Evolutionary Applications最新文献

{"title":"Trait Mapping Utilizing a Newly Constructed Genome for Allohexaploid Invasive Eurasian Watermilfoil (Myriophyllum spicatum) Reveals a Non-Target Site QTL Associated With Fluridone Resistance","authors":"Del Hannay,&nbsp;Gregory M. Chorak,&nbsp;Alex Harkess,&nbsp;Josh Clevenger,&nbsp;Josh T. Cuperus,&nbsp;Haley Hale,&nbsp;Laramie Aközbek,&nbsp;Zachary Meharg,&nbsp;Sarah B. Carey,&nbsp;Zachary Myers,&nbsp;Christine Queitsch,&nbsp;Arianna Stamatoyannopoulos,&nbsp;Ryan A. Thum","doi":"10.1111/eva.70193","DOIUrl":"10.1111/eva.70193","url":null,"abstract":"<p>Herbicides are a valuable tool in agricultural ecosystems to manage nuisance species. Due to the reliance on herbicides for weed control, herbicide resistance is a growing concern. Herbicides are also used extensively in aquatic and natural systems, but the genetics and evolutionary dynamics of resistance are not as frequently incorporated into management plans in these systems. In Eurasian watermilfoil, a widespread and heavily managed invasive aquatic weed in the United States, clonal lineages have been characterized as resistant to fluridone, a commonly used phytoene desaturase (PDS)-inhibitor herbicide. In order to locate genomic loci associated with herbicide resistance, we created an F2 mapping population segregating for fluridone resistance. Using this population, we examined the <i>pds</i> gene for amino acid alterations in resistant individuals and performed bulk segregant analysis between the highly resistant and susceptible F2 individuals. Additionally, we compared <i>pds</i> gene expression between resistant and susceptible strains in control and treated environments using RT-qPCR. We found no evidence of amino acid alterations to the <i>pds</i> gene in fluridone resistant individuals or increased <i>pds</i> expression in the resistant strain, either in the presence or absence of fluridone. Our QTL mapping identified a putative QTL on chromosome seven, while the gene encoding fluridone's target molecule, phytoene desaturase (PDS) is located on chromosomes 10–12. Our results indicate that fluridone resistance in the Eurasian watermilfoil strain isolated from Lake Lansing, MI, is due to at least one non-target site mechanism. Characterizing mechanisms of herbicide resistance within invasive plants enables effective and thoughtful herbicide usage, as well as the development of diagnostic biomarkers for resistance in unknown populations.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"19 1","pages":""},"PeriodicalIF":3.2,"publicationDate":"2026-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12789191/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145950912","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic Data Reveal Nonlocal Juvenile Recruitment and Variable Seasonal Movement of a Highly Mobile Marine Fish Across Alaska","authors":"Sara M. Schaal,&nbsp;Wes Larson,&nbsp;Johanna Vollenweider,&nbsp;Katharine Miller,&nbsp;Thilo Klenz,&nbsp;Jacek Maselko,&nbsp;Darcie Neff,&nbsp;Claire Tobin,&nbsp;Susanne McDermott,&nbsp;Ingrid Spies","doi":"10.1111/eva.70174","DOIUrl":"10.1111/eva.70174","url":null,"abstract":"<p>Movement patterns of marine fish are often difficult to accurately define given seasonal variation, ontogenetic shifts, and changing environmental conditions. However, outlining movement is crucial for understanding population dynamics, as well as for conservation and management efforts. Here, we evaluate seasonal adult movement and juvenile spatial distribution of Pacific cod (<i>Gadus macrocephalus</i>), a highly mobile and commercially important species, by developing and applying a genotyping-in-thousands by sequencing (GT-seq) panel. This panel identifies four genetically distinct stocks within Alaska waters with high confidence in assignment (97% average accuracy across stocks). The application of this panel to adult, summer-caught Pacific cod identified limited seasonal movement within and between populations, with the exception of those in the Northern Bering Sea (NBS). Two stocks occupied this region during the summer, non-spawning season, and mixed at variable proportions in a west-to-east gradient potentially tied to the directionality of sea-ice retreat in the NBS. Juvenile results indicated that although a predominant westward advection of larvae was prevalent in the Gulf of Alaska (GOA), two major deviations from this overall trend were apparent: (i) an eastward advection of a western GOA stock into the eastern GOA that varied interannually and (ii) a consistently high proportion of eastern GOA individuals in a western GOA narrow strait. These two deviating patterns suggest that mesoscale oceanographic processes play an important role in transport dynamics in the GOA that may be contrary to patterns expected based on the prevailing current. Taken together, our study provides novel insights into the movement dynamics of Pacific cod that can be leveraged by managers to help guide decision-making for the species. Additionally, this inexpensive genetic panel can continue to be applied to further explore important questions about the ecology of Pacific cod in Alaska waters.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"19 1","pages":""},"PeriodicalIF":3.2,"publicationDate":"2026-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12772979/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145916181","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Contemporary Evolution of an At-Risk Stickleback Population During a Severe Drought","authors":"Sarah Sanderson,&nbsp;Lucas Eckert,&nbsp;Rowan D. H. Barrett,&nbsp;Thomas E. Reimchen,&nbsp;Andrew P. Hendry","doi":"10.1111/eva.70189","DOIUrl":"10.1111/eva.70189","url":null,"abstract":"<p>Populations can be granted conservation status because they harbour a set of unique traits, evolutionary histories, or ecological roles. Such populations are often isolated and specialised and, as such, can be particularly vulnerable to environmental disturbances. Even if distinct populations survive and adapt to severe disturbances, they could show changes in the very traits that made them distinct in the first place. Here, we leverage a natural ‘experiment’ involving an unarmoured population of threespine stickleback (<i>Gasterosteus aculeatus</i>) in Rouge Lake (Haida Gwaii, BC)—a population listed as Special Concern under the Canadian Species at Risk Act. In 2015, Rouge Lake nearly dried up during a severe drought event; yet the stickleback population appeared to have fully recovered its abundance in subsequent years. Using phenotypic measurements, we assessed the extent to which evolution in this population was impacted by the drought. We document important shifts in several phenotypic traits, with the largest occurring in precisely the trait that made the population distinct and prompted its original conservation designation. Specifically, fish with no lateral plates (i.e., ‘unarmoured’) made up 51% of the population before the drought but only 13% after the drought. This shift held (13%–16% unarmoured) over the 4 years of our post-drought monitoring. Field observations support a strong demographic bottleneck, which we suggest might have been coupled with a shift in the selective regime. These findings underscore how populations of conservation concern are not only at risk of extinction; they are also at risk of losing the characteristics that make them unique. These dynamics highlight the need for policies to consider a population's evolutionary potential and develop more flexible approaches than simply considering single-timepoint assessments of diversity.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"19 1","pages":""},"PeriodicalIF":3.2,"publicationDate":"2026-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12772980/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145916225","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Using Historic and Contemporary Genomes to Assess the Genetic Consequences of a Population Decline in an Endangered Tern Population","authors":"Anna Schnelle,&nbsp;Robert E. Rollins,&nbsp;Ingo A. Müller,&nbsp;Martin Irestedt,&nbsp;Jacopo G. Cecere,&nbsp;Lorenzo Serra,&nbsp;Jorge S. Gutiérrez,&nbsp;Jose A. Masero,&nbsp;Markus Risch,&nbsp;Sandra Bouwhuis,&nbsp;Miriam Liedvogel","doi":"10.1111/eva.70192","DOIUrl":"10.1111/eva.70192","url":null,"abstract":"<p>Many migratory species have experienced severe population declines, but the genetic consequences of such declines are still rarely assessed. The last Central European population of gull-billed terns (<i>Gelochelidon nilotica</i>) has declined from 500 breeding pairs in the 1940s to 52 in 2025, whereas Mediterranean populations of this migratory waterbird still thrive. Here, we compare whole-genome sequencing (WGS) data among the declining population, two thriving populations and the ancestors of the declining population. We find comparable nucleotide diversity, but lower observed heterozygosity in the Central European population compared to the Mediterranean populations. The contemporary samples show some population structure as well, although admixture analyses and low genetic differentiation (<i>F</i>_ST) still suggest potential population connectivity. Museum specimens from the historic population reveal an increased level of genetic diversity compared to the contemporary population, with effective population size estimates suggesting two past population declines. While inbreeding coefficients (<i>F</i>_ROH) in the current Central European population are significantly higher than in the historic population, they are similar to those in the Mediterranean populations. These results suggest that population structure may be emerging, and that although inbreeding is not yet at worrisome levels in the last Central European population of gull-billed terns, it may be on the rise. If this endangered population remains small and isolation manifests, the effects of inbreeding depression may become more pronounced over time, potentially reducing fitness and increasing the risk of extinction.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"19 1","pages":""},"PeriodicalIF":3.2,"publicationDate":"2026-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12759046/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145898858","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Conservation Genomics of Apocynum venetum: Genetic Adaptation and Demographic History Across China's Saline-Alkali Ecosystems","authors":"Na Yuan,&nbsp;Chunlin Jia,&nbsp;Ruisen Lu,&nbsp;Xingxing Yuan,&nbsp;Xin Chen","doi":"10.1111/eva.70191","DOIUrl":"10.1111/eva.70191","url":null,"abstract":"<p><i>Apocynum venetum</i> L., a saline-alkali-tolerant plant valued for its high-quality bast fiber in textile manufacturing and medicinal compounds in traditional medicine, serves as a key economic species in saline-alkali regions with additional phytoremediation applications. However, its natural populations are becoming increasingly threatened by rapid environmental change and anthropogenic activities. To inform conservation and sustainable utilization, we generated a chromosome-level genome assembly of <i>A. venetum</i> (234.73 Mb; contig N50 = 19.11 Mb, scaffold N50 = 20.46 Mb) using PacBio HiFi, Illumina and Hi-C technologies, and performed whole-genome resequencing of 109 individuals spanning China's saline-alkali regions. Population genetic analyses revealed that the Xinjiang population exhibited the highest level of genetic diversity and strong genetic differentiation from the other populations. Demographic analyses indicated that most populations underwent significant population declines during the late Last Glacial Maximum, followed by recovery in western and northern populations, whereas the eastern coastal populations maintained consistently low effective population sizes. Genome-environment association analyses identified candidate adaptive loci, including a <i>flavonol 4′-sulfotransferase</i> (<i>4′-ST</i>) gene, potentially linked to saline-alkali tolerance and flavonoid biosynthesis. Our findings provide critical insights into the evolutionary history and adaptive mechanisms of <i>A. venetum</i>, offering genomic tools for conservation prioritization and the development of stress-resilient cultivars through marker-assisted breeding.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"19 1","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-12-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12745339/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145861364","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Defining Conservation Units in a Highly Diverse Species: A Case on Arctic Charr","authors":"Sam Fenton,&nbsp;Colin W. Bean,&nbsp;Samuel A. M. Martin,&nbsp;Samuel J. Poultney,&nbsp;Antony Smith,&nbsp;Elvira de Eyto,&nbsp;Kathryn R. Elmer,&nbsp;Colin E. Adams","doi":"10.1111/eva.70190","DOIUrl":"10.1111/eva.70190","url":null,"abstract":"<p>Defining appropriate conservation units is crucial to the protection and management of biodiversity. These delineations deliver further benefit when they include assessments of population vulnerability to extinction from pressures such as climate change. However, delineations and vulnerability assessments are particularly difficult within highly diverse species, such as the salmonid fish Arctic charr (<i>Salvelinus alpinus</i>), that show extensive phenotypic and genetic variation within and across locations, variable and complex life histories and broad geographic distributions. As yet, the nature and scope of Arctic charr diversity has not been characterised at the scale needed to delineate key conservation units in Scotland. To identify evolutionarily significant and vulnerable populations to prioritise for conservation, we conducted a genomic study of Arctic charr populations across Britain and Ireland with a focus on Scottish populations (<i>N</i> = 64 populations; 24,878 SNPs; 410 individuals). We found that most lake populations represented distinct genetic clusters, with limited gene flow between them and resulting in substantial genetic differentiation. Higher level groupings of genetic similarity across catchments likely reflect historic anadromy and migration, with populations primarily grouping east or west of the central watershed divide in Scotland. Analysing genetic offset, also known as genomic vulnerability, we identified strong inverse correlations between genetic vulnerability and latitude and distance to the sea, suggesting that more southern and more inland populations are more vulnerable to the effects of climate change. Additionally, patterns of vulnerability across several additional metrics identified other populations that may be at higher risk of loss. We further used our genetic data, along with phenotypic and geographic information, to identify populations of greatest evolutionary significance. This highlighted that the most important ones to protect are those in locations with multiple ecotypes, a key facet of functional Arctic charr biodiversity, and populations that are the only ones in their Hydrometric Area.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"19 1","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-12-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12745347/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145861297","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Pelagic Larval Duration and Isolation by Distance in Coastal Species","authors":"Atal Saha,&nbsp;Per Erik Jorde,&nbsp;Marte Sodeland,&nbsp;Lars Mørch Korslund,&nbsp;Halvor Knutsen","doi":"10.1111/eva.70187","DOIUrl":"10.1111/eva.70187","url":null,"abstract":"<p>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 <i>F</i>_ST-estimates regressed against distances measured along the prevailing coastal ocean current in the study region. We find a significant (<i>p</i> &lt; 0.05) correlation between species' PLD and IBD slopes, with a moderately strong correlation (<i>r</i>² &gt; 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.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"18 12","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12686963/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145720107","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Adaptive Potential and Genomic Vulnerability of Keystone Forest Tree Species to Climate Change: A Case Study in Scots Pine","authors":"Bartosz Łabiszak,&nbsp;Witold Wachowiak","doi":"10.1111/eva.70180","DOIUrl":"https://doi.org/10.1111/eva.70180","url":null,"abstract":"<p>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 (<i>Pinus sylvestris</i> 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 <i>P. sylvestris</i>, 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.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"18 12","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.70180","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145686326","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dogs of War: The Effect of War-Inflicted Environmental Damage on Free-Ranging Domestic Dogs","authors":"Mariia Martsiv,&nbsp;Ihor Dykyy,&nbsp;Małgorzata Witek,&nbsp;Piotr Chibowski,&nbsp;Giulia Cimarelli,&nbsp;Andre E. Moura,&nbsp;Małgorzata Pilot","doi":"10.1111/eva.70182","DOIUrl":"https://doi.org/10.1111/eva.70182","url":null,"abstract":"<p>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.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"18 12","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eva.70182","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145686325","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic Assignment at Different Geographical Levels: A Case Study in a Forest Tree Species (Pinus pinaster Ait.) Using SNP Markers","authors":"Sanna Olsson,&nbsp;Delphine Grivet,&nbsp;Marjana Westergren,&nbsp;Santiago C. González-Martínez,&nbsp;Ricardo Alía,&nbsp;Juan José Robledo-Arnuncio","doi":"10.1111/eva.70145","DOIUrl":"10.1111/eva.70145","url":null,"abstract":"<p>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 <i>Pinus pinaster</i>, 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: <i>RUBIAS</i>, which performs genetic stock identification and associated tasks, and <i>assignPOP</i>, 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 <i>P. pinaster</i> 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 <i>P. pinaster</i>, offering a useful tool for the management of forest genetic resources of this economically and ecologically important tree species.</p>","PeriodicalId":168,"journal":{"name":"Evolutionary Applications","volume":"18 12","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12670294/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145666681","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}