Molecular Ecology Resources最新文献

Belowground eukaryotic diversity serves a vital role in soil ecosystem functioning, yet the composition, structure, and macroecology of these communities are significantly under-characterized. The National Ecological Observatory Network (NEON) provides publicly available datasets from long-term surveillance of numerous taxa and ecosystem properties. However, this dataset is not routinely evaluated for its eukaryotic component, likely because analyzing metagenomes for eukaryotic sequences is hampered by low relative sequence abundance, large genomes, poorer eukaryote representation in public reference databases, and is not yet mainstream. We mined the NEON soil metagenome datasets for 18S rRNA sequences using a custom-built pipeline and produced a preliminary assessment of biodiversity trends in North American soil eukaryotes. We extracted ~800 18S rRNA reads per sample (~22,000 reads per site) from 1455 samples from 495 plots across 45 NEON sites in 11 biomes, which corresponded to 5183 genera in 35 phyla. To our knowledge, this represents the first large-scale soil eukaryote analysis of NEON data. We asked whether taxonomic richness paralleled patterns previously established ecological trends and found that eukaryotic richness was negatively correlated with pH, managed sites lowered eukaryotic richness by 47%, most biomes had a distinct eukaryotic community, and fire decreased eukaryotic richness. These findings parallel generally accepted ecological trends and support the notion that NEON soil metagenome datasets can and should be used to explore spatiotemporal patterns in soil eukaryote diversity, its association with ecosystem functioning, and its response to environmental changes in North America.

As a collection of all the genetic variants in the gene pool, the pangenome is a concept that will become fundamental to conservation genomic studies. Unfortunately, most pangenomic approaches developed for humans and model organisms are financially impractical for conservation genomic studies of threatened or endangered species due to the high costs associated with deep sequencing multiple individuals using long-read platforms. Here, by integrating metagenomic and iterative map-then-assemble approaches, we (1) propose novel workflows to construct graph pangenomes from multiple low-coverage short-read datasets; (2) benchmark these short-read pangenomes (both linear and graph) against a previously published long-read graph pangenome of the barn swallow; and (3) evaluate the utility of our workflows in population and conservation genomics. Our results indicate that economical short-read graph pangenomes can recover the vast majority of the variants identified through expensive long-read graph approaches, and that these variants accurately detect important biological signals (e.g., spatial structure and independent taxonomic delineations). These results mean that researchers can utilize their limited, conservation-oriented funding to more fully characterize all the variants in a particular gene pool for population-level analyses.

EXPRESSION OF CONCERN: L. Roman, B. Mayne, C. Anderson, Y. Kim, T. O'Dwyer, and N. Carlile, “A Novel Technique for Estimating Age and Demography of Long-Lived Seabirds (Genus Pterodroma) Using an Epigenetic Clock for Gould’s Petrel (Pterodroma leucoptera),” Molecular Ecology Resources 24, no. 7 (2024): e14003, https://doi.org/10.1111/1755-0998.14003.

This Expression of Concern is for the above article, published online on 29 July 2024 in Wiley Online Library (wileyonlinelibrary.com), and has been issued by agreement between the journal Editor-in-Chief, Ben Sibbett; and John Wiley & Sons Ltd. The Expression of Concern has been agreed upon following concerns raised by one of the authors, L. Roman, regarding potential inaccuracies in the data presented in the article. These concerns suggest the study may not be reproducible. The institution is currently investigating the matter and has requested that the Expression of Concern be published during the course of the investigation.

Species-specific non-invasive underwater DNA sampling remains largely understudied for marine invertebrates despite its potential to revolutionise biodiversity assessment of vulnerable species or fragile ecosystems. Comprehensive species-specific DNA barcode databases are essential for accurate species identification and taxonomic assignment, particularly at a time of increasingly employed metabarcoding monitoring of marine biodiversity. We present an in situ swab-based protocol adapted for underwater collection of genetic material, using Red Sea echinoderms as a case study. We sampled 308 individuals from over 50 species across all five echinoderm classes using a newly designed underwater sampling kit applying sterile buccal swabs and an underwater sampling container. The novel sampling protocol was compared to traditional tissue-based DNA extractions and tested for preservation conditions (fixatives, temperatures and durations). DNA yield from swabs was lower than from traditional tissue biopsies, yet sufficient for all downstream applications. Overall PCR amplification success was 88% (240/274 echinoderm swabs), with a 94% sequencing success rate (202/214), and no significant difference in DNA integrity between swab and tissue methods. Phylogenetic analyses of 231 specimens revealed 37 clades, including 20 novel Red Sea lineages and provisional identifications of cryptic and rare species. Our results demonstrate that underwater swabbing is a rapid (< 1 min per sample), cost-effective, and non-destructive, suitable for generating high-quality genetic data under challenging field conditions. We propose this protocol as an alternative to traditional DNA sampling, providing an efficient approach for studying at-risk ecosystems and species while prioritising conservation and sustainability and facilitating large-scale genetic screening of wild populations.

The authors (Zuo et al. 2025) reported that Figure 2A was inadvertently duplicated in place of Figure 2B. Consequently, the relevant figures (Figure 2B) need to be revised accordingly. This error does not alter the main conclusions of the study.

We apologize for this error.

Published version Figure 2:

Corrected version Figure 2:

A key application of phylogenetics in ecological studies is identifying unknown sequences with respect to known ones. This goal can be formalised as assigning taxonomic labels or inserting sequences into a reference phylogenetic tree (phylogenetic placement). Much attention has been paid to the phylogenetic placement of short fragments used in amplicon sequencing or metagenomics. However, placing longer pieces of DNA, such as assembled genomes, contigs, or long reads, is less studied. Placing long sequences should be easier than short reads due to their increased signal. However, handling larger inputs poses its own challenges including finding homologues and the computational burden. Here, we explore a phylogenetic placement method that uses k-mer frequencies to measure distances between long query sequences and reference genomes. Our proposed method, kf2vec, requires no alignment and can work on any region of the genome (needs no marker genes), thus simplifying analysis pipelines. A rich literature exists on using short k-mers frequencies to measure distances that correlate with phylogeny. Existing methods, however, have had moderate practical success despite enjoying strong theory. Instead of using predefined metrics, we train a deep neural network to estimate a distance from k-mer frequency vectors such that those distances match the path lengths on the reference phylogeny. The trained model is then used to characterise new samples. We demonstrate that kf2vec outperforms existing k-mer-based approaches in distance calculation and allows accurate phylogenetic placement and taxonomic identification of new samples from various types of long sequences.

Food availability is a fundamental driver of vertebrate spatial distributions, yet quantifying these relationships across taxonomic groups remains challenging in structurally complex ecosystems such as tropical rainforests. Understanding how resource heterogeneity shapes community structure is critical for advancing ecological theory and informing conservation strategies. We combined airborne environmental DNA (eDNA) sampling with ground-based fruit tree surveys in the Xishuangbanna tropical rainforest to test whether measurable animal genetic traces in the air reflect the fine-scale distribution of animals driven by fruit resources. Airborne eDNA sampling revealed a diverse vertebrate community, with 71 bird and 18 mammal species detected at high spatial resolution in tropical rainforests. By applying occupancy models to account for detection bias, we show that vertebrate occurrence patterns are significantly influenced by both the overall abundance of fruiting trees and, more importantly, the availability of small fruiting trees across locations. Our findings provide the first compelling airborne eDNA-based evidence that fine-scale fruit resource availability, particularly from small-fruited trees, contributes to the spatial distribution of vertebrates in tropical rainforests of Xishuangbanna, China. These spatial couplings between plants and animals highlight the value of airborne eDNA not only for biodiversity monitoring but also for testing trait-based ecological hypotheses (e.g., fruit size selection by frugivores) and advancing theory on community assembly in structurally complex ecosystems.

Nematodes are among the most diverse animals, yet only around 28,000 of an estimated one million species have been morphologically described. Their small size, morphological simplicity, and cryptic diversity complicate phylogenetic analyses. Traditional morphological and single-locus molecular approaches often lack resolution for both recent and ancient divergences. To address these limitations, we developed the first ultraconserved elements (UCEs) probe sets for two nematode families: Panagrolaimidae, a group of non-model organisms with limited genomic resources when compared to model taxa, and Rhabditidae, which includes the model species Caenorhabditis elegans. Our probe sets targeted 1612 loci for Panagrolaimidae and 100,397 for Rhabditidae. In vitro testing recovered up to 1457 loci in Panagrolaimidae, supporting robust phylogenetic reconstruction. Results were largely consistent with previous analyses, except for one strain reclassified as Neocephalobus halophilus BSS8. Using machine learning, we determined the minimum number of loci needed for accurate genus-level classification. For Rhabditidae, XGBoost achieved high accuracy with just 46 loci. For Panagrolaimidae, 39 loci were most informative. Our UCE-based approach offers a scalable and cost-effective framework for phylogenomics, enhancing taxonomic resolution and evolutionary inference in nematodes. It is well suited for biodiversity assessments and shallow, field-based sequencing, expanding research possibilities across this ecologically important phylum.

Ancient DNA (aDNA) analysis of archaeological dental calculus has provided a wealth of insights into ancient health, demography and lifestyles. However, the workflow for ancient metagenomics is still evolving, raising concerns about reproducibility. Few systematic investigations have examined how DNA extraction methods and library preparation protocols influence ancient oral microbiome recovery, despite evidence from modern populations suggesting that they do. This leaves a gap in our understanding of how wet-lab protocols impact aDNA recovery from dental calculus. In this study, we apply two DNA extraction and two library preparation methods in the aDNA field on dental calculus samples from Hungary and Niger. Samples from each context have similar chronological ages, but differences in their levels of aDNA preservation are notable, providing additional insights into how the efficacy of wet-lab protocols is impacted by sample preservation. Several metrics were employed to assess intra- and inter-sample variability, such as DNA fragment length recovery, GC content, clonality, endogenous content, DNA deamination and microbial composition. Our findings indicate that both DNA extraction and library preparation protocols can considerably impact ancient DNA recovery from archaeological dental calculus. Furthermore, no single protocol consistently outperformed the others across all assessments, and the effectiveness of specific protocol combinations depended on the preservation of the sample. These findings highlight the challenges of meta-analyses and underscore the need to account for technical variability. Lastly, our study raises the question of whether the field should strive to standardise methods for comparability or optimise protocols based on sample preservation and specific research objectives.

Obligate biotrophic plant pathogens like the powdery mildew fungi commit to a closely dependent relationship with their plant hosts and have lost the ability to grow and reproduce independently. Thus, at present, these organisms are not amenable to in vitro cultivation, which is a prerequisite for effective genetic modification and functional molecular studies. Saprotrophic fungi of the family Arachnopezizaceae are the closest known extant relatives of the powdery mildew fungi and may hold great potential for studying genetic components of their obligate biotrophic lifestyle. Here, we established telomere-to-telomere genome assemblies for two representatives of this family, Arachnopeziza aurata and A. aurelia. Both species harbour haploid genomes that are composed of 16 chromosomes at a genome size of 43.1 and 46.3 million base pairs, respectively, which, in contrast to most powdery mildew genomes that are transposon-enriched, show a repeat content below 5% and signs of repeat-induced point mutation. Both species could be grown in liquid culture and on standard solid media and were sensitive to common fungicides such as hygromycin and fenhexamid. We successfully expressed a red fluorescent protein and hygromycin resistance in A. aurata following polyethylene glycol-mediated protoplast transformation, demonstrating that Arachnopeziza species are amenable to genetic alterations, which may be expanded to include gene replacement, gene modification, and gene complementation in the future. With this work, we established a potential model system that promises to sidestep the need for genetic modification of powdery mildew fungi by using Arachnopeziza species as a proxy to uncover the molecular functions of powdery mildew proteins.