Molecular Ecology Resources

Papers
(The median citation count of Molecular Ecology Resources is 5. The table below lists those papers that are above that threshold based on CrossRef citation counts [max. 250 papers]. The publications cover those that have been published in the past four years, i.e., from 2020-10-01 to 2024-10-01.)
ArticleCitations
ASAP: assemble species by automatic partitioning724
Dsuite ‐ Fast D‐statistics and related admixture evidence from VCF files394
pixy: Unbiased estimation of nucleotide diversity and divergence in the presence of missing data262
CPGView: A package for visualizing detailed chloroplast genome structures256
Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird‐of‐paradise100
Extending approximate Bayesian computation with supervised machine learning to infer demographic history from genetic polymorphisms using DIYABC Random Forest79
SCycDB: A curated functional gene database for metagenomic profiling of sulphur cycling pathways73
Experimental support for genomic prediction of climate maladaptation using the machine learning approach Gradient Forests60
Reference genome and demographic history of the most endangered marine mammal, the vaquita56
Construction of a chromosome‐level genome and variation map for the Pacific oyster Crassostrea gigas53
Complex interactions between environmental DNA (eDNA) state and water chemistries on eDNA persistence suggested by meta‐analyses51
Strategies for sample labelling and library preparation in DNA metabarcoding studies50
Improving the reliability of eDNA data interpretation50
Chromosomal‐level genomes of three rice planthoppers provide new insights into sex chromosome evolution50
Integrating eDNA metabarcoding and simultaneous underwater visual surveys to describe complex fish communities in a marine biodiversity hotspot50
pr2‐primers: An 18S rRNA primer database for protists49
A high‐quality genome assembly of the eggplant provides insights into the molecular basis of disease resistance and chlorogenic acid synthesis48
A chromosome‐level assembly of the black tiger shrimp (Penaeus monodon) genome facilitates the identification of growth‐associated genes48
Improving metabarcoding taxonomic assignment: A case study of fishes in a large marine ecosystem48
eDNAFlow, an automated, reproducible and scalable workflow for analysis of environmental DNA sequences exploiting Nextflow and Singularity47
LEA 3: Factor models in population genetics and ecological genomics with R46
Bioinformatic pipelines combining denoising and clustering tools allow for more comprehensive prokaryotic and eukaryotic metabarcoding45
Benchmarking bioinformatic tools for fast and accurate eDNA metabarcoding species identification45
The changing face of genome assemblies: Guidance on achieving high‐quality reference genomes44
High‐quality chromosome‐level genomes of two tilapia species reveal their evolution of repeat sequences and sex chromosomes44
Chromosome‐level genome assembly for the largemouth bass Micropterus salmoides provides insights into adaptation to fresh and brackish water44
DiversityScanner: Robotic handling of small invertebrates with machine learning methods44
Successful application of ancient DNA extraction and library construction protocols to museum wet collection specimens43
RADSex: A computational workflow to study sex determination using restriction site‐associated DNA sequencing data43
SambaR: An R package for fast, easy and reproducible population‐genetic analyses of biallelic SNP data sets42
Automatic inference of demographic parameters using generative adversarial networks41
Testing genome skimming for species discrimination in the large and taxonomically difficult genus Rhododendron40
Apolygus lucorum genome provides insights into omnivorousness and mesophyll feeding39
The influence of intraspecific sequence variation during DNA metabarcoding: A case study of eleven fungal species39
Navigating the seven challenges of taxonomic reference databases in metabarcoding analyses38
f‐Statistics estimation and admixture graph construction with Pool‐Seq or allele count data using the R package poolfstat38
DILS: Demographic inferences with linked selection by using ABC38
The elephant grass (Cenchrus purpureus) genome provides insights into anthocyanidin accumulation and fast growth38
Commonly used Hardy–Weinberg equilibrium filtering schemes impact population structure inferences using RADseq data37
Assessment of current taxonomic assignment strategies for metabarcoding eukaryotes37
A large genome with chromosome‐scale assembly sheds light on the evolutionary success of a true toad (Bufo gargarizans)37
Nonlethal age estimation of three threatened fish species using DNA methylation: Australian lungfish, Murray cod and Mary River cod37
Model‐based genotype and ancestry estimation for potential hybrids with mixed‐ploidy36
Chromosome‐level reference genome assembly provides insights into aroma biosynthesis in passion fruit (Passiflora edulis)36
Barcode UK: A complete DNA barcoding resource for the flowering plants and conifers of the United Kingdom35
Chromosome‐level genome assembly of Sichuan pepper provides insights into apomixis, drought tolerance, and alkaloid biosynthesis35
Chromosome‐scale assembly of the genome of Salixdunnii reveals a male‐heterogametic sex determination system on chromosome 734
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 research34
Giant African snail genomes provide insights into molluscan whole‐genome duplication and aquatic–terrestrial transition34
A molecular‐based identification resource for the arthropods of Finland34
Assessing genome assembly quality prior to downstream analysis: N50 versus BUSCO33
A high‐quality genome of taro (Colocasia esculenta (L.) Schott), one of the world's oldest crops33
A chromosome‐scale genome assembly of the Mongolian oak (Quercus mongolica)32
BAGS: An automated Barcode, Audit & Grade System for DNA barcode reference libraries32
NOVOWrap: An automated solution for plastid genome assembly and structure standardization32
User‐friendly bioinformatics pipeline gDAT (graphical downstream analysis tool) for analysing rDNA sequences31
metaPR2: A database of eukaryotic 18S rRNA metabarcodes with an emphasis on protists31
A robust approach to estimate relative phytoplankton cell abundances from metagenomes31
Distinguishing between recent balancing selection and incomplete sweep using deep neural networks31
A chromosome‐scale assembly of the bilberry genome identifies a complex locus controlling berry anthocyanin composition31
Unlocking inaccessible historical genomes preserved in formalin30
Hybridization capture of larch (Larix Mill.) chloroplast genomes from sedimentary ancient DNA reveals past changes of Siberian forest30
A chromosome‐level genome assembly of the woolly apple aphid, Eriosoma lanigerum Hausmann (Hemiptera: Aphididae)30
Factors affecting the efficiency of molecular species delimitation in a species‐rich insect family30
Genome‐scale target capture of mitochondrial and nuclear environmental DNA from water samples29
Chromosome‐level assembly of the brown planthopper genome with a characterized Y chromosome29
MCycDB: A curated database for comprehensively profiling methane cycling processes of environmental microbiomes29
RepeatProfiler: A pipeline for visualization and comparative analysis of repetitive DNA profiles29
Limits and convergence properties of the sequentially Markovian coalescent29
Exhaustive reanalysis of barcode sequences from public repositories highlights ongoing misidentifications and impacts taxa diversity and distribution29
Quantitative monitoring of diverse fish communities on a large scale combining eDNA metabarcoding and qPCR28
Fast and accurate distance‐based phylogenetic placement using divide and conquer28
Nonrandom missing data can bias Principal Component Analysis inference of population genetic structure28
Taxon‐specific or universal? Using target capture to study the evolutionary history of rapid radiations28
Individual haplotyping of whale sharks from seawater environmental DNA28
Chromosome‐level genome assembly of the bean bug Riptortus pedestris27
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 i27
Chromosome‐level genome assembly of Lethenteron reissneri provides insights into lamprey evolution27
Towards reproducible metabarcoding data: Lessons from an international cross‐laboratory experiment27
Guidelines for standardizing the application of discriminant analysis of principal components to genotype data26
Design and implementation of multiplexed amplicon sequencing panels to serve genomic epidemiology of infectious disease: A malaria case study26
High quality haplotype‐resolved genome assemblies of Populus tomentosa Carr., a stabilized interspecific hybrid species widespread in Asia26
Detecting population declines via monitoring the effective number of breeders (Nb)25
High molecular weight DNA extraction strategies for long‐read sequencing of complex metagenomes25
Automated improvement of stickleback reference genome assemblies with Lep‐Anchor software25
The genomes of chicory, endive, great burdock and yacon provide insights into Asteraceae palaeo‐polyploidization history and plant inulin production25
The Meishan pig genome reveals structural variation‐mediated gene expression and phenotypic divergence underlying Asian pig domestication25
Extracting abundance information from DNA‐based data25
Long read sequencing of Toona sinensis (A. Juss) Roem: A chromosome‐level reference genome for the family Meliaceae25
Characterizing the spatial signal of environmental DNA in river systems using a community ecology approach24
A unified model of species abundance, genetic diversity, and functional diversity reveals the mechanisms structuring ecological communities24
Evaluating the role of reference‐genome phylogenetic distance on evolutionary inference24
The Ocean barcode atlas: A web service to explore the biodiversity and biogeography of marine organisms24
Chromosome‐scale genome assembly of areca palm (Areca catechu)24
snpfiltr: An R package for interactive and reproducible SNP filtering24
Population genomics provides insights into lineage divergence and local adaptation within the cotton bollworm24
A targeted amplicon sequencing panel to simultaneously identify mosquito species and Plasmodium presence across the entire Anopheles genus24
Detection and population genomics of sea turtle species via noninvasive environmental DNA analysis of nesting beach sand tracks and oceanic water24
A guide to avian museomics: Insights gained from resequencing hundreds of avian study skins24
Analysing landscape effects on dispersal networks and gene flow with genetic graphs24
Systematic review and meta‐analysis: Water type and temperature affect environmental DNA decay23
A step towards the validation of bacteria biotic indices using DNA metabarcoding for benthic monitoring23
Validated removal of nuclear pseudogenes and sequencing artefacts from mitochondrial metabarcode data23
A chromosome‐level genome of the mud crab (Scylla paramamosain estampador) provides insights into the evolution of chemical and light perception in this crustacean23
Why eDNA fractions need consideration in biomonitoring23
Short‐ and long‐read metabarcoding of the eukaryotic rRNA operon: Evaluation of primers and comparison to shotgun metagenomics sequencing22
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 nematode22
Speeding up the detection of invasive bivalve species using environmental DNA: A Nanopore and Illumina sequencing comparison22
TaxonTableTools: A comprehensive, platform‐independent graphical user interface software to explore and visualise DNA metabarcoding data21
Whole genome sequencing of silver carp (Hypophthalmichthys molitrix) and bighead carp (Hypophthalmichthys nobilis) provide novel insights into their evolution and speciation21
Metagenomics: A viable tool for reconstructing herbivore diet21
Environmental RNA degrades more rapidly than environmental DNA across a broad range of pH conditions21
Pairwise linkage disequilibrium estimation for polyploids21
Elucidating shark diets with DNA metabarcoding from cloacal swabs20
A chromosome‐level assembly of the harlequin ladybird Harmonia axyridis as a genomic resource to study beetle and invasion biology20
Chromosome level reference of Atlantic halibut Hippoglossushippoglossus provides insight into the evolution of sexual determination systems20
Batch effects in population genomic studies with low‐coverage whole genome sequencing data: Causes, detection and mitigation20
ddPCR surpasses classical qPCR technology in quantitating bacteria and fungi in the environment20
Whole‐genome sequencing of brown‐marbled grouper (Epinephelus fuscoguttatus) provides insights into adaptive evolution and growth differences20
Contaminations contaminate common databases20
A high‐quality genome assembly of Jasminum sambac provides insight into floral trait formation and Oleaceae genome evolution20
DNA barcoding of Cymbidium by genome skimming: Call for next‐generation nuclear barcodes20
Coming of age for COI metabarcoding of whole organism community DNA: Towards bioinformatic harmonisation20
High quality genome of Erigeron breviscapus provides a reference for herbal plants in Asteraceae20
An ecologist's guide for studying DNA methylation variation in wild vertebrates20
DROP: Molecular voucher database for identification of Drosophila parasitoids20
Chromosome‐level genome and population genomic analysis provide insights into the evolution and environmental adaptation of Jinjiang oysterCrassostrea ariakensis19
Efficiency of eDNA and iDNA in assessing vertebrate diversity and its abundance19
Chromosome‐level assembly of southern catfish (silurus meridionalis) provides insights into visual adaptation to nocturnal and benthic lifestyles19
A chromosome‐level genome assembly of rice leaffolder, Cnaphalocrocis medinalis19
DNA methylation as a tool to explore ageing in wild roe deer populations19
Canonical correlations reveal adaptive loci and phenotypic responses to climate in perennial ryegrass19
Joint identification of sex and sex‐linked scaffolds in non‐model organisms using low depth sequencing data19
Phylogenomic analyses of the genusDrosophilareveals genomic signals of climate adaptation19
Genomic analysis of Medicago ruthenica provides insights into its tolerance to abiotic stress and demographic history19
Reference genome of lumpfish Cyclopterus lumpus Linnaeus provides evidence of male heterogametic sex determination through the AMH pathway19
Fish eDNA metabarcoding from aquatic biofilm samples: Methodological aspects19
Biodiversity monitoring using environmental DNA18
Species discrimination in Schima (Theaceae): Next‐generation super‐barcodes meet evolutionary complexity18
Chromosome‐level genome assembly of the aphid parasitoid Aphidius gifuensis using Oxford Nanopore sequencing and Hi‐C technology18
ModEst: Accurate estimation of genome size from next generation sequencing data18
Optimal sample size for calibrating DNA methylation age estimators18
Generation of a chromosome‐level genome assembly for Pacific halibut (Hippoglossus stenolepis) and characterization of its sex‐determining genomic region18
Microbial networks inferred from environmental DNA data for biomonitoring ecosystem change: Strengths and pitfalls18
DNA barcoding uncovers cryptic diversity in minute herbivorous mites (Acari, Eriophyoidea)18
A high‐quality carabid genome assembly provides insights into beetle genome evolution and cold adaptation18
Pseudoreplication in genomic‐scale data sets18
Benchmarking the performance of Pool‐seq SNP callers using simulated and real sequencing data18
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 Basin18
Maximizing the acquisition of unique reads in noninvasive capture sequencing experiments17
Age prediction of green turtles with an epigenetic clock17
Novel quality metrics allow identifying and generating high‐quality assemblies of piRNA clusters17
Transposable element annotation in non‐model species: The benefits of species‐specific repeat libraries using semi‐automated EDTA and DeepTE de novo pipelines17
Chromosome‐level reference genome of the soursop (Annonamuricata): A new resource for Magnoliid research and tropical pomology17
Improved genome assembly of Chinese shrimp (Fenneropenaeus chinensis) suggests adaptation to the environment during evolution and domestication17
TransPi—a comprehensive TRanscriptome ANalysiS PIpeline for de novo transcriptome assembly17
FrogCap: A modular sequence capture probe‐set for phylogenomics and population genetics for all frogs, assessed across multiple phylogenetic scales17
Chromosome‐level assembly of the mangrove plant Aegiceras corniculatum genome generated through Illumina, PacBio and Hi‐C sequencing technologies17
Chromosomal‐scale genome assembly of Eleutherococcus senticosus provides insights into chromosome evolution in Araliaceae16
Successes and limitations of quantitative diet metabarcoding in a small, herbivorous mammal16
The genome of Draba nivalis shows signatures of adaptation to the extreme environmental stresses of the Arctic16
A chromosome‐anchored genome assembly for Lake Trout (Salvelinus namaycush)16
Chromosomal‐level genome of a sheet‐web spider provides insight into the composition and evolution of venom16
Spider webs as eDNA samplers: Biodiversity assessment across the tree of life16
Chromosome‐scale genomes reveal genomic consequences of inbreeding in the South China tiger: A comparative study with the Amur tiger16
The genomic architecture of the passerine MHC region: High repeat content and contrasting evolutionary histories of single copy and tandemly duplicated MHC genes16
Effective double‐digest RAD sequencing and genotyping despite large genome size16
Exon probe sets and bioinformatics pipelines for all levels of fish phylogenomics16
Chromosome‐level genome assembly reveals genomic architecture of northern range expansion in the mountain pine beetle, Dendroctonus ponderosae Hopkins (Coleoptera: Curculionidae)16
Chromosome‐level genome assembly of Paralithodes platypus provides insights into evolution and adaptation of king crabs16
Environmental nucleic acids: A field‐based comparison for monitoring freshwater habitats using eDNA and eRNA16
Phylogeographic model selection using convolutional neural networks16
EggLib 3: A python package for population genetics and genomics15
Genomic insights into the adaptation and evolution of the nautilus, an ancient but evolving “living fossil”15
The chromosome‐scale genome assembly, annotation and evolution of Rhododendron henanense subsp. lingbaoense15
Chromosome‐level genome assembly of the Arctic fox (Vulpes lagopus) using PacBio sequencing and Hi‐C technology15
Long‐ and short‐read metabarcoding technologies reveal similar spatiotemporal structures in fungal communities15
Origin matters: Using a local reference genome improves measures in population genomics15
Invertebrates for vertebrate biodiversity monitoring: Comparisons using three insect taxa as iDNA samplers15
Comparison of destructive and nondestructiveDNAextraction methods for the metabarcoding of arthropod bulk samples15
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 chelicer15
Chromosome‐scale inference of hybrid speciation and admixture with convolutional neural networks15
Hidden diversity of Ctenophora revealed by new mitochondrial COI primers and sequences15
mold, a novel software to compile accurate and reliable DNA diagnoses for taxonomic descriptions15
An ancient truncated duplication of the anti‐Müllerian hormone receptor type 2 gene is a potential conserved master sex determinant in the Pangasiidae catfish family15
The discernible and hidden effects of clonality on the genotypic and genetic states of populations: Improving our estimation of clonal rates15
The genome of low‐chill Chinese plum “Sanyueli” (Prunus salicina Lindl.) provides insights into the regulation of the chilling requirement of flower buds15
A high‐quality reference genome forFraxinus pennsylvanicafor ash species restoration and research14
DNA barcoding of fungal specimens using PacBio long‐read high‐throughput sequencing14
SCNIC: Sparse correlation network investigation for compositional data14
A chromosome level genome assembly of Propsilocerus akamusi to understand its response to heavy metal exposure14
Trio‐binned genomes of the woodrats Neotoma bryanti and Neotoma lepida reveal novel gene islands and rapid copy number evolution of xenobiotic metabolizing genes14
snpR: User friendly population genomics for SNP data sets with categorical metadata14
On‐site environmental DNA detection of species using ultrarapid mobile PCR14
HMS‐S‐S: A tool for the identification of Sulphur metabolism‐related genes and analysis of operon structures in genome and metagenome assemblies14
Chromosome‐level de novo genome assembly of Telopea speciosissima (New South Wales waratah) using long‐reads, linked‐reads and Hi‐C14
Understudied, underrepresented, and unknown: Methodological biases that limit detection of early diverging fungi from environmental samples14
Plastid Genome Assembly Using Long‐read data14
Estimating dispersal using close kin dyads: The kindisperse R package13
crabs—A software program to generate curated reference databases for metabarcoding sequencing data13
Chromosome‐level genome of Poropuntius huangchuchieni provides a diploid progenitor‐like reference genome for the allotetraploid Cyprinus carpio13
Utilizing paralogues for phylogenetic reconstruction has the potential to increase species tree support and reduce gene tree discordance in target enrichment data13
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 of13
Opening a next‐generation black box: Ecological trends for hundreds of species‐like taxa uncovered within a single bacterial >99% 16S rRNA operational taxonomic unit13
A chromosome‐level genome assembly enables the identification of the follicule stimulating hormone receptor as the master sex‐determining gene in the flatfish Solea senegalensis13
Chromosome‐level genome assembly of the endangered humphead wrasse Cheilinus undulatus: Insight into the expansion of opsin genes in fishes13
MAUI‐seq: Metabarcoding using amplicons with unique molecular identifiers to improve error correction13
Genotyping‐in‐thousands by sequencing (GT‐seq) of noninvasive faecal and degraded samples: A new panel to enable ongoing monitoring of Canadian polar bear populations13
Simultaneous genotyping of snails and infecting trematode parasites using high‐throughput amplicon sequencing13
Environmental DNA persistence and fish detection in captive sponges13
Amazonian mammal monitoring using aquatic environmental DNA13
Long‐read assembly of the Chinese indigenous Ningxiang pig genome and identification of genetic variations in fat metabolism among different breeds13
A comprehensive analysis comparing linear and generalized linear models in detecting adaptive SNPs13
Predicting amphibian intraspecific diversity with machine learning: Challenges and prospects for integrating traits, geography, and genetic data13
The first high‐quality chromosomal genome assembly of a medicinal and edible plant Arctium lappa13
Practical application of the linkage disequilibrium method for estimating contemporary effective population size: A review13
Exploring the vertebrate fauna of the Bird’s Head Peninsula (Indonesia, West Papua) through DNA barcodes13
Passive sampling of environmental DNA in aquatic environments using 3D‐printed hydroxyapatite samplers13
Development of DNA methylation‐based epigenetic age predictors in loblolly pine (Pinus taeda)13
Regarding the F‐word: The effects of data filtering on inferred genotype‐environment associations13
The practice and promise of temporal genomics for measuring evolutionary responses to global change13
eDNAssay: A machine learning tool that accurately predicts qPCR cross‐amplification12
A pile of pipelines: An overview of the bioinformatics software for metabarcoding data analyses12
Chromosome level assembly reveals a unique immune gene organization and signatures of evolution in the common pheasant12
Comparison of materials for rapid passive collection of environmental DNA12
Culture‐enriched community profiling improves resolution of the vertebrate gut microbiota12
A chromosome‐level genome assembly for the tertiary relict plant Tetracentron sinense oliv. (trochodendraceae)12
High‐throughput sequencing of faeces provides evidence for dispersal of parasites and pathogens by migratory waterbirds12
The genome sequence of Samia ricini, a new model species of lepidopteran insect12
Chromosome‐level genome assembly of burbot (Lota lota) provides insights into the evolutionary adaptations in freshwater12
A multitiered sequence capture strategy spanning broad evolutionary scales: Application for phylogenetic and phylogeographic studies of orchids12
epiGBS2: Improvements and evaluation of highly multiplexed, epiGBS‐based reduced representation bisulfite sequencing12
A chromosome‐level genome of Antechinus flavipes provides a reference for an Australian marsupial genus with male death after mating12
Assessing the utility of marine filter feeders for environmental DNA (eDNA) biodiversity monitoring12
NGSEP 4: Efficient and accurate identification of orthogroups and whole‐genome alignment12
Chromosome‐level genome reference and genome editing of the tea geometrid12
Complex genetic admixture histories reconstructed with Approximate Bayesian Computation12
Using target capture to address conservation challenges: Population‐level tracking of a globally‐traded herbal medicine12
Assessing candidate DNA barcodes for Chinese and internationally traded timber species11
Recovered microbiome of an oviparous lizard differs across gut and reproductive tissues, cloacal swabs, and faeces11
A library preparation optimized for metagenomics of RNA viruses11
A reference‐free approach to analyse RADseq data using standard next generation sequencing toolkits11
Deciphering the molecular signal from past and alive bacterial communities in aquatic sedimentary archives11
Development of epigenetic biomarkers for the identification of sex and thermal stress in fish using DNA methylation analysis and machine learning procedures11
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 nucle11
A genome‐wide SNP genotyping resource for tropical pine tree species11
Optimal sequence similarity thresholds for clustering of molecular operational taxonomic units inDNAmetabarcoding studies11
A chromosome‐scale genome assembly and annotation of the spring orchid (Cymbidium goeringii)11
A chromosome‐level genome of Portunus trituberculatus provides insights into its evolution, salinity adaptation and sex determination11
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