Molecular Ecology Resources

Article	Citations
Bayesian tests for random mating in polyploids	334
A road map for in vivo evolution experiments with blood‐borne parasitic microbes	95
Issue Information	70
Good from far, but far from good: The impact of a reference genome on evolutionary inference	64
The endangered White Sands pupfish (Cyprinodon tularosa) genome reveals low diversity and heterogenous patterns of differentiation	62
Chromosome‐Level Genome Assembly of the Loach Goby Rhyacichthys aspro Offers Insights Into Gobioidei Evolution	61
Revisiting the Briggs Ancient DNA Damage Model: A Fast Maximum Likelihood Method to Estimate Post‐Mortem Damage	61
Evaluating the use of lake sedimentary DNA in palaeolimnology: A comparison with long‐term microscopy‐based monitoring of the phytoplankton community	59
The voice of the little giants: Arcellinida testate amoebae in environmental DNA‐based bioindication, from taxonomy free to haplotypic level	59
Chromosome‐scale assembly and whole‐genome sequencing of 266 giant panda roundworms provide insights into their evolution, adaptation and potential drug targets	58
detectEVE: Fast, Sensitive and Precise Detection of Endogenous Viral Elements in Genomic Data	50
Stomach Content DNA (scDNA) Detection and Quantification for Predator Diet Assessment Using High‐Throughput Nanofluidic Chip Technology: Species‐Specific qPCR Assay Pa	50
Benchmarking the Mantel test and derived methods for testing association between distance matrices	50
Molecular assays of pollen use consistently reflect pollinator visitation patterns in a system of flowering plants	45
Fast‐tracking bespoke DNA reference database generation from museum collections for biomonitoring and conservation	44
Molecular diet analysis in mussels and other metazoan filter feeders and an assessment of their utility as natural eDNA samplers	43
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	43
DNA barcoding of Chinese snakes reveals hidden diversity and conservation needs	42
A chromosome‐scale genome assembly and annotation of the spring orchid (Cymbidium goeringii)	42
Use of 16S rRNA gene sequences to identify cyanobacteria that can grow in far‐red light	42
metaPR2: A database of eukaryotic 18S rRNA metabarcodes with an emphasis on protists	40
Alignment‐free methods for polyploid genomes: Quick and reliable genetic distance estimation	40
Collecting baleen whale blow samples by drone: A minimally intrusive tool for conservation genetics	39
A second unveiling: Haplotig masking of the eastern oyster genome improves population‐level inference	39
Particle size influences decay rates of environmental DNA in aquatic systems	38

The topological nature of tag jumping in environmental DNA metabarcoding studies	38
Potential PCR amplification bias in identifying complex ecological patterns: Higher species compositional homogeneity revealed in smaller‐size coral reef zooplankton by metatranscriptomics	37
MaxTemp: A Method to Maximise Precision of the Temporal Method for Estimating Ne in Genetic Monitoring Programs	37
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Chromosome‐level genome assembly reveals genomic architecture of northern range expansion in the mountain pine beetle, Dendroctonus ponderosae Hopkins (Coleoptera: Curculionidae)	35
The chromosome‐scale assembly of the Canary Islands endemic spiderDysdera silvatica(Arachnida, Araneae) sheds light on the origin and genome structure of chemoreceptor gene families in chelicer	35
A needle in a haystack: A new metabarcoding approach to survey diversity at the species level of Arcellinida (Amoebozoa: Tubulinea)	35
Single‐molecule long‐read sequencing reveals extensive genomic and transcriptomic variation between maize and its wild relative teosinte (Zea mays ssp. parviglumis)	35
Deciphering the molecular signal from past and alive bacterial communities in aquatic sedimentary archives	34
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Improved genome assembly of Chinese shrimp (Fenneropenaeus chinensis) suggests adaptation to the environment during evolution and domestication	33
SPEDE‐sampler: An R Shiny application to assess how methodological choices and taxon sampling can affect Generalized Mixed Yule Coalescent output and interpretation	33
Beyond taxonomy: Validating functional inference approaches in the context of fish‐farm impact assessments	33
Demogenomic inference from spatially and temporally heterogeneous samples	32
Simulating plasticity as a framework for understanding habitat selection and its role in adaptive capacity and extinction risk through an expansion of CDMetaPOP	32
Fishing for DNA? Designing baits for population genetics in target enrichment experiments: Guidelines, considerations and the new tool supeRbaits	32
Beware of Plant DNA in Animal Dietary Metabarcoding: Lessons From a Strictly Insectivorous Bat	32
Monitoring of multiple fish species by quantitative environmental DNA metabarcoding surveys over two summer seasons	32
Inference of the distribution of fitness effects of mutations is affected by single nucleotide polymorphism filtering methods, sample size and population structure	32
Cover Image	31
Species discrimination in Schima (Theaceae): Next‐generation super‐barcodes meet evolutionary complexity	31
The proof is in the poo: Non‐invasive method to detect endoparasitic infection	31
Contemporary Ne estimation using temporally spaced data with linked loci	31
Pedigree simulations reveal that maternity assignment is reliable in populations with conspecific brood parasitism, incomplete parental sampling and kin structure	30
Strategies for sample labelling and library preparation in DNA metabarcoding studies	30
DNA methylation‐based biomarkers for ageing long‐lived cetaceans	30
When barcoding fails: Genome chimerization (admixing) and reticulation obscure phylogenetic and taxonomic relationships	30
Batch effects in population genomic studies with low‐coverage whole genome sequencing data: Causes, detection and mitigation	30
Performance of DNA metabarcoding, standard barcoding and morphological approaches in the identification of insect biodiversity	29
MycoAI: Fast and accurate taxonomic classification for fungal ITS sequences	29
A comprehensive framework for detecting copy number variants from single nucleotide polymorphism data: ‘rCNV’, a versatile r package for paralogue and CNV detection	29
Exploring the vertebrate fauna of the Bird’s Head Peninsula (Indonesia, West Papua) through DNA barcodes	28
Assessing the impact of USER‐treatment on hyRAD capture applied to ancient DNA	28
Comparative analysis of fish environmental DNA reveals higher sensitivity achieved through targeted sequence‐based metabarcoding	28
The great tit HapMap project: A continental‐scale analysis of genomic variation in a songbird	28
The Long and the Short of It: Nanopore‐Based eDNA Metabarcoding of Marine Vertebrates Works; Sensitivity and Species‐Level Assignment Depend on Amplicon Lengths	28
Proteomic fingerprinting enables quantitative biodiversity assessments of species and ontogenetic stages in Calanus congeners (Copepoda, Crustacea) from the Arctic Ocean	28
Chromosome‐level genome of Entada phaseoloides provides insights into genome evolution and biosynthesis of triterpenoid saponins	27
Comparing eDNA and Transect Methods for Aquatic Biodiversity Assessment in Lakes and Ponds	27
Evaluating the Benefits and Limits of Multiple Displacement Amplification With Whole‐Genome Oxford Nanopore Sequencing	27
Allelic bias when performing in‐solution enrichment of ancient human DNA	26
GenAPoPop 1.0: A user‐friendly software to analyse genetic diversity and structure from partially clonal and selfed autopolyploid organisms	26
pr2‐primers: An 18S rRNA primer database for protists	26
Evaluating the role of reference‐genome phylogenetic distance on evolutionary inference	26
Recovering the genomes hidden in museum wet collections	25
Non‐invasive age estimation based on faecal DNA using methylation‐sensitive high‐resolution melting for Indo‐Pacific bottlenose dolphins	25
A roadmap to robust discriminant analysis of principal components	25
Cover Image	25
Coalescent‐based species delimitation meets deep learning: Insights from a highly fragmented cactus system	25
Do not be scared of the genome's 5th base—Explaining phenotypic variability and evolutionary dynamics through DNA methylation analysis	25

Issue Information	25
Bee foraging preferences, microbiota and pathogens revealed by direct shotgun metagenomics of honey	25
A Long‐Term Ecological Research Data Set From the Marine Genetic Monitoring Program ARMS‐MBON 2018–2020	24
Lessons from assembling UCEs: A comparison of common methods and the case of Clavinomia (Halictidae)	24
Quantifying uncertainty in inferences of landscape genetic resistance due to choice of individual‐based genetic distance metric	24
Replicate DNA metabarcoding can discriminate seasonal and spatial abundance shifts in river macroinvertebrate assemblages	24
Evolutionary history and seascape genomics of Harbour porpoises (Phocoena phocoena) across environmental gradients in the North Atlantic and adjacent waters	24
Detecting clonemate pairs in multicellular diploid clonal species based on a shared heterozygosity index	24
Genomic Prediction of Individual Inbreeding Levels for the Management of Genetic Diversity in Populations With Small Effective Size	24
Enhancing metabarcoding efficiency and ecological insights through integrated taxonomy and DNA reference barcoding: A case study on beach meiofauna	24
ParAquaSeq, a Database of Ecologically Annotated rRNA Sequences Covering Zoosporic Parasites Infecting Aquatic Primary Producers in Natural and Industrial S	24
A consensus protocol for the recovery of mercury methylation genes from metagenomes	23
COInr and mkCOInr: Building and customizing a nonredundant barcoding reference database from BOLD and NCBI using a semi‐automated pipeline	23
Environmental RNA can distinguish life stages in amphibian populations	23
On‐site environmental DNA detection of species using ultrarapid mobile PCR	22
Plastid Genome Assembly Using Long‐read data	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
Detection and population genomics of sea turtle species via noninvasive environmental DNA analysis of nesting beach sand tracks and oceanic water	22
FreshOmics: A manually curated and standardized –omics database for investigating freshwater microbiomes	22
Improved high‐throughput MHC typing for non‐model species using long‐read sequencing	22
Chromosome‐scale genome assembly of areca palm (Areca catechu)	21
Comparative genomics of a vertically transmitted thiotrophic bacterial ectosymbiont and its close free‐living relative	21
Pseudoreplication in genomic‐scale data sets	21
Testing the applicability of environmental DNA metabarcoding to landscape genetics	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	21
SLRfinder: A method to detect candidate sex‐linked regions with linkage disequilibrium clustering	21
Issue Information	21
Leveraging an existing whole‐genome resequencing population data set to characterize toll‐like receptor gene diversity in a threatened bird	21
Limits and convergence properties of the sequentially Markovian coalescent	20
The accuracy of predicting maladaptation to new environments with genomic data	20
Prey ration, temperature, and predator species influence digestion rates of prey DNA inferred from qPCR and metabarcoding	20
An exploration of assembly strategies and quality metrics on the accuracy of the rewarewa (Knightia excelsa) genome	20
The unknown unknown: A framework for assessing environmental DNA assay specificity against unsampled taxa	20
New deep learning‐based methods for visualizing ecosystem properties using environmental DNA metabarcoding data	20
A dynamic ancestral graph model and GPU‐based simulation of a community based on metagenomic sampling	20
MuDoGeR: Multi‐Domain Genome recovery from metagenomes made easy	20
A collaborative backbone resource for comparative studies of subterranean evolution: The World Asellidae database	20
Missing genotype imputation in non‐model species using self‐organizing maps	20
Unlocking inaccessible historical genomes preserved in formalin	20
Three Novel Spider Genomes Unveil Spidroin Diversification and Hox Cluster Architecture: Ryuthela nishihirai (Liphistiidae), Uloborus plumipes (Uloboridae) and Cheiracanthium punctori	20
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A bioinformatic toolkit to simultaneously identify sex and sex‐linked regions	19
Conservation in a litre of air	19
High‐quality genomes reveal significant genetic divergence and cryptic speciation in the model organism Folsomia candida (collembola)	19
Environmental DNA metabarcoding of freshwater fish in Malaysian tropical rivers using short‐read nanopore sequencing as a potential biomonitoring tool	19
The year of the tiger and the year of tiger genomes!	19
Tools and applications for integrative analysis of DNA methylation in social insects	18
Genome architecture used to supplement species delineation in two cryptic marine ciliates	18
TransPi—a comprehensive TRanscriptome ANalysiS PIpeline for de novo transcriptome assembly	18
Detailed DNA barcoding of mayflies in a small European country proved how far we are from having comprehensive barcode reference libraries	18
CRISPR‐Cas9 enrichment, a new strategy in microbial metagenomics to investigate complex genomic regions: The case of an environmental integron	18
Contemporary issues, current best practice and ways forward in soil protist ecology	18
Identification and quantification of chimeric sequencing reads in a highly multiplexed RAD‐seq protocol	18
Launching insectphylo.org; a new hub facilitating construction and use of synthesis molecular phylogenies of insects	18
Using metatranscriptomics to estimate the diversity and composition of zooplankton communities	17
Assessing the limits of local ancestry inference from small reference panels	17
MOSCA 2.0: A bioinformatics framework for metagenomics, metatranscriptomics and metaproteomics data analysis and visualization	17
The WZA: A window‐based method for characterizing genotype–environment associations	17
A targeted amplicon sequencing panel to simultaneously identify mosquito species and Plasmodium presence across the entire Anopheles genus	17
Influence of RNA‐Seq library construction, sampling methods, and tissue harvesting time on gene expression estimation	17
SEGUL: Ultrafast, memory‐efficient and mobile‐friendly software for manipulating and summarizing phylogenomic datasets	17
Issue Information	16
Management and conservation implications of cryptic population substructure for two commercially exploited fishes (Merluccius spp.) in southern Africa	16
Inferring the timing and strength of natural selection and gene migration in the evolution of chicken from ancient DNA data	16
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Exhaustive reanalysis of barcode sequences from public repositories highlights ongoing misidentifications and impacts taxa diversity and distribution	16
Testing genome skimming for species discrimination in the large and taxonomically difficult genus Rhododendron	16
Bayesian StairwayPlot for Inferring Single Population Demographic Histories From Site Frequency Spectra	16
A Short‐Read Amplicon Sequencing Protocol and Bioinformatic Pipeline for Ecological Surveillance of Dipteran Disease Vectors	16
Log‐ratio analysis of microbiome data with many zeroes is library size dependent	16
Correcting for Bias in Estimates of θw$$ {\theta}_w $$ and Tajima's D$$ D $$ From Missing Data in Next‐Generation Sequencing	16
Who are you? A framework to identify and report genetic sample mix‐ups	16
RNA allows identifying the consumption of carrion prey	16
A high‐quality carabid genome assembly provides insights into beetle genome evolution and cold adaptation	15
Species delimitation with limited sampling: An example from rare trapdoor spider genus Cyclocosmia (Mygalomorphae, Halonoproctidae)	15
Validating a Target‐Enrichment Design for Capturing Uniparental Haplotypes in Ancient Domesticated Animals	15
Genome and gene evolution of seahorse species revealed by the chromosome‐level genome of Hippocampus abdominalis	15
A High‐Throughput Ancient DNA Extraction Method for Large‐Scale Sample Screening	15
Machine learning in molecular ecology	15

High quality haplotype‐resolved genome assemblies of Populus tomentosa Carr., a stabilized interspecific hybrid species widespread in Asia	15
Long‐ and short‐read metabarcoding technologies reveal similar spatiotemporal structures in fungal communities	14
RIDGE, a tool tailored to detect gene flow barriers across species pairs	14
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Individual haplotyping of whale sharks from seawater environmental DNA	14
A molecular‐based identification resource for the arthropods of Finland	14
DNA barcodes highlight genetic diversity patterns in rodents from lowland desert and Andean areas in Argentina	14
Efficiency of eDNA and iDNA in assessing vertebrate diversity and its abundance	14
Express barcoding with NextGenPCR and MinION for species‐level sorting of ecological samples	14
Comparative genomics reveals the dynamic evolutionary history of cement protein genes of barnacles from intertidal to deep‐sea hydrothermal vents	13
Chromosome‐level genome assembly of the mirid predator Cyrtorhinus lividipennis Reuter (Hemiptera: Miridae), an important natural enemy in the rice ecosystem	13
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Environmental DNA phylogeography: Successful reconstruction of phylogeographic patterns of multiple fish species from cups of water	13
Next‐generation bioinformatics: An ultrafast and user‐friendly tool for phylogenomic data exploration	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
Genome of the butterfly hillstream loach provides insights into adaptations to torrential mountain stream life	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
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
Estimation of spatial demographic maps from polymorphism data using a neural network	13
Genetic variation and domestication of horses revealed by 10 chromosome‐level genomes and whole‐genome resequencing	13
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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
A chromosomal level genome sequence for Quasipaa spinosa (Dicroglossidae) reveals chromosomal evolution and population diversity	13
Macrobial airborne environmental DNA analysis: A review of progress, challenges, and recommendations for an emerging application	13
quickLD: An efficient software for linkage disequilibrium analyses	13
The answer, my friend, is blowin’ in the wind: Blow sampling provides a new dimension to whale population monitoring	13
Scaling‐up RADseq methods for large datasets of non‐invasive samples: Lessons for library construction and data preprocessing	12
Polly: An R package for genotyping microsatellites and detecting highly polymorphic DNA markers from short‐read data	12
Affordable de novo generation of fish mitogenomes using amplification‐free enrichment of mitochondrial DNA and deep sequencing of long fragments	12
Taxon‐specific or universal? Using target capture to study the evolutionary history of rapid radiations	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
Quantitative assessment of reef foraminifera community from metabarcoding data	12
Issue Information	12
A guide to avian museomics: Insights gained from resequencing hundreds of avian study skins	12
CCS‐Consensuser: A Haplotype‐Aware Consensus Generator for PacBio Amplicon Sequences	12
Delimiting the rare, endangered and actively speciating	12
Application of palaeogenetic techniques to historic mollusc shells reveals phylogeographic structure in a New Zealand abalone	12
DROP: Molecular voucher database for identification of Drosophila parasitoids	12
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Identifying loci under selection via explicit demographic models	12
Simultaneous genotyping of snails and infecting trematode parasites using high‐throughput amplicon sequencing	12