Evolutionary Applications最新文献

Quantitative resistances are essential tools for mitigating epidemics in managed plant ecosystems. However, their deployment can drive evolutionary changes in pathogen life-history traits, making predictions of epidemic development challenging. To investigate these effects, we developed a demo-genetic model that explicitly captures feedbacks between the pathogen's population demography and its genetic composition. The model also links within-host multiplication and between-host transmission, and is built on the assumption that the coexistence of susceptible and resistant hosts imposes divergent selection pressures on the pathogen population at the landscape scale. We simulated contrasting landscapes of perennial host plants with varying proportions of resistant plants and resistance efficiencies. Our simulations confirmed that deploying resistances with nearly complete efficiency (> 99.99%) effectively reduces the severity of epidemics caused by pathogen introduction and promotes the specialization of infectious genotypes to either susceptible or resistant hosts. Conversely, the use of partial resistances induces limited evolutionary changes, often resulting in pathogen maladaptation to both susceptible and resistant hosts. Notably, deploying resistances with strong (89%) or moderate (60%) efficiencies can, under certain conditions, lead to higher host mortality compared to entirely susceptible populations. This counterintuitive outcome arises from the maladaptation of infectious genotypes to their hosts, which prolongs the lifespan of infected hosts and can increase inoculum pressure. We further compared simulations of the full model with those of simplified versions in which (i) the contribution of infected plants to disease transmission did not depend on the pathogen load they carried, (ii) plant landscapes were not spatially explicit. These comparisons highlighted the essential role of these components in shaping model predictions. Finally, we discuss the conditions that may lead to detrimental outcomes of quantitative resistance deployments in managed perennial plants.

The agromyzid leafminer Liriomyza trifolii (Burgess) is an important polyphagous pest of vegetable crops and ornamental plants. It is native to the Americas but has spread throughout the world over the past 50 years. Previous molecular research has indicated that this species contains highly distinct mitochondrial lineages suggestive of cryptic species. To better interpret the mitochondrial divergence, we used anchored hybrid enrichment datasets in order to conduct genome-wide phylogenetic analyses. We found that individuals of L. trifolii from pepper and tomatillo populations form a monophyletic group (“PT group”) distinct from the remaining L. trifolii (“non-PT group”). These results corroborate previous mitochondrial and nuclear datasets and indicate an absence of gene flow between the PT and non-PT groups. This is consistent with previous work on reproductive isolation and oviposition preferences, and provides substantial evidence that the PT group represents a distinct and previously unrecognized species. The presence of two species within a nominally single pest species has important implications for management. Although there was only weak genetic differentiation between geographically disparate groups of non-PT L. trifolii, a monophyletic group of Chinese specimens was found in a coalescent-based analysis that is concordant with the history of invasions in Asia. Our study provides important new insight into geographic and host-associated structure in L. trifolii.

Dispersal impacts individual fitness and influences local dynamics, stability and adaptation in interconnected populations. Anadromous salmonid fishes are renowned for their precise homing and adaptations to local aquatic environments, while navigating between multiple connected habitats. However, recent studies have demonstrated considerable straying among systems, generating metapopulation dynamics among connected subpopulations or demes. Salmonids constitute valuable economic and ecological resources, yet many populations are declining due to multifaceted anthropogenic-induced disturbances. This context of reduced populations inhabiting altered environments may impact both population viability and dispersal. To explore if metapopulation processes are present among impacted neighbouring populations of anadromous brown trout (Salmo trutta), a 4-year study of individual (N = 84) dispersal behaviour (using biotelemetry) and genetic analysis was conducted in four populations, connected by an extensive (> 200 km), semi-enclosed fjord system, Sognefjorden, Norway. To estimate the demographic status of each study population, life-table matrices were built, from which a potential source–sink structure among demes could be identified. Sognefjorden brown trout formed a metapopulation consisting of multiple sink populations, primarily supplemented from a single source. Only one population exhibited intrinsic growth (i.e., λ > 1), with excess recruits in this population attributed to high survival within the fjord. Among potential spawners, dispersal movements were performed by 55% of the total population, with individual age and migration extent affecting the probability of this behaviour. Successful dispersal (straying) was performed by 25% of the total spawning population. The extensive hydroscape generated directional gene flow from the innermost to outermost populations, with the highest rates observed among neighbouring populations. Although most dispersal resulted in unsuccessful spawning events and/or was not intended for spawning (e.g., conducted for overwintering purposes), connectivity among population demes was significant. This connectivity likely enhances the overall resilience of the metapopulation to variation and shifts in contemporary conditions within the fjord.

Anthropogenic pollution can have detrimental effects on organismal physiology, behavior, and fitness, but the underlying genomic mechanisms mediating these effects are not well understood. Epigenetic regulation, such as DNA methylation, has been proposed as a potential mechanism mediating these effects, but currently, there are few studies in wild populations. Here, we examined the methylation patterns of liver tissues from black guillemot (Cepphus grylle) in regions of the Canadian Arctic with different histories of exposure to polycyclic aromatic compounds (PACs)—contaminants associated with hydrocarbons and petrochemicals. As compared to a reference site with minimal PAC exposure, the two sites with exposure to anthropogenic sources of PACs (shipping and spills) shared more differentially methylated regions (DMRs) than they did with the site experiencing chronic exposure to natural PACs (a hydrocarbon seep). Furthermore, we found that guillemots that have been exposed to anthropogenic PACs are characterized by having DMRs with significantly greater ratios of hypermethylated to hypomethylated DNA versus the population experiencing chronic exposure to natural PACs. However, birds from all three sites with elevated PAC exposure shared a core set of DMRs, implying that there are some consistent methylation responses to this family of compounds. Taken together, these results imply that the specific composition and exposure length of PACs can influence the direction of the epigenetic response. The identified DMRs serve as a genomic resource for further research investigating the functional role of DNA methylation in response to anthropogenic oil pollution.

Pesticide resistance presents some of the best examples of evolution by natural selection in action. An exceptionally well-documented case from recent years is the evolution of resistance to the diamide chlorantraniliprole in the striped rice stem-borer Chilo suppressalis in China. Prior to the registration of chlorantraniliprole, C. suppressalis had evolved resistance to almost all other available pesticides. Using data from resistance monitoring and laboratory analysis, the quantitative dynamics of chlorantraniliprole resistance evolution in C. suppressalis and other lepidopteran pests in China are collated and analysed. The results reveal the rapid evolution of high levels of chlorantraniliprole resistance in C. suppressalis causing control failure across China, primarily driven by the origin and spread of multiple identified major mutations of the target site. Some of the same mutations also drove the parallel evolution of chlorantraniliprole resistance in other lepidopteran pests. As well as providing an exceptional example of evolution by natural selection in action, the evolution of chlorantraniliprole resistance in C. suppressalis in China also provides a cautionary tale for resistance management.

Ecological restoration has emerged as a prominent conservation and management strategy widely touted for its utility in evaluating ecological theories when designed experimentally. In comparison, restoration has been underutilized to investigate evolution-oriented questions, despite the importance of evolutionary processes in conservation and management settings. Here, we leverage an experimental restoration approach using the eastern oyster, Crassostrea virginica, an economically valuable and ecologically important reef-building foundation species. Previous small-scale manipulations of oyster source identity highlight the potential evolutionary implications of sources used in restoration, yet have rarely been empirically evaluated at the scale of a restored reef. We sourced juvenile oysters from four commercial hatcheries spanning a broad geographic range along the Atlantic coast of the United States to build restored oyster reefs of diverse initial source composition in a single New England estuary. We characterized four distinct genetic clusters associated with hatchery source using SNP genotyping data and examined whether the frequencies of these genetic clusters on our mixed reefs shifted over the course of our restoration experiment. We documented strong shifts in the relative abundance of certain genetic lineages, consistent with differential mortality among oyster sources. Further, we found significant variation in ecologically relevant traits, including multi-parasite infection patterns and oyster size, associated with source identity. Oyster condition index, a commonly used proxy for oyster health, was associated with higher relative mortality over time. Our research highlights how evolutionary processes can influence restoration demographics and how, concurrently, restoration can serve as a powerful platform for gaining fundamental, and sometimes unexpected, insights into eco-evolutionary dynamics.

Increasingly frequent marine heatwaves devastate coral reefs around the world, so there is great interest in finding warm-adapted coral populations that could be used as sources for assisted gene flow and restoration. Here, we evaluated the relative power of various environmental factors to explain coral genetic variation, suggestive of differential local adaptation to these factors, across the Florida Keys Reef Tract. We applied a machine learning population genomic method (RDAforest) to two coral species—the mustard hill coral Porites astreoides and the lettuce coral Agaricia agaricites—sampled from 65 sites covering the whole reef tract. Both species comprised three genetically distinct lineages distributed across depths in a remarkably similar way. Within these lineages, there was additional genetic divergence explained by depth, but even more within-lineage variation was cumulatively explained by water chemistry parameters related to nitrogen, phosphorus, silicate, and salinity. Visualizing the predicted environment-associated genetic variation on a geographic map suggests that these associations reflect adaptation to certain aspects of the inshore-offshore environmental gradient, and, to a lesser extent, to difference of Middle and Lower Keys from the rest of the reef tract. Thermal parameters, most notably maximal monthly thermal anomaly, were also consistently identified as putative drivers of genetic divergence, but had a relatively low explanatory power compared to depth and water chemistry. Overall, our results indicate that temperature was not the most important driver of coral genetic divergence in the Florida Keys, and underscore depth and water chemistry as more important environmental factors from the corals' perspective. Our study emphasizes the need for considering a variety of environmental variables, rather than solely focusing on temperature, when predicting how corals may respond to transplantation.

Teat number is an important economic trait in pigs, affecting piglet health and survival. While numerous GWAS have identified candidate genes for teat number in Duroc, Landrace, and Large White pigs, the causal genes remain unclear, largely due to a lack of transcriptional and epigenetic studies on mammary placodes in 26-day-old pig embryos, a critical stage for teat formation. Erhualian and Bamaxiang pigs, derived from Chinese wild boars, serve as ideal models for studying genetic variation in teat number, with Erhualian averaging nearly 20 teats and Bamaxiang around 10. This study collected mammary placodes from these breeds at embryonic day 26 and performed ATAC-seq and RNA-seq to explore chromatin accessibility and gene expression. Results indicate widespread chromatin accessibility across mammary placodes. Of the 30,806 open chromatin regions (OCRs) identified, only 30 showed breed-specific differences, suggesting conserved accessibility patterns across breeds. OCRs are enriched in intergenic and promoter regions, and significantly overlap with QTL intervals for teat number. RNA-seq revealed 4432 differentially expressed genes between the two breeds, including WTN10B and WNT6, indicating breed-specific gene expression patterns. Combining ATAC-seq and RNA-seq results identified three protein-coding genes (ENSSSCG00000031037, ENSSSCG00000032042, and ENSSSCG00000039180) near 48.80 Mb on SSC14 that are associated with teat number according to pheWAS and GWAS data. FISH analysis confirmed that ENSSSCG00000031037 is specifically expressed in epithelial cells of mammary placodes, and this region is under stronger selection in Erhualian pigs, suggesting its role in the breed's higher teat number. In conclusion, this study integrates ATAC-seq and RNA-seq to construct a chromatin accessibility and gene expression map of pig mammary placodes. It identifies ENSSSCG00000031037, ENSSSCG00000032042, and ENSSSCG00000039180 as key candidate genes driving teat number differences, providing insights for understanding QTL intervals and identifying causal genes linked to teat number in pigs.

Global climate change will impact the geographic distribution of plant populations. The rapid changes will require range shifts and the adaptation of plants. The recent global spread of crops across different continents shows how plants successfully coped with drastically different environments. One such spread was the introduction of the nutritious pseudocereal amaranth to India. Three different species of grain amaranth have been domesticated in different regions of the Americas. The crops have later been introduced to India, likely within the last five centuries, where it is now grown across the subcontinent. We used whole genome sequencing data of over 300 accessions to study the introduction of grain amaranth to India to understand the factors, allowing the successful establishment of crops to novel environments. Despite a population bottleneck during the introduction, Indian amaranths have comparable genetic diversity to those in the Americas. Although gene-flow between the three grain amaranth species was common in the Americas, the three species did not show signs of gene-flow in India. Correspondingly, genetic differentiation between species was higher within India than in the native range, indicating strong isolation between otherwise interbreeding populations. We further identified genomic regions under selection in India that potentially enabled the adaptation to the new environment. Our results suggest that introduced crop populations can act as reservoirs of genetic diversity, providing additional adaptive potential and resilience to future environmental change.

Staghorn Acropora corals are ecological keystone species in shallow lagoons and back reef habitats throughout the tropics. Their widespread decline coupled with their amenability for asexual propagation propelled them to the forefront of global coral restoration efforts—albeit frequently without much scientific input. To guide these efforts and as a blueprint for similar projects, we conducted a comprehensive population genomic study of Acropora cf. pulchra, a major restoration target species in the Indo-West Pacific. Our results revealed that A. cf. pulchra populations in the Mariana Islands are characterized by large clonal clusters and extremely low levels of genetic diversity. Differentiation among populations followed a significant isolation-by-distance pattern and delineated two distinct metapopulations on Guam. Our investigation identified critical population genetic parameters, necessitating targeted management strategies, and provides actionable guidelines for effective conservation efforts. For management and conservation, two populations emerged as pivotal connectivity hubs with elevated genetic diversity. For restoration, we show that A. cf. pulchra populations demonstrated a suitability for extensive asexual propagation and provide guidelines on how to best apply that. To preserve and augment genetic diversity, strategies to mitigate inbreeding are crucial until sexual reproduction can be fully integrated into restoration protocols. Critical sites for restoration include local connectivity hubs, fringing lagoons that connect metapopulations, and back reefs around a particularly isolated population. These findings offer crucial insights into the genetic landscape of a keystone coral species and provide actionable recommendations for coral conservation and restoration. By advocating for the preservation of population connectivity and the promotion of genotypic, genetic, and symbiont diversity in coral restoration, our study serves as a blueprint for leveraging population genomic studies to enhance the efficacy and resilience of restoration projects on remote islands.