Molecular Ecology Resources

Article	Citations
Issue Information	541
Revisiting the Briggs Ancient DNA Damage Model: A Fast Maximum Likelihood Method to Estimate Post‐Mortem Damage	183
Chromosome‐Level Genome Assembly of the Loach Goby Rhyacichthys aspro Offers Insights Into Gobioid	83
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	82
Characterising Soil Eukaryotic Diversity From NEON Metagenomics Datasets	71
An Accessible Metagenomic Strategy Allows for Better Characterisation of Invertebrate Bulk Samples	60
A second unveiling: Haplotig masking of the eastern oyster genome improves population‐level inference	60
Bayesian tests for random mating in polyploids	58
Use of 16S rRNA gene sequences to identify cyanobacteria that can grow in far‐red light	58
Issue Information	55
Issue Information	55
The topological nature of tag jumping in environmental DNA metabarcoding studies	53
Evaluating the use of lake sedimentary DNA in palaeolimnology: A comparison with long‐term microscopy‐based monitoring of the phytoplankton community	52
Fast‐tracking bespoke DNA reference database generation from museum collections for biomonitoring and conservation	52
An Innovative Binding‐Protein‐Based dsRNA Extraction Method: Comparison of Cost‐Effectiveness of Virus Detection Methods Using High‐Throughput Sequen	50
detectEVE : Fast, Sensitive and Precise Detection of Endogenous Viral Elements in Genomic Data	49
Stomach Content DNA ( scDNA ) Detection and Quantification for Predator Diet Assessment Using High	48
DNA barcoding of Chinese snakes reveals hidden diversity and conservation needs	48
The Pan‐Genome of 1107 Spotted Sea Bass Accessions Reveals Gene Evolution Patterns During Domestication Selection	41
Benchmarking the Mantel test and derived methods for testing association between distance matrices	41
Issue Information	40
GeneMiner2 : Accurate and Automated Recovery of Genes From Genome Skimming Data	39
The voice of the little giants: Arcellinida testate amoebae in environmental DNA‐based bioindication, from taxonomy free to haplotypic level	37
Collecting baleen whale blow samples by drone: A minimally intrusive tool for conservation genetics	37
Particle size influences decay rates of environmental DNA in aquatic systems	37

Molecular diet analysis in mussels and other metazoan filter feeders and an assessment of their utility as natural eDNA samplers	37
Saprotrophic Arachnopeziza Species as New Resources to Study the Obligate Biotrophic Lifestyle of Powdery Mildew Fungi	36
Potential PCR amplification bias in identifying complex ecological patterns: Higher species compositional homogeneity revealed in smaller‐size coral reef zooplankton by metatranscriptomics	36
	36
MaxTemp : A Method to Maximise Precision of the Temporal Method for Estimating	35
Beware of Plant DNA in Animal Dietary Metabarcoding: Lessons From a Strictly Insectivorous Bat	34
Inference of the distribution of fitness effects of mutations is affected by single nucleotide polymorphism filtering methods, sample size and population structure	34
Monitoring of multiple fish species by quantitative environmental DNA metabarcoding surveys over two summer seasons	33
RETRACTION : Age Prediction of Green Turtles With an Epigenetic Clock	33
Simulating plasticity as a framework for understanding habitat selection and its role in adaptive capacity and extinction risk through an expansion of CDMetaPOP	32
The FORGENIUS Genomic Resources: New Genotyping Tools and Genomic Data for 23 Forest Tree Species and Their Genetic Conservation Units	32
OligoN‐Design: A Simple and Versatile Tool to Design Specific Probes and Primers From Large Heterogeneous Datasets	32
PopGenHelpR : An R Package to Streamline and Facilitate Informed Population Genomic Analyses and Visualization of Genetic Ancestry, Diversity and Differentiation	32
Independent Avian Epigenetic Clocks for Ageing and Development	31
Demogenomic inference from spatially and temporally heterogeneous samples	31
GenAPoPop 1.0: A user‐friendly software to analyse genetic diversity and structure from partially clonal and selfed autopolyploid organisms	30
A needle in a haystack: A new metabarcoding approach to survey diversity at the species level of Arcellinida (Amoebozoa: Tubulinea)	30
Towards Large‐Scale Museomics Projects: A Cost‐Effective and High‐Throughput Extraction Method for Obtaining Historical DNA From Museum Insect Specimens	30
Proteomic fingerprinting enables quantitative biodiversity assessments of species and ontogenetic stages in Calanus congeners (Copepoda, Crustacea) from the Arctic Ocean	29
The proof is in the poo: Non‐invasive method to detect endoparasitic infection	28
Evaluating the Benefits and Limits of Multiple Displacement Amplification With Whole‐Genome Oxford Nanopore Sequencing	27
A Field‐Deployable eDNA Metabarcoding Workflow Including De Novo Reference Assembly for Characterising Understudied Biodiversity Hotspots	27
Scoop That Poop: Optimising Faecal Sample Pre‐Processing for Parasite Metabarcoding	27
DNA methylation‐based biomarkers for ageing long‐lived cetaceans	26
Methylome Profiling of a Deuterostome Invertebrate Using Oxford Nanopore Technology ( ONT )	26
The Long and the Short of It: Nanopore‐Based eDNA Metabarcoding of Marine Vertebrates Works; Sensitivity and Species‐Level Assignment Depend on Ampli	26
A comprehensive framework for detecting copy number variants from single nucleotide polymorphism data: ‘rCNV’, a versatile r package for paralogue and CNV detection	26
MycoAI: Fast and accurate taxonomic classification for fungal ITS sequences	25
The great tit HapMap project: A continental‐scale analysis of genomic variation in a songbird	24
Wild Pedigree exploreR (wpeR): Streamlined Analysis and Visualization of Wild Pedigrees in Time and Space	24
Scaling Up Species Delimitation From DNA Barcodes to Whole Organelle Genomes: Strong Evidence for Discordance Among Genes and Methods for the Red Alg	24
Comparing eDNA and Transect Methods for Aquatic Biodiversity Assessment in Lakes and Ponds	23
Performance of DNA metabarcoding, standard barcoding and morphological approaches in the identification of insect biodiversity	23
Issue Information	22
Genomic Prediction of Individual Inbreeding Levels for the Management of Genetic Diversity in Populations With Small Effective Size	22
Comparative analysis of fish environmental DNA reveals higher sensitivity achieved through targeted sequence‐based metabarcoding	22
Do not be scared of the genome's 5th base—Explaining phenotypic variability and evolutionary dynamics through DNA methylation analysis	22
ParAquaSeq, a Database of Ecologically Annotated rRNA Sequences Covering Zoosporic Parasites Infecting Aquatic Primary Producers in Natural and Industrial Systems	21
Robust, Open‐Source and Automation‐Friendly DNA Extraction Protocol for Hologenomic Research	21
Quaternary Habitat Fluctuations and Demographic Dynamics in Turtles Inferred From Environmental Niche Modelling and Whole Genome Data	21
Allelic bias when performing in‐solution enrichment of ancient human DNA	21
Evaluating the Molecular Potential and Interpretability of DNA in Historical Spirit Collection Media	21
Reliable Inference of Phylogenomic Relationship via Assembly‐Based Strategy Accommodating Raw Reads and Proteins	21
A consensus protocol for the recovery of mercury methylation genes from metagenomes	21
Non‐invasive age estimation based on faecal DNA using methylation‐sensitive high‐resolution melting for Indo‐Pacific bottlenose dolphins	21
Replicate DNA metabarcoding can discriminate seasonal and spatial abundance shifts in river macroinvertebrate assemblages	21
A roadmap to robust discriminant analysis of principal components	21
COInr and mkCOInr : Building and customizing a nonredundant barcoding reference database from	21
Evolutionary history and seascape genomics of Harbour porpoises (Phocoena phocoena) across environmental gradients in the North Atlantic and adjacent waters	20
A Long‐Term Ecological Research Data Set From the Marine Genetic Monitoring Program ARMS‐MBON 2018–2020	20

Enhancing metabarcoding efficiency and ecological insights through integrated taxonomy and DNA reference barcoding: A case study on beach meiofauna	20
Environmental RNA can distinguish life stages in amphibian populations	20
Quantifying uncertainty in inferences of landscape genetic resistance due to choice of individual‐based genetic distance metric	20
Detecting clonemate pairs in multicellular diploid clonal species based on a shared heterozygosity index	20
Plastid Genome Assembly Using Long‐read data	19
Issue Information	19
Comparative genomics of a vertically transmitted thiotrophic bacterial ectosymbiont and its close free‐living relative	19
FreshOmics: A manually curated and standardized –omics database for investigating freshwater microbiomes	19
Lessons from assembling UCEs: A comparison of common methods and the case of Clavinomia (Halictidae)	19
Correction to “Complete Mitochondrial Genomes of Eleven Extinct or Possibly Extinct Bird Species”	19
Missing genotype imputation in non‐model species using self‐organizing maps	18
SLRfinder : A method to detect candidate sex‐linked regions with linkage disequilibrium clustering	18
A collaborative backbone resource for comparative studies of subterranean evolution: The World Asellidae database	18
Ultraconserved Elements and Machine Learning Classifiers Enable Robust Phylogenetics and Taxonomy in Model and Non‐Model Nematodes	18
Epigenetic Age Estimation for Hawaiian False Killer Whales ( Pseudorca crassidens ) in the Absence of ‘Known‐Age’ Individuals	18
Balancing Barcoding and Genomics: gDNA Quality in Insect Vouchers After HotSHOT DNA Extraction	18
The accuracy of predicting maladaptation to new environments with genomic data	17
Metabarcoding using nanopore long‐read sequencing for the unbiased characterization of apicomplexan haemoparasites	17
Phylogenomic and syntenic data demonstrate complex evolutionary processes in early radiation of the rosids	17
Testing the applicability of environmental DNA metabarcoding to landscape genetics	17
New deep learning‐based methods for visualizing ecosystem properties using environmental DNA metabarcoding data	17
Unravelling the Web of Life: Incomplete Lineage Sorting and Hybridisation as Primary Mechanisms Over Polyploidisation in the Evolutionary Dynamics of Pear Species	17
DNA Barcode Reference Library for European Ants: A Roadmap for Phylogeography and Species Discovery	17
Fragmentation of Long Reads Enables Reliable Mitogenome Assembly From Whole‐Genome Amplification Data With Pervasive Palindromic Reads	16
Correction to “ epiGBS2 : Improvements and Evaluation of Highly Multiplexed, epiGBS ‐Based Reduced	16
The unknown unknown: A framework for assessing environmental DNA assay specificity against unsampled taxa	16
High‐quality genomes reveal significant genetic divergence and cryptic speciation in the model organism Folsomia candida (collembola)	16
Beyond Presence and Absence: Using eDNA and Microsatellite Genotyping to Estimate Densities of Microscopic Life Forms in Wild Populations	16
Assessing the limits of local ancestry inference from small reference panels	15
The year of the tiger and the year of tiger genomes!	15
Issue Information	15
Prey ration, temperature, and predator species influence digestion rates of prey DNA inferred from qPCR and metabarcoding	15
Accelerating Moss Identification Through the Development of Specific DNA Barcodes Based on the Whole Chloroplast Genome	15
RDAforest: Identifying Environmental Drivers of Polygenic Adaptation	15
Three Novel Spider Genomes Unveil Spidroin Diversification and Hox Cluster Architecture: Ryuthela nishihirai (Liphistiidae), Uloborus plumipes (Uloboridae) and Cheiracanthium punctori	15
MOSCA 2.0: A bioinformatics framework for metagenomics, metatranscriptomics and metaproteomics data analysis and visualization	15
Influence of RNA‐Seq library construction, sampling methods, and tissue harvesting time on gene expression estimation	15
CRISPR‐Cas9 enrichment, a new strategy in microbial metagenomics to investigate complex genomic regions: The case of an environmental integron	14
Contemporary issues, current best practice and ways forward in soil protist ecology	14
The WZA : A window‐based method for characterizing genotype–environment associations	14
MuDoGeR: Multi‐Domain Genome recovery from metagenomes made easy	14
Launching insectphylo.org; a new hub facilitating construction and use of synthesis molecular phylogenies of insects	14
Detailed DNA barcoding of mayflies in a small European country proved how far we are from having comprehensive barcode reference libraries	14
Environmental DNA metabarcoding of freshwater fish in Malaysian tropical rivers using short‐read nanopore sequencing as a potential biomonitoring tool	14
Conservation in a litre of air	13
Moss‐Accumulated eDNA Is a Promising Source for Terrestrial Biodiversity Surveys Across the Tree of Life and Biomes	13
Correction to “Advancing Yeast Identification Using High‐Throughput DNA Barcode Data From a Curated Culture Collection”	13
SEGUL: Ultrafast, memory‐efficient and mobile‐friendly software for manipulating and summarizing phylogenomic datasets	13
Management and conservation implications of cryptic population substructure for two commercially exploited fishes (Merluccius spp.) in southern Africa	13
Machine Learning Enables Alignment‐Free Distance Calculation and Phylogenetic Placement Using k ‐Mer Frequencies	13
Correcting for Bias in Estimates of θw and Tajima's D From Missing Data in Next‐Generation Sequencing	13
	13
Validating a Target‐Enrichment Design for Capturing Uniparental Haplotypes in Ancient Domesticated Animals	13
A Short‐Read Amplicon Sequencing Protocol and Bioinformatic Pipeline for Ecological Surveillance of Dipteran Disease Vectors	12
RIDGE , a tool tailored to detect gene flow barriers across species pairs	12
From Gene Copies to Cell Numbers: Advancing Quantitative Approaches in Protistan Ecology Using Digital PCR	12
	12
	12
Species delimitation with limited sampling: An example from rare trapdoor spider genus Cyclocosmia (Mygalomorphae, Halonoproctidae)	12
Genome Assemblies for Seven Families of Birds From the Global South	12
A High‐Throughput Ancient DNA Extraction Method for Large‐Scale Sample Screening	12
	12
Bayesian StairwayPlot for Inferring Single Population Demographic Histories From Site Frequency Spectra	12
Individual Identification of Prey in Carnivore Scats	12
	12
Temporal Variability in Effective Size (N̂e) Identifies Potential Sources of Discrepancies Between Mark Recapture and Close Kin Mark Recapture Estimates of Population Abundance	12
A Logratio Approach to the Analysis of Autosomal Genotype Frequencies Across Multiple Samples	11
Macrobial airborne environmental DNA analysis: A review of progress, challenges, and recommendations for an emerging application	11
Quantitative assessment of reef foraminifera community from metabarcoding data	11
Estimation of spatial demographic maps from polymorphism data using a neural network	11
An empirical test of the estimation of historical effective population size using Drosophila melanogaster	11
Chromosome‐level genome assembly of Pedicularis kansuensis illuminates genome evolution of facultative parasitic plant	11
Genetic variation and domestication of horses revealed by 10 chromosome‐level genomes and whole‐genome resequencing	11
Next‐generation bioinformatics: An ultrafast and user‐friendly tool for phylogenomic data exploration	11
Scaling‐up RADseq methods for large datasets of non‐invasive samples: Lessons for library construction and data preprocessing	11
Quantifying Soil Microbiome Abundance by Metatranscriptomics and Complementary Molecular Techniques—Cross‐Validation and Perspectives	11
Issue Information	11
Genomes of Two Monophagous Weevils and Their Host Plant Provide Insights Into Evolution of Plant Defence and Insect Counter‐Defence	11
The answer, my friend, is blowin’ in the wind: Blow sampling provides a new dimension to whale population monitoring	11
Environmental DNA phylogeography: Successful reconstruction of phylogeographic patterns of multiple fish species from cups of water	11

Delimiting the rare, endangered and actively speciating	10
Express barcoding with NextGenPCR and MinION for species‐level sorting of ecological samples	10
Issue Information	10
CCS ‐Consensuser: A Haplotype‐Aware Consensus Generator for PacBio Amplicon Sequences	10
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	10
Next‐Generation Snow Leopard Population Assessment Tool: Multiplex‐ PCR SNP Panel for Individual Identification From Faeces	10
A Post‐Mortem Molecular Damage Profile in the Ancient Human Mitochondrial DNA	10
Affordable de novo generation of fish mitogenomes using amplification‐free enrichment of mitochondrial DNA and deep sequencing of long fragments	10
Comparative genomics reveals the dynamic evolutionary history of cement protein genes of barnacles from intertidal to deep‐sea hydrothermal vents	10
A Computational Ecological Genetic Model of Phenotypic Plasticity in Species Interactions	10
A Novel Protistan Trait Database Reveals Functional Redundancy and Complementarity in Terrestrial Protists (Amoebozoa and Rhizaria)	10
Chromosome‐level genomes of two armyworms, Mythimna separata and Mythimna loreyi, provide insights into the biosynthesis and reception of sex pheromones	10
Polly: An R package for genotyping microsatellites and detecting highly polymorphic DNA markers from short‐read data	10
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	10
Comparison of Environmental DNA and Bulk DNA Metabarcoding for Assessing Terrestrial Arthropod Div	10
Navigating Cetacean Mitochondrial Genome Data: Identifying Coverage and Deficiencies in Public Repositories	10
Application of palaeogenetic techniques to historic mollusc shells reveals phylogeographic structure in a New Zealand abalone	10
Chromosome‐level genome assembly of a triploid poplar Populus alba ‘Berolinensis’	10
MetaZooGene Intercalibration Experiment ( MZG ‐ ICE ): Metabarcodin	10