Molecular Ecology Resources

Article	Citations
ASAP: assemble species by automatic partitioning	706
Dsuite ‐ Fast D‐statistics and related admixture evidence from VCF files	386
pixy: Unbiased estimation of nucleotide diversity and divergence in the presence of missing data	257
CPGView: A package for visualizing detailed chloroplast genome structures	244
Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird‐of‐paradise	100
Extending approximate Bayesian computation with supervised machine learning to infer demographic history from genetic polymorphisms using DIYABC Random Forest	78
SCycDB: A curated functional gene database for metagenomic profiling of sulphur cycling pathways	68
Experimental support for genomic prediction of climate maladaptation using the machine learning approach Gradient Forests	60
Reference genome and demographic history of the most endangered marine mammal, the vaquita	55
Construction of a chromosome‐level genome and variation map for the Pacific oyster Crassostrea gigas	52
Improving the reliability of eDNA data interpretation	50
Strategies for sample labelling and library preparation in DNA metabarcoding studies	49
Chromosomal‐level genomes of three rice planthoppers provide new insights into sex chromosome evolution	49
pr2‐primers: An 18S rRNA primer database for protists	49
Integrating eDNA metabarcoding and simultaneous underwater visual surveys to describe complex fish communities in a marine biodiversity hotspot	49
A chromosome‐level assembly of the black tiger shrimp (Penaeus monodon) genome facilitates the identification of growth‐associated genes	48
Complex interactions between environmental DNA (eDNA) state and water chemistries on eDNA persistence suggested by meta‐analyses	48
Improving metabarcoding taxonomic assignment: A case study of fishes in a large marine ecosystem	48
LEA 3: Factor models in population genetics and ecological genomics with R	46
eDNAFlow, an automated, reproducible and scalable workflow for analysis of environmental DNA sequences exploiting Nextflow and Singularity	46
Bioinformatic pipelines combining denoising and clustering tools allow for more comprehensive prokaryotic and eukaryotic metabarcoding	45
Chromosome‐level genome assembly for the largemouth bass Micropterus salmoides provides insights into adaptation to fresh and brackish water	44
Benchmarking bioinformatic tools for fast and accurate eDNA metabarcoding species identification	44
DiversityScanner: Robotic handling of small invertebrates with machine learning methods	44
A high‐quality genome assembly of the eggplant provides insights into the molecular basis of disease resistance and chlorogenic acid synthesis	44

High‐quality chromosome‐level genomes of two tilapia species reveal their evolution of repeat sequences and sex chromosomes	44
The changing face of genome assemblies: Guidance on achieving high‐quality reference genomes	43
RADSex: A computational workflow to study sex determination using restriction site‐associated DNA sequencing data	43
Successful application of ancient DNA extraction and library construction protocols to museum wet collection specimens	43
The quest for absolute abundance: The use of internal standards for DNA‐based community ecology	43
Automatic inference of demographic parameters using generative adversarial networks	41
Testing genome skimming for species discrimination in the large and taxonomically difficult genus Rhododendron	40
Apolygus lucorum genome provides insights into omnivorousness and mesophyll feeding	39
SambaR: An R package for fast, easy and reproducible population‐genetic analyses of biallelic SNP data sets	39
f‐Statistics estimation and admixture graph construction with Pool‐Seq or allele count data using the R package poolfstat	38
New approaches to species delimitation and population structure of anthozoans: Two case studies of octocorals using ultraconserved elements and exons	38
The influence of intraspecific sequence variation during DNA metabarcoding: A case study of eleven fungal species	38
The elephant grass (Cenchrus purpureus) genome provides insights into anthocyanidin accumulation and fast growth	38
DILS: Demographic inferences with linked selection by using ABC	37
Assessment of current taxonomic assignment strategies for metabarcoding eukaryotes	36
A large genome with chromosome‐scale assembly sheds light on the evolutionary success of a true toad (Bufo gargarizans)	36
Navigating the seven challenges of taxonomic reference databases in metabarcoding analyses	36
A chromosome‐scale assembly of the black gram (Vigna mungo) genome	35
Model‐based genotype and ancestry estimation for potential hybrids with mixed‐ploidy	35
Chromosome‐scale assembly of the genome of Salixdunnii reveals a male‐heterogametic sex determination system on chromosome 7	34
Chromosome‐level genome assembly of Sichuan pepper provides insights into apomixis, drought tolerance, and alkaloid biosynthesis	34
Commonly used Hardy–Weinberg equilibrium filtering schemes impact population structure inferences using RADseq data	34
Barcode UK: A complete DNA barcoding resource for the flowering plants and conifers of the United Kingdom	34
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	34
Chromosome‐level reference genome assembly provides insights into aroma biosynthesis in passion fruit (Passiflora edulis)	34
Nonlethal age estimation of three threatened fish species using DNA methylation: Australian lungfish, Murray cod and Mary River cod	34
Giant African snail genomes provide insights into molluscan whole‐genome duplication and aquatic–terrestrial transition	33
A molecular‐based identification resource for the arthropods of Finland	33
A high‐quality genome of taro (Colocasia esculenta (L.) Schott), one of the world's oldest crops	33
Assessing genome assembly quality prior to downstream analysis: N50 versus BUSCO	33
BAGS: An automated Barcode, Audit & Grade System for DNA barcode reference libraries	32
NOVOWrap: An automated solution for plastid genome assembly and structure standardization	32
A chromosome‐scale genome assembly of the Mongolian oak (Quercus mongolica)	32
User‐friendly bioinformatics pipeline gDAT (graphical downstream analysis tool) for analysing rDNA sequences	31
A robust approach to estimate relative phytoplankton cell abundances from metagenomes	31
Distinguishing between recent balancing selection and incomplete sweep using deep neural networks	31
A chromosome‐scale assembly of the bilberry genome identifies a complex locus controlling berry anthocyanin composition	31
Unlocking inaccessible historical genomes preserved in formalin	30
metaPR2: A database of eukaryotic 18S rRNA metabarcodes with an emphasis on protists	30
Factors affecting the efficiency of molecular species delimitation in a species‐rich insect family	30
Hybridization capture of larch (Larix Mill.) chloroplast genomes from sedimentary ancient DNA reveals past changes of Siberian forest	30
A chromosome‐level genome assembly of the woolly apple aphid, Eriosoma lanigerum Hausmann (Hemiptera: Aphididae)	30
Chromosome‐level assembly of the brown planthopper genome with a characterized Y chromosome	29
RepeatProfiler: A pipeline for visualization and comparative analysis of repetitive DNA profiles	29
Limits and convergence properties of the sequentially Markovian coalescent	28
Quantitative monitoring of diverse fish communities on a large scale combining eDNA metabarcoding and qPCR	28
Genome‐scale target capture of mitochondrial and nuclear environmental DNA from water samples	28
Taxon‐specific or universal? Using target capture to study the evolutionary history of rapid radiations	28
Exhaustive reanalysis of barcode sequences from public repositories highlights ongoing misidentifications and impacts taxa diversity and distribution	28
Fast and accurate distance‐based phylogenetic placement using divide and conquer	28

Nonrandom missing data can bias Principal Component Analysis inference of population genetic structure	28
Individual haplotyping of whale sharks from seawater environmental DNA	28
MCycDB: A curated database for comprehensively profiling methane cycling processes of environmental microbiomes	27
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	27
Chromosome‐level genome assembly of Lethenteron reissneri provides insights into lamprey evolution	27
Towards reproducible metabarcoding data: Lessons from an international cross‐laboratory experiment	27
Guidelines for standardizing the application of discriminant analysis of principal components to genotype data	26
Chromosome‐level genome assembly of the bean bug Riptortus pedestris	26
High quality haplotype‐resolved genome assemblies of Populus tomentosa Carr., a stabilized interspecific hybrid species widespread in Asia	26
Extracting abundance information from DNA‐based data	25
The genomes of chicory, endive, great burdock and yacon provide insights into Asteraceae palaeo‐polyploidization history and plant inulin production	25
Automated improvement of stickleback reference genome assemblies with Lep‐Anchor software	25
Long read sequencing of Toona sinensis (A. Juss) Roem: A chromosome‐level reference genome for the family Meliaceae	25
Detecting population declines via monitoring the effective number of breeders (Nb)	24
A unified model of species abundance, genetic diversity, and functional diversity reveals the mechanisms structuring ecological communities	24
A guide to avian museomics: Insights gained from resequencing hundreds of avian study skins	24
Analysing landscape effects on dispersal networks and gene flow with genetic graphs	24
Characterizing the spatial signal of environmental DNA in river systems using a community ecology approach	24
Detection and population genomics of sea turtle species via noninvasive environmental DNA analysis of nesting beach sand tracks and oceanic water	24
High molecular weight DNA extraction strategies for long‐read sequencing of complex metagenomes	24
The Meishan pig genome reveals structural variation‐mediated gene expression and phenotypic divergence underlying Asian pig domestication	24
snpfiltr: An R package for interactive and reproducible SNP filtering	24
Population genomics provides insights into lineage divergence and local adaptation within the cotton bollworm	24
A targeted amplicon sequencing panel to simultaneously identify mosquito species and Plasmodium presence across the entire Anopheles genus	23
Validated removal of nuclear pseudogenes and sequencing artefacts from mitochondrial metabarcode data	23
Systematic review and meta‐analysis: Water type and temperature affect environmental DNA decay	23
Evaluating the role of reference‐genome phylogenetic distance on evolutionary inference	23
A chromosome‐level genome of the mud crab (Scylla paramamosain estampador) provides insights into the evolution of chemical and light perception in this crustacean	23
Chromosome‐scale genome assembly of areca palm (Areca catechu)	23
The Ocean barcode atlas: A web service to explore the biodiversity and biogeography of marine organisms	23
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	22
Short‐ and long‐read metabarcoding of the eukaryotic rRNA operon: Evaluation of primers and comparison to shotgun metagenomics sequencing	22
Design and implementation of multiplexed amplicon sequencing panels to serve genomic epidemiology of infectious disease: A malaria case study	22
Why eDNA fractions need consideration in biomonitoring	22
TaxonTableTools: A comprehensive, platform‐independent graphical user interface software to explore and visualise DNA metabarcoding data	21
Pairwise linkage disequilibrium estimation for polyploids	21
Metagenomics: A viable tool for reconstructing herbivore diet	21
Environmental RNA degrades more rapidly than environmental DNA across a broad range of pH conditions	21
Speeding up the detection of invasive bivalve species using environmental DNA: A Nanopore and Illumina sequencing comparison	21
A step towards the validation of bacteria biotic indices using DNA metabarcoding for benthic monitoring	21
ddPCR surpasses classical qPCR technology in quantitating bacteria and fungi in the environment	20
Whole‐genome sequencing of brown‐marbled grouper (Epinephelus fuscoguttatus) provides insights into adaptive evolution and growth differences	20
A chromosome‐level assembly of the harlequin ladybird Harmonia axyridis as a genomic resource to study beetle and invasion biology	20
Batch effects in population genomic studies with low‐coverage whole genome sequencing data: Causes, detection and mitigation	20
DNA barcoding of Cymbidium by genome skimming: Call for next‐generation nuclear barcodes	20
Contaminations contaminate common databases	20
Whole genome sequencing of silver carp (Hypophthalmichthys molitrix) and bighead carp (Hypophthalmichthys nobilis) provide novel insights into their evolution and speciation	20
Chromosome‐level assembly of southern catfish (silurus meridionalis) provides insights into visual adaptation to nocturnal and benthic lifestyles	19
Elucidating shark diets with DNA metabarcoding from cloacal swabs	19
Genomics of natural history collections for understanding evolution in the wild	19
High quality genome of Erigeron breviscapus provides a reference for herbal plants in Asteraceae	19
DNA methylation as a tool to explore ageing in wild roe deer populations	19
Chromosome‐level genome and population genomic analysis provide insights into the evolution and environmental adaptation of Jinjiang oysterCrassostrea ariakensis	19
Untangling ITS2 genotypes of algal symbionts in zooxanthellate corals	19
Detecting selected haplotype blocks in evolve and resequence experiments	19
Chromosome level reference of Atlantic halibut Hippoglossushippoglossus provides insight into the evolution of sexual determination systems	19
Phylogenomic analyses of the genusDrosophilareveals genomic signals of climate adaptation	19
DROP: Molecular voucher database for identification of Drosophila parasitoids	19
Canonical correlations reveal adaptive loci and phenotypic responses to climate in perennial ryegrass	19
Coming of age for COI metabarcoding of whole organism community DNA: Towards bioinformatic harmonisation	19
A chromosome‐level genome assembly of rice leaffolder, Cnaphalocrocis medinalis	19
Fish eDNA metabarcoding from aquatic biofilm samples: Methodological aspects	19
A high‐quality genome assembly of Jasminum sambac provides insight into floral trait formation and Oleaceae genome evolution	19
Genomic analysis of Medicago ruthenica provides insights into its tolerance to abiotic stress and demographic history	19
Pseudoreplication in genomic‐scale data sets	18
Species discrimination in Schima (Theaceae): Next‐generation super‐barcodes meet evolutionary complexity	18
A high‐quality carabid genome assembly provides insights into beetle genome evolution and cold adaptation	18
Reference genome of lumpfish Cyclopterus lumpus Linnaeus provides evidence of male heterogametic sex determination through the AMH pathway	18
Benchmarking the performance of Pool‐seq SNP callers using simulated and real sequencing data	18
Microbial networks inferred from environmental DNA data for biomonitoring ecosystem change: Strengths and pitfalls	18
ModEst: Accurate estimation of genome size from next generation sequencing data	18
Biodiversity monitoring using environmental DNA	18
Molecular dating for phylogenies containing a mix of populations and species by using Bayesian and RelTime approaches	18
Efficiency of eDNA and iDNA in assessing vertebrate diversity and its abundance	18
Optimal sample size for calibrating DNA methylation age estimators	17
Joint identification of sex and sex‐linked scaffolds in non‐model organisms using low depth sequencing data	17
The predator problem and PCR primers in molecular dietary analysis: Swamped or silenced; depth or breadth?	17
Improved genome assembly of Chinese shrimp (Fenneropenaeus chinensis) suggests adaptation to the environment during evolution and domestication	17
Novel quality metrics allow identifying and generating high‐quality assemblies of piRNA clusters	17
Maximizing the acquisition of unique reads in noninvasive capture sequencing experiments	17

Chromosome‐level reference genome of the soursop (Annonamuricata): A new resource for Magnoliid research and tropical pomology	17
Chromosome‐level de novo genome assembly of Sarcophaga peregrina provides insights into the evolutionary adaptation of flesh flies	17
Chromosome‐level genome assembly of the aphid parasitoid Aphidius gifuensis using Oxford Nanopore sequencing and Hi‐C technology	17
Genetic landscape clustering of a large DNA barcoding data set reveals shared patterns of genetic divergence among freshwater fishes of the Maroni Basin	17
TransPi—a comprehensive TRanscriptome ANalysiS PIpeline for de novo transcriptome assembly	17
FrogCap: A modular sequence capture probe‐set for phylogenomics and population genetics for all frogs, assessed across multiple phylogenetic scales	17
An ecologist's guide for studying DNA methylation variation in wild vertebrates	17
DNA barcoding uncovers cryptic diversity in minute herbivorous mites (Acari, Eriophyoidea)	17
Chromosome‐level assembly of the mangrove plant Aegiceras corniculatum genome generated through Illumina, PacBio and Hi‐C sequencing technologies	17
Effective double‐digest RAD sequencing and genotyping despite large genome size	16
Chromosomal‐level genome of a sheet‐web spider provides insight into the composition and evolution of venom	16
Chromosome‐level genome assembly reveals genomic architecture of northern range expansion in the mountain pine beetle, Dendroctonus ponderosae Hopkins (Coleoptera: Curculionidae)	16
The genome of Draba nivalis shows signatures of adaptation to the extreme environmental stresses of the Arctic	16
Environmental nucleic acids: A field‐based comparison for monitoring freshwater habitats using eDNA and eRNA	16
Generation of a chromosome‐level genome assembly for Pacific halibut (Hippoglossus stenolepis) and characterization of its sex‐determining genomic region	16
Chromosomal‐scale genome assembly of Eleutherococcus senticosus provides insights into chromosome evolution in Araliaceae	16
The genomic architecture of the passerine MHC region: High repeat content and contrasting evolutionary histories of single copy and tandemly duplicated MHC genes	16
A chromosome‐anchored genome assembly for Lake Trout (Salvelinus namaycush)	16
Phylogeographic model selection using convolutional neural networks	16
Spider webs as eDNA samplers: Biodiversity assessment across the tree of life	16
Transposable element annotation in non‐model species: The benefits of species‐specific repeat libraries using semi‐automated EDTA and DeepTE de novo pipelines	16
Hidden diversity of Ctenophora revealed by new mitochondrial COI primers and sequences	15
EggLib 3: A python package for population genetics and genomics	15
Invertebrates for vertebrate biodiversity monitoring: Comparisons using three insect taxa as iDNA samplers	15
Comparison of destructive and nondestructive DNA extraction methods for the metabarcoding of arthropod bulk samples	15
The discernible and hidden effects of clonality on the genotypic and genetic states of populations: Improving our estimation of clonal rates	15
Long‐ and short‐read metabarcoding technologies reveal similar spatiotemporal structures in fungal communities	15
Chromosome‐scale genomes reveal genomic consequences of inbreeding in the South China tiger: A comparative study with the Amur tiger	15
Genomic insights into the adaptation and evolution of the nautilus, an ancient but evolving “living fossil”	15
Age prediction of green turtles with an epigenetic clock	15
Exon probe sets and bioinformatics pipelines for all levels of fish phylogenomics	15
Chromosome‐scale inference of hybrid speciation and admixture with convolutional neural networks	15
Origin matters: Using a local reference genome improves measures in population genomics	15
Chromosome‐level genome assembly of Paralithodes platypus provides insights into evolution and adaptation of king crabs	15
mold, a novel software to compile accurate and reliable DNA diagnoses for taxonomic descriptions	15
The chromosome‐scale genome assembly, annotation and evolution of Rhododendron henanense subsp. lingbaoense	15
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	15
The genome of low‐chill Chinese plum “Sanyueli” (Prunus salicina Lindl.) provides insights into the regulation of the chilling requirement of flower buds	15
Chromosome‐level de novo genome assembly of Telopea speciosissima (New South Wales waratah) using long‐reads, linked‐reads and Hi‐C	14
Understudied, underrepresented, and unknown: Methodological biases that limit detection of early diverging fungi from environmental samples	14
On‐site environmental DNA detection of species using ultrarapid mobile PCR	14
Chromosome‐level genome assembly of the Arctic fox (Vulpes lagopus) using PacBio sequencing and Hi‐C technology	14
Successes and limitations of quantitative diet metabarcoding in a small, herbivorous mammal	14
snpR: User friendly population genomics for SNP data sets with categorical metadata	14
SCNIC: Sparse correlation network investigation for compositional data	14
An ancient truncated duplication of the anti‐Müllerian hormone receptor type 2 gene is a potential conserved master sex determinant in the Pangasiidae catfish family	14
Trio‐binned genomes of the woodrats Neotoma bryanti and Neotoma lepida reveal novel gene islands and rapid copy number evolution of xenobiotic metabolizing genes	14
DNA barcoding of fungal specimens using PacBio long‐read high‐throughput sequencing	14
A chromosome level genome assembly of Propsilocerus akamusi to understand its response to heavy metal exposure	14
A high‐quality reference genome for Fraxinus pennsylvanica for ash species restoration and research	14