Evolutionary Applications最新文献

Nutria (Myocastor coypus) are semi-aquatic rodents native to South America, introduced to the USA for fur farming during the early twentieth century. This species' herbivory can cause extensive damage to agriculture and wetland ecosystems. Though declared eradicated from California, USA, in the 1970s, nutria populations were recently discovered in the state's Central Valley and subsequently the Sacramento–San Joaquin Delta, areas of agricultural and conservation significance. We report the use of a combination of nuclear single nucleotide polymorphisms (SNPs) and mitochondrial (mtDNA; cytochrome b locus) markers to characterize the source and demographic history of the current invasion, with the goal of informing eradication efforts. Our study is the first to develop a SNP dataset for nutria, utilizing 6809 loci to characterize genetic diversity in comparison to several potential source populations. Multivariate analysis and Bayesian clustering of the SNP dataset found the greatest similarity to invasive nutria in central Oregon, USA, with minimal genetic differentiation in the Central Valley excluding the leading edges of the invasion. Cytochrome b sequencing resulted in a single contemporary California haplotype shared with nutria in Oregon and Washington but also detected in museum samples from California fur farms predating eradication. Mantel tests found genetic differentiation among nutria in the Central Valley was best explained by ecological distance along rivers, while estimated effective migration surface (eems) analysis indicated gene flow was characterized by infrequent dispersal followed by rapid expansion in large, protected areas of emergent wetland habitat. These combined findings suggest contemporary California nutria represent a recent introduction that underwent rapid expansion. Our data further support treating the Central Valley as a single eradication unit while investing additional resources in targeting dispersal corridors to best achieve management goals. This study presents the first characterization of a regional nutria invasion within the larger context of global population and phylogenetics.

Crestel, D., A. Vergnet, F. Clota, M.O. Blanc, T. Navarro, S. Lallement, F. Moulard, D. McKenzie, F. Allal, M. Vandeputte 2025. Lallement S, et al. “Do European Seabass Larvae Grow Better in Their Natural Temperature Regime?” Evolutionary Applications 18, no. 2: e70083.

(1) The title 2.4.3 “Rearing in four different thermal regimes” was incorrect. This should be “Rearing in three different thermal regimes”.

(2) In the first paragraph of section 3.3, the text “At 20 dph, when fish moved from 13°C to the four thermal regimes, […]” was incorrect. This should be “At 20 dph, when fish moved from 13°C to the three thermal regimes, […]”.

We apologize for this error.

The use of resistant plants is an effective alternative to chemical products. But their sustainability is often compromised by the rapid adaptation of pathogen populations. For the cyst nematode Globodera pallida, a major parasite of potato, several quantitative trait loci (QTLs) conferring resistance have been identified, but their individual use could lead to resistance breakdown. Combining several resistance loci within a single potato genotype has been proposed as a strategy to improve both efficacy and durability. However, the evolutionary pathways leading to the circumvention of this pyramidal resistance remain unknown. The combination of experimental evolution, phenotyping and genome scan enabled us to study the genomic basis of G. pallida adaptation to individual (GpaV_spl, GpaXI_spl) and pyramidal (GpaV + XI_spl) resistance QTLs. Experimental evolution over 10 generations revealed that adaptation to GpaV + XI_spl pyramidal resistance was more difficult than to individual QTLs, but was nevertheless possible. Genomic analyses identified distinct regions under selection for each resistance, with a strong overlap between the adaptation to GpaV_spl and to GpaV + XI_spl, but a weaker overlap between the adaptation to GpaXI_spl and to the pyramidal resistance. Known effector genes involved in immune suppression were systematically found in the selected regions, confirming their potential role in virulence. In addition, a two-generations experiment demonstrated that prior adaptation, particularly to GpaV_spl, facilitated adaptation to pyramidal resistance. These results highlight the existence of preferential evolutionary trajectories favored by genomic proximity between nematode lineages adapted to different resistances. Our results show that pyramidal resistance can be compromised by the prior deployment of its individual components, and underline the importance of taking evolutionary pathways into account in resistance deployment.

Maerl beds, formed by free-living coralline red algae, are biodiversity-rich and carbon-storing habitats of high conservation value but remain understudied at the genomic level. Here, we present the first draft genomes and population genomic analyses for two dominant maerl-forming species in the north-east Atlantic, Phymatolithon calcareum and Lithothamnion corallioides. Using maerl samples genotyped at over 15,000 single nucleotide polymorphisms (SNPs) across England, Wales and additional European sites, we assessed clonal diversity, population structure and potential adaptation to environmental gradients. P. calcareum generally showed moderate clonal diversity, though extreme clonality driven by a single genet (multi-locus lineage) was detected at certain sites. In comparison, L. corallioides displayed high clonal diversity, with most maerl samples representing distinct genets, although local dominance of a single genet was occasionally observed. Contrasting clonal dynamics have important implications for resilience, as populations dominated by a few clones may be more sensitive to environmental change. Population structure analyses in both species revealed strong genetic differentiation between sites, consistent with limited dispersal, while genomic associations identified candidate SNPs linked to climate in P. calcareum, albeit explaining only a small proportion of the observed genetic variation. Genomic offset analyses suggested that certain populations may require greater shifts in allele frequencies to avoid being maladapted to mid-century climate scenarios. Together, these findings highlight both genetically diverse and potentially vulnerable maerl populations, some of which fall within existing marine protected areas. Integrating genomic insights with ecological monitoring will help inform conservation and restoration strategies for these irreplaceable, high natural capital value habitats.

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.