Evolutionary Applications最新文献

Dispersal among populations is crucial both for demographic stability and for the evolutionary potential of species. In marine organisms, dispersal has been shown to be prevalent during pelagic early life stages. Consequently, pelagic larval duration (PLD) has been proposed as an important driver of gene flow in marine species and is influencing genetic differentiation among populations. Despite this prediction, empirical studies have often failed to find the expected correlation between PLD and genetic metrics of gene flow. This could mean either that PLD is a poor predictor of gene flow or that differences in methodology, oceanography or sampling design across studies obscure the underlying mechanisms of gene flow. In the present study, we address these issues by using a consistent sampling design for 10 coastal species with previously published genetic data (ddRAD and microsatellites), and that differ in PLD. We investigate gene flow using an isolation-by-distance (IBD) model with pairwise F_ST-estimates regressed against distances measured along the prevailing coastal ocean current in the study region. We find a significant (p < 0.05) correlation between species' PLD and IBD slopes, with a moderately strong correlation (r² > 0.5), These findings support the notion of PLD as a key factor determining dispersal and gene flow among populations of coastal species. Our findings reiterate genetics as a useful tool for inferring population dispersal in marine organisms when potentially confounding factors are eliminated by adopting a consistent sampling design.

A better understanding of the possible adaptive response and genomic vulnerability of forest trees is needed to properly assist future forest management and develop adequate resilience strategies to changing environments. Scots pine (Pinus sylvestris L.), a keystone species with extensive distribution and a broad ecological niche, is expected to be directly impacted by climate change due to maladaptation and associated fitness declines. Despite extensive studies that have clarified the broad-scale history and genetic structure of the species, understanding the genetic basis for local adaptation and the extent of genomic offset in Scots pine remains incomplete. Here, we used thousands of genotyped SNP markers in 39 natural populations (440 trees) along a broad latitudinal gradient of species distribution to examine molecular signatures of local adaptation. Specifically, this landscape genomics approach aimed to assess fine-scale patterns of SNPs associated with environmental gradients, estimate genomic offset as a proxy for exposure and sensitivity components of vulnerability, and evaluate the adaptive response of populations to projected climate shifts. The variation of outlier SNPs, which exhibit selection signatures between genetically very similar populations in the analysed distribution range, was highly correlated with mean annual temperature, a key limiting factor for the growth and survival of tree species. Furthermore, our simulation results indicated a high genomic offset on a large spatial scale in P. sylvestris, with the time frame required to close the offset gap by natural selection estimated to be in the range of hundreds of years. We evaluate the genomic offset in the coming decades and indicate the optimal allelic frequency spectra required in the future to ensure resilience of Scots pine populations. We discuss forest assisted migration (FAM) as a management strategy, involving the relocation of genotypes to areas with matching environmental conditions. By evaluating adaptive responses, the study adds to the discussion on the long-term sustainability of forest ecosystems.

Wars impose unprecedented environmental damage that has rarely been studied in real time. Domestic dogs are an accessible model species during war times, because they enable data collection without specialised equipment and skills, which can be performed without creating additional danger to humans or animals involved. We compared phenotypic traits in Ukrainian dogs living close to the front line with those from other regions of Ukraine. We found significant differences in frequencies and diversity of multiple morphological traits, consistent with mortality-based selection at the front line. We also found differences in age structure and frequency of diseases and injuries, consistent with high mortality of old and ill individuals. The front-line population had low average BMI and stable isotope analysis suggested malnutrition and low trophic level. Our study shows that wars can be factors of strong and fast natural selection, with the effects comparable to large-scale natural or anthropogenic disasters.

Genetic markers can assist in the identification of the stock origin in different organisms. Comparative studies of forest tree provenances have demonstrated that forest tree populations differ in performance across environments and at multiple geographic levels: populations nested within regions nested within gene pools. These levels are critical for conservation and sustainable use of genetic resources: regions of provenance are key units for seed marketing, while populations guide reproductive material collection under most seed regulations. Despite their potential, genetic methods have rarely been applied to identify forest tree origins due to methodological (sufficient number of highly discriminatory markers) and practical (construction of a baseline composed of a representative selection of samples) challenges. In our study, we analyzed a genomic dataset comprising 10,185 SNPs from 1579 samples of Pinus pinaster, a species with strong population structure, across 86 populations, 45 regions of provenance, and 10 gene pools, to discriminate among these hierarchical levels and assign individuals to them. We used two software packages to evaluate the reliability of our baseline dataset (i.e., reference data) for genetic discrimination and assignment: RUBIAS, which performs genetic stock identification and associated tasks, and assignPOP, implementing a supervised machine-learning genetic-assignment framework. Using numerical validation analyses, we assessed their suitability and limitations for origin inference at each geographical level. Our results indicate that origin assignment is reliable in P. pinaster at the gene pool and region of provenance levels, but less so at the population level, provided that the 10 K SNP markers and a comprehensive genetic baseline are used. Incomplete baselines may result in wrong assignments at any hierarchical level, irrespective of sampling intensity for sampled candidate origins. We provide an extensive and publicly available baseline for P. pinaster, offering a useful tool for the management of forest genetic resources of this economically and ecologically important tree species.

Hatchery programs can provide fishery and conservation benefits, but can also inadvertently threaten wild populations through genetic and ecological interactions. Two common, and non-mutually exclusive, strategies for mitigating the genetic impacts of hatchery programs on wild populations are reducing the number of hatchery-origin fish spawning in the wild and integrating wild-origin individuals into the hatchery broodstock. We compared the robustness of these two strategies to imperfect implementation (variation around target proportions of hatchery-origin spawners in the wild and wild-origin brood stock) using a quantitative population genetic model. Simulations revealed that incorporating wild-origin broodstock was more robust to both short- and long-term implementation errors compared to minimizing hatchery-origin spawners in the wild. Furthermore, relatively low levels of hatchery integration were required to achieve most of the increase in robustness, provided that the average proportion of hatchery-origin spawners was correspondingly low. We checked these findings against empirically observed levels of implementation error by parametrizing the model using data from hatchery programs in Washington and Oregon. These findings suggest that integrated hatchery programs can pose a smaller genetic risk to wild populations than segregated programs, given realistic levels of implementation error.

Blue mussels (Mytilus spp.) are ecologically and economically important bivalves widespread in both hemispheres. Their relevance to coastal ecosystems and the aquaculture industry has made them extensively studied. The Mytilus complex consists of distinct genetic lineages, including Mytilus edulis, Mytilus galloprovincialis, Mytilus trossulus, and their fertile hybrids. In overlapping areas, they create complex hybrid zones, which have been investigated along European coasts, employing multi-marker approaches. However, knowledge gaps still exist in the North-east Atlantic region, in the middle of their hybrid zone around the island of Ireland, regarding their genomic composition, population structure and connectivity. This study addresses these gaps by genotyping 781 individuals from 26 sites encompassing Ireland's hybrid zone, including both wild and farmed stocks from varying environmental conditions. Using a selected panel of 72 SNP markers we examined relationships among genotypic composition, genetic diversity, isolation by distance (IBD) and environmental variables to identify drivers of Mytilus genetic structure. Results confirmed two distinct genetic lineages and their hybrids, with a clear geographic pattern: the east coast of Ireland is dominated by pure M. edulis genotype populations, while the south, west and north coasts exhibit varying degrees of admixture with M. galloprovincialis genotype. Pure M. galloprovincialis populations were identified at specific sites on the west and north coast. Sea current resistance and wave height were significant predictors for both genotype composition and genetic differentiation. This study corroborates previous findings and provides the first comprehensive investigation of Irish Mytilus spp. population structure and connectivity using a multi-marker approach. The findings highlight the importance of understanding the Mytilus complex's composition and population dynamics to inform sustainable aquaculture practices and monitor potential climate change-driven shifts in the North-east Atlantic region.

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.