Evolutionary Applications最新文献

The risk of climate maladaptation is increasing for numerous species, including trees. Developing robust methods to assess population maladaptation remains a critical challenge. Genomic offset approaches aim to predict climate maladaptation by characterizing the genomic changes required for populations to maintain their fitness under changing climates. In this study, we assessed the risk of climate maladaptation in European populations of English yew (Taxus baccata), a long-lived tree with a patchy distribution across Europe, the Atlas Mountains, and the Near East, where many populations are small or threatened. We found evidence suggesting local climate adaptation by analyzing 8616 SNPs in 475 trees from 29 European T. baccata populations, with climate explaining 18.1% of genetic variance and 100 unlinked climate-associated loci identified via genotype-environment association (GEA). Then, we evaluated the deviation of populations from the overall gene-climate association to assess variability in local adaptation or different adaptation trajectories across populations and found the highest deviations in low latitude populations. Moreover, we predicted genomic offsets and successfully validated these predictions using phenotypic traits assessed in plants from 26 populations grown in a comparative experiment. Finally, we integrated information from current local adaptation, genomic offset, historical genetic differentiation, and effective migration rates to show that Mediterranean and high-elevation T. baccata populations face higher vulnerability to climate change than low-elevation Atlantic and continental populations. Our study demonstrates the practical use of the genomic offset framework in conservation genetics, offers insights for its further development, and highlights the need for a population-centered approach that incorporates additional statistics and data sources to credibly assess climate vulnerability in wild plant populations.

The restoration of swampland is vital for the recovery of both biodiversity and cultural values in Aotearoa New Zealand. Syzygium maire, an endemic wetland tree species, is a focus of many wetland restoration efforts. Formerly widespread, extant populations are small, fragmented, and under pressure from myrtle rust. Restoration initiatives may be unknowingly compounding these threats to the species by failing to represent the complete genetic diversity of populations. What genetic diversity remains in remnants and how it is distributed is not known. We therefore aimed to assess the national scale population structure, genetic diversity, and adaptive potential of S. maire to inform species conservation. We identified over 760,000 high-quality single nucleotide variants in 269 reproductive age trees from across the species' range, using low coverage whole genome resequencing. At a national scale, we found five distinct regional-scale genetic clusters, which in turn exhibit local structure and admixture. In the North Island: Northland, Bay of Plenty in the central east, Taranaki in the central west, and Greater Wellington/Manawatū in the south. A single cluster was identified in the South Island, Marlborough. Within-cluster substructure was particularly evident for Greater Wellington/Manawatū. Genetic diversity and fixation indices (F_ST) were relatively uniform across all clusters, and there was some evidence of north to south increase in kinship and shorter time since radiation. These patterns are likely to reflect glaciation cycles that resulted in complex contractions into local microrefugia and subsequent re-radiations of the species over time. Genotype by environment analysis detected genetic variants potentially contributing to environmental adaptation, notably precipitation seasonality. Restoration and conservation goals would best be served by capturing diversity within regional clusters. Information on the geographic and environmentally structured distribution of this tree's genetic diversity supports conservation and restoration strategies through ensuring the complete extant diversity is captured, identifying regions at most risk of genetic degradation, and facilitating planning regarding the movement of adaptive diversity in a changing environment.

The sterile insect technique (SIT), traditionally reliant on gamma irradiation, has been an effective strategy for controlling Bactrocera dorsalis. However, strict regulations governing gamma radiation sources and the limited research on the responses of B. dorsalis to X-ray irradiation have hindered the further development of SIT. This study demonstrated that X-ray dosage, pupal age, and their interaction significantly influenced the emergence parameters of B. dorsalis. Further experiments revealed that irradiating 8-day-old pupae resulted in a significant reduction in flight ability, lifespan, and fecundity in emerging adults. However, optimized doses ranging from 70 to 100 Gy effectively induced complete sterility while exerting minimal adverse effects on male quality. X-ray irradiation induced notable shifts in the gut microbiota composition of B. dorsalis, marked by a reduction in the abundance of Enterobacter, Citrobacter, and Proteus, accompanied by an enrichment of Providencia. Additionally, broad correlations among dominant bacterial genera were observed. Transcriptomic analysis further indicated that irradiation had a profound impact on gene expression in both male and female adults, with 100 and 34 differentially expressed genes (DEGs) identified in females and males, respectively. Gene Ontology (GO) enrichment analysis revealed six enriched GO terms common to both sexes. Correlation analysis suggested potential associations between specific differentially abundant bacterial genera and DEGs. These findings optimize X-ray-based SIT for B. dorsalis and provide new insights into its effects on gut microbiota and gene expression, offering theoretical support for the refinement of SIT strategies.

Biodiversity is under increasing pressure from environmental change, although the scope and severity of these impacts remain incompletely understood. For many species, a lack of information about population-specific responses to future environmental change hinders the development of effective conservation strategies. Here, we use an East African reed frog species complex as a model to explore spatial variation in vulnerability to future environmental changes. Our sampling across two threatened biodiversity hotspots spans the entire geographic range of H. mitchelli and H. rubrovermiculatus in Kenya, Tanzania, and Malawi. Using genome-wide (ddRAD-seq) data, we evaluate levels of neutral genetic diversity and local adaptations across sampling localities. We then integrate spatial approaches (genomic offset, modeled dispersal barriers, and Species Distribution Models) to predict how populations may respond differently to future environmental changes, such as climate warming and predicted land use changes. Based on our analyses, we characterize population structure and identify region-specific management needs that reflect genetic variation among populations and the uneven impacts of predicted change across the landscape. Peripheral populations are most vulnerable to future environmental changes due to (i) low levels of neutral genetic diversity (Malawi and Pare mountains in Tanzania), (ii) putative signals of local adaptation to wetter conditions with predicted disruptions to genotype–environment associations (i.e., high genomic offset, Kenya and Northern Tanzania), and (iii) the projected contraction of suitable habitat, which is a pervasive threat to the species complex in general. Populations in Northern, Central, and Southern Tanzania show the lowest vulnerability to environmental change and may serve as important reservoirs of genetic diversity for potential future genetic rescue initiatives. Our study highlights how populations across different parts of species ranges may be unevenly affected by future global changes and provides a framework to predict which conservation actions may help mitigate these effects.

With global environmental change, mismatches between seasonal movements of species and environmental conditions are increasingly impacting survival and persistence. Atlantic salmon (Salmo salar) perform long-distance marine migrations culminating in a return to natal rivers, the timing of which varies among and within populations. Global declines of salmon raise the possibility that phenological mismatches could be a contributing factor; however, the underlying genetic architecture of run timing remains poorly understood. Here, we use a 220 K SNP Array to examine the association of genetic variation with run timing at a population level for 11 North American rivers. We also ask what the potential vulnerability of run timing is to future climate change by estimating trait-specific genomic offsets, i.e., predicted shifts in allele frequencies at loci associated with run timing under projected climate change, yielding relative estimates for each population. Detected associations suggest a polygenic basis for run timing, including a large structural variant and maturation-associated genes previously characterised in Atlantic salmon (six6, vgll3), and ppfia2, a migration-timing gene conserved across vertebrates. Genomic offsets associated with climate change impacts for run timing were highest in more northern populations, suggesting potential maladaptation in future migrations. By describing the genetic architecture of run timing in North American Atlantic salmon and possible impacts of climate change on the persistence of life-history strategies, results from this study contribute towards a better understanding of this complex life-history trait to inform future conservation management.

Coastal organisms live in a dynamic environment where a myriad of environmental stressors, including climate change, ocean acidification, and human harvesting, act on variable spatio-temporal scales. Each of these stressors may impose unique selective forces on a population, shaping a species' adaptive potential and its ability to persist under future climatic conditions. Genomic investigations of adaptive responses to environmental and anthropogenic disturbances remain rare, especially in marine systems. Here, we use whole genome sequencing data from the owl limpet, Lottia gigantea, and outlier detection methods to pinpoint signals of selection (1) across long-standing environmental gradients spanning the species' distribution, (2) at the poleward edge of the species' range where it experienced a recent expansion, and (3) between sites vulnerable to or protected from human size-selective harvesting within California. Loci associated with environmental gradients across the entire range show the strongest differentiation at the southern end of the species' range, potentially driven by adaptation to sea surface temperature and pH. Additional ad-hoc outlier analyses revealed a distinct set of loci potentially under selection in the expanded range, with different functional roles than the range-wide outliers. Despite demographic models suggesting that protection from harvesting has a positive impact on the abundance of large individuals, we did not find strong signals of selection or changes in genetic diversity between sites differing in harvesting vulnerability. Our findings suggest that range-wide environmental selective signals established over longer time scales are distinct from those imposed by climatic anomalies at finer spatio-temporal scales. We found that climatic variation has a stronger selective imprint than human harvesting, and thus conservation interventions should consider prioritizing the maintenance of climate-related adaptive potential. Understanding how climatic trends and anomalies interact with anthropogenic pressures will allow us to make more informed decisions to sustain the evolutionary capacity of L. gigantea and other key coastal species.

Introgression of domesticated genomes influences the evolutionary trajectory of wild populations. Genetic markers are used to quantify admixture in wild populations subjected to introgression from non-native conspecifics. However, markers can be under direct and indirect selection which may influence admixture estimates and quantification of fitness consequences thereafter. We expanded the Atlantic salmon eco-genetic model IBSEM to compute individual fish phenotype and domestication admixture using markers under variable strengths of selection. Following 50 years of 5%–25% domesticated conspecifics on the spawning grounds, the recipient wild population showed an increase in adult size at age and a decline in adult abundance, both of which scaled with the degree of intrusion. In the following 50-year recovery period without further escapees, traits started to but did not completely revert to pre-impact levels. Neutral and weakly selected markers gave higher admixture estimates than markers under stronger degrees of selection. The disparity increased during the recovery period where neutral markers and their corresponding admixture estimates “lingered” in the wild population, whereas admixture based on markers under selection declined as the population recovered. During the recovery period, the strength in the relationship between individual fish admixture and size at age was also eroded when computed using neutral markers, but less so for the markers under selection. Collectively, these observations illustrate how markers under selection mirror the fitness and phenotypic changes in the population, while neutral markers reflect demographic history and can therefore not be uncritically used to infer fitness consequences. Our results also suggest that management guidelines used in Norway and some other countries, setting 10% domesticated escapees in a river and/or 10% domestication admixture in wild populations as the limit for a “large” impact, will provide a high level of protection for wild salmon populations.

Extreme climatic temperature stress induced by global warming poses a severe threat to the survival of marine invertebrates. The plasma membrane functions as a natural barrier and serves as the first responder to ambient temperature through dynamic modulation of its fluidity. However, the adaptive mechanisms of membrane lipid remodeling in response to temperature fluctuations remain poorly understood in marine organisms. Oysters, the most widely cultivated shellfish globally, hold significant economic and ecological importance. We characterized the changes in plasma membrane lipid composition of two congeneric oyster species—the northern/cold-adapted Crassostrea gigas and the southern/warm-adapted Crassostrea angulata—under short-term acute heat and cold stress, including changes in lipid subclass content, glycerophospholipid acyl chain length, and glycerophospholipid unsaturation. Our results revealed sphingolipids and sterol lipids content may play a more critical role in short-term temperature adaptation, while glycerophospholipid alterations may prioritize dynamic lipid modifications over abundance changes. Notably, the relatively cold tolerant C. gigas exhibited higher lipid unsaturation and shorter acyl chain lengths, with a preferential modulation of glycerophospholipid acyl chain length, while the heat tolerant C. angulata regulated fatty acid unsaturation to maintain membrane fluidity for temperature adaptation. Divergent membrane lipid remodeling strategies in two congeneric oysters provide new insights into the adaptation mechanisms of membrane fluidity in marine organisms, informing risk assessment for aquaculture industries under global warming. The identification of key components such as phosphatidylethanolamine, sphingosine, ceramide phosphates, and cold and heat adapted lipid molecules provides important biomarkers for predicting the adaptive potential of marine organisms to future extreme climate.

The spatial structure and dynamics of populations are important considerations when defining management units in organisms that are harvested as natural resources. In the Eastern Pacific, Pacific Sardine range from Chile to Alaska, the northernmost state of the United States (U.S.), and once supported an expansive and productive fishery. Along its North American range, it is hypothesized to comprise three subpopulations: a northern and southern subpopulation, which primarily occur off the coast of the U.S. and Baja California, Mexico (M.X.), respectively, and a third in the Gulf of California, M.X. We used low coverage whole genome sequencing to generate genotype likelihoods for millions of SNPs in 317 individuals collected from the Gulf of California, M.X., to Oregon, U.S., to assess population structure in Pacific Sardine. Differentiation across the genome was driven by variation at several putative chromosomal inversions ranging in size from ~21 MB to 0.89 MB, although none of the putative inversions showed any evidence of geographic differentiation. Our results support panmixia across an impressive ~4000 km range.

Mud crab (Scylla paramamosain) is an economically important aquaculture crustacean species in China and Southeast Asia countries. However, the catches of wild mud crabs declined sharply due to overfishing and environmental pollution. Therefore, it is necessary to understand the current genetic resources and population history of mud crab (S. paramamosain), which would provide appropriate guidelines for genetic resource management and breeding programs. To achieve this goal, a total of 146 mud crabs from four geographic populations in the southeast coast of China were collected for whole genome resequencing to investigate the genetic diversity, population genetic structure, and runs of homozygosity (ROHs). Results showed that the nucleotide diversity (π) ranged from 0.00157 to 0.00160, with observed heterozygosity (0.248–0.257) approximately equal to expected heterozygosity (0.260–0.265), indicating that these populations were near Hardy–Weinberg equilibrium, albeit with relatively low polymorphism. The results of PCA, population structure, phylogenetic tree, and linkage disequilibrium (LD) analysis consistently indicated weak genetic differentiation among different geographic populations. ROHs detection revealed 47,142 ROHs in mud crabs, with over 60% shorter than 0.1 Mb. Moreover, the average genomic inbreeding coefficient estimated by ROHs (F_ROH = 0.0293) and homozygous sites (F_HOM = 0.0389) suggested relatively low inbreeding in mud crab populations. Notably, 29 candidate genes were identified in potential ROH islands, including growth and development-related genes (IARS and UNC79), which may play an important role in the adaptive evolution of mud crabs. Overall, our results would provide valuable insights for conserving, managing, and improving the genetic resources of mud crabs (S. paramamosain).