Evolutionary Applications

Understanding the genetic structure of keystone species within river networks is essential for effective conservation and management. While population differentiation of anadromous species often occurs between river systems, less research has been conducted on differentiation within rivers with smaller catchment areas. In this study, we investigated the population genetic structure of wild Atlantic salmon (Salmo salar) across the small-scale river Ronne [a] system in southernmost Sweden using Restriction-site Associated DNA sequencing (RADseq). Although the Admixture analysis did not detect clearly defined genetic clusters, significant pairwise FST values and DAPC revealed emerging population differentiation among the Ronne [a] tributaries. The observed patterns are consistent with a system characterized by connectivity, where genetic flow is present but can be reduced by behavioral and ecological factors such as spawning homing behavior and selective movements. These findings suggest that, despite overall connectivity, Atlantic salmon populations in the Ronne [a] catchment area may function as partially independent sub-populations. This highlights the importance of conservation and management strategies in fragmented river systems to consider population genetic structure to support resilient salmon populations under ongoing anthropogenic pressures.

Many economically important insect pests reproduce through asexual or partially asexual life cycles, yet how reproductive mode influences insecticide resistance management remains unclear. The choice of resistance management strategy has been suggested to differ for sexual and asexual pests. For instance, current IRAC guidance suggests that pesticide mixtures are less effective in non-mating pests than in sexually reproducing populations. Here, stochastic evolutionary simulations are used to compare resistance evolution under sequences and mixtures across four reproductive modes observed in pests of economic importance: sexual reproduction, obligate parthenogenesis, cyclical parthenogenesis and haplodiploidy. Contrary to current expectations, mixtures are not disadvantaged in asexual populations and, in some cases, lead to delayed resistance evolution compared to sexually reproducing populations. These differences arise as the result of reduced genetic recombination which constrained the assembly and spread of multi-resistant genotypes. Overall, these findings suggest that mixtures remain a viable resistance management strategy for pests with asexual reproduction.

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.

Selection for disease resistance forms one of the most highlighted areas of aquaculture breeding. A breeding program for Arctic charr has been operating in Sweden for over 40 years, making it the oldest of its kind worldwide for this species. However, the lack of available genomic resources prevented selection for any disease-resistance traits. A 72k Axiom SNP array was produced in this study and used to assess the potential to select for charr resistant to bacterial kidney disease (BKD), which is currently a major threat to the industry. Following a challenge experiment with Renibacterium salmoninarum, the causative agent of BKD, relevant phenotypic proxies were collected from approximately 2,000 charr. Thereafter, those animals were genotyped with the new 72k SNP array. The magnitude of the estimated variance components suggested potential for breeding for BKD resistance in charr, with relevant heritabilities ranging from 0.05 to 0.56 depending on the resistance proxy used. In addition, GWAS suggested that BKD resistance is a polygenic trait. Furthermore, genomic prediction approaches indicated that BKD-resistant animals can be identified using their SNP genotypes. Accuracies, expressed as Pearson correlation coefficients, when BKD resistance was analysed as a continuous trait, ranged from 0.42 to 0.52. In the scenario where BKD resistance was treated as a binary trait, the efficiency of genomic prediction was assessed using ROC curves, with an area under the curve of 0.72. Finally, no unfavourable correlations were found with growth traits. The developed 72k SNP array has the potential of being a pivotal tool for the Swedish Arctic charr breeding program. Moreover, our data support the use of genomic prediction in breeding BKD-resistant Arctic charr. As a critical next step, further validations in actual industry conditions would be required.

Genomic signatures can provide key insight into the evolutionary history and remaining adaptive potential of threatened populations. As demographic decline erodes both diversity and the processes maintaining it, understanding how remaining variation is distributed becomes increasingly important for conserving species like the staghorn coral, Acropora cervicornis, a foundational but critically endangered Caribbean reef-builder. We analyzed 46 high-coverage A. cervicornis genomes from 10 locations across the tropical western Atlantic to evaluate neutral and adaptive structure, genomic diversity, demographic history, inbreeding, and connectivity, and generated a regional haplotype reference panel for future genomic monitoring. Genome-wide analyses recovered recurring regional substructure, but differentiation was modest and partly explained by isolation-by-distance and spatial variation in effective migration. Subpopulations had similar levels of genomic diversity, shared demographic history, and limited evidence of local adaptation. These patterns support interpreting sampled Caribbean populations as a single evolutionarily significant unit (ESU) containing multiple regional management units (MUs), rather than as deeply divergent evolutionary lineages. Despite substantial retained variation and low current inbreeding, estimated contemporary effective population size was small, suggesting an increased vulnerability to the effects of drift as demographic collapse continues, especially if structure is reinforced by isolated management. Together, our findings emphasize the urgent need for interventions that preserve and enhance genomic diversity, including risk-managed assisted gene flow. Supported by the haplotype reference panel developed here, these strategies will require coordinated efforts across regional entities to conserve and restore A. cervicornis as a jointly managed, single ESU.

Many rare saproxylic (deadwood-dwelling) beetles are among Europes most threatened insects, yet the relative importance of local microhabitat quality versus broad-scale landscape connectivity in shaping their genetic integrity remains poorly understood. We evaluated environmental drivers for 13 saproxylic beetle species--rare old-growth specialists, common taxa, and economically significant pests--across eight major forest complexes in Poland, using double digest restriction-site associated DNA sequencing (ddRAD-seq) paired with plot-level structural inventories and estimated effective migration surfaces (EEMS) modelling. A beta generalized linear mixed model identified deadwood diversity as the only significant within-species predictor of observed heterozygosity ({beta} = 0.041, 95% CI 0.0227-0.0586, p < 10-); total deadwood volume, forest age, time since logging, stump density, and veteran tree density were not significant. Management-category contrasts in observed heterozygosity (Ho) and the inbreeding coefficient (Fis) were non-significant after Tukey adjustment. Predictor x ecological-tier interactions did not differ detectably between rare and common species for five of six structural predictors; time since last logging was the exception ({chi}{superscript 2} = 4.56, p = 0.033). EEMS patterns differed among species and fell into three broad groups: regional lineage barriers, asymmetrical corridors, and surfaces close to isolation- by-distance expectations. These results associate plot-level heterozygosity with deadwood diversity and show that regional gene-flow patterns cannot be generalised across saproxylic beetles. Conservation planning should therefore combine local deadwood restoration with species-specific assessment of landscape connectivity.

Mining pollution is an important stressor of freshwater communities worldwide. Persistence in these environments requires adaptation, yet identifying the mechanisms responsible in wild systems remains challenging due to differing water chemistries and genetic backgrounds. Parallel evolution presents a powerful framework for identifying adaptive mechanisms through repeated directional change. Here, we seek to understand the mechanisms that enable brown trout (Salmo trutta) to survive in metal-polluted rivers. Using low-coverage Whole Genome Resequencing (lc-WGS) we analyse paired metal-polluted and non-polluted brown trout populations across the British Isles. Metal-impacted populations show reduced nucleotide diversity and increased genomic divergence from paired control populations. We observe strong signatures of parallel adaptation in populations with shared geography, emphasising the importance of standing genetic variation in rapid adaptation to pollution. We identify a candidate region of 0.5 Mb on chr25 that shows strong parallel adaptation across multiple pairwise comparisons, including a shared signal among populations experiencing highly divergent water chemistries. The chr25 region contains the genes oestrogen receptor (esr2b) and a potassium-gated ion channel (kcnh5b), both of which are linked to developmental and osmoregulatory functions known to be disrupted by metals. Using population branch statistics (PBS) and scans for selective sweeps, we also identify population-specific candidate loci, yet putatively selected regions repeatedly converge on shared gene families and functional pathways. Our findings reveal both parallel and unique evolutionary responses to anthropogenic pollution in wild fish, highlighting convergent adaptive pathways to diverse pollutants in teleosts.

The European flat oyster (Ostrea edulis), like numerous other oyster species, has been exploited for millennia and cultivated and translocated for centuries. Following a severe population decline, and in the context of ongoing conservation and restoration programs, genetic considerations must now be addressed to avoid mistakes. The objective of our study was to complement population genetic studies conducted at various scales along European coasts. Our sampling primarily targeted the French Atlantic, English Channel, and Mediterranean coasts, aiming to provide a fine-scale genetic characterization of populations in these regions. By integrating SNP array and low-coverage sequencing datasets, we obtained a comprehensive overview of the population genetic structure of Ostrea edulis across western Europe. Most previously identified clusters in Western Europe were confirmed. In France, populations assigned to these clusters exhibited notable within-patch homogeneity. However, two key findings emerged: (1) an extensive overlap zone between the Atlantic and western Mediterranean clusters, spanning at least from southern Portugal to southern France, and (2) the detection of a novel, clearly distinct cryptic cluster east of the English Channel, whose geographic range remains to be better delineated. These insights are critical for informing management decisions, particularly as restoration and conservation plans are currently being implemented across the species range.

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.

Sustainable management of commercial and recreational fisheries depends on accurately resolving population connectivity, across both ecological and evolutionary timescales. However, dispersal can vary markedly among life stages, making stock connectivity difficult to resolve using single-method approaches that often differ in spatio-temporal resolution. Here, we integrated population genomics, otolith stable isotope chemistry, and mark-recapture analyses to provide a multi-faceted assessment of stock connectivity in mulloway (Argyrosomus japonicus). Mulloway are a commercially, culturally, and recreationally important estuary associated fish distributed throughout the Indo-Pacific region, including south-eastern Australia where this study was conducted. Genome-wide single nucleotide polymorphism (SNP) analyses revealed significant genetic differentiation between regions influenced by different current systems, but limited structure within regions across distances exceeding 900 km. In contrast, otolith {delta}13C and {delta}18O signatures revealed fine-scale spatial structuring among estuaries, consistent with prolonged occupancy of local habitats. Mark-recapture analyses supported this interpretation, with most fish exhibiting strong estuarine fidelity over extended periods despite occasional long-distance coastal movements. Reconstructed age structures from fish otoliths revealed remarkably similar cohort composition among estuaries, with populations dominated by cohorts originating from a major recruitment pulse centred on 2011-2012, likely associated with a broad-scale flood-driven spawning and recruitment event. Together, our findings indicate that mulloway fisheries function as regionally connected networks of partially independent estuarine assemblages, where strong local residency is periodically offset by dispersive individuals and episodic recruitment events that maintain long-term demographic and genetic connectivity. Consequently, local estuarine populations may be vulnerable to localised depletion despite broader regional connectivity, particularly where sustained fishing pressure coincides with reductions in freshwater flows that constrain spawning and recruitment. More broadly, our study demonstrates the value of integrating complementary approaches to identify biological connections and define meaningful management units in species with complex life histories.

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.

The global invasion of the Asian tiger mosquito Aedes albopictus has led to an increase in arboviral disease, including within Mesoamerica. Understanding vector invasion routes is important for public health because it directs biosecurity and identifies sources of adaptive allele spread. Panama is an important hub of global trade with opportunities for Aedes introduction through both maritime and overland routes but dispersal into the Isthmus has not yet been investigated. We therefore sought to investigate the population structure and invasion history of Ae. albopictus into Panama, targeting both its mitogenome and associated Wolbachia. Historical demographic analysis with Bayesian phylogeographic diffusion models and estimates of divergence revealed that Panamanian Ae. albopictus and its associated Wolbachia have a convergent evolutionary history resulting from multiple introductions. Both could be traced to Asian-derived lineages introduced via the Americas, with invasion primarily through the maritime trade of the Panama Canal rather than overland dispersal from neighboring Costa Rica. An investigation of the relative density of Wolbachia in Panama revealed that both the strains wAlbB and wAlbA were at a notably lower density compared to other worldwide locations. This finding has implications for arbovirus transmission and raises important questions about how Wolbachia density is impacted by the environment and impacts on population control. Overall, the Panama Canal is a key route for vector introductions into Mesoamerica.

Prolonged use of the few insecticide classes available for long-lasting insecticidal nets (LLINs) and indoor residual spraying (IRS) has driven widespread physiological resistance of malaria vector mosquitoes to this limited arsenal of active ingredients. However, recent innovations like next-generation LLINs (NG-LLINs) containing two complementary insecticides and new insecticide classes for IRS offer new opportunities for pre-emptive resistance management by deploying more diversified actives as mixtures, combinations, rotations or mosaics. Here a deterministic model of mosquito foraging behaviour was formulated to predict the probabilities of deterrence, mortality or successful feeding across repeated feeding attempts in scenarios with different combinations of NG-LLINs and/or IRS micro-mosaics with varying levels of insecticide diversification between neighbouring houses. Final fates were classified based on whether or not the mosquito eventually died or successfully fed, and whether the latter occurred indoors or outdoors after exposure to zero, one or several IRS insecticides. The primary outcome was the probability that a single F mosquito carrying a novel resistance trait to a new IRS insecticide successfully feeds, survives and reproduces, thereby establishing those traits within the population. The secondary outcome was the selection coefficient governing the spread of such novel resistance traits from the F generation onwards. For highly anthropophagic and endophagic vectors like Anopheles funestus, combining NG-LLINs with IRS micro-mosaics using two insecticides may reduce emergence rates for novel resistance traits against IRS insecticides by approximately 2 to 2.5-fold, mainly through direct killing by NG-LLINs, although exposure to both IRS actives when forced to visit multiple houses also contributes to a lesser extent. However, such resistance management benefits are fundamentally constrained by outdoor feeding behaviours that limit or completely prevent indoor insecticide exposure. Increasing IRS micro-mosaic insecticide diversity beyond two actives is unlikely to further dampen resistance emergence rates because few mosquitoes survive long enough without feeding to encounter several IRS treatments. Once a resistance trait becomes established in the vector population, selection coefficients remain consistently high enough to force the spread of those traits, regardless of intervention combination. For more exophagic, zoophagic vectors like An. arabiensis, NG-LLINs plus IRS micro-mosaics are not expected to provide any meaningful resistance management benefit because frequent outdoor feeding, often on animals, allows them to largely avoid insecticide exposure altogether. Exclusively indoor-focused vector control strategies may not satisfactorily slow insecticide resistance emergence and spread, so new outdoor protection measures that close these coverage gaps with complementary insecticides will be needed.

Genomic health estimates help inform conservation and management decisions, with genetic load and runs-of-homozygosity (ROH) being two key metrics. White-tailed deer (Odocoileus virginianus) and mule deer (O. hemionus) are found throughout North America, with some populations declining or of conversation concern. Using genome-wide data from samples across their range, we provide the first estimate of genetic load in mule deer, and revisit ROH estimates using model-based approaches. These updated estimates of ROH notable showed elevated inbreeding in the Key deer, consistent with current conservation designations. We also detected a relatively high number loss-of function mutations in mule deer that we attributed to historical bottlenecks. Notably, we observed an increased overall genetic load in O. hemionus from the Pacific Northwest.

Climate change is driving the decline of coral populations around the world such that many are unlikely to recover without human intervention. Assisted sexual reproduction is one intervention proposed to enhance genetic diversity and support population recovery, yet its genetic outcomes remain poorly quantified. We evaluated genome-wide relatedness and genetic diversity in 168 restoration genets of the endangered Caribbean coral Acropora palmata, including 153 sexually produced offspring derived from multi-parent batch and biparental crosses. We detected high relatedness within multi-parent batch cross cohorts, with many genets comprising only one or a few full-sibling groups, indicating highly unequal parental contributions. Nucleotide diversity was lower in one batch cross cohort relative to founder populations, but the absolute difference was small and runs of homozygosity were relatively short indicating that inbreeding depression is not yet a concern. These patterns suggest that common larval propagation approaches can successfully generate large numbers of new genets but underscore the need to manage inbreeding risk, especially in small breeding stocks such as the Caribbean Acropora spp. Specifically, our results highlight the need for comprehensive genetic management to integrate assisted sexual reproduction into coral restoration, including parentage tracking, broodstock rotation, and relatedness-informed outplanting designs.

The Atlantic surfclam, Spisula solidissima solidissima supports multimillion dollar harvests in the western North Atlantic, including Georges Bank and Mid-Atlantic Bight populations along the continental shelf. Surfclam populations in this part of the Exclusive Economic Zone (3-200 nm from shore) are managed as a single unit, but demographic connectivity has never been tested directly. This study analyzed >8,500 SNPs in 548 Atlantic surfclams sampled across the USA harvested range to infer population structure, genomic diversity, and gene flow patterns. Genomic analyses included eight sampled and 10 reference Spisula solidissima similis samples, a morphologically cryptic nominal subspecies previously known only from nearshore habitats. Novel morphologically cryptic population structure was identified in S.s. solidissima. One operational taxonomic unit (OTU-A) was found only in the inshore region of southern New England, south of Cape Cod. The other population unit, OTU-B, was found offshore and in Cape Cod Bay. The federal fishing grounds only had OTU-B clams. Populations within each OTU were connected by gene flow, justifying current fishery management practices. Nearshore state waters had mixed OTU stocks. Hybridization was analyzed between the two OTUs and between the two subspecies based on nuclear SNPs and asymmetrical mitochondrial DNA introgression. Finally, we demonstrated the utility of a novel SNP panel for diagnosing all three taxa and their hybrids.

European white oaks grow from the Mediterranean coast to Southern Scandinavia, a huge environmental gradient that has likely fostered environmental adaptation. In the face of climate change, leveraging adaptations through assisted gene flow could help improve drought tolerance and maintain forest health, but requires an understanding of the species-specific patterns of adaptation to be successful at the target location. In this study, three common gardens were established in Switzerland, Tuerkiye, and Austria for two European white oak species (Quercus robur, and Q. pubescens) using provenances from Central and Southern Europe. Almost 900 oak seedlings were measured at key water-use efficiency and life history traits for their first two year of life and genotyped with low coverage whole-genome sequencing. Trait heritability and environmental adaptation were then explored through pedigree-free animal models, while the genomic architecture of traits was mapped using a genome wide association study ("GWAS"). Across the species, the heritability of measured traits was moderate to high, but common garden had a strong impact, signalling an environmental effect on the phenotype. Adaptation to precipitation seasonality was detected in key productivity and growth traits for both species, but had a small effect on absolute trait values. The GWAS identified a striking 150 kbp association in the Cyclic Nucleotide-Gated Ion Channel gene family with leaf d13C values. This gene family is involved in stomata opening and likely impacts the intrinsic water use efficiency under stress. Together, the strong signals of phenotypic plasticity and rather weak signals of climatic adaptation in seedlings suggest that assisted gene flow in these two white oaks is relevant only for highly drought-sensitive populations, if conducted managers should focus on seeds sources with high precipitation seasonality and smaller leaf sizes.

Tree populations can respond to climate change through migration, phenotypic plasticity, or genetic evolution. Despite long generation times of forest tree species, recent studies suggest that their evolutionary responses may occur rapidly. Using oaks as a model system, we synthesize evidence from 88 common garden studies and from historical, retrospective and longitudinal approaches to explore how populations have adapted to climatic variability across different biomes, and assess the consistency and pace of evolutionary responses across spatial and temporal climatic gradients. We found that approximately 61% of the studies exhibited significant differences among populations but climatic drivers and adaptive strategies differed among biomes. Temperature-related clines predominated in temperate regions, with populations from warmer origins showing longer growing seasons and higher growth potential. In seasonally dry biomes, aridity favored increased drought tolerance in Mediterranean populations but drought avoidance in tropical populations. Allochronic studies revealed genetic changes over decades to millenia in response to climate changes, with warming associated with increased growth and reduced specific leaf area in temperate oaks. Thus, spatial differentiation and temporal evolution were generally congruent in direction for most traits except for leaf unfolding, while short-term evolutionary rates exceeded long-term estimates by two to three orders of magnitude. In summary, provenance trials can provide useful information on the direction of climate-driven evolution for some traits, but may underestimate its contemporary pace. More studies are needed to evaluate whether standing genetic variation of forest tree species is sufficient to track current climate change.

A comprehensive understanding of life history is vital to successful species conservation and management. When different life history stages are accompanied by considerable morphological or cryptic variation, such as the egg and larval phases exhibited by most fishes, genomic tools are essential for identifying species so that early-life ecology questions can be studied. Genotyping-in-thousands by sequencing (GT-seq) has recently emerged as a targeted and efficient approach for species identification. We leveraged existing genomic and transcriptomic data to develop a GT-seq panel capable of differentiating the members of the Coregonus artedi complex, a radiation of salmonids in the Laurentian Great Lakes whose members are indistinguishable with mitochondrial DNA barcoding loci and are the focus of bi-national conservation initiatives. Our panel of 494 loci was able to assign fishes in the C. artedi complex to species and lake. We examined cross-amplification in other coregonines with overlapping distributions and found that congeneric Lake Whitefish (C. clupeaformis) cross-amplified at 94% of loci and confamilial Round and Pygmy Whitefish (Prosopium spp.) cross-amplified at 42% and 38% of loci, respectively. We adapted bioinformatic probes to account for Prosopium-specific variants including 22 new SNPs and developed a whitelist of 428 SNPs capable of distinguishing these whitefishes. Finally, we demonstrated performance by identifying 3,066 coregonine larvae and juveniles collected in spring 2019-2021 from Lake Superior. These results hold promise for future insights into the species-specific ecology of early life coregonines and demonstrate the flexibility of GT-seq panels, which may cross-amplify hundreds of informative genome-wide loci in related taxa.

Biodiversity losses continue to outpace traditional management, underscoring the need to understand adaptive capacity and the potential for interventions to increase fitness under climate change. We undertook a genome-wide association study on 156 Acropora palmata genets to investigate the genomic basis of areal growth, endosymbiont association, and thermal tolerance. Seven peaks on chromosomes 1, 3 and 14 were associated with endosymbiont shuffling and two peaks on chromosome 4 were associated with areal growth. As variants were located in non-coding regions we incorporated additional data from an independent field-transplant experiment to investigate their relationship with patterns of gene expression. Intersection of these datasets implicated melanocortin-like receptor activity and Ran GTPase activating protein 1 in endosymbiont composition and surface area growth, respectively. Results indicate that growth and endosymbiont associations may represent more viable intervention targets than temperature tolerance and highlight the need to better understand the role of non-coding variation in basic biology and development of restoration interventions.