Molecular Ecology Resources

Article	Citations
MitoFinder: Efficient automated large‐scale extraction of mitogenomic data in target enrichment phylogenomics	781
ASAP: assemble species by automatic partitioning	566
Dsuite ‐ Fast D‐statistics and related admixture evidence from VCF files	317
pixy: Unbiased estimation of nucleotide diversity and divergence in the presence of missing data	205
CPGView: A package for visualizing detailed chloroplast genome structures	164
Genetic structure and insecticide resistance characteristics of fall armyworm populations invading China	114
Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird‐of‐paradise	93
The genetic adaptations of fall armyworm Spodoptera frugiperda facilitated its rapid global dispersal and invasion	87
Evaluation of primer pairs for microbiome profiling from soils to humans within the One Health framework	56
Extending approximate Bayesian computation with supervised machine learning to infer demographic history from genetic polymorphisms using DIYABC Random Forest	56
Reference genome and demographic history of the most endangered marine mammal, the vaquita	52
SCycDB: A curated functional gene database for metagenomic profiling of sulphur cycling pathways	50
Experimental support for genomic prediction of climate maladaptation using the machine learning approach Gradient Forests	49
A demonstration of conservation genomics for threatened species management	47
Deep learning for population size history inference: Design, comparison and combination with approximate Bayesian computation	46
Complex interactions between environmental DNA (eDNA) state and water chemistries on eDNA persistence suggested by meta‐analyses	45
bitacora: A comprehensive tool for the identification and annotation of gene families in genome assemblies	44
Improving metabarcoding taxonomic assignment: A case study of fishes in a large marine ecosystem	44
Chromosome‐level analysis of the Crassostrea hongkongensis genome reveals extensive duplication of immune‐related genes in bivalves	44
Construction of a chromosome‐level genome and variation map for the Pacific oyster Crassostrea gigas	44
Chromosomal‐level genomes of three rice planthoppers provide new insights into sex chromosome evolution	42
Integrating eDNA metabarcoding and simultaneous underwater visual surveys to describe complex fish communities in a marine biodiversity hotspot	41
A chromosome‐level assembly of the black tiger shrimp (Penaeus monodon) genome facilitates the identification of growth‐associated genes	41
eDNAFlow, an automated, reproducible and scalable workflow for analysis of environmental DNA sequences exploiting Nextflow and Singularity	40
Combining genotype, phenotype, and environmental data to delineate site‐adjusted provenance strategies for ecological restoration	39

Evaluation of model fit of inferred admixture proportions	39
Automatic inference of demographic parameters using generative adversarial networks	39
Improving the reliability of eDNA data interpretation	39
Bioinformatic pipelines combining denoising and clustering tools allow for more comprehensive prokaryotic and eukaryotic metabarcoding	39
A high‐quality genome assembly of the eggplant provides insights into the molecular basis of disease resistance and chlorogenic acid synthesis	39
The quest for absolute abundance: The use of internal standards for DNA‐based community ecology	38
The changing face of genome assemblies: Guidance on achieving high‐quality reference genomes	37
Comparing diversity levels in environmental samples: DNA sequence capture and metabarcoding approaches using 18S and COI genes	37
The influence of intraspecific sequence variation during DNA metabarcoding: A case study of eleven fungal species	37
DiversityScanner: Robotic handling of small invertebrates with machine learning methods	37
High‐quality chromosome‐level genomes of two tilapia species reveal their evolution of repeat sequences and sex chromosomes	36
RADSex: A computational workflow to study sex determination using restriction site‐associated DNA sequencing data	36
Strategies for sample labelling and library preparation in DNA metabarcoding studies	36
Chromosome‐level genome assembly for the largemouth bass Micropterus salmoides provides insights into adaptation to fresh and brackish water	36
Error, noise and bias in de novo transcriptome assemblies	36
Benchmarking bioinformatic tools for fast and accurate eDNA metabarcoding species identification	35
Rapid and accurate species identification for ecological studies and monitoring using CRISPR‐based SHERLOCK	35
Successful application of ancient DNA extraction and library construction protocols to museum wet collection specimens	34
Italian odonates in the Pandora's box: A comprehensive DNA barcoding inventory shows taxonomic warnings at the Holarctic scale	34
A chromosome‐level genome assembly of the parasitoid wasp Pteromalus puparum	34
pr2‐primers: An 18S rRNA primer database for protists	33
The elephant grass (Cenchrus purpureus) genome provides insights into anthocyanidin accumulation and fast growth	33
SambaR: An R package for fast, easy and reproducible population‐genetic analyses of biallelic SNP data sets	33
New approaches to species delimitation and population structure of anthozoans: Two case studies of octocorals using ultraconserved elements and exons	33
Model‐based genotype and ancestry estimation for potential hybrids with mixed‐ploidy	32
Museomics identifies genetic erosion in two butterfly species across the 20th century in Finland	32
Testing genome skimming for species discrimination in the large and taxonomically difficult genus Rhododendron	32
LEA 3: Factor models in population genetics and ecological genomics with R	32
DNA metabarcoding for biodiversity monitoring in a national park: Screening for invasive and pest species	32
De novo sequencing and chromosomal‐scale genome assembly of leopard coral grouper, Plectropomus leopardus	32
A large genome with chromosome‐scale assembly sheds light on the evolutionary success of a true toad (Bufo gargarizans)	32
A chromosome‐scale assembly of the black gram (Vigna mungo) genome	31
Assessment of current taxonomic assignment strategies for metabarcoding eukaryotes	31
Apolygus lucorum genome provides insights into omnivorousness and mesophyll feeding	31
Applying f4‐statistics and admixture graphs: Theory and examples	31
Estimating and accounting for genotyping errors in RAD‐seq experiments	31
BAGS: An automated Barcode, Audit & Grade System for DNA barcode reference libraries	31
Chromosome‐level reference genome assembly provides insights into aroma biosynthesis in passion fruit (Passiflora edulis)	30
A new method of metabarcoding Microsporidia and their hosts reveals high levels of microsporidian infections in mosquitoes (Culicidae)	30
Building a global genomics observatory: Using GEOME (the Genomic Observatories Metadatabase) to expedite and improve deposition and retrieval of genetic data and metadata for biodiversity research	30
Chromosome‐level assembly of the melon thrips genome yields insights into evolution of a sap‐sucking lifestyle and pesticide resistance	30
DILS: Demographic inferences with linked selection by using ABC	29
An optimized method for the extraction of ancient eukaryote DNA from marine sediments	29
Giant African snail genomes provide insights into molluscan whole‐genome duplication and aquatic–terrestrial transition	29
Tagsteady: A metabarcoding library preparation protocol to avoid false assignment of sequences to samples	29
Chromosome‐level genome assembly of Sichuan pepper provides insights into apomixis, drought tolerance, and alkaloid biosynthesis	29
Nonlethal age estimation of three threatened fish species using DNA methylation: Australian lungfish, Murray cod and Mary River cod	28
A high‐quality genome of taro (Colocasia esculenta (L.) Schott), one of the world's oldest crops	28
A chromosome‐level genome assembly of the woolly apple aphid, Eriosoma lanigerum Hausmann (Hemiptera: Aphididae)	27
A chromosome‐scale assembly of the bilberry genome identifies a complex locus controlling berry anthocyanin composition	27

Chromosome‐scale assembly of the genome of Salixdunnii reveals a male‐heterogametic sex determination system on chromosome 7	27
f‐Statistics estimation and admixture graph construction with Pool‐Seq or allele count data using the R package poolfstat	27
Distinguishing between recent balancing selection and incomplete sweep using deep neural networks	27
Barcode UK: A complete DNA barcoding resource for the flowering plants and conifers of the United Kingdom	27
A molecular‐based identification resource for the arthropods of Finland	27
A robust approach to estimate relative phytoplankton cell abundances from metagenomes	26
A de novo chromosome‐level genome assembly of Coregonus sp. “Balchen”: One representative of the Swiss Alpine whitefish radiation	26
More affordable and effective noninvasive single nucleotide polymorphism genotyping using high‐throughput amplicon sequencing	26
A chromosome‐scale genome assembly of the Mongolian oak (Quercus mongolica)	26
Assessing genome assembly quality prior to downstream analysis: N50 versus BUSCO	26
Identifying error and accurately interpreting environmental DNA metabarcoding results: A case study to detect vertebrates at arid zone waterholes	26
Versatile simulations of admixture and accurate local ancestry inference with mixnmatch and ancestryinfer	26
Fast and accurate distance‐based phylogenetic placement using divide and conquer	25
Chromosome‐level genome assembly of Lethenteron reissneri provides insights into lamprey evolution	25
Simulation with RADinitio improves RADseq experimental design and sheds light on sources of missing data	25
Genome‐scale target capture of mitochondrial and nuclear environmental DNA from water samples	25
User‐friendly bioinformatics pipeline gDAT (graphical downstream analysis tool) for analysing rDNA sequences	25
Hybridization capture of larch (Larix Mill.) chloroplast genomes from sedimentary ancient DNA reveals past changes of Siberian forest	25
Unlocking inaccessible historical genomes preserved in formalin	25
RepeatProfiler: A pipeline for visualization and comparative analysis of repetitive DNA profiles	25
Development of a highly efficient 50K single nucleotide polymorphism genotyping array for the large and complex genome of Norway spruce (Picea abies L. Karst) by whole genome resequencing and i	25
Chromosome‐level genome assembly of a cyprinid fish Onychostoma macrolepis by integration of nanopore sequencing, Bionano and Hi‐C technology	24
Commonly used Hardy–Weinberg equilibrium filtering schemes impact population structure inferences using RADseq data	24
Environmental DNA analysis shows high potential as a tool for estimating intraspecific genetic diversity in a wild fish population	24
Chromosome‐level genome assembly of the East Asian common octopus (Octopus sinensis) using PacBio sequencing and Hi‐C technology	24
Factors affecting the efficiency of molecular species delimitation in a species‐rich insect family	24
Chromosome‐level assembly of the brown planthopper genome with a characterized Y chromosome	24
Quantitative evaluation of intraspecific genetic diversity in a natural fish population using environmental DNA analysis	24
Chromosome‐level genome assembly of the bean bug Riptortus pedestris	24
Towards reproducible metabarcoding data: Lessons from an international cross‐laboratory experiment	24
Development of a single nucleotide polymorphism array for population genomic studies in four European pine species	24
Exhaustive reanalysis of barcode sequences from public repositories highlights ongoing misidentifications and impacts taxa diversity and distribution	24
Chromosome‐level genome assembly of the greenfin horse‐faced filefish (Thamnaconus septentrionalis) using Oxford Nanopore PromethION sequencing and Hi‐C technology	23
Chromosomal‐level reference genome of the incense tree Aquilaria sinensis	23
Species delimitation and geography	23
Chromosomal‐level genome assembly of the scimitar‐horned oryx: Insights into diversity and demography of a species extinct in the wild	23
High molecular weight DNA extraction strategies for long‐read sequencing of complex metagenomes	23
Individual haplotyping of whale sharks from seawater environmental DNA	23
Validated removal of nuclear pseudogenes and sequencing artefacts from mitochondrial metabarcode data	22
metaPR2: A database of eukaryotic 18S rRNA metabarcodes with an emphasis on protists	22
Automated improvement of stickleback reference genome assemblies with Lep‐Anchor software	22
Chromosome‐level genome assembly of an important pine defoliator, Dendrolimus punctatus (Lepidoptera; Lasiocampidae)	22
NOVOWrap: An automated solution for plastid genome assembly and structure standardization	22
Metagenomic analysis of historical herbarium specimens reveals a postmortem microbial community	22
Limits and convergence properties of the sequentially Markovian coalescent	21
Nonrandom missing data can bias Principal Component Analysis inference of population genetic structure	21
De novo assemblies of Luffa acutangula and Luffa cylindrica genomes reveal an expansion associated with substantial accumulation of transposable elements	21
One panel to rule them all: DArTcap genotyping for population structure, historical demography, and kinship analyses, and its application to a threatened shark	21
Detecting population declines via monitoring the effective number of breeders (Nb)	21
A unified model of species abundance, genetic diversity, and functional diversity reveals the mechanisms structuring ecological communities	21
Analysing landscape effects on dispersal networks and gene flow with genetic graphs	21
Detection and population genomics of sea turtle species via noninvasive environmental DNA analysis of nesting beach sand tracks and oceanic water	20
Genomic basis of environmental adaptation in the leathery sea squirt (Styela clava)	20
Long read sequencing of Toona sinensis (A. Juss) Roem: A chromosome‐level reference genome for the family Meliaceae	20
Navigating the seven challenges of taxonomic reference databases in metabarcoding analyses	20
Taxon‐specific or universal? Using target capture to study the evolutionary history of rapid radiations	20
Evaluating the role of reference‐genome phylogenetic distance on evolutionary inference	20
Improved de novo chromosome‐level genome assembly of the vulnerable walnut tree Juglans mandshurica reveals gene family evolution and possible genome basis of resistance to lesion nematode	20
Chromosome‐level reference genome assembly and gene editing of the dead‐leaf butterfly Kallima inachus	20
The genomes of chicory, endive, great burdock and yacon provide insights into Asteraceae palaeo‐polyploidization history and plant inulin production	20
Quantitative monitoring of diverse fish communities on a large scale combining eDNA metabarcoding and qPCR	20
Detecting selected haplotype blocks in evolve and resequence experiments	19
A DNA mini‐barcode for marine macrophytes	19
High quality genome of Erigeron breviscapus provides a reference for herbal plants in Asteraceae	19
A GT‐seq panel for walleye (Sander vitreus) provides important insights for efficient development and implementation of amplicon panels in non‐model organisms	19
High quality haplotype‐resolved genome assemblies of Populus tomentosa Carr., a stabilized interspecific hybrid species widespread in Asia	19
Chromosome‐level assembly of southern catfish (silurus meridionalis) provides insights into visual adaptation to nocturnal and benthic lifestyles	19
Chromosome‐level genome assembly of the greenhouse whitefly (Trialeurodes vaporariorum Westwood)	19
A chromosome‐scale genome assembly of Antheraea pernyi (Saturniidae, Lepidoptera)	19
Hybridization ddRAD‐sequencing for population genomics of nonmodel plants using highly degraded historical specimen DNA	19
Chromosome‐level genome assembly of the coastal horseshoe crab (Tachypleus gigas)	19
A targeted amplicon sequencing panel to simultaneously identify mosquito species and Plasmodium presence across the entire Anopheles genus	19
The Meishan pig genome reveals structural variation‐mediated gene expression and phenotypic divergence underlying Asian pig domestication	19
Elucidating shark diets with DNA metabarcoding from cloacal swabs	19
Chromosome‐scale genome assembly of areca palm (Areca catechu)	19
A guide to avian museomics: Insights gained from resequencing hundreds of avian study skins	19
The Ocean barcode atlas: A web service to explore the biodiversity and biogeography of marine organisms	19
Characterizing the spatial signal of environmental DNA in river systems using a community ecology approach	19
TaxonTableTools: A comprehensive, platform‐independent graphical user interface software to explore and visualise DNA metabarcoding data	18
Make every species count: fastachar software for rapid determination of molecular diagnostic characters to describe species	18

Canonical correlations reveal adaptive loci and phenotypic responses to climate in perennial ryegrass	18
Chromosome level reference of Atlantic halibut Hippoglossushippoglossus provides insight into the evolution of sexual determination systems	18
Population genomics provides insights into lineage divergence and local adaptation within the cotton bollworm	18
Systematic review and meta‐analysis: Water type and temperature affect environmental DNA decay	18
Contaminations contaminate common databases	18
Environmental RNA degrades more rapidly than environmental DNA across a broad range of pH conditions	18
Untangling ITS2 genotypes of algal symbionts in zooxanthellate corals	17
Molecular dating for phylogenies containing a mix of populations and species by using Bayesian and RelTime approaches	17
snpfiltr: An R package for interactive and reproducible SNP filtering	17
Pairwise linkage disequilibrium estimation for polyploids	17
Coming of age for COI metabarcoding of whole organism community DNA: Towards bioinformatic harmonisation	17
Genomics of natural history collections for understanding evolution in the wild	17
Extracting abundance information from DNA‐based data	17
DNA methylation as a tool to explore ageing in wild roe deer populations	17
A chromosome‐level genome of the mud crab (Scylla paramamosain estampador) provides insights into the evolution of chemical and light perception in this crustacean	17
Sampling schemes and drift can bias admixture proportions inferred by structure	17
Benchmarking the performance of Pool‐seq SNP callers using simulated and real sequencing data	17
Whole genome sequencing of silver carp (Hypophthalmichthys molitrix) and bighead carp (Hypophthalmichthys nobilis) provide novel insights into their evolution and speciation	17
Whole‐genome sequencing of brown‐marbled grouper (Epinephelus fuscoguttatus) provides insights into adaptive evolution and growth differences	16
A high‐quality genome assembly of Jasminum sambac provides insight into floral trait formation and Oleaceae genome evolution	16
Evaluation of the R package ‘resistancega’: A promising approach towards the accurate optimization of landscape resistance surfaces	16
Metagenomics: A viable tool for reconstructing herbivore diet	16
Genomic analysis of Medicago ruthenica provides insights into its tolerance to abiotic stress and demographic history	16
A chromosome‐level assembly of the harlequin ladybird Harmonia axyridis as a genomic resource to study beetle and invasion biology	16
Speeding up the detection of invasive bivalve species using environmental DNA: A Nanopore and Illumina sequencing comparison	16
Batch effects in population genomic studies with low‐coverage whole genome sequencing data: Causes, detection and mitigation	16
MCycDB: A curated database for comprehensively profiling methane cycling processes of environmental microbiomes	16
Maximizing the acquisition of unique reads in noninvasive capture sequencing experiments	15
Guidelines for standardizing the application of discriminant analysis of principal components to genotype data	15
Joint identification of sex and sex‐linked scaffolds in non‐model organisms using low depth sequencing data	15
Microbial networks inferred from environmental DNA data for biomonitoring ecosystem change: Strengths and pitfalls	15
Short‐ and long‐read metabarcoding of the eukaryotic rRNA operon: Evaluation of primers and comparison to shotgun metagenomics sequencing	15
Why eDNA fractions need consideration in biomonitoring	15
ModEst: Accurate estimation of genome size from next generation sequencing data	15
Reference genome of lumpfish Cyclopterus lumpus Linnaeus provides evidence of male heterogametic sex determination through the AMH pathway	15
A chromosome‐anchored genome assembly for Lake Trout (Salvelinus namaycush)	15
Fish eDNA metabarcoding from aquatic biofilm samples: Methodological aspects	15
Chromosome‐level de novo genome assembly of Sarcophaga peregrina provides insights into the evolutionary adaptation of flesh flies	15
DNA barcoding uncovers cryptic diversity in minute herbivorous mites (Acari, Eriophyoidea)	15
Chromosome‐level assembly of the mangrove plant Aegiceras corniculatum genome generated through Illumina, PacBio and Hi‐C sequencing technologies	15
A step towards the validation of bacteria biotic indices using DNA metabarcoding for benthic monitoring	15
Linked‐read sequencing enables haplotype‐resolved resequencing at population scale	15
Chromosome‐level reference genome of the soursop (Annonamuricata): A new resource for Magnoliid research and tropical pomology	15
Phylogeographic model selection using convolutional neural networks	15
Exon probe sets and bioinformatics pipelines for all levels of fish phylogenomics	15
Chromosome‐level genome and population genomic analysis provide insights into the evolution and environmental adaptation of Jinjiang oysterCrassostrea ariakensis	15
A high‐quality carabid genome assembly provides insights into beetle genome evolution and cold adaptation	15
Design and implementation of multiplexed amplicon sequencing panels to serve genomic epidemiology of infectious disease: A malaria case study	15
FrogCap: A modular sequence capture probe‐set for phylogenomics and population genetics for all frogs, assessed across multiple phylogenetic scales	14
Effective double‐digest RAD sequencing and genotyping despite large genome size	14
DROP: Molecular voucher database for identification of Drosophila parasitoids	14
Understudied, underrepresented, and unknown: Methodological biases that limit detection of early diverging fungi from environmental samples	14
Invertebrates for vertebrate biodiversity monitoring: Comparisons using three insect taxa as iDNA samplers	14
Generation of a chromosome‐level genome assembly for Pacific halibut (Hippoglossus stenolepis) and characterization of its sex‐determining genomic region	14
Improved genome assembly of Chinese shrimp (Fenneropenaeus chinensis) suggests adaptation to the environment during evolution and domestication	14
Chromosome‐level hybrid de novo genome assemblies as an attainable option for nonmodel insects	14
A chromosome‐level genome assembly of rice leaffolder, Cnaphalocrocis medinalis	14
Phylogenomic analyses of the genusDrosophilareveals genomic signals of climate adaptation	14
Chromosome‐level genome assembly of Paralithodes platypus provides insights into evolution and adaptation of king crabs	14