Molecular Ecology Resources最新文献

{"title":"A Museum-Curated, Voucher-Backed 12S Barcode Reference Library for Fishes of the Ecuadorian Amazon","authors":"Evan W. Hessels,&nbsp;José V. Montoya,&nbsp;Corey Yuen,&nbsp;Jonathan Valdiviezo-Rivera,&nbsp;Blanca Rios-Touma,&nbsp;Gabriela Echevarría,&nbsp;Nathan K. Lujan","doi":"10.1111/1755-0998.70220","DOIUrl":"10.1111/1755-0998.70220","url":null,"abstract":"<p>Environmental DNA (eDNA) metabarcoding is an emerging method that promises to expedite and improve biodiversity surveys by identifying species from the genetic material they shed into the environment. eDNA methods offer many advantages over conventional specimen-based surveys, but their effectiveness hinges on reference libraries, which for highly biodiverse regions such as the Ecuadorian Amazon are too often incomplete, inconsistently curated and disconnected from morphological voucher specimens needed to reliably identify and revise taxa. To address this gap, we collected approximately 5000 fish specimens and 1500 tissues of an estimated 311 morphologically defined species from Ecuador's Aguarico, Napo and Pastaza river basins, and built a new, rigorously curated, museum voucher–backed 12S reference library spanning 748 barcodes from over 303 species across 12 orders, 46 families and 171 genera. When tested against unknown haplotypes from concurrently collected eDNA samples, the library nearly doubled the proportion identified to species (40.0%, vs. 21.3% using GenBank). It also enabled the empirical estimation of new species-level barcode thresholds: 0.4% for the full-length barcode, 0.9% for a general vertebrate mini-barcode, and 0.6% for a fish-specific mini-barcode. By linking museum vouchers, updated taxonomy, and operational scalability, this reference library helps transform eDNA metabarcoding from an exciting possibility to a practical tool for understanding, monitoring and safeguarding Amazonian freshwater biodiversity.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"26 8","pages":""},"PeriodicalIF":5.9,"publicationDate":"2026-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.70220","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149331875","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Genome and Population Structure of the Spruce Beetle, Dendroctonus rufipennis (Kirby, 1837), a Transcontinental Pest of North American Spruce","authors":"Erin O. Campbell,&nbsp;Philip D. Batista,&nbsp;Véronique Lévesque-Tremblay,&nbsp;Catherine Béliveau,&nbsp;Kathia Bernier,&nbsp;Kateryna Romanenko,&nbsp;Ward B. Strong,&nbsp;Katherine P. Bleiker,&nbsp;Dezene P. W. Huber,&nbsp;Christopher I. Keeling","doi":"10.1111/1755-0998.70209","DOIUrl":"10.1111/1755-0998.70209","url":null,"abstract":"<p>The spruce bark beetle <i>Dendroctonus rufipennis</i> (Family: Curculionidae; Subfamily Scolytinae) is a major forest insect pest throughout the transcontinental range of spruce species (<i>Picea</i> spp.) in North America. Here, we present an annotated, near chromosome-level, genome assembly of 271 Mb, with 86% of the assembly contained in 16 pseudochromosomes and containing 17,778 predicted gene models. We also annotated 13 protein-coding genes, 2 rRNAs, and 22 tRNAs in its 19,637 bp mitochondrial genome. In addition, we present the annotated complete nuclear and mitochondrial genomes of an associated endoparasitic nematode, <i>Contortylenchus</i> sp. T'it'q'et (Order: Tylenchida; Family: Allantonematidae). Its nuclear genome assembly was 76.2 Mb, with 99.8% of the assembly contained in nine pseudochromosomes and containing 12,208 predicted gene models. We also annotated 12 protein-coding genes, 2 rRNAs, and 22 tRNAs in its extremely AT-rich, 15,509 bp mitochondrial genome. Population genomic analyses revealed broad consistencies with past microsatellite work, supporting the hypothesis of multiple range expansions from glacial refugia. Our analyses also identified alternate modes of population diversification which suggest that both neutral and non-neutral processes may be shaping current population genetic structure across the spruce beetle range.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"26 8","pages":""},"PeriodicalIF":5.9,"publicationDate":"2026-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13717379/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149284338","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Comparison of Two Species-Discriminatory SNP Sets for Taxonomic Assignment in Hybridizing European White Oaks (Quercus sect. Quercus)","authors":"Christian Rellstab,&nbsp;Erwan Guichoux,&nbsp;Felix Gugerli,&nbsp;Antoine Kremer,&nbsp;Oliver Reutimann","doi":"10.1111/1755-0998.70221","DOIUrl":"10.1111/1755-0998.70221","url":null,"abstract":"<p>Species identification is essential for conservation, forest management, and understanding ecological and evolutionary dynamics, such as adaptive introgression and maintenance of species boundaries in hybridizing taxa. Species-discriminatory marker sets have been shown to be more accurate than morphological identification, especially in hybridizing species complexes, and provide a more affordable alternative to genome-wide analyses. However, to our knowledge, no species complex exists for which several marker sets are available, let alone have been compared to each other. Moreover, it remains unclear how well marker sets can be applied to additional, closely related species. Here, we compared two independently developed SNP sets, one derived from amplicon sequencing and one from whole-genome sequencing, for three morphologically similar and hybridizing European white oak species <i>sensu lato</i> (<i>Quercus robur</i>, <i>Q. petraea</i>, and <i>Q. pubescens</i>). We applied the SNP sets to 560 samples, including samples of known pure ancestry, controlled crosses, natural populations, and four additional white oak species. Congruency between SNP sets was very high, but species assignment was slightly more accurate for the reference samples used in the development of the respective SNP set. Ancestry coefficients for first-generation hybrids were more precise with the SNP set based on whole-genome data. In a natural population, there was limited congruency between SNP sets in quantifying admixture. Notably, the SNP sets were able to identify up to two additional white oak species. Our study highlights the great potential of species-discriminatory SNP sets in science and practice, while demonstrating that ascertainment bias should not be neglected, and accurate introgression assessments may require genome-wide analyses.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"26 8","pages":""},"PeriodicalIF":5.9,"publicationDate":"2026-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.70221","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149293558","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Active Filtration of Airborne eDNA for Vertebrate Surveys in Tropical Caves","authors":"Christina Lynggaard,&nbsp;Kasun Harshana Bodawatta,&nbsp;Rafael de Fraga,&nbsp;Vitoria Catarina Cardoso Martins,&nbsp;Alexandre Aleixo,&nbsp;Valéria da C. Tavares,&nbsp;Leonardo C. Trevelin,&nbsp;Markus Gastauer,&nbsp;Kristine Bohmann","doi":"10.1111/1755-0998.70218","DOIUrl":"10.1111/1755-0998.70218","url":null,"abstract":"<p>Hidden from sunlight, caves are remarkable subterraneous ecosystems that host a wide range of animals, including unique species. Conventional cave biodiversity surveys can be physically challenging, disturb sensitive vertebrate communities, or require animal collection. Here we evaluate the use of metabarcoding of airborne environmental DNA (eDNA) as a non-invasive method for surveying cave vertebrates. We collected 55 samples by filtering air for 24 h at three light zones (outside, and in twilight and dark zones inside the cave) in three tropical caves in Amazonian Brazil. Using two metabarcoding primer sets targeting mammal and vertebrate DNA, we detected 123 wild vertebrate taxa encompassing mammals, birds, amphibians, and a reptile, of which 74 were identified to genus level. Genus richness in the twilight zone was significantly higher than outside the caves. Vertebrate diversity was also highest in the twilight zone, and community composition differed significantly between light zones and caves. Mammals and amphibians were mostly detected in the twilight and dark zones, whereas birds were more frequently detected outside the cave and in the twilight zone. While preliminary, our results show that caves with smaller entrances yielded more homogeneous communities in the twilight and dark zones. We detected eight of the 13 bat species and one of the four amphibian species recorded in previous surveys, while also detecting taxa not previously recorded in the caves, demonstrating complementarity with conventional surveys. As airborne eDNA requires minimal human presence in cave interiors, it reduces disturbance to sensitive fauna, lowers safety risks to surveyors, and offers a scalable method to complement conventional cave biodiversity surveys in tropical regions.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"26 8","pages":""},"PeriodicalIF":5.9,"publicationDate":"2026-10-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13712314/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149284278","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"sandwrm: An R Package for Estimating Wright's Neighbourhood Size and Species-Level Genetic Diversity","authors":"Zachary B. Hancock,&nbsp;Gideon S. Bradburd","doi":"10.1111/1755-0998.70212","DOIUrl":"https://doi.org/10.1111/1755-0998.70212","url":null,"abstract":"<p>In most natural populations, individuals in close proximity are more related on average than those at greater distances; this pattern gives rise to geographic population genetic structure. Despite extensive theoretical work on spatial population genetics, few empirical methods exist to estimate the components of theoretical models of genetic relatedness in continuous space. One classic model of relatedness in continuous space is the Wright-Malécot model, which predicts that the probability of identity-by-descent decays as a function of geographic distances. The shape of this decay curve is dictated by the dynamics of local dispersal and mating, as well as population density. This model can be reformulated to describe the probability of identity-by-state, in which case the curve decays to an asymptote, the value of which is determined by the historical demography of the population. Collectively, these features can be modelled in a likelihood-based framework to estimate neighbourhood size—a localized measure of the rate of genetic drift—and long-term diversity from pairwise genetic and geographic distance. In this article, we introduce the R package <span>sandwrm</span> (Spatial Analysis of Neighbourhood size and Diversity using WRight-Malécot), which takes a Bayesian approach to estimate key parameters of populations that are both dispersal-limited (i.e., do not traverse the entire range in a single generation) and distributed continuously across a landscape. The <span>R</span> package can be installed from the GitHub repository, https://github.com/zachbhancock/sandwrm.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"26 7","pages":""},"PeriodicalIF":5.9,"publicationDate":"2026-10-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.70212","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149259203","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Comparative Survey of Historical DNA Degradation From Vertebrate Museum Specimens: Unexpected Utility of Fluid-Preserved Specimens","authors":"Alexander T. Salis,&nbsp;Nasrin Ali,&nbsp;Shiva Karmakar,&nbsp;Jasleen Kaur,&nbsp;Brian Tilston Smith,&nbsp;Christopher J. Raxworthy","doi":"10.1111/1755-0998.70206","DOIUrl":"10.1111/1755-0998.70206","url":null,"abstract":"<p>Advances in museomics have expanded from dry and skeletal specimens to now include fluid-preserved material as a source of DNA. However, our understanding of patterns of DNA degradation across specimens and tissue types remains limited, hindering justification for targeting optimal DNA sources from museum voucher specimens. Here we quantify DNA quality across taxonomic groups (amphibians, squamates, and birds) and tissue types to benchmark DNA yield, fragmentation, endogenous content, and DNA damage in fluid-preserved specimens versus more commonly used sources (frozen tissues, dried skins, and skeletons). Our tests showed that fluid-preserved material had smaller fragments, decreased endogenous content, and increased deamination with age, indicative of extensive degradation over even short timescales. Unexpectedly, formalin-fixed fluid-preserved specimens did not show clear declines in DNA yield or fragment length with specimen age, suggesting formalin fixation initially fragments DNA but may partly decouple subsequent fragment-length patterns from specimen age. DNA yield, fragment size, and endogenous content across tissue types in fluid-preserved specimens showed both time- and tissue-type dependent patterns. DNA from liver had the highest quality metrics in younger specimens but performed worse in the oldest specimens. In older specimens, the optimal tissue types included skin, muscle or bone across taxonomic groups. However, substantial variation between individual specimens of the same preparation type and age indicated that collection history also influences DNA degradation. Our comparative analyses reinforce earlier findings that fluid-preserved specimens of all ages are viable DNA sources. We use these findings to refine DNA sampling strategies for incorporating fluid-preserved voucher specimens into museomic research.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"26 7","pages":""},"PeriodicalIF":5.9,"publicationDate":"2026-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13682614/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149226849","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Accounting for Variability Across Years, Depths, and Non-Target Reads Improves Quantification of Root Community Composition in Plant Mixtures","authors":"Emma K. Rice,&nbsp;Jason C. Keagy,&nbsp;Terrence H. Bell,&nbsp;Liana T. Burghardt,&nbsp;Jason P. Kaye,&nbsp;Carolyn J. Lowry","doi":"10.1111/1755-0998.70214","DOIUrl":"10.1111/1755-0998.70214","url":null,"abstract":"<p>One key challenge in characterizing plant communities is determining the relative abundance of distinct species in root biomass. Metabarcoding is increasingly used to estimate a species' proportion in root mass based on its proportion in sample reads, but results have been mixed in accurately converting sequencing output to species mass in mixture. We created calibration mixtures from four focal plant species to determine how the association between a species' proportion in mass and its proportion in sequencing reads of the <i>rbcL</i> chloroplast gene varied across sample years, soil depth, and non-target proportion of reads. We also determined whether including these explanatory variables in prediction models could improve accuracy. We found the association between a species' proportion in reads and its proportion in mass varied across years and non-target proportion of reads, and to a lesser extent, rooting depth, and incorporating these explanatory factors into prediction models improved prediction accuracy. A secondary objective was to determine the number of calibration levels and sequencing depth required to accurately predict a species' proportion in mass. Through simulations, we estimated that 42 calibration samples (seven proportional levels * three years * two depths) and 700 reads per sample consistently obtained accurate predictions for simple mixtures. The association between a species' proportion in mass and proportion in reads can vary considerably, and our study suggests that measuring and explaining this variation can lead to more accurate predictions of the relative abundance of plants within root biomass using metabarcoding.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"26 7","pages":""},"PeriodicalIF":5.9,"publicationDate":"2026-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.70214","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149190423","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Establishing Practical and Cost-Effective Methodologies for Preservation and Extraction of Environmental RNA (eRNA) From Aquatic Samples","authors":"Elise D. Snyder,&nbsp;Teya C. Broyles,&nbsp;Sarah A. Molinaro,&nbsp;Mark A. Davis","doi":"10.1111/1755-0998.70216","DOIUrl":"10.1111/1755-0998.70216","url":null,"abstract":"<p>Sampling environmental nucleic acids (eDNA and eRNA, collectively eNA) in aquatic systems facilitates the efficient exploration of the distribution of aquatic species. Since eRNA is inherently less stable than eDNA, eRNA may yield more spatiotemporally precise information about organisms, but this volatility also poses unique methodological challenges, making it unclear whether eDNA protocols are suitable for eRNA samples. To address this gap, we conducted experiments using naturally occurring eRNA and eDNA from the mitochondrial cytochrome b (CytB) gene from largemouth bass (<i>Micropterus salmoides</i>) along with DNA and RNA extracted from bluegill tissue (<i>Lepomis megalotis</i>). We first conducted a degradation experiment to test the efficacy of refrigeration for eRNA preservation (specifically mitochondrial messenger eRNA, emRNA), given its widespread use for eDNA samples. We then compared a suite of approaches for the long-term preservation and co-extraction of emRNA and eDNA in the laboratory. Despite the potential that the instability of eRNA might render eDNA approaches unsuitable, we found that methods developed for eDNA samples can be readily repurposed for emRNA. Contrary to our hypothesis that refrigeration of water samples might not efficiently preserve emRNA in the short term, samples in a cooler on ice showed no decrease in concentration or detectability over 25 h for largemouth bass (Tukey's, all <i>p</i> &gt; 0.3). Filtration time (i.e., time spent at room temperature) also slightly reduced eRNA yields, with concentration decreasing as filtration time increased for largemouth bass emRNA (LM, <i>p</i> = 0.05), highlighting the importance of cold conditions throughout processing. Additionally, as we hypothesized, a low-cost chloroform extraction protocol yielded equivalent emRNA quantities to more expensive commercial kits for both largemouth bass and bluegill (Tukey's, <i>p</i> between methods &gt; 0.8), in some cases even yielding higher concentrations than these methods. Overall, these results demonstrate the possible practical feasibility of eRNA sampling and provide guidance for future work on eRNA in natural systems.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"26 7","pages":""},"PeriodicalIF":5.9,"publicationDate":"2026-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13662609/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149178232","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Signal of Admixture Can Decay Rapidly When Using Clustering-Based Methods","authors":"Josia Shemuel,&nbsp;Sonal Singhal,&nbsp;Craig Moritz,&nbsp;Stephen M. Zozaya","doi":"10.1111/1755-0998.70215","DOIUrl":"10.1111/1755-0998.70215","url":null,"abstract":"<p>Gene flow shapes evolutionary trajectories by introducing novel alleles, facilitating or retarding adaptation or eroding divergence among populations. Studies commonly infer gene flow through estimates of genetic admixture from methods that cluster individuals by allele-frequency similarity. However, the ability of these methods to reliably detect historical admixture remains poorly understood, particularly under spatially restricted dispersal and across a range of migration rates. Here, we evaluate how signals of admixture arise and decay during and after gene flow across a range of within- and between-population dispersal rates, using three common inference methods: ADMIXTURE, sNMF and PopCluster. Using forward-time simulations in a two-dimensional landscape, we modelled two metapopulations that diverged in isolation, experienced a pulse of secondary contact and subsequently returned to isolation. All three methods systematically underestimated admixture, with the bias increasing once gene flow ceased: inferred admixture averaged 56% of the true value at the end of gene flow, declined to 23% after 1000 generations and fell below 5% by 2000 generations, even where true admixture exceeded 20%. This underestimation was accompanied by corresponding overestimation of barrier strength, assessed using a metric analogous to cline width. Both patterns reflect the erosion of allele-frequency differences upon which these methods depend, which coincides with the rapid re-establishment of Hardy–Weinberg and linkage equilibrium following secondary contact. Our simulations show that, at least in some scenarios, the clustering-based admixture methods evaluated here cannot recover the signal of historical gene flow from present-day samples.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"26 7","pages":""},"PeriodicalIF":5.9,"publicationDate":"2026-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13659251/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149163320","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Historical Plant Embryos as Alternative Sources of Ancient DNA for Whole Genome Sequencing","authors":"Hong Phuong Le,&nbsp;Stefano Porrelli,&nbsp;Yoon Kyung Lee,&nbsp;Simon Juraver,&nbsp;Flora Pennec,&nbsp;Mark Nesbitt,&nbsp;Koji Numaguchi,&nbsp;Rafal Marek Gutaker","doi":"10.1111/1755-0998.70210","DOIUrl":"10.1111/1755-0998.70210","url":null,"abstract":"<p>Natural history and agricultural collections contain hundreds of millions of specimens classified in terms of time, space and taxonomy. Since the first success of ancient DNA (aDNA) isolation in the 1980s, these repositories, including herbaria for plants, have been intensively used to support studies in taxonomy, macroevolution and genetic responses to anthropogenic activities. For herbarium specimens, aDNA is usually extracted from leaf samples and is highly fragmented (typically length of 50–100 bp). To optimise the amount of data retrieved and minimise destructive sampling, we isolated DNA from an unconventional plant tissue type—seed embryos. We carried out whole-genome sequencing and compared sequenced DNA quality between embryo and leaf tissue from the same specimen. We evaluated endogenous DNA proportion, median fragment length, damage fraction per site (<i>λ</i>), decay rates (<i>k</i>), nucleotide misincorporations and library complexity for three species: cultivated rice <i>Oryza sativa</i>, wild rice <i>O. rufipogon</i> and wild barley <i>Hordeum spontaneum</i>. In <i>O. sativa</i>, embryos exhibited significantly higher endogenous content and median fragment length than leaves. The superior DNA preservation was likely due to the protective role of the seed husk, which might play an important role in DNA preservation in plants collected in the tropics. By contrast, in temperate <i>H. spontaneum</i>, tissue type had minimal impact on DNA quality. Despite the minuscule size of the embryos, all derived genomic libraries were highly complex, sufficient for deep whole genome sequencing. These results highlight seed embryos as a promising alternative aDNA source for herbarium specimens, economic botany and anthropological museum collections.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":"26 7","pages":""},"PeriodicalIF":5.9,"publicationDate":"2026-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.70210","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149126185","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}