Molecular Ecology Resources

Article	Citations
Molecular diet analysis in mussels and other metazoan filter feeders and an assessment of their utility as natural eDNA samplers	393
Bayesian tests for random mating in polyploids	97
Chromosome‐Level Genome Assembly of the Loach Goby Rhyacichthys aspro Offers Insights Into Gobioidei Evolution	75
Stomach Content DNA (scDNA) Detection and Quantification for Predator Diet Assessment Using High‐Throughput Nanofluidic Chip Technology: Species‐Specific qPCR Assay Pa	74
Benchmarking the Mantel test and derived methods for testing association between distance matrices	67
Evaluating the use of lake sedimentary DNA in palaeolimnology: A comparison with long‐term microscopy‐based monitoring of the phytoplankton community	63
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	62
Collecting baleen whale blow samples by drone: A minimally intrusive tool for conservation genetics	59
Fast‐tracking bespoke DNA reference database generation from museum collections for biomonitoring and conservation	58
detectEVE: Fast, Sensitive and Precise Detection of Endogenous Viral Elements in Genomic Data	56
Revisiting the Briggs Ancient DNA Damage Model: A Fast Maximum Likelihood Method to Estimate Post‐Mortem Damage	52
A road map for in vivo evolution experiments with blood‐borne parasitic microbes	49
Issue Information	49
A chromosome‐scale genome assembly and annotation of the spring orchid (Cymbidium goeringii)	48
The topological nature of tag jumping in environmental DNA metabarcoding studies	47
metaPR2: A database of eukaryotic 18S rRNA metabarcodes with an emphasis on protists	45
Use of 16S rRNA gene sequences to identify cyanobacteria that can grow in far‐red light	44
An Accessible Metagenomic Strategy Allows for Better Characterisation of Invertebrate Bulk Samples	43
DNA barcoding of Chinese snakes reveals hidden diversity and conservation needs	43
The voice of the little giants: Arcellinida testate amoebae in environmental DNA‐based bioindication, from taxonomy free to haplotypic level	42
Particle size influences decay rates of environmental DNA in aquatic systems	42
Good from far, but far from good: The impact of a reference genome on evolutionary inference	41
A second unveiling: Haplotig masking of the eastern oyster genome improves population‐level inference	41
Chromosome‐scale assembly and whole‐genome sequencing of 266 giant panda roundworms provide insights into their evolution, adaptation and potential drug targets	40
An Innovative Binding‐Protein‐Based dsRNA Extraction Method: Comparison of Cost‐Effectiveness of Virus Detection Methods Using High‐Throughput Sequencing	39

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Independent Avian Epigenetic Clocks for Ageing and Development	38
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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	37
Simulating plasticity as a framework for understanding habitat selection and its role in adaptive capacity and extinction risk through an expansion of CDMetaPOP	36
Beware of Plant DNA in Animal Dietary Metabarcoding: Lessons From a Strictly Insectivorous Bat	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
RETRACTION: Age Prediction of Green Turtles With an Epigenetic Clock	35
Potential PCR amplification bias in identifying complex ecological patterns: Higher species compositional homogeneity revealed in smaller‐size coral reef zooplankton by metatranscriptomics	35
MaxTemp: A Method to Maximise Precision of the Temporal Method for Estimating Ne in Genetic Monitoring Programs	35
Monitoring of multiple fish species by quantitative environmental DNA metabarcoding surveys over two summer seasons	35
Chromosome‐level genome assembly reveals genomic architecture of northern range expansion in the mountain pine beetle, Dendroctonus ponderosae Hopkins (Coleoptera: Curculionidae)	34
Fishing for DNA? Designing baits for population genetics in target enrichment experiments: Guidelines, considerations and the new tool supeRbaits	34
Demogenomic inference from spatially and temporally heterogeneous samples	34
Towards Large‐Scale Museomics Projects: A Cost‐Effective and High‐Throughput Extraction Method for Obtaining Historical DNA From Museum Insect Specimens	34
MycoAI: Fast and accurate taxonomic classification for fungal ITS sequences	32
A needle in a haystack: A new metabarcoding approach to survey diversity at the species level of Arcellinida (Amoebozoa: Tubulinea)	32
A comprehensive framework for detecting copy number variants from single nucleotide polymorphism data: ‘rCNV’, a versatile r package for paralogue and CNV detection	32
Cover Image	32
When barcoding fails: Genome chimerization (admixing) and reticulation obscure phylogenetic and taxonomic relationships	32
Deciphering the molecular signal from past and alive bacterial communities in aquatic sedimentary archives	32
Assessing the impact of USER‐treatment on hyRAD capture applied to ancient DNA	31
Proteomic fingerprinting enables quantitative biodiversity assessments of species and ontogenetic stages in Calanus congeners (Copepoda, Crustacea) from the Arctic Ocean	31
Comparing eDNA and Transect Methods for Aquatic Biodiversity Assessment in Lakes and Ponds	31
The proof is in the poo: Non‐invasive method to detect endoparasitic infection	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)	30
The great tit HapMap project: A continental‐scale analysis of genomic variation in a songbird	29
Species discrimination in Schima (Theaceae): Next‐generation super‐barcodes meet evolutionary complexity	29
Strategies for sample labelling and library preparation in DNA metabarcoding studies	28
Scaling Up Species Delimitation From DNA Barcodes to Whole Organelle Genomes: Strong Evidence for Discordance Among Genes and Methods for the Red Alga Dasyclonium	28
DNA methylation‐based biomarkers for ageing long‐lived cetaceans	27
Evaluating the Benefits and Limits of Multiple Displacement Amplification With Whole‐Genome Oxford Nanopore Sequencing	27
Quaternary Habitat Fluctuations and Demographic Dynamics in Turtles Inferred From Environmental Niche Modelling and Whole Genome Data	27
GenAPoPop 1.0: A user‐friendly software to analyse genetic diversity and structure from partially clonal and selfed autopolyploid organisms	27
Comparative analysis of fish environmental DNA reveals higher sensitivity achieved through targeted sequence‐based metabarcoding	27
Robust, Open‐Source and Automation‐Friendly DNA Extraction Protocol for Hologenomic Research	27
Batch effects in population genomic studies with low‐coverage whole genome sequencing data: Causes, detection and mitigation	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
Issue Information	27
Performance of DNA metabarcoding, standard barcoding and morphological approaches in the identification of insect biodiversity	27
A roadmap to robust discriminant analysis of principal components	26
Non‐invasive age estimation based on faecal DNA using methylation‐sensitive high‐resolution melting for Indo‐Pacific bottlenose dolphins	26
Coalescent‐based species delimitation meets deep learning: Insights from a highly fragmented cactus system	25
A consensus protocol for the recovery of mercury methylation genes from metagenomes	25
Do not be scared of the genome's 5th base—Explaining phenotypic variability and evolutionary dynamics through DNA methylation analysis	25
Plastid Genome Assembly Using Long‐read data	25
Replicate DNA metabarcoding can discriminate seasonal and spatial abundance shifts in river macroinvertebrate assemblages	25
Improved high‐throughput MHC typing for non‐model species using long‐read sequencing	25
Allelic bias when performing in‐solution enrichment of ancient human DNA	24

Evolutionary history and seascape genomics of Harbour porpoises (Phocoena phocoena) across environmental gradients in the North Atlantic and adjacent waters	24
ParAquaSeq, a Database of Ecologically Annotated rRNA Sequences Covering Zoosporic Parasites Infecting Aquatic Primary Producers in Natural and Industrial Systems	24
Recovering the genomes hidden in museum wet collections	24
A Long‐Term Ecological Research Data Set From the Marine Genetic Monitoring Program ARMS‐MBON 2018–2020	24
Detection and population genomics of sea turtle species via noninvasive environmental DNA analysis of nesting beach sand tracks and oceanic water	23
Genomic Prediction of Individual Inbreeding Levels for the Management of Genetic Diversity in Populations With Small Effective Size	23
Detecting clonemate pairs in multicellular diploid clonal species based on a shared heterozygosity index	23
Lessons from assembling UCEs: A comparison of common methods and the case of Clavinomia (Halictidae)	23
Environmental RNA can distinguish life stages in amphibian populations	22
COInr and mkCOInr: Building and customizing a nonredundant barcoding reference database from BOLD and NCBI using a semi‐automated pipeline	22
Bee foraging preferences, microbiota and pathogens revealed by direct shotgun metagenomics of honey	22
Enhancing metabarcoding efficiency and ecological insights through integrated taxonomy and DNA reference barcoding: A case study on beach meiofauna	22
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
Comparative genomics of a vertically transmitted thiotrophic bacterial ectosymbiont and its close free‐living relative	21
Issue Information	21
SLRfinder: A method to detect candidate sex‐linked regions with linkage disequilibrium clustering	21
The unknown unknown: A framework for assessing environmental DNA assay specificity against unsampled taxa	21
Quantifying uncertainty in inferences of landscape genetic resistance due to choice of individual‐based genetic distance metric	21
Phylogenomic and syntenic data demonstrate complex evolutionary processes in early radiation of the rosids	21
Metabarcoding using nanopore long‐read sequencing for the unbiased characterization of apicomplexan haemoparasites	20
Testing the applicability of environmental DNA metabarcoding to landscape genetics	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
Leveraging an existing whole‐genome resequencing population data set to characterize toll‐like receptor gene diversity in a threatened bird	20
A collaborative backbone resource for comparative studies of subterranean evolution: The World Asellidae database	20
FreshOmics: A manually curated and standardized –omics database for investigating freshwater microbiomes	20
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Missing genotype imputation in non‐model species using self‐organizing maps	19
Environmental DNA metabarcoding of freshwater fish in Malaysian tropical rivers using short‐read nanopore sequencing as a potential biomonitoring tool	19
Unlocking inaccessible historical genomes preserved in formalin	19
Prey ration, temperature, and predator species influence digestion rates of prey DNA inferred from qPCR and metabarcoding	19
Unravelling the Web of Life: Incomplete Lineage Sorting and Hybridisation as Primary Mechanisms Over Polyploidisation in the Evolutionary Dynamics of Pear Species	19
RDAforest: Identifying Environmental Drivers of Polygenic Adaptation	18
Accelerating Moss Identification Through the Development of Specific DNA Barcodes Based on the Whole Chloroplast Genome	18
Influence of RNA‐Seq library construction, sampling methods, and tissue harvesting time on gene expression estimation	18
Using metatranscriptomics to estimate the diversity and composition of zooplankton communities	18
Genome architecture used to supplement species delineation in two cryptic marine ciliates	18
A bioinformatic toolkit to simultaneously identify sex and sex‐linked regions	18
A dynamic ancestral graph model and GPU‐based simulation of a community based on metagenomic sampling	18
MuDoGeR: Multi‐Domain Genome recovery from metagenomes made easy	18
Tools and applications for integrative analysis of DNA methylation in social insects	18
The year of the tiger and the year of tiger genomes!	18
Issue Information	17
Assessing the limits of local ancestry inference from small reference panels	17
Identification and quantification of chimeric sequencing reads in a highly multiplexed RAD‐seq protocol	17
Correction to “epiGBS2: Improvements and Evaluation of Highly Multiplexed, epiGBS‐Based Reduced Representation Bisulfite Sequencing”	17
CRISPR‐Cas9 enrichment, a new strategy in microbial metagenomics to investigate complex genomic regions: The case of an environmental integron	17
The WZA: A window‐based method for characterizing genotype–environment associations	16
TransPi—a comprehensive TRanscriptome ANalysiS PIpeline for de novo transcriptome assembly	16
Conservation in a litre of air	16
Contemporary issues, current best practice and ways forward in soil protist ecology	16
Beyond Presence and Absence: Using eDNA and Microsatellite Genotyping to Estimate Densities of Microscopic Life Forms in Wild Populations	16
MOSCA 2.0: A bioinformatics framework for metagenomics, metatranscriptomics and metaproteomics data analysis and visualization	16
SEGUL: Ultrafast, memory‐efficient and mobile‐friendly software for manipulating and summarizing phylogenomic datasets	16
Correcting for Bias in Estimates of θw and Tajima's D From Missing Data in Next‐Generation Sequencing	16
Three Novel Spider Genomes Unveil Spidroin Diversification and Hox Cluster Architecture: Ryuthela nishihirai (Liphistiidae), Uloborus plumipes (Uloboridae) and Cheiracanthium punctori	16
High‐quality genomes reveal significant genetic divergence and cryptic speciation in the model organism Folsomia candida (collembola)	16
Launching insectphylo.org; a new hub facilitating construction and use of synthesis molecular phylogenies of insects	16
Detailed DNA barcoding of mayflies in a small European country proved how far we are from having comprehensive barcode reference libraries	15
RNA allows identifying the consumption of carrion prey	15
Validating a Target‐Enrichment Design for Capturing Uniparental Haplotypes in Ancient Domesticated Animals	15
A Short‐Read Amplicon Sequencing Protocol and Bioinformatic Pipeline for Ecological Surveillance of Dipteran Disease Vectors	15
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Inferring the timing and strength of natural selection and gene migration in the evolution of chicken from ancient DNA data	15
A High‐Throughput Ancient DNA Extraction Method for Large‐Scale Sample Screening	15
Machine learning in molecular ecology	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
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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	14
Genomes of Two Monophagous Weevils and Their Host Plant Provide Insights Into Evolution of Plant Defence and Insect Counter‐Defence	14
Express barcoding with NextGenPCR and MinION for species‐level sorting of ecological samples	14
Genome and gene evolution of seahorse species revealed by the chromosome‐level genome of Hippocampus abdominalis	14
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HMS‐S‐S: A tool for the identification of Sulphur metabolism‐related genes and analysis of operon structures in genome and metagenome assemblies	14
Comparative genomics reveals the dynamic evolutionary history of cement protein genes of barnacles from intertidal to deep‐sea hydrothermal vents	14
Quantifying Soil Microbiome Abundance by Metatranscriptomics and Complementary Molecular Techniques—Cross‐Validation and Perspectives	14
Estimation of spatial demographic maps from polymorphism data using a neural network	14
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A molecular‐based identification resource for the arthropods of Finland	14

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Management and conservation implications of cryptic population substructure for two commercially exploited fishes (Merluccius spp.) in southern Africa	14
Chromosome‐level genome assembly of Pedicularis kansuensis illuminates genome evolution of facultative parasitic plant	14
Species delimitation with limited sampling: An example from rare trapdoor spider genus Cyclocosmia (Mygalomorphae, Halonoproctidae)	14
Next‐generation bioinformatics: An ultrafast and user‐friendly tool for phylogenomic data exploration	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
An empirical test of the estimation of historical effective population size using Drosophila melanogaster	13
Affordable de novo generation of fish mitogenomes using amplification‐free enrichment of mitochondrial DNA and deep sequencing of long fragments	13
Genetic variation and domestication of horses revealed by 10 chromosome‐level genomes and whole‐genome resequencing	13
Environmental DNA phylogeography: Successful reconstruction of phylogeographic patterns of multiple fish species from cups of water	13
Quantitative assessment of reef foraminifera community from metabarcoding data	13
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	13
Macrobial airborne environmental DNA analysis: A review of progress, challenges, and recommendations for an emerging application	13
Chromosome‐level genome assembly of the mirid predator Cyrtorhinus lividipennis Reuter (Hemiptera: Miridae), an important natural enemy in the rice ecosystem	13
The answer, my friend, is blowin’ in the wind: Blow sampling provides a new dimension to whale population monitoring	13
DNA barcodes highlight genetic diversity patterns in rodents from lowland desert and Andean areas in Argentina	13
Delimiting the rare, endangered and actively speciating	12
A Post‐Mortem Molecular Damage Profile in the Ancient Human Mitochondrial DNA	12
Scaling‐up RADseq methods for large datasets of non‐invasive samples: Lessons for library construction and data preprocessing	12
Chromosome‐level genomes of two armyworms, Mythimna separata and Mythimna loreyi, provide insights into the biosynthesis and reception of sex pheromones	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
Application of palaeogenetic techniques to historic mollusc shells reveals phylogeographic structure in a New Zealand abalone	12
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CCS‐Consensuser: A Haplotype‐Aware Consensus Generator for PacBio Amplicon Sequences	12
Phylogenomic analyses of the genusDrosophilareveals genomic signals of climate adaptation	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
Next‐Generation Snow Leopard Population Assessment Tool: Multiplex‐PCR SNP Panel for Individual Identification From Faeces	12
Issue Information	12
A chromosomal level genome sequence for Quasipaa spinosa (Dicroglossidae) reveals chromosomal evolution and population diversity	12
Chromosome‐level genome assembly of a triploid poplar Populus alba ‘Berolinensis’	12
Taxon‐specific or universal? Using target capture to study the evolutionary history of rapid radiations	12