Evolutionary Applications最新文献

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.

Drought has been identified as one of the important environmental factors in the context of climate change due to its interaction with other biotic and abiotic stresses. However, only a few studies have reported the effect of breeding on forest adaptability to climate change. Using a common garden experiment with seedlings from families of Scots pine (Pinus sylvestris L.) from northern Sweden, we have found differences in drought tolerance between seedlings from breeding stands and those from natural forests. We performed a genetic analysis including high-throughput image-based phenotyping of seedling canopy and root traits and conducted metabolomic and hormone analyses with the aerial parts of the seedlings. Our results indicate that root architecture traits associated with drought tolerance exhibit moderate to high heritability. Analyses of seedling architecture reveal that families from breeding stands have higher drought resistance but lower genetic variation than the ones from natural forests, especially in the case of canopy traits. Metabolomic and hormone analyses of the aerial parts of the seedlings also support that the breeding stands may have a higher capacity to withstand or deal with drought conditions as compared to the natural forests. For example, increase in abscisic acid along with increase in tryptophan and auxin conjugates in the breeding stands compared to the natural forests under drought conditions may contribute to alleviation of drought response in the breeding stands. The methodology employed to evaluate drought tolerance and plant architecture in this study might be useful for future research and forest management focused on climate change adaptability.

Pest management programmes can operate more effectively when movement patterns of target species are known. As individual insects are difficult to track, genomic data can instead be used to infer movement patterns based on pest population structure and connectivity. These data can also provide critical information about cryptic taxa relevant to management. Here we present the first genomic investigation of Aedes vigilax, the Australian saltmarsh mosquito, a major arbovirus vector across Australasia. We used a ddRAD pool-seq approach and a draft genome assembly to investigate genetic variation in 60 Ae. vigilax pools from across Australia but with a focus on urban Newcastle and Sydney, NSW. There was strong genetic structure between samples from the west and east coasts of Australia, and additional structure that differentiated east coast populations. Within Newcastle and Sydney, contrasting patterns of genetic structure were evident. In Newcastle, there was no differentiation among subregions up to 60 km apart. In Sydney, samples from one urban subregion were differentiated from others < 3 km apart, and this structure was stable across sampling years. Heterozygosity and Tajima's D indicated no bottlenecks in Newcastle or Sydney populations, suggesting this structure represents a gene flow barrier. Nuclear differentiation patterns contrast with previous mtDNA data indicating two COI clades in the east coast, one of which was also present in Western Australia. The panmixia over 60 km across the Newcastle region corroborates previous field observations of high dispersal capacity in this mosquito. These findings indicate specific challenges that may hinder local suppression strategies for this species.

There is growing evidence for the role of introgressive hybridization in promoting species adaptation (i.e., adaptive introgression) owing to increasing genomic studies on a diversity of taxa over the past decades. However, introgressive hybridization was, and still is, regarded as a homogenizing process hindering the evolutionary process of adaptation to selection pressures. Despite methodological advances, key gaps remain in understanding how adaptive introgression due to hybridization functions across taxonomic groups and biological levels. This study has three objectives: (1) to explore historical trends in the understanding of adaptive introgression, particularly its genomic and functional dimensions; (2) to investigate structural organismal characteristics influencing patterns of adaptive introgression; and (3) to evaluate how adaptive introgression interacts with counteracting evolutionary mechanisms. We carried out a systematic review of the adaptive introgression literature and a multidimensional meta-analysis. The current knowledge trends have been shaped by the genomic revolution. Since 2012, genomic studies have contributed to establishing a clearer understanding of adaptive introgression. The amount and variety of published studies increased from bacteria to mammals across a complexity gradient, focusing on the genomic level and progressively having consequences at a greater number of levels of biological organization (from physiological and demographic to behavioral/ecological). Testing for tendencies, our study also revealed evolutionary mechanisms linked to adaptive introgression co-occurring with divergence forces, demonstrating that these processes are not mutually exclusive, even when they act in opposite directions, i.e., convergence and divergence, such as autosomal introgression (versus islands of differentiation in sex-linked chromosomes), balancing selection (versus genetic drift), or sexual selection (versus assortative mating). This balance is mediated by environmental conditions as they are frequently reported in the studies, regardless of the organisms' structural complexity, shaping the path of the evolutionary process of introgressing species. Studying introgression patterns has important implications for understanding adaptation in rapidly changing environments.

The large yellow croaker is one of the most important marine aquaculture species in China, yet its intensive farming industry faces challenges from various pathogens, particularly white spot disease caused by Cryptocaryon irritans. This study aimed to address the issue of white spot disease through genetic breeding. We implemented two consecutive generations of genomic selection (GS) of large yellow croaker against Cryptocaryon irritans, resulting in three continuous generations for subsequent analyses. Challenge tests demonstrated significantly higher 96-h survival rates in the selected generations compared to corresponding controls, with increases of 18.5% and 79.7%, respectively. Survival analysis confirmed that the two selected generations exhibited significantly stronger resistance to C. irritans. By merging the genotype files across generations, a comprehensive dataset containing 1844 individuals and 28,637 SNPs was created. Genomic Estimated Breeding Values (GEBVs) showed steady increases across the three consecutive generations, while genetic structure analysis revealed progressive population differentiation resulting from the two rounds of GS. Through genome-wide selection signature scanning, we identified five positive selection regions (PSRs) distributed across four chromosomes. These regions were enriched for multiple biological pathways related to energy metabolism, immune response, and cell death, including the HIF-1 signaling pathway, NOD-like receptor signaling pathway, and apoptosis. Within these pathways, we identified key candidate genes, including crebbp in the HIF-1 signaling pathway and traf2 involved in immune regulation, both significantly associated with resistance to C. irritans. Our results validate the effectiveness of GS in selective breeding of large yellow croaker against C. irritans and demonstrate that just two consecutive generations of GS can induce substantial differentiation in genetic structure. This approach facilitates the identification of candidate genes and biological pathways associated with disease resistance.