Molecular Ecology Resources最新文献

Genetic introgression of domesticated plants and animals into wild populations occurs globally. Such introgression disrupts adaptive potential, reduces fitness in wild populations and threatens intraspecific genetic variation. The best-documented case of farmed introgression into wild populations is that of the Atlantic salmon (Salmo salar). Norway is the world's largest producer of farmed Atlantic salmon, and the industry is growing in Iceland and other countries. In Norway, genetic introgression resulting from farmed escapees breeding with wild conspecifics has been documented in approximately two-thirds of 250 salmon populations studied. This comprehensive quantification has been possible due to a panel of genetic markers diagnostic of farmed introgression. Improved genomic resources, continued selection and genetic drift in the farmed breeding lines, as well as new breeding lines in commercial production, call for an updated tool to quantify farmed genetic introgression. Here, we present second-generation panels of genetic markers diagnostic of farmed introgression in Norway and the first panels of genetic markers diagnostic of farmed introgression in Iceland. We show that these diagnostic markers provide increased power to detect introgression compared to the first-generation panel, as well as increased power compared to a genome-wide marker set. Improved accuracy will benefit the ongoing monitoring of farmed introgression and facilitate research into the ecological and functional effects of farmed introgression in wild populations.

Understanding the strengths and limitations of different environmental DNA substrates is essential for optimising terrestrial vertebrate surveys and monitoring. However, the performance of newly explored substrates (airborne eDNA, vegetation swabs, spiderwebs) compared to longstanding eDNA sources (water and soil) is uncertain. Using a metabarcoding approach, we assessed vertebrate eDNA diversity across seven substrates: three airborne DNA collection methods (a powered “active” fan system and two passive collection methods), spider webs, vegetation swabs (including swabbing tree trunks and leaves), water, and soil at Perth Zoo and Karakamia Wildlife Sanctuary. Active air sampling and spider webs yielded the highest taxonomic richness (Zoo: 83 and 62 taxa; Karakamia: 44 and 40, respectively), with no significant difference in the community composition, suggesting they capture eDNA from similar sources; however, all substrates contributed unique taxa detections. Passive airborne DNA collection, though less efficient than active samplers (mean taxonomic richness per sample: Zoo: 14.8 vs. 5.8; Karakamia: 6.9 vs. 2.7), showed potential as their low cost and simplicity may enable increased replication or longer deployment times, potentially improving detections. Our direct comparison of terrestrial eDNA substrates shows that airborne DNA sampling offers a genuine advance for terrestrial vertebrate biomonitoring. However, substrate-specific biases were evident, with vegetation swabs favouring arboreal mammals, while water was dominated by aquatic and semi-aquatic species, highlighting the influence of species ecology on DNA deposition. eDNA studies targeting terrestrial vertebrates must consider the heterogeneity of vertebrate DNA distribution across ecosystems and the need for careful selection of eDNA substrates.

Effective monitoring of aquatic biodiversity is critical for conservation, yet current approaches such as mitochondrial COI barcoding and microsatellite markers exhibit limitations in resolution, sensitivity, and scalability, particularly for detecting low-abundance or degraded DNA in mixed aquatic samples. To address these challenges, we developed a novel Multiple Nucleotide Polymorphism (MNP) marker system tailored to S. prenanti, an endangered endemic fish species emblematic of biodiversity crises in the Yangtze River. Through restriction-site associated DNA sequencing, we identified 115 genome-wide MNP markers. These markers demonstrated ultrasensitive detection (~1 DNA copy/reaction) and high specificity (mean discriminative power = 0.77, calculated as the probability that two random samples differ at a locus). When applied to environmental DNA from the Yangtze River, the MNP system revealed substantial genetic diversity among 86 samples (84% average differentiation rate) and quantified the contribution of artificially stocked fish to natural populations, identified 567 shared alleles between stocked and wild populations. By outperforming traditional methods in analysing fragmented DNA and enabling high-throughput applications, this MNP framework provides a transformative approach for conservation genetics. Our scalable solution bridges the gap between genetic research and conservation action, offering global applicability for aquatic biodiversity monitoring.

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.