Evolutionary Applications最新文献

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).

Understanding crop domestication offers crucial insights into the evolutionary processes that drive population divergence and adaptation. It also informs the identification of genetically diverse wild germplasm, which is essential for breeding and conservation efforts. While domestication has been extensively studied in many Mediterranean fruit trees, the evolutionary history of the almond (Prunus dulcis) remains comparatively underexplored. To address this, we analyzed 209 wild and cultivated almond accessions sampled across Eurasia and genotyped with 23 microsatellite markers. Using population genetics and coalescent-based inference, we reconstructed the domestication history of P. dulcis and its relationships with wild relatives. Bayesian clustering revealed four genetically distinct clusters of cultivated almonds: Turkish, Caucasian–Central Asian, Southern Spanish, and European/North American. These groups were differentiated from wild almond species—including Prunus turcomanica, Prunus orientalis, Prunus fenzliana, and Prunus spinosissima—each forming its gene pool across the Middle East and Central Asia. Approximate Bayesian Computation (ABC) supported a single domestication event in the Middle East, originating from either P. orientalis or P. turcomanica, with subsequent gene flow from P. fenzliana and P. spinosissima into the Turkish and Central Asian cultivated gene pools, respectively. We also inferred reciprocal introgression from cultivated almonds back into wild populations. Notably, sharka resistance—caused by plum pox virus (PPV)—was identified in three P. dulcis clusters and P. fenzliana, suggesting that resistance may have arisen independently or been maintained through crop–wild introgression. Together, our results highlight a complex and protracted domestication history for almond, shaped by contributions from multiple wild relatives and recurrent gene flow. These findings enhance our understanding of perennial crop evolution and underscore the value of wild germplasm in breeding programs aimed at increasing resilience in fruit trees.

The main theory of the evolution of virulence relies on a trade-off between virulence and transmission rate. However, it has been difficult to measure the required trade-off. A recent transmission decomposition framework explains that this might be partly due to a lack of information about the parasite's survival in the environment outside its hosts, where the parasite finds itself during transmission to its next host. In this study, we used parasite lines of the microsporidian Vavraia culicis with varying levels of virulence upon infecting their host, the mosquito Anopheles gambiae, to explore the interaction between parasite-driven virulence within its host and its survival outside of the host. The parasite lines with greater virulence and growth within their hosts had a cost in their intrinsic ability to withstand the environment, irrespective of temperature. These results underscore the importance of considering the full context of transmission and other parasite fitness traits in studying and predicting the evolution and spread of infectious diseases.

Genomic tools are becoming increasingly necessary for mitigating biodiversity loss and guiding management decisions in the context of climate change. Freshwater fish species are particularly susceptible to the impacts of changing environments, including kokanee, the resident form of sockeye salmon (Oncorhynchus nerka), which has already been negatively impacted by increases in extreme temperature throughout its distribution. A previous study using whole genome resequencing of wild kokanee stocks identified 1412 environmentally associated SNPs and demonstrated genomic offset, a measure of climate vulnerability, to be significantly correlated with higher increases in extreme warm temperatures across much of the species' range in western Canada. Here, we aimed to operationalize this information for fisheries management by first developing a Genotyping-in-Thousands by sequencing (GT-seq) panel populated exclusively with environment associated SNPs. We then evaluated the robustness of the GT-seq panel relative to the signal in the whole genome resequencing baseline and demonstrated a novel application of donor and recipient importance (DI/RI) analysis to inform recreational fisheries stocking decisions. We found that a reduced GT-seq panel of 616 SNPs exhibited a significant positive correlation with those calculated from the full set of 1412 SNPs across the climate change scenarios tested; similar results were obtained when adding new reference populations not included in the original whole genome resequencing baseline. The DI/RI analysis revealed clear spatial trends, with populations situated in the warmest regions of southern interior British Columbia (Canada) having the highest probability for successful translocations to different recipient locations to the north. Similarly, candidate recipient lakes for stocking at the center of the distribution had higher recipient importance values than those located towards the eastern and western range peripheries. Although further refinement is required, pairing targeted genotyping with genomic offset and DI/RI predictions holds great promise for informing freshwater fisheries management moving forward.

Habitat loss and fragmentation are major drivers of biodiversity decline, reducing connectivity among populations and leading to genetic isolation, loss of diversity, increased inbreeding, and reduced fitness. Translocations that promote gene flow by introducing genetically distinct individuals—a process known as genetic rescue—can mitigate these effects by increasing genetic diversity, alleviating inbreeding, and improving adaptive capacity. However, a limited understanding of a population's demographic history, genetic differentiation, and connectivity can hinder the effective application of genetic rescue. We used the Stephens' kangaroo rat (Dipodomys stephensi), a species threatened by habitat loss and fragmentation in southern California, as a model for developing range-wide genetic management strategies. We analyzed mitochondrial DNA and microsatellite data to investigate genetic structure and estimate both historical and recent demographic patterns, and we used landscape resistance modeling to assess the impacts of natural and anthropogenic barriers on gene flow. Genetic analyses suggest a relatively recent diversification of Stephens' kangaroo rat populations, with higher allelic diversity concentrated in central populations and reduced diversity in isolated northern and southern populations. Although natural geographic features explain much of the genetic structure, landscape resistance models showed that anthropogenic barriers (e.g., roads, development) play a key role in current genetic isolation and are expected to continue driving population differentiation. To guide management, we used population viability simulations to test translocation strategies aimed at reversing genetic erosion. Repeated translocations were far more effective than single events at boosting heterozygosity and population persistence. The frequency and size of translocations were less important than their continued implementation. For very small populations, concurrent habitat restoration to increase carrying capacity was essential to prevent extirpation. Our findings highlight the value of integrating genetic, demographic, and landscape data into conservation planning. This approach is broadly applicable to other species experiencing habitat fragmentation and population isolation.