Molecular Ecology Resources最新文献

{"title":"An Optimised Method to Identify Reintroduced Swift Foxes (Vulpes velox) Through SNP Genotyping of Non-Invasively Collected Scat Samples Using In-Solution Hybridisation Capture.","authors":"L D Parker, K R Todd, D L Nelson, N Songsasen, M G Campana, W J McShea, M Songer, T Messerly, H Shamon, J E Maldonado","doi":"10.1111/1755-0998.70017","DOIUrl":"https://doi.org/10.1111/1755-0998.70017","url":null,"abstract":"<p><p>Genomic methods have become increasingly common in wildlife population studies over the past two decades. While noninvasive genetic sampling has been prevalent since the 1990s, the field has lagged in the adoption of high-throughput sequencing methods. In-solution hybridisation capture offers an efficient way to enrich and sequence degraded, low-quantity DNA with a large percentage of exogenous content (e.g., scat samples) for specific targets of interest. Despite their frequent use in ancient and historical DNA applications, hybridisation capture techniques have not been widely adopted for noninvasive genetic samples. Previous studies demonstrated that capture enrichment of single-nucleotide polymorphism (SNP) loci enables genotyping of field-collected kit fox and coyote scats to effectively identify species, individuals and sex. Here, we expanded on this work by (1) investigating whether probes designed for kit foxes can generate multi-locus SNP genotypes and identify sex in closely related swift foxes (Vulpes velox), (2) assessing the capability of the resulting genotypes to differentiate among swift foxes by calculating identity-by-state values between samples from the same individual, (3) exploring the impact of replicate index polymerase chain reactions (PCRs) on genotyping success, and (4) exploring the performance of the marker set for inference of population genetic structure. We applied these methods to samples from swift foxes reintroduced to the Fort Belknap Indian Reservation, Montana, and showed a success rate of 85%. Our developed methodology can be applied to monitor the success of swift fox reintroduction efforts by estimating dispersal, survival, and reproduction. We also showed that probes designed and optimised for one species can produce informative genotypes from closely related species, highlighting their versatility for broader applications in wildlife population studies.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e70017"},"PeriodicalIF":5.5,"publicationDate":"2025-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144740759","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effects of Vacuum-Heat-Assisted Sample Desiccation on Microbiome Surveys.","authors":"Stilianos Louca, Claire E Mullin","doi":"10.1111/1755-0998.70020","DOIUrl":"https://doi.org/10.1111/1755-0998.70020","url":null,"abstract":"<p><p>Sample preservation in the field and during transport can be a logistical challenge for microbiome surveys, particularly in remote areas. Sample desiccation eliminates the need for complicated cold chains and dangerous preservatives. However, the effects of desiccation on modern microbiome workflows such as gene-centric metagenomic profiling and metagenome-assembled genome (MAG) binning, remain poorly understood. In addition, most common desiccation tools such as lyophilisation cannot easily be deployed in the field. Here, we describe a proof-of-principle sample desiccator using vacuum and heat, specifically built for deployment in the field and exhibiting low power consumption and cost. We then test the effects of vacuum-heat-assisted sample desiccation followed by storage at room temperature, in comparison to conventional freezing, on multiple soil and animal faecal samples, via metagenomic and 16S rRNA amplicon sequencing. We consider multiple metrics related to the success of DNA extraction, sequencing, contig assembly, OTU clustering, gene annotation and MAG construction, as well as effects on inferred microbial community composition. We find that the impact of drying on considered success metrics was almost always either minor, non-significant or positive. For a subset of source materials we observed moderate but statistically significant differences in terms of inferred microbial taxonomic and genetic composition. We conclude that vacuum- and heat-assisted desiccation can be a useful, practical and cost-effective tool for microbiome field surveys, when a high consistency with frozen samples is not required.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e70020"},"PeriodicalIF":5.5,"publicationDate":"2025-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144726278","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Linkage Mapping vs. Association: A Comparison of Two RADseq-Based Approaches to Identify Markers for Homomorphic Sex Chromosomes in Large Genomes.","authors":"James France, Wiesław Babik, Katarzyna Dudek, Marzena Marszałek, Ben Wielstra","doi":"10.1111/1755-0998.70019","DOIUrl":"https://doi.org/10.1111/1755-0998.70019","url":null,"abstract":"<p><p>Reliable tools for the identification of genetic sex are invaluable in many fields of biology, but their design requires knowledge of sex-linked sequences, which is lacking in many taxa. Restriction-site-associated DNA sequencing (RADseq) is widely used to identify sex-linked markers, but multiple distinct strategies are employed, and it is often not obvious which is most suitable. In this study, we compare two approaches for using RADseq to identify sex-linked markers. We use the common newt, Lissotriton vulgaris, as our study system, providing a challenging combination of homomorphic sex chromosomes and an exceptionally large genome. We attempt an associative approach, sequencing 60 adult newts of known-sex individuals, and compare this to a linkage mapping approach utilising a family of 146 offspring with unknown sex. After optimisation for a highly paralogous genome, the associative approach identifies five Y-chromosome-linked markers in L. vulgaris, and we design a robust PCR protocol for molecular sexing of four more related species. Via the linkage approach, we construct a high-density map featuring 10,763 markers, matching the observed karyotype of L. vulgaris and showing broad synteny with the Iberian ribbed newt (Pleurodeles waltl). However, without incorporating the markers identified via the association-based approach, we cannot confidently distinguish a sex-determining region in the linkage map, either by analysing marker density or by identifying clusters of paternal markers. We conclude that linkage mapping alone is unlikely to yield sex-linked markers in organisms with very small sex-determining regions, whereas association-based RADseq can still be effective under these conditions.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e70019"},"PeriodicalIF":5.5,"publicationDate":"2025-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144697221","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative Analyses of Four Reference Genomes Reveal Exceptional Diversity and Weak Linked Selection in the Yellow Monkeyflower (Mimulus guttatus) Complex.","authors":"John T Lovell, Rachel Walstead, Amelia Lawrence, Evan Stark-Dykema, Matthew C Farnitano, Avril Harder, Tomáš Brůna, Kerrie Barry, David Goodstein, Jerry Jenkins, Anna Lipzen, LoriBeth Boston, Jenell Webber, Mansi Chovatia, Joanne Eichenberger, Jayson Talag, Jane Grimwood, Jeremy Schmutz, John K Kelly, Andrea L Sweigart, Lila Fishman, John H Willis","doi":"10.1111/1755-0998.70012","DOIUrl":"https://doi.org/10.1111/1755-0998.70012","url":null,"abstract":"<p><p>Yellow monkeyflowers (Mimulus guttatus complex, Phrymaceae) are a powerful system for studying ecological adaptation, reproductive variation, and genome evolution. To initiate pan-genomics in this group, we present four chromosome-scale assemblies and annotations of accessions spanning a broad evolutionary spectrum: two from a single M. guttatus population, one from the closely related selfing species M. nasutus, and one from a more divergent species M. tilingii. All assemblies are highly complete and resolve centromeric and repetitive regions. Comparative analyses reveal such extensive structural variation in repeat-rich, gene-poor regions that large portions of the genome are unalignable across accessions. As a result, this Mimulus pan-genome is primarily informative in genic regions, underscoring limitations of resequencing approaches in such polymorphic taxa. We document gene presence-absence, investigate the recombination landscape using high-resolution linkage data, and quantify nucleotide diversity. Surprisingly, pairwise differences at fourfold synonymous sites are exceptionally high-even in regions of very low recombination-reaching ~3.2% within a single M. guttatus population, ~7% within the interfertile M. guttatus species complex (approximately equal to SNP divergence between great apes and Old World monkeys), and ~7.4% between that complex and the reproductively isolated M. tilingii. Genome-wide patterns of nucleotide variation show little evidence of linked selection, and instead suggest that the concentration of genes (and likely selected sites) in high-recombination regions may buffer diversity loss. These assemblies, annotations, and comparative analyses provide a robust genomic foundation for Mimulus research and offer new insights into the interplay of recombination, structural variation, and molecular evolution in highly diverse plant genomes.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e70012"},"PeriodicalIF":5.5,"publicationDate":"2025-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144688488","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"wholeskim: Utilising Genome Skims for Taxonomically Annotating Ancient DNA Metagenomes.","authors":"Lucas Elliott, Frédéric Boyer, Teo Lemane, Inger Greve Alsos, Eric Coissac","doi":"10.1111/1755-0998.70001","DOIUrl":"https://doi.org/10.1111/1755-0998.70001","url":null,"abstract":"<p><p>Inferring community composition from shotgun sequencing of environmental DNA is highly dependent on the completeness of reference databases used to assign taxonomic information as well as the pipeline used. While the number of complete, fully assembled reference genomes is increasing rapidly, their taxonomic coverage is generally too sparse to use them to build complete reference databases that span all or most of the target taxa. Low-coverage, whole genome sequencing, or skimming, provides a cost-effective and scalable alternative source of genome-wide information in the interim. Without enough coverage to assemble large contigs of nuclear DNA, much of the utility of a genome skim in the context of taxonomic annotation is found in its short read form. However, previous methods have not been able to fully leverage the data in this format. We demonstrate the utility of wholeskim, a pipeline for the indexing of k-mers present in genome skims and subsequent querying of these indices with short DNA reads. Wholeskim expands on the functionality of kmindex, a software which utilises Bloom filters to efficiently index and query billions of k-mers. Using a collection of thousands of plant genome skims, wholeskim is the only software that is able to index and query the skims in their unassembled form. It is able to correctly annotate 1.16× more simulated reads and 2.48× more true sedaDNA reads in 0.32× of the time required by Holi, another metagenomic pipeline that uses genome skims in their assembled form as its reference database input. We also explore the effects of taxonomic and genomic completeness of the reference database on the accuracy and sensitivity of read assignment. Increasing the genomic coverage of the genome skims used as reference increases the number of correctly annotated reads, but with diminishing returns after ~1× depth of coverage. Increasing taxonomic coverage clearly reduces the number of false negative taxa in the dataset, but we also demonstrate that it does not greatly impact false positive annotations.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e70001"},"PeriodicalIF":5.5,"publicationDate":"2025-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144673544","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"RETRACTION: Nonlethal Age Estimation of Three Threatened Fish Species Using DNA Methylation: Australian Lungfish, Murray Cod and Mary River Cod.","authors":"","doi":"10.1111/1755-0998.70018","DOIUrl":"https://doi.org/10.1111/1755-0998.70018","url":null,"abstract":"","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e70018"},"PeriodicalIF":5.5,"publicationDate":"2025-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144673543","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"RETRACTION: Age Prediction of Green Turtles With an Epigenetic Clock.","authors":"","doi":"10.1111/1755-0998.70016","DOIUrl":"https://doi.org/10.1111/1755-0998.70016","url":null,"abstract":"<p><strong>Retraction: </strong>B. Mayne, W. Mustin, V. Baboolal, F. Casella, K. Ballorain, M. Barret, M. A. Vanderklift, A. D. Tucker, D. Korbie, S. Jarman and O. Berry, \"Age Prediction of Green Turtles With an Epigenetic Clock,\" Molecular Ecology Resources 22, no. 6 (2022): 2275-2284, https://doi.org/10.1111/1755-0998.13621. The above article, published online on 15 April 2022 in Wiley Online Library (wileyonlinelibrary.com), has been retracted by agreement between the journal Editors-in-Chief, Shawn Narum and Ben Sibbett; and John Wiley & Sons Ltd. The retraction has been agreed upon following an alert from one of the authors, S. Jarman, identifying that the results shown in Figure 2 are inaccurate and do not represent a real relationship between age and DNA methylation. Consequently, the editors consider the results and conclusions invalid. The authors, S. Jarman, B. Mayne, M. A. Vanderklift, O. Berry, K. Ballorain and M. Barret agree with the decision to retract this article.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e70016"},"PeriodicalIF":5.5,"publicationDate":"2025-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144648082","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Historical Collections of Tropical Marine Mammals Are an Excellent Resource for Ancient DNA.","authors":"Lydia Hildebrand Furness, Richard Sabin, Marianne Strand Torvanger, Oliver Kersten, James H Barrett, Bastiaan Star","doi":"10.1111/1755-0998.70015","DOIUrl":"https://doi.org/10.1111/1755-0998.70015","url":null,"abstract":"<p><p>The ability to predict ancient DNA sequencing success in natural history collections is critical to reducing the amount of destructive sampling of a finite resource. So far, studies investigating such success have predominantly focused on taxa with ranges restricted to temperate or cold environments at northern latitudes, which likely aids DNA preservation. Here, we report remarkably high aDNA sequencing success in Sirenia, herbivorous marine mammals of which the distribution is currently constrained to the global tropics. We investigate 91 samples from 85 specimens comprising all four contemporary species and one extinct species, comparing different sample types (cranial/post-cranial bone, skin and cartilage), species, collections, and material age. We obtained remarkably high (e.g., > 20%) endogenous DNA preservation for the majority (e.g., ~57% percent) of samples. Sequencing success was linked to sample type, with cranial bones (including petrous and tympanic bones) yielding significantly higher endogenous DNA. Additionally, we obtained variable, but potentially superior DNA results for preserved cartilage and hide samples that can be associated with historical bone. Although such tissue is not always present, this type of material is easy to sample, with very limited destructive impacts on the associated bones, and we therefore highlight its untapped potential as a source of DNA. Overall, our results show the high success of ancient DNA retrieval from historical collections of species with a tropical distribution, expanding on the types of specimens that are available for temporal genomic analyses.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e70015"},"PeriodicalIF":5.5,"publicationDate":"2025-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144648080","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multi-Tool Marine Metabarcoding Bioassessment for Baselining and Monitoring Species and Communities in Kelp Habitats.","authors":"Giulia Maiello, Marilla R Lippert, Erika F Neave, Erik A Hanson, Stephen R Palumbi, Stefano Mariani","doi":"10.1111/1755-0998.70010","DOIUrl":"https://doi.org/10.1111/1755-0998.70010","url":null,"abstract":"<p><p>The astonishing biological diversity found in Californian kelp forests requires efficient and robust monitoring tools to better understand ecological trends and mitigate against loss or disruption of ecosystem services due to human pressure and climate changes. With environmental DNA (eDNA) metabarcoding becoming a popular biodiversity assessment approach, we set out to evaluate a combination of powerful, rapid and sustainable eDNA solutions for characterising marine community composition in kelp-dominated habitats along the central California coast, in the newly proposed Chumash Heritage National Marine Sanctuary. We employed and compared the efficiency of several eDNA collection approaches, including 'traditional' surface water filtration, the collection of organisms encrusting cobble rocks and various deployments of an artificial passive sampler, the metaprobe (i.e., attached to divers, dangled from a boat and cast from the shore using a fishing rod). By combining the information from fish specific (Tele02 12S) and universal metazoan (COI) markers, we 'captured' 501 unique marine taxa, belonging to at least 36 phyla, over 400 of which were identified to genus/species level, and including 52 vertebrate species typical of Californian kelp forest ecosystems. Despite differences in the type of biodiversity returned by the tested sampling methods, the overall community structure of the surveyed area was highly spatially structured and strongly influenced by the biogeographic break around Point Conception (Humqaq). We discuss the benefits of integrating eDNA metabarcoding in existing monitoring programs and devising a reproducible approach to monitor faunal changes in kelp forest habitats and beyond.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e70010"},"PeriodicalIF":5.5,"publicationDate":"2025-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144648081","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Conserved Sequence Identification Within Large Genomic Datasets Using 'Unikseq2': Application in Environmental DNA Assay Development.","authors":"Mark Louie D Lopez, René L Warren, Michael J Allison, Lauren Coombe, Jacob J Imbery, Inanc Birol, Caren C Helbing","doi":"10.1111/1755-0998.70014","DOIUrl":"https://doi.org/10.1111/1755-0998.70014","url":null,"abstract":"<p><p>Identification of conserved genomic sequences and their utilisation as anchor points for clade detection and/or characterisation is a mainstay in ecological studies. For environmental DNA (eDNA) assays, effective processing of large genomic datasets is crucial for reliable species detection in biodiversity monitoring. While considerable focus has been on developing robust species-targeted assays, eDNA assays with broader taxonomic coverage (e.g., detecting any species within a taxonomic group such as fish), can significantly streamline environmental monitoring, especially when detecting individual species' DNA proves challenging. Designing such assays requires identifying conserved regions representing the target taxonomic group, a chiefly manual task that is often labor-intensive and error-prone, particularly when working with large sequence datasets. To address these challenges, we present unikseq2, an enhanced, alignment-free, k-mer-based tool for identifying unique and conserved sequences. It introduces a new functionality to identify sequence conservation among target species, enabling more informed marker selection for applications such as universal primer design. This automates sequence selection in large-scale mitochondrial genome datasets eliminating the need for manual inspection of computationally costly multiple sequence alignments. Herein, we demonstrate unikseq2's capabilities by developing and validating eDNA assays for various taxa, including Osteichthyes (bony fishes), the Salmonidae family (salmon and trout), Myotis bats and Cervus deer. Unikseq2-based eDNA assays allow for accurate detection across multiple taxonomic levels, from genus to class, enhancing the flexibility, scalability and reliability of eDNA tools in environmental monitoring. By leveraging genomic data from public repositories, unikseq2 supports efficient, reproducible assay design, making it an invaluable tool for a wide range of ecological and biodiversity research applications.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e70014"},"PeriodicalIF":5.5,"publicationDate":"2025-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144606956","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}