Molecular Ecology Resources

Article	Citations
ASAP: assemble species by automatic partitioning	795
pixy: Unbiased estimation of nucleotide diversity and divergence in the presence of missing data	293
CPGView: A package for visualizing detailed chloroplast genome structures	256
Extending approximate Bayesian computation with supervised machine learning to infer demographic history from genetic polymorphisms using DIYABC Random Forest	79
SCycDB: A curated functional gene database for metagenomic profiling of sulphur cycling pathways	73
Experimental support for genomic prediction of climate maladaptation using the machine learning approach Gradient Forests	66
Reference genome and demographic history of the most endangered marine mammal, the vaquita	56
Construction of a chromosome‐level genome and variation map for the Pacific oyster Crassostrea gigas	56
Improving metabarcoding taxonomic assignment: A case study of fishes in a large marine ecosystem	54
Chromosomal‐level genomes of three rice planthoppers provide new insights into sex chromosome evolution	54
Integrating eDNA metabarcoding and simultaneous underwater visual surveys to describe complex fish communities in a marine biodiversity hotspot	53
Improving the reliability of eDNA data interpretation	53
pr2‐primers: An 18S rRNA primer database for protists	53
eDNAFlow, an automated, reproducible and scalable workflow for analysis of environmental DNA sequences exploiting Nextflow and Singularity	53
Complex interactions between environmental DNA (eDNA) state and water chemistries on eDNA persistence suggested by meta‐analyses	52
A chromosome‐level assembly of the black tiger shrimp (Penaeus monodon) genome facilitates the identification of growth‐associated genes	51
Strategies for sample labelling and library preparation in DNA metabarcoding studies	50
LEA 3: Factor models in population genetics and ecological genomics with R	49
A high‐quality genome assembly of the eggplant provides insights into the molecular basis of disease resistance and chlorogenic acid synthesis	48
Benchmarking bioinformatic tools for fast and accurate eDNA metabarcoding species identification	48
High‐quality chromosome‐level genomes of two tilapia species reveal their evolution of repeat sequences and sex chromosomes	46
SambaR: An R package for fast, easy and reproducible population‐genetic analyses of biallelic SNP data sets	46
Navigating the seven challenges of taxonomic reference databases in metabarcoding analyses	45
Bioinformatic pipelines combining denoising and clustering tools allow for more comprehensive prokaryotic and eukaryotic metabarcoding	45
DiversityScanner: Robotic handling of small invertebrates with machine learning methods	44

The changing face of genome assemblies: Guidance on achieving high‐quality reference genomes	44
DILS: Demographic inferences with linked selection by using ABC	43
Successful application of ancient DNA extraction and library construction protocols to museum wet collection specimens	43
Automatic inference of demographic parameters using generative adversarial networks	43
RADSex: A computational workflow to study sex determination using restriction site‐associated DNA sequencing data	43
Testing genome skimming for species discrimination in the large and taxonomically difficult genus Rhododendron	40
The influence of intraspecific sequence variation during DNA metabarcoding: A case study of eleven fungal species	39
Assessment of current taxonomic assignment strategies for metabarcoding eukaryotes	39
f‐Statistics estimation and admixture graph construction with Pool‐Seq or allele count data using the R package poolfstat	38
Commonly used Hardy–Weinberg equilibrium filtering schemes impact population structure inferences using RADseq data	37
Nonlethal age estimation of three threatened fish species using DNA methylation: Australian lungfish, Murray cod and Mary River cod	37
A large genome with chromosome‐scale assembly sheds light on the evolutionary success of a true toad (Bufo gargarizans)	37
Chromosome‐level reference genome assembly provides insights into aroma biosynthesis in passion fruit (Passiflora edulis)	36
Chromosome‐level genome assembly of Sichuan pepper provides insights into apomixis, drought tolerance, and alkaloid biosynthesis	36
Model‐based genotype and ancestry estimation for potential hybrids with mixed‐ploidy	36
Barcode UK: A complete DNA barcoding resource for the flowering plants and conifers of the United Kingdom	35
A molecular‐based identification resource for the arthropods of Finland	34
Chromosome‐scale assembly of the genome of Salixdunnii reveals a male‐heterogametic sex determination system on chromosome 7	34
metaPR2: A database of eukaryotic 18S rRNA metabarcodes with an emphasis on protists	34
Assessing genome assembly quality prior to downstream analysis: N50 versus BUSCO	33
NOVOWrap: An automated solution for plastid genome assembly and structure standardization	32
A chromosome‐scale genome assembly of the Mongolian oak (Quercus mongolica)	32
Guidelines for standardizing the application of discriminant analysis of principal components to genotype data	31
A robust approach to estimate relative phytoplankton cell abundances from metagenomes	31
User‐friendly bioinformatics pipeline gDAT (graphical downstream analysis tool) for analysing rDNA sequences	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
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
Unlocking inaccessible historical genomes preserved in formalin	30
MCycDB: A curated database for comprehensively profiling methane cycling processes of environmental microbiomes	29
RepeatProfiler: A pipeline for visualization and comparative analysis of repetitive DNA profiles	29
Limits and convergence properties of the sequentially Markovian coalescent	29
Exhaustive reanalysis of barcode sequences from public repositories highlights ongoing misidentifications and impacts taxa diversity and distribution	29
Genome‐scale target capture of mitochondrial and nuclear environmental DNA from water samples	29
Chromosome‐level assembly of the brown planthopper genome with a characterized Y chromosome	29
High quality haplotype‐resolved genome assemblies of Populus tomentosa Carr., a stabilized interspecific hybrid species widespread in Asia	28
The Meishan pig genome reveals structural variation‐mediated gene expression and phenotypic divergence underlying Asian pig domestication	28
snpfiltr: An R package for interactive and reproducible SNP filtering	28
Quantitative monitoring of diverse fish communities on a large scale combining eDNA metabarcoding and qPCR	28
Individual haplotyping of whale sharks from seawater environmental DNA	28
Fast and accurate distance‐based phylogenetic placement using divide and conquer	28
The genomes of chicory, endive, great burdock and yacon provide insights into Asteraceae palaeo‐polyploidization history and plant inulin production	28
Nonrandom missing data can bias Principal Component Analysis inference of population genetic structure	28
Towards reproducible metabarcoding data: Lessons from an international cross‐laboratory experiment	28
Taxon‐specific or universal? Using target capture to study the evolutionary history of rapid radiations	28
Chromosome‐level genome assembly of the bean bug Riptortus pedestris	27
Chromosome‐level genome assembly of Lethenteron reissneri provides insights into lamprey evolution	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
Systematic review and meta‐analysis: Water type and temperature affect environmental DNA decay	26

A step towards the validation of bacteria biotic indices using DNA metabarcoding for benthic monitoring	26
Design and implementation of multiplexed amplicon sequencing panels to serve genomic epidemiology of infectious disease: A malaria case study	26
Detecting population declines via monitoring the effective number of breeders (Nb)	25
Extracting abundance information from DNA‐based data	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
High molecular weight DNA extraction strategies for long‐read sequencing of complex metagenomes	25
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	25
DNA barcoding of Cymbidium by genome skimming: Call for next‐generation nuclear barcodes	24
TaxonTableTools: A comprehensive, platform‐independent graphical user interface software to explore and visualise DNA metabarcoding data	24
Why eDNA fractions need consideration in biomonitoring	24
Detection and population genomics of sea turtle species via noninvasive environmental DNA analysis of nesting beach sand tracks and oceanic water	24
Evaluating the role of reference‐genome phylogenetic distance on evolutionary inference	24
A targeted amplicon sequencing panel to simultaneously identify mosquito species and Plasmodium presence across the entire Anopheles genus	24
A guide to avian museomics: Insights gained from resequencing hundreds of avian study skins	24
Chromosome‐scale genome assembly of areca palm (Areca catechu)	24
Analysing landscape effects on dispersal networks and gene flow with genetic graphs	24
A unified model of species abundance, genetic diversity, and functional diversity reveals the mechanisms structuring ecological communities	24
Characterizing the spatial signal of environmental DNA in river systems using a community ecology approach	24
Population genomics provides insights into lineage divergence and local adaptation within the cotton bollworm	24
Speeding up the detection of invasive bivalve species using environmental DNA: A Nanopore and Illumina sequencing comparison	24
The Ocean barcode atlas: A web service to explore the biodiversity and biogeography of marine organisms	24
Pairwise linkage disequilibrium estimation for polyploids	24
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
Validated removal of nuclear pseudogenes and sequencing artefacts from mitochondrial metabarcode data	23
Environmental RNA degrades more rapidly than environmental DNA across a broad range of pH conditions	23
Fish eDNA metabarcoding from aquatic biofilm samples: Methodological aspects	22
Short‐ and long‐read metabarcoding of the eukaryotic rRNA operon: Evaluation of primers and comparison to shotgun metagenomics sequencing	22
Metagenomics: A viable tool for reconstructing herbivore diet	22
ModEst: Accurate estimation of genome size from next generation sequencing data	22
Whole genome sequencing of silver carp (Hypophthalmichthys molitrix) and bighead carp (Hypophthalmichthys nobilis) provide novel insights into their evolution and speciation	22
The genomic architecture of the passerine MHC region: High repeat content and contrasting evolutionary histories of single copy and tandemly duplicated MHC genes	20
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
An ecologist's guide for studying DNA methylation variation in wild vertebrates	20
Genomic analysis of Medicago ruthenica provides insights into its tolerance to abiotic stress and demographic history	20
Elucidating shark diets with DNA metabarcoding from cloacal swabs	20
Practical application of the linkage disequilibrium method for estimating contemporary effective population size: A review	20
Chromosome level reference of Atlantic halibut Hippoglossushippoglossus provides insight into the evolution of sexual determination systems	20
Batch effects in population genomic studies with low‐coverage whole genome sequencing data: Causes, detection and mitigation	20
Chromosome‐level genome and population genomic analysis provide insights into the evolution and environmental adaptation of Jinjiang oysterCrassostrea ariakensis	20
Coming of age for COI metabarcoding of whole organism community DNA: Towards bioinformatic harmonisation	20
A chromosome‐level assembly of the harlequin ladybird Harmonia axyridis as a genomic resource to study beetle and invasion biology	20
A chromosome‐level genome assembly of rice leaffolder, Cnaphalocrocis medinalis	20
A high‐quality genome assembly of Jasminum sambac provides insight into floral trait formation and Oleaceae genome evolution	20
DROP: Molecular voucher database for identification of Drosophila parasitoids	20
Environmental nucleic acids: A field‐based comparison for monitoring freshwater habitats using eDNA and eRNA	19
DNA methylation as a tool to explore ageing in wild roe deer populations	19
Reference genome of lumpfish Cyclopterus lumpus Linnaeus provides evidence of male heterogametic sex determination through the AMH pathway	19
Joint identification of sex and sex‐linked scaffolds in non‐model organisms using low depth sequencing data	19
Efficiency of eDNA and iDNA in assessing vertebrate diversity and its abundance	19
Chromosome‐level assembly of southern catfish (silurus meridionalis) provides insights into visual adaptation to nocturnal and benthic lifestyles	19
Phylogenomic analyses of the genusDrosophilareveals genomic signals of climate adaptation	19
Canonical correlations reveal adaptive loci and phenotypic responses to climate in perennial ryegrass	19
The predator problem and PCR primers in molecular dietary analysis: Swamped or silenced; depth or breadth?	18
Genetic landscape clustering of a large DNA barcoding data set reveals shared patterns of genetic divergence among freshwater fishes of the Maroni Basin	18
Pseudoreplication in genomic‐scale data sets	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
DNA barcoding uncovers cryptic diversity in minute herbivorous mites (Acari, Eriophyoidea)	18
Optimal sample size for calibrating DNA methylation age estimators	18
Chromosomal‐level genome of a sheet‐web spider provides insight into the composition and evolution of venom	18
Chromosome‐level genome assembly of the aphid parasitoid Aphidius gifuensis using Oxford Nanopore sequencing and Hi‐C technology	18
A high‐quality carabid genome assembly provides insights into beetle genome evolution and cold adaptation	18
Biodiversity monitoring using environmental DNA	18
Generation of a chromosome‐level genome assembly for Pacific halibut (Hippoglossus stenolepis) and characterization of its sex‐determining genomic region	18
Species discrimination in Schima (Theaceae): Next‐generation super‐barcodes meet evolutionary complexity	18
TransPi—a comprehensive TRanscriptome ANalysiS PIpeline for de novo transcriptome assembly	17
Age prediction of green turtles with an epigenetic clock	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
Spider webs as eDNA samplers: Biodiversity assessment across the tree of life	17
Chromosome‐level assembly of the mangrove plant Aegiceras corniculatum genome generated through Illumina, PacBio and Hi‐C sequencing technologies	17
Transposable element annotation in non‐model species: The benefits of species‐specific repeat libraries using semi‐automated EDTA and DeepTE de novo pipelines	17
FrogCap: A modular sequence capture probe‐set for phylogenomics and population genetics for all frogs, assessed across multiple phylogenetic scales	17
Improved genome assembly of Chinese shrimp (Fenneropenaeus chinensis) suggests adaptation to the environment during evolution and domestication	17
The genome of Draba nivalis shows signatures of adaptation to the extreme environmental stresses of the Arctic	16
A chromosome‐anchored genome assembly for Lake Trout (Salvelinus namaycush)	16
Phylogeographic model selection using convolutional neural networks	16

Exon probe sets and bioinformatics pipelines for all levels of fish phylogenomics	16
Successes and limitations of quantitative diet metabarcoding in a small, herbivorous mammal	16
Chromosome‐scale genomes reveal genomic consequences of inbreeding in the South China tiger: A comparative study with the Amur tiger	16
A pile of pipelines: An overview of the bioinformatics software for metabarcoding data analyses	16
Plastid Genome Assembly Using Long‐read data	16
The chromosome‐scale genome assembly, annotation and evolution of Rhododendron henanense subsp. lingbaoense	16
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	16
DNA barcoding of fungal specimens using PacBio long‐read high‐throughput sequencing	16
Genomic insights into the adaptation and evolution of the nautilus, an ancient but evolving “living fossil”	16
Effective double‐digest RAD sequencing and genotyping despite large genome size	16
Chromosomal‐scale genome assembly of Eleutherococcus senticosus provides insights into chromosome evolution in Araliaceae	16
Chromosome‐level genome assembly reveals genomic architecture of northern range expansion in the mountain pine beetle, Dendroctonus ponderosae Hopkins (Coleoptera: Curculionidae)	16
Understudied, underrepresented, and unknown: Methodological biases that limit detection of early diverging fungi from environmental samples	16
Comparison of destructive and nondestructiveDNAextraction 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
Hidden diversity of Ctenophora revealed by new mitochondrial COI primers and sequences	15
Chromosome‐level genome assembly of the Arctic fox (Vulpes lagopus) using PacBio sequencing and Hi‐C technology	15
Invertebrates for vertebrate biodiversity monitoring: Comparisons using three insect taxa as iDNA samplers	15
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	15
Estimation of the contemporary effective population size from SNP data while accounting for mating structure	15
Chromosome‐scale inference of hybrid speciation and admixture with convolutional neural networks	15
EggLib 3: A python package for population genetics and genomics	15
Long‐ and short‐read metabarcoding technologies reveal similar spatiotemporal structures in fungal communities	15
High‐throughput sequencing‐based microsatellite genotyping for polyploids to resolve allele dosage uncertainty and improve analyses of genetic diversity, structure and differentiation: A case study of	15
Chromosome‐level de novo genome assembly of Telopea speciosissima (New South Wales waratah) using long‐reads, linked‐reads and Hi‐C	15
Origin matters: Using a local reference genome improves measures in population genomics	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
mold, a novel software to compile accurate and reliable DNA diagnoses for taxonomic descriptions	15
SCNIC: Sparse correlation network investigation for compositional data	14
Chromosome‐level genome assemblies of two cotton‐melon aphid Aphis gossypii biotypes unveil mechanisms of host adaption	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
Predicting amphibian intraspecific diversity with machine learning: Challenges and prospects for integrating traits, geography, and genetic data	14
On‐site environmental DNA detection of species using ultrarapid mobile PCR	14
HMS‐S‐S: A tool for the identification of Sulphur metabolism‐related genes and analysis of operon structures in genome and metagenome assemblies	14
snpR: User friendly population genomics for SNP data sets with categorical metadata	14
A chromosome level genome assembly of Propsilocerus akamusi to understand its response to heavy metal exposure	14
A high‐quality reference genome forFraxinus pennsylvanicafor ash species restoration and research	14
Development of DNA methylation‐based epigenetic age predictors in loblolly pine (Pinus taeda)	13
Exploring the vertebrate fauna of the Bird’s Head Peninsula (Indonesia, West Papua) through DNA barcodes	13
Simultaneous genotyping of snails and infecting trematode parasites using high‐throughput amplicon sequencing	13
Regarding the F‐word: The effects of data filtering on inferred genotype‐environment associations	13
The practice and promise of temporal genomics for measuring evolutionary responses to global change	13
The first high‐quality chromosomal genome assembly of a medicinal and edible plant Arctium lappa	13
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	13
Utilizing paralogues for phylogenetic reconstruction has the potential to increase species tree support and reduce gene tree discordance in target enrichment data	13
Environmental DNA persistence and fish detection in captive sponges	13
Opening a next‐generation black box: Ecological trends for hundreds of species‐like taxa uncovered within a single bacterial >99% 16S rRNA operational taxonomic unit	13
A comprehensive analysis comparing linear and generalized linear models in detecting adaptive SNPs	13
Chromosome‐level genome assembly of the endangered humphead wrasse Cheilinus undulatus: Insight into the expansion of opsin genes in fishes	13
Estimating dispersal using close kin dyads: The kindisperse R package	13
Chromosome‐level genome of Poropuntius huangchuchieni provides a diploid progenitor‐like reference genome for the allotetraploid Cyprinus carpio	13
Amazonian mammal monitoring using aquatic environmental DNA	13
Passive sampling of environmental DNA in aquatic environments using 3D‐printed hydroxyapatite samplers	13
Long‐read assembly of the Chinese indigenous Ningxiang pig genome and identification of genetic variations in fat metabolism among different breeds	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
MAUI‐seq: Metabarcoding using amplicons with unique molecular identifiers to improve error correction	13
crabs—A software program to generate curated reference databases for metabarcoding sequencing data	13
High‐throughput sequencing of faeces provides evidence for dispersal of parasites and pathogens by migratory waterbirds	12
NGSEP 4: Efficient and accurate identification of orthogroups and whole‐genome alignment	12
A multitiered sequence capture strategy spanning broad evolutionary scales: Application for phylogenetic and phylogeographic studies of orchids	12
Complex genetic admixture histories reconstructed with Approximate Bayesian Computation	12
Using target capture to address conservation challenges: Population‐level tracking of a globally‐traded herbal medicine	12
eDNAssay: A machine learning tool that accurately predicts qPCR cross‐amplification	12
Assessing the utility of marine filter feeders for environmental DNA (eDNA) biodiversity monitoring	12
Chromosome‐level genome assembly of burbot (Lota lota) provides insights into the evolutionary adaptations in freshwater	12
Chromosome‐level genome reference and genome editing of the tea geometrid	12
Optimal sequence similarity thresholds for clustering of molecular operational taxonomic units inDNAmetabarcoding studies	12
epiGBS2: Improvements and evaluation of highly multiplexed, epiGBS‐based reduced representation bisulfite sequencing	12
Chromosome level assembly reveals a unique immune gene organization and signatures of evolution in the common pheasant	12
Comparison of materials for rapid passive collection of environmental DNA	12
Culture‐enriched community profiling improves resolution of the vertebrate gut microbiota	12
A chromosome‐level genome assembly for the tertiary relict plant Tetracentron sinense oliv. (trochodendraceae)	12
A chromosome‐level genome of Antechinus flavipes provides a reference for an Australian marsupial genus with male death after mating	12
Deciphering the molecular signal from past and alive bacterial communities in aquatic sedimentary archives	11
Genomic library preparation and hybridization capture of formalin‐fixed tissues and allozyme supernatant for population genomics and considerations for combining capture‐ and RADseq‐based single nucle	11
A library preparation optimized for metagenomics of RNA viruses	11
Invertebrate methylomes provide insight into mechanisms of environmental tolerance and reveal methodological biases	11
Pitfalls in the statistical analysis of microbiome amplicon sequencing data	11
Genome‐wide association study analysis to resolve the key regulatory mechanism of biomineralization in Pinctada fucata martensii	11
msGBS: A new high‐throughput approach to quantify the relative species abundance in root samples of multispecies plant communities	11
Assessing candidate DNA barcodes for Chinese and internationally traded timber species	11
A chromosome‐scale genome assembly and annotation of the spring orchid (Cymbidium goeringii)	11
Development of epigenetic biomarkers for the identification of sex and thermal stress in fish using DNA methylation analysis and machine learning procedures	11
Comparing genome‐based estimates of relatedness for use in pedigree‐based conservation management	11
Sequencing platform shifts provide opportunities but pose challenges for combining genomic data sets	11
Obtaining deeper insights into microbiome diversity using a simple method to block host and nontargets in amplicon sequencing	11
When barcoding fails: Genome chimerization (admixing) and reticulation obscure phylogenetic and taxonomic relationships	11
Benchmarking DNA methylation assays in a reef‐building coral	11
Recovered microbiome of an oviparous lizard differs across gut and reproductive tissues, cloacal swabs, and faeces	11
A reference‐free approach to analyse RADseq data using standard next generation sequencing toolkits	11
A chromosome‐level genome of Portunus trituberculatus provides insights into its evolution, salinity adaptation and sex determination	11
MrIML: Multi‐response interpretable machine learning to model genomic landscapes	11
A chromosomal assembly of the soybean cyst nematode genome	11
A chromosome‐scale reference genome assembly of yellow mangrove (Bruguiera parviflora) reveals a whole genome duplication event associated with the Rhizophoraceae lineage	11
A genome‐wide SNP genotyping resource for tropical pine tree species	11