Evolutionary Applications最新文献

As an essential species across European forests, Scots pine (Pinus sylvestris L.) plays a vital ecological and economic role, yet its physiological variability underlying its adaptive potential remains underexplored. Understanding this intraspecific variability is crucial for uncovering the genetic basis of adaptation. Traditional genetic evaluations require large sample sizes and are time-consuming, whereas hyperspectral sensing/imaging enables rapid, nondestructive assessment of physiological traits across many individuals, facilitating more efficient exploration of adaptive variation. We assessed needle functional traits (NFTs) linked to foliar structure, water content, and pigment composition in clonal seed orchards over two seasons, integrating hyperspectral measurements at needle and canopy levels with genotyping using a new 50 K single-nucleotide polymorphism (SNP) array. Linear mixed models revealed substantial genetic variation, with the carotenoid-to-total-chlorophyll ratio showing the highest heritability (0.29) among pigment traits, and structural/water-related traits reaching heritability values up to 0.38. Significant genetic correlations were observed between stress-related traits (pigment content, equivalent water thickness) and reflectance, suggesting that spectral traits could serve as proxies for indirect selection of adaptive traits or in breeding programs. Low genotype-by-environment interaction and stable clonal performance across years further underscore the reliability of these traits for identifying resilient genotypes. Overall, our findings highlight hyperspectral phenotyping and NFTs as promising tools for accelerating climate-adaptive breeding in Scots pine.

Biological invasions significantly threaten global biodiversity and disrupt the stability of ecosystems worldwide. Effective responses to environmental stressors are crucial for invasion success; however, the underlying epigenetic regulatory mechanisms remain poorly understood, especially regarding the interplay among multiple regulatory layers such as DNA methylation and microRNAs (miRNAs). Here we employed an integrative multi-omics approach to investigate the model invasive Ciona robusta subjected to repeated salinity stress. Focusing on canonical osmotic regulation pathways, we revealed a dynamic and coordinated regulation of stress-responsive gene expression, with miRNAs and DNA methylation playing distinct yet complementary roles across functional pathways/genes and distinct regions within the same genes. Regulating osmolyte shifts during repeated stress, miRNAs emerged as dominant regulators through widespread and flexible targeting of genes, whereas DNA methylation contributed more selectively. Notably, both mechanisms co-regulated certain genes via spatially distinct genomic regions, supporting a multilayered model of gene regulation. Furthermore, we observed significantly reduced methylation levels in miRNA-targeted genes, suggesting an evolutionary structural complementarity between the two epigenetic systems. Moreover, the permutation test revealed that dual regulation was a non-random event. Interestingly, miRNAs and DNA methylation did not converge on a limited set of stress-related pathways; instead, they provided complementary regulation across multiple functions, while dual regulation did not directly amplify gene expression changes. Together, these findings underscore the critical role of complex interplay among epigenetic processes in enabling rapid phenotypic plasticity and provide novel insights into the molecular mechanisms underlying invasion success under environmental stress.

Marine biological invasions, increasingly facilitated by maritime transport, represent a major dimension of global change, threatening biodiversity, ecosystem services, and human well-being worldwide. Although the factors shaping invasion success have been widely studied, the evolutionary processes occurring during the transport stage remain poorly understood. Using high-salinity selection experiments with the model invasive ascidian Ciona robusta, we tested whether transport-related stress imposed genotype-dependent filtering. We quantified survival dynamics and employed whole-genome resequencing together with transcriptomic profiling to characterize genome-wide responses to environmental filtering. Survival analyses revealed significant mortality differences among genotypes under hypersaline conditions. Whole-genome resequencing of survivors identified genomic regions with marked genetic differentiation and allele frequency shifts, particularly in osmoregulatory genes such as solute carriers and ion channels. Transcriptomic profiling further demonstrated genotype-specific expression patterns consistent with stress responses, highlighting the functional relevance of candidate variants. Collectively, our findings show that transport stress drives genotype-dependent survival and functional genomic signatures consistent with selection. Acknowledging transport as an evolutionary filter and integrating such processes into invasion risk frameworks are essential for developing effective management and prevention measures in an era of accelerating global trade and climate change.

Jing-Li Xuan, Sonja J. Scheffer, John Soghigian, Brian Cassel, Matthew L. Lewis, Shu-Peng Li, Jian-Yang Guo, Wan-Xue Liu, Brian M. Wiegmann. 2025. Population Phylogenomics and Genetic Structure of the Polyphagous Leafminer, Liriomyza trifolii (Burgess) (Diptera: Agromyzidae). Evolutionary Applications 18, no. 7: e70132.

An author, Dr. Ravindra C. Joshi, was omitted from the author list in the published version. This author provided valuable specimens used in this study, who should be in the author list. Therefore, the correct author list should be “Jing-Li Xuan, Sonja J. Scheffer, John Soghigian, Brian Cassel, Matthew L. Lewis, Shu-Peng Li, Jian-Yang Guo, Ravindra C. Joshi, Wan-Xue Liu, Brian M. Wiegmann.”

We apologize for this author omission.

Animals are increasingly exposed to multiple co-occurring stressors. Environmental factors such as seasonal time constraints (TC), predation risk, and pollutants strongly influence fitness-related traits in aquatic organisms. Yet, the interactive effects of such stressors, especially across life stages, remain unclear. We examined immediate and delayed effects of predator cue exposure during the post-overwintering egg stage and the larval stage, both subjected to early- or late-season photoperiods, and how these factors interacted with subsequent larval exposure to predator cues and copper in the damselfly Lestes sponsa. Copper was used due to its known effects as a pesticide on aquatic invertebrates. We measured immediate effects of egg predator cue on egg hatching (development time), carry-over effects on larval survival and growth rate, and behavioural (activity, resting, freezing, feeding) and physiological (oxidative damage, cellular energy allocation) traits after larval exposure to metal and predator cues. Several pairwise stressor interactions occurred, but none were modified by a third stressor. Predator cues during the egg stage delayed hatching under strong TC and led to sex-specific carry-over effects: males had reduced growth under strong TC. Copper increased oxidative damage only under weak TC, suggesting that strong TC can induce a hormetic antioxidant response. Short-term copper exposure did not affect survival, behaviour, or net energy budget. However, predator exposure during the egg stage modified energy allocation, increasing it under weak TC and reducing it under strong TC, indicating context-dependent trade-offs. Behavioural responses were shaped by predator cues and TC; fast-growing larvae under strong TC increased activity and feeding, while predator-exposed individuals reduced these behaviours. These findings show how environmental stressors interact across life stages and traits, shaping plastic, sex-specific responses. By integrating natural and anthropogenic stressors with life-history timing, our study advances understanding of how ecological and evolutionary processes shape stress responses.

Population genetics is concerned with the variability of genetic diversity in populations subjected to different evolutionary forces. One concrete application of this research is international genetic diversity conservation policies. Our perspective manuscript is a plea for research activities and policies that control their environmental consequences, for example, carbon emissions due to technical choices, and are emancipated from the main economic model. We have indeed witnessed a profound transformation in population genetic studies due to the proliferation of molecular markers and DNA sequencing tools. We analyze the underlying assumptions, and even the beliefs, of the scientific community regarding the quantophrenic use of markers when very significant results on the determinants of genetic diversity are already available. We also discuss the implications of these practices for conservation genetics policy at the international level. The community is indeed defending an approach that aims to describe effective population sizes on a large scale, without considering the environmental costs of these actions. In this paper, we also discuss the “knowledge hypothesis,” that is, that knowledge would lead to effective action. We argue that both the meaning (through the associated promises) and the materiality (the environmental footprint of practices) must be considered in order to rebuild the discipline.

Large epidemiological impacts resulting from disease vector control interventions are typically associated with significant disruption of vector populations. While vector density is a frequently measured response, impacts on demography and connectivity are suspected but rarely quantified. We analysed low-coverage whole-genome sequence data of 893 Anopheles gambiae mosquitoes collected between 2014 and 2015 during a cluster-randomized control trial (cRCT) in Burkina Faso to compare a pyrethroid-only net (ITN) with a pyrethroid-pyriproxyfen (ITN-PPF) net. Despite reductions of clinical malaria by 12% and vector density by 22% in the ITN-PPF arm, we found no significant changes in An. gambiae population genetic structure or diversity. We found remarkably low population differentiation and a lack of discernible clustering by treatment, time, or space. Nucleotide diversity and inbreeding coefficient remained stable between treatments, and genome-wide scans showed no putative signatures of selection between trial arms. These results show that ITN-PPF did not alter An. gambiae genetic structure, possibly due to large, vagile populations in West Africa. More widely, this is the first evidence that epidemiologically meaningful reductions in vector density may not impact genetic diversity or connectivity and challenges what constitutes adequate vector control in large populations.

Phytoplankton respond to their environment through genetic adaptation and plasticity to maintain fitness. This poses challenges when growing microalgae for industrial applications because, inherently, outdoor mass cultivation may lead to adaptations that alter desirable phenotypic traits and environmental niches. Here, we used common garden experiments to quantify the plasticity and adaptive responses to seasonal and geographic climate variation of Nannochloropsis, a microalga commonly used in biotechnology. An initially monoclonal strain was grown outdoors across four locations in Hawaii, Texas, California, and New Mexico. Following 17 and 22 months of cultivation outdoors, we collected samples during winter and summer, respectively, and we compared strains' growth from the four sites across temperature and light gradients in the laboratory. Despite hundreds of generations of exposure to divergent climates, with ~20°C and three-fold differences in daily light intensity, strains showed only minor differences in performance. Thermal performance varied more among seasons than sites, whereas light performance varied with both season and site. Our study indicates that Nannochloropsis exhibits broad plasticity in response to light and temperature, which may inhibit genetic adaptation in space or time. Highly variable field conditions, with daily and seasonal climate fluctuations, may favor plasticity and prevent the rapid adaptation often seen in laboratory studies of microorganisms in constant environments.

As global temperatures rise and become more variable, the capacity of domestic species to adapt, while maintaining production efficiency, is becoming a pressing concern. In this context, genotype-by-environment (GxE) interactions pose a significant challenge for selective breeding, as traits that perform well in one environment may not in another. These interactions complicate the design of breeding programmes that aim to ensure long-term resilience while optimising short-term productivity. Genomic Offsets—a metric that can quantify the mismatch between current and future genotype–environment associations, predicting potential genetic mismatch to environmental change—may offer a promising solution. In this perspective piece, we explore potential applications of genomic offsets in agriculture and aquaculture, including their use as tools for risk assessment, selective breeding and cryopreservation. We discuss how genomic offsets can overcome hurdles posed by GxE interactions, addressing practical considerations such as data requirements and methodological frameworks, and needed validation efforts. By predicting genetic mismatches and guiding the selection of individuals best suited for changing environmental conditions, our proposed Adaptive Breeding Framework may help breeders proactively enhance the resilience of farmed populations.

The brown planthopper (BPH, Nilaparvata lugens) is a major rice pest in Asia, causing significant yield losses. As BPH cannot overwinter in temperate regions, East Asian populations are wind-borne migratory insects originating from tropical regions. The identification of precise migratory patterns is essential for forecasting BPH outbreaks and implementing effective pest management strategies. Despite extensive studies using meteorological data, field population observations, and whole-genome analyses, the BPH migratory pathways to East Asia remain unclear. To address this question, we conducted population genomics analyses using 454 BPH individuals densely collected from China, Korea, and Vietnam between 2017 and 2022. We showed that BPH migration into East Asia exhibits substantial annual variation and involves genomically distinct overwintering origins. Principal component analysis revealed two major groups with whole-genome differentiation. This separation was confirmed by statistically significant F_ST estimates, suggesting migration pathways involving at least two overwintering populations. Ancestry coefficient analysis further confirmed the complexity of the ancestry of East Asian BPH. These results demonstrate the complex migratory dynamics of East Asian BPH populations, possibly with the influence of differential selective pressures among overwintering origins. Given the heterogeneity of migratory pathways to East Asia, we argue for temporally and geographically dense field monitoring with the incorporation of genetic information to enhance early warning and BPH management strategies.