Molecular Ecology Resources

Article	Citations
An Innovative Binding‐Protein‐Based dsRNA Extraction Method: Comparison of Cost‐Effectiveness of Virus Detection Methods Using High‐Throughput Sequencing	401
The voice of the little giants: Arcellinida testate amoebae in environmental DNA‐based bioindication, from taxonomy free to haplotypic level	107
Collecting baleen whale blow samples by drone: A minimally intrusive tool for conservation genetics	77
Particle size influences decay rates of environmental DNA in aquatic systems	70
metaPR2: A database of eukaryotic 18S rRNA metabarcodes with an emphasis on protists	65
The topological nature of tag jumping in environmental DNA metabarcoding studies	64
Use of 16S rRNA gene sequences to identify cyanobacteria that can grow in far‐red light	63
Chromosome‐Level Genome Assembly of the Loach Goby Rhyacichthys aspro Offers Insights Into Gobioidei Evolution	61
Evaluating the use of lake sedimentary DNA in palaeolimnology: A comparison with long‐term microscopy‐based monitoring of the phytoplankton community	57
Stomach Content DNA (scDNA) Detection and Quantification for Predator Diet Assessment Using High‐Throughput Nanofluidic Chip Technology: Species‐Specific qPCR Assay Pa	57
A minimally invasive, field‐applicable CRISPR/Cas biosensor to aid in the detection of Pseudogymnoascus destructans, the causative fungal agent of white‐nose syndrome in bats	55
Fast‐tracking bespoke DNA reference database generation from museum collections for biomonitoring and conservation	54
detectEVE: Fast, Sensitive and Precise Detection of Endogenous Viral Elements in Genomic Data	49
A road map for in vivo evolution experiments with blood‐borne parasitic microbes	47
Issue Information	47
A chromosome‐scale genome assembly and annotation of the spring orchid (Cymbidium goeringii)	44
Revisiting the Briggs Ancient DNA Damage Model: A Fast Maximum Likelihood Method to Estimate Post‐Mortem Damage	44
Bayesian tests for random mating in polyploids	44
DNA barcoding of Chinese snakes reveals hidden diversity and conservation needs	42
Characterising Soil Eukaryotic Diversity From NEON Metagenomics Datasets	42
Molecular diet analysis in mussels and other metazoan filter feeders and an assessment of their utility as natural eDNA samplers	42
A second unveiling: Haplotig masking of the eastern oyster genome improves population‐level inference	41
An Accessible Metagenomic Strategy Allows for Better Characterisation of Invertebrate Bulk Samples	41
Benchmarking the Mantel test and derived methods for testing association between distance matrices	41
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Inference of the distribution of fitness effects of mutations is affected by single nucleotide polymorphism filtering methods, sample size and population structure	39
Simulating plasticity as a framework for understanding habitat selection and its role in adaptive capacity and extinction risk through an expansion of CDMetaPOP	37
Beware of Plant DNA in Animal Dietary Metabarcoding: Lessons From a Strictly Insectivorous Bat	36
Potential PCR amplification bias in identifying complex ecological patterns: Higher species compositional homogeneity revealed in smaller‐size coral reef zooplankton by metatranscriptomics	36
SPEDE‐sampler: An R Shiny application to assess how methodological choices and taxon sampling can affect Generalized Mixed Yule Coalescent output and interpretation	36
Monitoring of multiple fish species by quantitative environmental DNA metabarcoding surveys over two summer seasons	36
RETRACTION: Age Prediction of Green Turtles With an Epigenetic Clock	35
Demogenomic inference from spatially and temporally heterogeneous samples	34
Saprotrophic Arachnopeziza Species as New Resources to Study the Obligate Biotrophic Lifestyle of Powdery Mildew Fungi	34
Towards Large‐Scale Museomics Projects: A Cost‐Effective and High‐Throughput Extraction Method for Obtaining Historical DNA From Museum Insect Specimens	34
MaxTemp: A Method to Maximise Precision of the Temporal Method for Estimating Ne in Genetic Monitoring Programs	34
Independent Avian Epigenetic Clocks for Ageing and Development	33
Cover Image	33
Fishing for DNA? Designing baits for population genetics in target enrichment experiments: Guidelines, considerations and the new tool supeRbaits	33
A needle in a haystack: A new metabarcoding approach to survey diversity at the species level of Arcellinida (Amoebozoa: Tubulinea)	33
Assessing the impact of USER‐treatment on hyRAD capture applied to ancient DNA	32
Scaling Up Species Delimitation From DNA Barcodes to Whole Organelle Genomes: Strong Evidence for Discordance Among Genes and Methods for the Red Alga Dasyclonium	32
Comparing eDNA and Transect Methods for Aquatic Biodiversity Assessment in Lakes and Ponds	32
Comparative analysis of fish environmental DNA reveals higher sensitivity achieved through targeted sequence‐based metabarcoding	31
The proof is in the poo: Non‐invasive method to detect endoparasitic infection	31
GenAPoPop 1.0: A user‐friendly software to analyse genetic diversity and structure from partially clonal and selfed autopolyploid organisms	31
The great tit HapMap project: A continental‐scale analysis of genomic variation in a songbird	31
Proteomic fingerprinting enables quantitative biodiversity assessments of species and ontogenetic stages in Calanus congeners (Copepoda, Crustacea) from the Arctic Ocean	31
Chromosome‐level genome of Entada phaseoloides provides insights into genome evolution and biosynthesis of triterpenoid saponins	30
Methylome Profiling of a Deuterostome Invertebrate Using Oxford Nanopore Technology ( ONT )	29
When barcoding fails: Genome chimerization (admixing) and reticulation obscure phylogenetic and taxonomic relationships	29
DNA methylation‐based biomarkers for ageing long‐lived cetaceans	28
Evaluating the Benefits and Limits of Multiple Displacement Amplification With Whole‐Genome Oxford Nanopore Sequencing	28
A comprehensive framework for detecting copy number variants from single nucleotide polymorphism data: ‘rCNV’, a versatile r package for paralogue and CNV detection	28
MycoAI: Fast and accurate taxonomic classification for fungal ITS sequences	28
Performance of DNA metabarcoding, standard barcoding and morphological approaches in the identification of insect biodiversity	27
Species discrimination in Schima (Theaceae): Next‐generation super‐barcodes meet evolutionary complexity	27
Batch effects in population genomic studies with low‐coverage whole genome sequencing data: Causes, detection and mitigation	27
Issue Information	27
The Long and the Short of It: Nanopore‐Based eDNA Metabarcoding of Marine Vertebrates Works; Sensitivity and Species‐Level Assignment Depend on Amplicon Lengths	27
Evolutionary history and seascape genomics of Harbour porpoises (Phocoena phocoena) across environmental gradients in the North Atlantic and adjacent waters	26
A roadmap to robust discriminant analysis of principal components	26
Do not be scared of the genome's 5th base—Explaining phenotypic variability and evolutionary dynamics through DNA methylation analysis	26
Recovering the genomes hidden in museum wet collections	26
Replicate DNA metabarcoding can discriminate seasonal and spatial abundance shifts in river macroinvertebrate assemblages	26
Allelic bias when performing in‐solution enrichment of ancient human DNA	25
Lessons from assembling UCEs: A comparison of common methods and the case of Clavinomia (Halictidae)	25
Detecting clonemate pairs in multicellular diploid clonal species based on a shared heterozygosity index	25
ParAquaSeq, a Database of Ecologically Annotated rRNA Sequences Covering Zoosporic Parasites Infecting Aquatic Primary Producers in Natural and Industrial Systems	25
Genomic Prediction of Individual Inbreeding Levels for the Management of Genetic Diversity in Populations With Small Effective Size	24
Quantifying uncertainty in inferences of landscape genetic resistance due to choice of individual‐based genetic distance metric	23
Bee foraging preferences, microbiota and pathogens revealed by direct shotgun metagenomics of honey	23
Enhancing metabarcoding efficiency and ecological insights through integrated taxonomy and DNA reference barcoding: A case study on beach meiofauna	23
A consensus protocol for the recovery of mercury methylation genes from metagenomes	23

Genotyping‐in‐thousands by sequencing (GT‐seq) of noninvasive faecal and degraded samples: A new panel to enable ongoing monitoring of Canadian polar bear populations	22
A Long‐Term Ecological Research Data Set From the Marine Genetic Monitoring Program ARMS‐MBON 2018–2020	22
Detection and population genomics of sea turtle species via noninvasive environmental DNA analysis of nesting beach sand tracks and oceanic water	22
Quaternary Habitat Fluctuations and Demographic Dynamics in Turtles Inferred From Environmental Niche Modelling and Whole Genome Data	22
Plastid Genome Assembly Using Long‐read data	22
Environmental RNA can distinguish life stages in amphibian populations	22
SLRfinder: A method to detect candidate sex‐linked regions with linkage disequilibrium clustering	22
Robust, Open‐Source and Automation‐Friendly DNA Extraction Protocol for Hologenomic Research	22
COInr and mkCOInr: Building and customizing a nonredundant barcoding reference database from BOLD and NCBI using a semi‐automated pipeline	22
Non‐invasive age estimation based on faecal DNA using methylation‐sensitive high‐resolution melting for Indo‐Pacific bottlenose dolphins	22
Leveraging an existing whole‐genome resequencing population data set to characterize toll‐like receptor gene diversity in a threatened bird	21
Comparative genomics of a vertically transmitted thiotrophic bacterial ectosymbiont and its close free‐living relative	21
A collaborative backbone resource for comparative studies of subterranean evolution: The World Asellidae database	21
Missing genotype imputation in non‐model species using self‐organizing maps	21
The unknown unknown: A framework for assessing environmental DNA assay specificity against unsampled taxa	21
Phylogenomic and syntenic data demonstrate complex evolutionary processes in early radiation of the rosids	20
FreshOmics: A manually curated and standardized –omics database for investigating freshwater microbiomes	20
Unravelling the Web of Life: Incomplete Lineage Sorting and Hybridisation as Primary Mechanisms Over Polyploidisation in the Evolutionary Dynamics of Pear Species	20
The accuracy of predicting maladaptation to new environments with genomic data	20
New deep learning‐based methods for visualizing ecosystem properties using environmental DNA metabarcoding data	20
Ultraconserved Elements and Machine Learning Classifiers Enable Robust Phylogenetics and Taxonomy in Model and Non‐Model Nematodes	20
Testing the applicability of environmental DNA metabarcoding to landscape genetics	20
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Metabarcoding using nanopore long‐read sequencing for the unbiased characterization of apicomplexan haemoparasites	19
Prey ration, temperature, and predator species influence digestion rates of prey DNA inferred from qPCR and metabarcoding	19
Issue Information	19
Tools and applications for integrative analysis of DNA methylation in social insects	18
Three Novel Spider Genomes Unveil Spidroin Diversification and Hox Cluster Architecture: Ryuthela nishihirai (Liphistiidae), Uloborus plumipes (Uloboridae) and Cheiracanthium punctori	18
MuDoGeR: Multi‐Domain Genome recovery from metagenomes made easy	18
Influence of RNA‐Seq library construction, sampling methods, and tissue harvesting time on gene expression estimation	18
A dynamic ancestral graph model and GPU‐based simulation of a community based on metagenomic sampling	18
Accelerating Moss Identification Through the Development of Specific DNA Barcodes Based on the Whole Chloroplast Genome	18
High‐quality genomes reveal significant genetic divergence and cryptic speciation in the model organism Folsomia candida (collembola)	18
The year of the tiger and the year of tiger genomes!	17
Contemporary issues, current best practice and ways forward in soil protist ecology	17
MOSCA 2.0: A bioinformatics framework for metagenomics, metatranscriptomics and metaproteomics data analysis and visualization	17
CRISPR‐Cas9 enrichment, a new strategy in microbial metagenomics to investigate complex genomic regions: The case of an environmental integron	17
Conservation in a litre of air	17
Assessing the limits of local ancestry inference from small reference panels	17
Detailed DNA barcoding of mayflies in a small European country proved how far we are from having comprehensive barcode reference libraries	17
Beyond Presence and Absence: Using eDNA and Microsatellite Genotyping to Estimate Densities of Microscopic Life Forms in Wild Populations	16
Environmental DNA metabarcoding of freshwater fish in Malaysian tropical rivers using short‐read nanopore sequencing as a potential biomonitoring tool	16
TransPi—a comprehensive TRanscriptome ANalysiS PIpeline for de novo transcriptome assembly	16
The WZA: A window‐based method for characterizing genotype–environment associations	16
RDAforest: Identifying Environmental Drivers of Polygenic Adaptation	16
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Identification and quantification of chimeric sequencing reads in a highly multiplexed RAD‐seq protocol	16
Correcting for Bias in Estimates of θw and Tajima's D From Missing Data in Next‐Generation Sequencing	16
Correction to “epiGBS2: Improvements and Evaluation of Highly Multiplexed, epiGBS‐Based Reduced Representation Bisulfite Sequencing”	16
SEGUL: Ultrafast, memory‐efficient and mobile‐friendly software for manipulating and summarizing phylogenomic datasets	16
Genome architecture used to supplement species delineation in two cryptic marine ciliates	16
Issue Information	16
Launching insectphylo.org; a new hub facilitating construction and use of synthesis molecular phylogenies of insects	16
RNA allows identifying the consumption of carrion prey	15
Who are you? A framework to identify and report genetic sample mix‐ups	15
RIDGE, a tool tailored to detect gene flow barriers across species pairs	15
Genome and gene evolution of seahorse species revealed by the chromosome‐level genome of Hippocampus abdominalis	15
Inferring the timing and strength of natural selection and gene migration in the evolution of chicken from ancient DNA data	15
Validating a Target‐Enrichment Design for Capturing Uniparental Haplotypes in Ancient Domesticated Animals	15
A High‐Throughput Ancient DNA Extraction Method for Large‐Scale Sample Screening	15
Management and conservation implications of cryptic population substructure for two commercially exploited fishes (Merluccius spp.) in southern Africa	14
A molecular‐based identification resource for the arthropods of Finland	14
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DNA barcodes highlight genetic diversity patterns in rodents from lowland desert and Andean areas in Argentina	14
Bayesian StairwayPlot for Inferring Single Population Demographic Histories From Site Frequency Spectra	14
Efficiency of eDNA and iDNA in assessing vertebrate diversity and its abundance	14
Machine Learning Enables Alignment‐Free Distance Calculation and Phylogenetic Placement Using k ‐Mer Frequencies	14
Affordable de novo generation of fish mitogenomes using amplification‐free enrichment of mitochondrial DNA and deep sequencing of long fragments	14
The answer, my friend, is blowin’ in the wind: Blow sampling provides a new dimension to whale population monitoring	14
Species delimitation with limited sampling: An example from rare trapdoor spider genus Cyclocosmia (Mygalomorphae, Halonoproctidae)	14
A Short‐Read Amplicon Sequencing Protocol and Bioinformatic Pipeline for Ecological Surveillance of Dipteran Disease Vectors	14
Machine learning in molecular ecology	14
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A chromosome‐level genome assembly enables the identification of the follicule stimulating hormone receptor as the master sex‐determining gene in the flatfish Solea senegalensis	14
Quantitative assessment of reef foraminifera community from metabarcoding data	13
Express barcoding with NextGenPCR and MinION for species‐level sorting of ecological samples	13
Genomes of Two Monophagous Weevils and Their Host Plant Provide Insights Into Evolution of Plant Defence and Insect Counter‐Defence	13
Next‐generation bioinformatics: An ultrafast and user‐friendly tool for phylogenomic data exploration	13

Comparative genomics reveals the dynamic evolutionary history of cement protein genes of barnacles from intertidal to deep‐sea hydrothermal vents	13
Temporal Variability in Effective Size (N̂e) Identifies Potential Sources of Discrepancies Between Mark Recapture and Close Kin Mark Recapture Estimates of Population Abundance	13
Chromosome‐level genome assembly of Pedicularis kansuensis illuminates genome evolution of facultative parasitic plant	13
An empirical test of the estimation of historical effective population size using Drosophila melanogaster	13
Macrobial airborne environmental DNA analysis: A review of progress, challenges, and recommendations for an emerging application	13
Quantifying Soil Microbiome Abundance by Metatranscriptomics and Complementary Molecular Techniques—Cross‐Validation and Perspectives	13
Environmental DNA phylogeography: Successful reconstruction of phylogeographic patterns of multiple fish species from cups of water	13
Estimation of spatial demographic maps from polymorphism data using a neural network	12
Issue Information	12
Chromosome‐level genome assembly of a triploid poplar Populus alba ‘Berolinensis’	12
A guide to avian museomics: Insights gained from resequencing hundreds of avian study skins	12
Delimiting the rare, endangered and actively speciating	12
Next‐Generation Snow Leopard Population Assessment Tool: Multiplex‐PCR SNP Panel for Individual Identification From Faeces	12
Scaling‐up RADseq methods for large datasets of non‐invasive samples: Lessons for library construction and data preprocessing	12
HMS‐S‐S: A tool for the identification of Sulphur metabolism‐related genes and analysis of operon structures in genome and metagenome assemblies	12
CCS‐Consensuser: A Haplotype‐Aware Consensus Generator for PacBio Amplicon Sequences	12
Utilizing paralogues for phylogenetic reconstruction has the potential to increase species tree support and reduce gene tree discordance in target enrichment data	12
Polly: An R package for genotyping microsatellites and detecting highly polymorphic DNA markers from short‐read data	12
Issue Information	12
A chromosomal level genome sequence for Quasipaa spinosa (Dicroglossidae) reveals chromosomal evolution and population diversity	12
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Genetic variation and domestication of horses revealed by 10 chromosome‐level genomes and whole‐genome resequencing	12
A Novel Protistan Trait Database Reveals Functional Redundancy and Complementarity in Terrestrial Protists (Amoebozoa and Rhizaria)	12
Integration of De Novo Chromosome‐Level Genome and Population Resequencing of Peganum (Nitrariaceae): A Case Study of Speciation and Evolutionary Trajectories in Arid Central Asia	12