Molecular Ecology Resources

Article	Citations
Issue Information	507
A road map for in vivo evolution experiments with blood‐borne parasitic microbes	164
Revisiting the Briggs Ancient DNA Damage Model: A Fast Maximum Likelihood Method to Estimate Post‐Mortem Damage	80
Fast‐tracking bespoke DNA reference database generation from museum collections for biomonitoring and conservation	76
Chromosome‐Level Genome Assembly of the Loach Goby Rhyacichthys aspro Offers Insights Into Gobioid	75
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	67
Characterising Soil Eukaryotic Diversity From NEON Metagenomics Datasets	64
DNA barcoding of Chinese snakes reveals hidden diversity and conservation needs	59
An Accessible Metagenomic Strategy Allows for Better Characterisation of Invertebrate Bulk Samples	58
detectEVE : Fast, Sensitive and Precise Detection of Endogenous Viral Elements in Genomic Data	57
A second unveiling: Haplotig masking of the eastern oyster genome improves population‐level inference	55
Use of 16S rRNA gene sequences to identify cyanobacteria that can grow in far‐red light	54
Molecular diet analysis in mussels and other metazoan filter feeders and an assessment of their utility as natural eDNA samplers	53
Particle size influences decay rates of environmental DNA in aquatic systems	52
Bayesian tests for random mating in polyploids	52
Stomach Content DNA ( scDNA ) Detection and Quantification for Predator Diet Assessment Using High	51
Issue Information	51
GeneMiner2 : Accurate and Automated Recovery of Genes From Genome Skimming Data	50
Collecting baleen whale blow samples by drone: A minimally intrusive tool for conservation genetics	49
The voice of the little giants: Arcellinida testate amoebae in environmental DNA‐based bioindication, from taxonomy free to haplotypic level	49
Issue Information	49
Benchmarking the Mantel test and derived methods for testing association between distance matrices	47
An Innovative Binding‐Protein‐Based dsRNA Extraction Method: Comparison of Cost‐Effectiveness of Virus Detection Methods Using High‐Throughput Sequen	45
metaPR 2 : A database of eukaryotic 18S rRNA	40
Evaluating the use of lake sedimentary DNA in palaeolimnology: A comparison with long‐term microscopy‐based monitoring of the phytoplankton community	40

The topological nature of tag jumping in environmental DNA metabarcoding studies	39
Potential PCR amplification bias in identifying complex ecological patterns: Higher species compositional homogeneity revealed in smaller‐size coral reef zooplankton by metatranscriptomics	38
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Saprotrophic Arachnopeziza Species as New Resources to Study the Obligate Biotrophic Lifestyle of Powdery Mildew Fungi	36
A needle in a haystack: A new metabarcoding approach to survey diversity at the species level of Arcellinida (Amoebozoa: Tubulinea)	36
OligoN‐Design: A Simple and Versatile Tool to Design Specific Probes and Primers From Large Heterogeneous Datasets	35
Simulating plasticity as a framework for understanding habitat selection and its role in adaptive capacity and extinction risk through an expansion of CDMetaPOP	35
Monitoring of multiple fish species by quantitative environmental DNA metabarcoding surveys over two summer seasons	34
Demogenomic inference from spatially and temporally heterogeneous samples	34
Independent Avian Epigenetic Clocks for Ageing and Development	33
Beware of Plant DNA in Animal Dietary Metabarcoding: Lessons From a Strictly Insectivorous Bat	32
MaxTemp : A Method to Maximise Precision of the Temporal Method for Estimating	32
Scaling Up Species Delimitation From DNA Barcodes to Whole Organelle Genomes: Strong Evidence for Discordance Among Genes and Methods for the Red Alg	31
PopGenHelpR : An R Package to Streamline and Facilitate Informed Population Genomic Analyses and Visualization of Genetic Ancestry, Diversity and Differentiation	31
The FORGENIUS Genomic Resources: New Genotyping Tools and Genomic Data for 23 Forest Tree Species and Their Genetic Conservation Units	31
RETRACTION : Age Prediction of Green Turtles With an Epigenetic Clock	31
Towards Large‐Scale Museomics Projects: A Cost‐Effective and High‐Throughput Extraction Method for Obtaining Historical DNA From Museum Insect Specimens	31
Inference of the distribution of fitness effects of mutations is affected by single nucleotide polymorphism filtering methods, sample size and population structure	31
Proteomic fingerprinting enables quantitative biodiversity assessments of species and ontogenetic stages in Calanus congeners (Copepoda, Crustacea) from the Arctic Ocean	30
GenAPoPop 1.0: A user‐friendly software to analyse genetic diversity and structure from partially clonal and selfed autopolyploid organisms	30
Comparative analysis of fish environmental DNA reveals higher sensitivity achieved through targeted sequence‐based metabarcoding	30
The Long and the Short of It: Nanopore‐Based eDNA Metabarcoding of Marine Vertebrates Works; Sensitivity and Species‐Level Assignment Depend on Ampli	29
Evaluating the Benefits and Limits of Multiple Displacement Amplification With Whole‐Genome Oxford Nanopore Sequencing	29
Performance of DNA metabarcoding, standard barcoding and morphological approaches in the identification of insect biodiversity	29
The great tit HapMap project: A continental‐scale analysis of genomic variation in a songbird	28
Methylome Profiling of a Deuterostome Invertebrate Using Oxford Nanopore Technology ( ONT )	28
Species discrimination in Schima (Theaceae): Next‐generation super‐barcodes meet evolutionary complexity	28
Scoop That Poop: Optimising Faecal Sample Pre‐Processing for Parasite Metabarcoding	28
The proof is in the poo: Non‐invasive method to detect endoparasitic infection	27
A Field‐Deployable eDNA Metabarcoding Workflow Including De Novo Reference Assembly for Characterising Understudied Biodiversity Hotspots	27
MycoAI: Fast and accurate taxonomic classification for fungal ITS sequences	27
Chromosome‐level genome of Entada phaseoloides provides insights into genome evolution and biosynthesis of triterpenoid saponins	27
A comprehensive framework for detecting copy number variants from single nucleotide polymorphism data: ‘rCNV’, a versatile r package for paralogue and CNV detection	27
DNA methylation‐based biomarkers for ageing long‐lived cetaceans	26
Comparing eDNA and Transect Methods for Aquatic Biodiversity Assessment in Lakes and Ponds	26
Allelic bias when performing in‐solution enrichment of ancient human DNA	25
Genomic Prediction of Individual Inbreeding Levels for the Management of Genetic Diversity in Populations With Small Effective Size	25
Do not be scared of the genome's 5th base—Explaining phenotypic variability and evolutionary dynamics through DNA methylation analysis	25
Quaternary Habitat Fluctuations and Demographic Dynamics in Turtles Inferred From Environmental Niche Modelling and Whole Genome Data	25
Issue Information	25
A roadmap to robust discriminant analysis of principal components	24
Lessons from assembling UCEs: A comparison of common methods and the case of Clavinomia (Halictidae)	24
A Long‐Term Ecological Research Data Set From the Marine Genetic Monitoring Program ARMS‐MBON 2018–2020	23
Evolutionary history and seascape genomics of Harbour porpoises (Phocoena phocoena) across environmental gradients in the North Atlantic and adjacent waters	23
Reliable Inference of Phylogenomic Relationship via Assembly‐Based Strategy Accommodating Raw Reads and Proteins	23
Detecting clonemate pairs in multicellular diploid clonal species based on a shared heterozygosity index	23
Quantifying uncertainty in inferences of landscape genetic resistance due to choice of individual‐based genetic distance metric	23
Robust, Open‐Source and Automation‐Friendly DNA Extraction Protocol for Hologenomic Research	22
Recovering the genomes hidden in museum wet collections	22
Non‐invasive age estimation based on faecal DNA using methylation‐sensitive high‐resolution melting for Indo‐Pacific bottlenose dolphins	22

Plastid Genome Assembly Using Long‐read data	21
A consensus protocol for the recovery of mercury methylation genes from metagenomes	21
Environmental RNA can distinguish life stages in amphibian populations	21
Evaluating the Molecular Potential and Interpretability of DNA in Historical Spirit Collection Media	20
COInr and mkCOInr : Building and customizing a nonredundant barcoding reference database from	20
FreshOmics: A manually curated and standardized –omics database for investigating freshwater microbiomes	20
Ultraconserved Elements and Machine Learning Classifiers Enable Robust Phylogenetics and Taxonomy in Model and Non‐Model Nematodes	20
Replicate DNA metabarcoding can discriminate seasonal and spatial abundance shifts in river macroinvertebrate assemblages	20
Comparative genomics of a vertically transmitted thiotrophic bacterial ectosymbiont and its close free‐living relative	20
Issue Information	20
New deep learning‐based methods for visualizing ecosystem properties using environmental DNA metabarcoding data	20
Enhancing metabarcoding efficiency and ecological insights through integrated taxonomy and DNA reference barcoding: A case study on beach meiofauna	20
ParAquaSeq, a Database of Ecologically Annotated rRNA Sequences Covering Zoosporic Parasites Infecting Aquatic Primary Producers in Natural and Industrial Systems	20
Phylogenomic and syntenic data demonstrate complex evolutionary processes in early radiation of the rosids	20
SLRfinder : A method to detect candidate sex‐linked regions with linkage disequilibrium clustering	19
Balancing Barcoding and Genomics: gDNA Quality in Insect Vouchers After HotSHOT DNA Extraction	19
The unknown unknown: A framework for assessing environmental DNA assay specificity against unsampled taxa	19
Leveraging an existing whole‐genome resequencing population data set to characterize toll‐like receptor gene diversity in a threatened bird	19
Epigenetic Age Estimation for Hawaiian False Killer Whales ( Pseudorca crassidens ) in the Absence of ‘Known‐Age’ Individuals	19
Testing the applicability of environmental DNA metabarcoding to landscape genetics	18
DNA Barcode Reference Library for European Ants: A Roadmap for Phylogeography and Species Discovery	18
The accuracy of predicting maladaptation to new environments with genomic data	18
Beyond Presence and Absence: Using eDNA and Microsatellite Genotyping to Estimate Densities of Microscopic Life Forms in Wild Populations	18
Missing genotype imputation in non‐model species using self‐organizing maps	18
Metabarcoding using nanopore long‐read sequencing for the unbiased characterization of apicomplexan haemoparasites	18
Unravelling the Web of Life: Incomplete Lineage Sorting and Hybridisation as Primary Mechanisms Over Polyploidisation in the Evolutionary Dynamics of Pear Species	18
A collaborative backbone resource for comparative studies of subterranean evolution: The World Asellidae database	18
Influence of RNA‐Seq library construction, sampling methods, and tissue harvesting time on gene expression estimation	17
Genome architecture used to supplement species delineation in two cryptic marine ciliates	17
Conservation in a litre of air	17
Issue Information	17
Accelerating Moss Identification Through the Development of Specific DNA Barcodes Based on the Whole Chloroplast Genome	17
Correction to “ epiGBS2 : Improvements and Evaluation of Highly Multiplexed, epiGBS ‐Based Reduced	17
High‐quality genomes reveal significant genetic divergence and cryptic speciation in the model organism Folsomia candida (collembola)	17
Launching insectphylo.org; a new hub facilitating construction and use of synthesis molecular phylogenies of insects	17
Three Novel Spider Genomes Unveil Spidroin Diversification and Hox Cluster Architecture: Ryuthela nishihirai (Liphistiidae), Uloborus plumipes (Uloboridae) and Cheiracanthium punctori	16
MOSCA 2.0: A bioinformatics framework for metagenomics, metatranscriptomics and metaproteomics data analysis and visualization	16
CRISPR‐Cas9 enrichment, a new strategy in microbial metagenomics to investigate complex genomic regions: The case of an environmental integron	16
MuDoGeR: Multi‐Domain Genome recovery from metagenomes made easy	16
Detailed DNA barcoding of mayflies in a small European country proved how far we are from having comprehensive barcode reference libraries	16
SEGUL: Ultrafast, memory‐efficient and mobile‐friendly software for manipulating and summarizing phylogenomic datasets	16
RDAforest: Identifying Environmental Drivers of Polygenic Adaptation	16
Identification and quantification of chimeric sequencing reads in a highly multiplexed RAD ‐seq protocol	15
Environmental DNA metabarcoding of freshwater fish in Malaysian tropical rivers using short‐read nanopore sequencing as a potential biomonitoring tool	15
The WZA : A window‐based method for characterizing genotype–environment associations	15
The year of the tiger and the year of tiger genomes!	15
Contemporary issues, current best practice and ways forward in soil protist ecology	15
Correcting for Bias in Estimates of θw and Tajima's D From Missing Data in Next‐Generation Sequencing	15
Assessing the limits of local ancestry inference from small reference panels	15
Correction to “Advancing Yeast Identification Using High‐Throughput DNA Barcode Data From a Curated Culture Collection”	14
Prey ration, temperature, and predator species influence digestion rates of prey DNA inferred from qPCR and metabarcoding	14
RIDGE , a tool tailored to detect gene flow barriers across species pairs	14
A Short‐Read Amplicon Sequencing Protocol and Bioinformatic Pipeline for Ecological Surveillance of Dipteran Disease Vectors	14
A High‐Throughput Ancient DNA Extraction Method for Large‐Scale Sample Screening	14
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Machine Learning Enables Alignment‐Free Distance Calculation and Phylogenetic Placement Using k ‐Mer Frequencies	14
RNA allows identifying the consumption of carrion prey	14
Management and conservation implications of cryptic population substructure for two commercially exploited fishes (Merluccius spp.) in southern Africa	14
Bayesian StairwayPlot for Inferring Single Population Demographic Histories From Site Frequency Spectra	14
Species delimitation with limited sampling: An example from rare trapdoor spider genus Cyclocosmia (Mygalomorphae, Halonoproctidae)	14
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Temporal Variability in Effective Size (N̂e) Identifies Potential Sources of Discrepancies Between Mark Recapture and Close Kin Mark Recapture Estimates of Population Abundance	13
Next‐generation bioinformatics: An ultrafast and user‐friendly tool for phylogenomic data exploration	13
Environmental DNA phylogeography: Successful reconstruction of phylogeographic patterns of multiple fish species from cups of water	13
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Comparative genomics reveals the dynamic evolutionary history of cement protein genes of barnacles from intertidal to deep‐sea hydrothermal vents	13
HMS‐S‐S: A tool for the identification of Sulphur metabolism‐related genes and analysis of operon structures in genome and metagenome assemblies	13
Issue Information	13
Validating a Target‐Enrichment Design for Capturing Uniparental Haplotypes in Ancient Domesticated Animals	13
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Moss‐Accumulated eDNA Is a Promising Source for Terrestrial Biodiversity Surveys Across the Tree of Life and Biomes	13
A Logratio Approach to the Analysis of Autosomal Genotype Frequencies Across Multiple Samples	13
Macrobial airborne environmental DNA analysis: A review of progress, challenges, and recommendations for an emerging application	13
Quantitative assessment of reef foraminifera community from metabarcoding data	12
Scaling‐up RADseq methods for large datasets of non‐invasive samples: Lessons for library construction and data preprocessing	12
The answer, my friend, is blowin’ in the wind: Blow sampling provides a new dimension to whale population monitoring	12
Genetic variation and domestication of horses revealed by 10 chromosome‐level genomes and whole‐genome resequencing	12
Quantifying Soil Microbiome Abundance by Metatranscriptomics and Complementary Molecular Techniques—Cross‐Validation and Perspectives	12
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	12

Genomes of Two Monophagous Weevils and Their Host Plant Provide Insights Into Evolution of Plant Defence and Insect Counter‐Defence	12
Estimation of spatial demographic maps from polymorphism data using a neural network	12
Chromosome‐level genome assembly of Pedicularis kansuensis illuminates genome evolution of facultative parasitic plant	12
Chromosome‐level genome assembly of a triploid poplar Populus alba ‘Berolinensis’	11
Express barcoding with NextGenPCR and MinION for species‐level sorting of ecological samples	11
Polly: An R package for genotyping microsatellites and detecting highly polymorphic DNA markers from short‐read data	11
CCS ‐Consensuser: A Haplotype‐Aware Consensus Generator for PacBio Amplicon Sequences	11
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	11
Application of palaeogenetic techniques to historic mollusc shells reveals phylogeographic structure in a New Zealand abalone	11
Affordable de novo generation of fish mitogenomes using amplification‐free enrichment of mitochondrial DNA and deep sequencing of long fragments	11
A Computational Ecological Genetic Model of Phenotypic Plasticity in Species Interactions	11
Issue Information	11
A Post‐Mortem Molecular Damage Profile in the Ancient Human Mitochondrial DNA	11
Utilizing paralogues for phylogenetic reconstruction has the potential to increase species tree support and reduce gene tree discordance in target enrichment data	11
An empirical test of the estimation of historical effective population size using Drosophila melanogaster	11
Delimiting the rare, endangered and actively speciating	11
MetaZooGene Intercalibration Experiment ( MZG ‐ ICE ): Metabarcodin	11
Chromosome‐level genomes of two armyworms, Mythimna separata and Mythimna loreyi, provide insights into the biosynthesis and reception of sex pheromones	11
Next‐Generation Snow Leopard Population Assessment Tool: Multiplex‐ PCR SNP Panel for Individual Identification From Faeces	11