyping assay to implement these candidate panel SNPs for ongoing management. This would enable consistency over time with genetic studies and be a foundational tool for repeated evaluation of conservation actions such as reintroductions and augmentations. Lay SummaryWe identified genetic markers to help track and protect one of the rarest trout in the United States. This work supports long-term conservation by making it easier to monitor isolated populations and measure the success of efforts to restore the species.

The Democratic Republic of Congo (DRC) suffers from one of the highest malaria burdens worldwide, but information on its Anopheles vector populations is relatively limited. Preventative malaria control in DRC is reliant on pyrethroid-treated nets, raising concerns over the potential impacts of insecticide resistance. We sampled Anopheles gambiae from three geographically distinct populations (Kimpese, Kapolowe and Mikalayi) in southern DRC, collecting from three sub-sites per population and characterising mosquito collections from each for resistance to pyrethroids using WHO tube bioassays. Resistance to each of three different pyrethroids was generally high in An. gambiae with <92% mortality in all tests, but varied between collections, with mosquitoes from Kimpese being the most resistant. Whole genome sequencing of 165 An. gambiae revealed evidence for genetic differentiation between Kimpese and Kapolowe / Mikalayi, but not between the latter two sample sites despite separation of approximately 800km. Surprisingly, there was evidence of population structure at a small spatial scale between collection subsites in Kimpese, despite separation of just tens of kilometres. Intra-population (H12) and inter-population (FST) genome scans identified multiple peaks corresponding to genes associated with insecticide resistance such as the voltage gated sodium channel (Vgsc) target site on chromosome 2L, a Cyp6 cytochrome P450 cluster on chromosome arm 2R, and the Cyp9k1 P450 gene on chromosome X. In addition, in the Kimpese subsites, the P450 redox partner gene Cpr showed evidence for contemporary selection (H12) and population differentiation (FST) meriting further exploration as a potential resistance associated marker.

Caribou, listed as a species at risk across Canada, have experienced a wide range of evolutionary and selective pressures at multiple scales, from large-scale range shifts and recolonisations driven by glacial cycles to more localized contemporary habitat degradation and fragmentation. Given these multi-scale evolutionary forces, genetic variation and diversity are expected to be hierarchically structured. Characterising hierarchical population structure is crucial to understanding a species evolutionary history and informing effective conservation and management strategies. In this study, we analysed genomic diversity and variation in woodland caribou (Rangifer tarandus caribou) across western Canada using genotypes from [~]33,000 Single Nucleotide Polymorphism (SNP) loci from 759 geo-referenced individuals spanning 45 pre-defined subpopulations. We employed genetic clustering methods and measures of genetic differentiation to characterize hierarchical population structure in the region and tested for latitudinal changes in heterozygosity resulting from post-glacial recolonisation and hybridisation. Our results confirm that woodland caribou genetic diversity and differentiation occur at multiple hierarchical levels, reflecting post-glacial recolonisation patterns and landscape heterogeneity. Notably, the major genetic clusters identified in our study do not align with current conservation units for the species in this region. We also observe elevated heterozygosity in the mid-latitudes of the sampled range, indicative of hybridisation following secondary contact during post-glacial recolonisation. These findings underscore the need to consider and include genetic diversity at all hierarchical levels in conservation planning, as wide-ranging species often experience diverse and complex evolutionary histories and pressures.