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Nanopore raw read accuracy has improved to over 99%, making it a potential tool for metabarcoding. For broad adoption, guidelines on quality filtering are needed to ensure reliable taxonomic unit recovery. This study aims to provide those guidelines for a fungal metabarcoding context and to apply them to a case study of ectomycorrhizae in the decaying bark of Fagus sylvatica. We introduce the eNano pipeline to test two standard metabarcoding approaches: (1) Reference-based mapping leveraging UNITE's species hypothesis system (SH approach); (2) Constructing 98% OTUs (OTU approach). Our results demonstrate that both approaches are effective with Nanopore data. When using a reference database, we recommend strict mapping criteria rather than Phred-based filtering. Leveraging the SH-system further enhances reproducibility and facilitates cross-study communication. For the 98% OTUs, filtering reads at ≥Q25 is recommended. Our case study reveals that the decay gradient is a primary determinant of community composition and that specific mycorrhizal fungi colonize decaying bark. Complementing our metabarcoding results with root tip morphotypification, we identify Laccaria amethystina and Tomentella sublilacina as key ectomycorrhizae of saplings on decaying logs. These findings demonstrate that Nanopore sequencing can provide valuable ecological insights and support its broader use in fungal metabarcoding as read quality continues to improve. [ABSTRACT FROM AUTHOR]

Premise Methods Results Discussion Hybridization capture kits are now commonly used for reduced representation approaches in genomic sequencing, with both universal and clade‐specific kits available. Here, we present a probe kit targeting 799 low‐copy genes for the plant family Annonaceae.This new version of the kit combines the original 469 genes from the previous Annonaceae kit with 334 genes from the universal Angiosperms353 kit. We also compare the results obtained using the original Angiosperms353 kit with our custom approach using a subset of specimens. Parsimony‐informative sites and the results of maximum likelihood phylogenetic inference were assessed for combined matrices using the genera Asimina and Deeringothamnus.The Annonaceae799 genes derived from the Angiosperms353 kit have extremely high recovery rates. Off‐target reads were also detected. When evaluating size, the proportion of on‐ and off‐target regions, and the number of parsimony‐informative sites, the genes incorporated from the Angiosperms353 panel generally outperformed the genes from the original Annonaceae probe kit.We demonstrated that the new sequences from the Angiosperms353 probe set are variable and relevant for future studies on species‐level phylogenomics and within‐species studies in the Annonaceae. The integration of kits also establishes a connection between projects and makes new genes available for phylogenetic and population studies. [ABSTRACT FROM AUTHOR]

Aim: Islands are 'nature's laboratories of evolution'. Most island biogeographical studies have focussed on remote volcanic island chains. Here, we challenge island biogeographical patterns using a slowly evolving recent colonist present on five islands in a nonlinear chronosequence island chain. Location: The Lesser Antilles (Caribbean). Taxon: Magnolia dodecapetala (Magnoliaceae). Methods: Genetic diversity was characterised using Sanger sequencing of 21 individuals amplified for 11 DNA markers, plus microsatellite data of 195 individuals genotyped with 19 simple sequence repeat (SSR) markers. Sanger sequencing data were used to construct a Bayesian phylogenetic hypothesis, while SSR markers were used to run approximate Bayesian computation (ABC) demographic analyses and calculate population statistics. Results: Both types of molecular data support stepwise colonisation, decoupled from known island ages. The ABC analyses support a north to south migration while the Sanger sequencing data indicate a mixture of island progression rule and stepping stone dispersal. The SSR data show strong genetic structuring per island and significant inbreeding in all populations except in Saint Lucia. The lowest genetic diversity is found in the population from Saint Vincent. A high amount of genetic linkage occurs in a subpopulation from Dominica. Main Conclusions: Biogeographical patterns in the complex geological setting of the Lesser Antilles are uncovered using a slowly evolving study species. All genetic data support treating each island as distinct Management Units for conservation and call for a re‐evaluation of the species limits. Inbreeding threatens the survival of island populations and the populations of Saint Vincent and Dominica represent conservation priorities. [ABSTRACT FROM AUTHOR]

Genetic data on threatened plant populations can facilitate the development of adequate conservation strategies to reduce extinction risk. Such data are particularly important for species affected by habitat fragmentation such as Magnolia cubensis subsp. acunae, a Critically Endangered magnolia subspecies endemic to Cuba. Using genetic data from 67 individuals, we aimed to evaluate the effect of habitat fragmentation on two subpopulations in the Guamuhaya mountain range, in Topes de Collantes Protected Natural Landscape and Lomas de Banao Ecological Reserve. We characterize the structure and genetic diversity of these subpopulations, with the objective of managing their conservation more effectively. We used Landsat satellite images to determine land-cover types at the two locations and calculated indices of habitat fragmentation. For genetic analyses, we extracted DNA from the leaf tissue of individuals from the two subpopulations and used 11 microsatellite markers to genotype them. We calculated heterozygosity, allelic richness and the F-statistics, to evaluate genetic variability. The montane rainforest in Topes de Collantes was most affected by habitat fragmentation, with smaller patches of more irregular shapes, compared to submontane forest at this location and both montane and submontane forests in Lomas de Banao. Genetic diversity was higher in Topes de Collantes, but we found no genetic differentiation between subpopulations. Our findings suggest the two subpopulations can be considered a single evolutionary unit and conservation entity. We propose to use individuals from both subpopulations for reinforcement to increase the overall genetic diversity of the subspecies. [ABSTRACT FROM AUTHOR]