Molecular Ecology Resources

Article	Citations
Issue Information	345
Revisiting the Briggs Ancient DNA Damage Model: A Fast Maximum Likelihood Method to Estimate Post‐Mortem Damage	73
Stomach Content DNA (scDNA) Detection and Quantification for Predator Diet Assessment Using High‐Throughput Nanofluidic Chip Technology: Species‐Specific qPCR Assay Pa	66
Chromosome‐Level Genome Assembly of the Loach Goby Rhyacichthys aspro Offers Insights Into Gobioidei Evolution	66
detectEVE: Fast, Sensitive and Precise Detection of Endogenous Viral Elements in Genomic Data	65
A road map for in vivo evolution experiments with blood‐borne parasitic microbes	62
The endangered White Sands pupfish (Cyprinodon tularosa) genome reveals low diversity and heterogenous patterns of differentiation	61
Good from far, but far from good: The impact of a reference genome on evolutionary inference	61
Molecular assays of pollen use consistently reflect pollinator visitation patterns in a system of flowering plants	61
Chromosome‐scale assembly and whole‐genome sequencing of 266 giant panda roundworms provide insights into their evolution, adaptation and potential drug targets	53
Fast‐tracking bespoke DNA reference database generation from museum collections for biomonitoring and conservation	52
The topological nature of tag jumping in environmental DNA metabarcoding studies	50
A second unveiling: Haplotig masking of the eastern oyster genome improves population‐level inference	49
Bayesian tests for random mating in polyploids	46
A minimally invasive, field‐applicable CRISPR/Cas biosensor to aid in the detection of Pseudogymnoascus destructans, the causative fungal agent of white‐nose syndrome in bats	45
Evaluating the use of lake sedimentary DNA in palaeolimnology: A comparison with long‐term microscopy‐based monitoring of the phytoplankton community	44
Alignment‐free methods for polyploid genomes: Quick and reliable genetic distance estimation	43
An Innovative Binding‐Protein‐Based dsRNA Extraction Method: Comparison of Cost‐Effectiveness of Virus Detection Methods Using High‐Throughput Sequencing	43
The voice of the little giants: Arcellinida testate amoebae in environmental DNA‐based bioindication, from taxonomy free to haplotypic level	41
Use of 16S rRNA gene sequences to identify cyanobacteria that can grow in far‐red light	41
A chromosome‐scale genome assembly and annotation of the spring orchid (Cymbidium goeringii)	40
Benchmarking the Mantel test and derived methods for testing association between distance matrices	40
DNA barcoding of Chinese snakes reveals hidden diversity and conservation needs	39
An Accessible Metagenomic Strategy Allows for Better Characterisation of Invertebrate Bulk Samples	39
Molecular diet analysis in mussels and other metazoan filter feeders and an assessment of their utility as natural eDNA samplers	38

Collecting baleen whale blow samples by drone: A minimally intrusive tool for conservation genetics	37
Particle size influences decay rates of environmental DNA in aquatic systems	37
Potential PCR amplification bias in identifying complex ecological patterns: Higher species compositional homogeneity revealed in smaller‐size coral reef zooplankton by metatranscriptomics	36
metaPR2: A database of eukaryotic 18S rRNA metabarcodes with an emphasis on protists	36
MaxTemp: A Method to Maximise Precision of the Temporal Method for Estimating Ne in Genetic Monitoring Programs	35
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Beware of Plant DNA in Animal Dietary Metabarcoding: Lessons From a Strictly Insectivorous Bat	34
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	34
Towards Large‐Scale Museomics Projects: A Cost‐Effective and High‐Throughput Extraction Method for Obtaining Historical DNA From Museum Insect Specimens	34
Improved genome assembly of Chinese shrimp (Fenneropenaeus chinensis) suggests adaptation to the environment during evolution and domestication	34
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Inference of the distribution of fitness effects of mutations is affected by single nucleotide polymorphism filtering methods, sample size and population structure	33
Fishing for DNA? Designing baits for population genetics in target enrichment experiments: Guidelines, considerations and the new tool supeRbaits	33
Simulating plasticity as a framework for understanding habitat selection and its role in adaptive capacity and extinction risk through an expansion of CDMetaPOP	33
Single‐molecule long‐read sequencing reveals extensive genomic and transcriptomic variation between maize and its wild relative teosinte (Zea mays ssp. parviglumis)	33
Demogenomic inference from spatially and temporally heterogeneous samples	32
Chromosome‐level genome assembly reveals genomic architecture of northern range expansion in the mountain pine beetle, Dendroctonus ponderosae Hopkins (Coleoptera: Curculionidae)	32
Deciphering the molecular signal from past and alive bacterial communities in aquatic sedimentary archives	32
A needle in a haystack: A new metabarcoding approach to survey diversity at the species level of Arcellinida (Amoebozoa: Tubulinea)	32
SPEDE‐sampler: An R Shiny application to assess how methodological choices and taxon sampling can affect Generalized Mixed Yule Coalescent output and interpretation	32
Batch effects in population genomic studies with low‐coverage whole genome sequencing data: Causes, detection and mitigation	31
Cover Image	31
Evaluating the Benefits and Limits of Multiple Displacement Amplification With Whole‐Genome Oxford Nanopore Sequencing	31
Monitoring of multiple fish species by quantitative environmental DNA metabarcoding surveys over two summer seasons	31
Comparing eDNA and Transect Methods for Aquatic Biodiversity Assessment in Lakes and Ponds	31
A comprehensive framework for detecting copy number variants from single nucleotide polymorphism data: ‘rCNV’, a versatile r package for paralogue and CNV detection	30
Pedigree simulations reveal that maternity assignment is reliable in populations with conspecific brood parasitism, incomplete parental sampling and kin structure	30
The proof is in the poo: Non‐invasive method to detect endoparasitic infection	30
Comparative analysis of fish environmental DNA reveals higher sensitivity achieved through targeted sequence‐based metabarcoding	30
Species discrimination in Schima (Theaceae): Next‐generation super‐barcodes meet evolutionary complexity	30
Assessing the impact of USER‐treatment on hyRAD capture applied to ancient DNA	29
MycoAI: Fast and accurate taxonomic classification for fungal ITS sequences	29
Proteomic fingerprinting enables quantitative biodiversity assessments of species and ontogenetic stages in Calanus congeners (Copepoda, Crustacea) from the Arctic Ocean	29
Performance of DNA metabarcoding, standard barcoding and morphological approaches in the identification of insect biodiversity	28
GenAPoPop 1.0: A user‐friendly software to analyse genetic diversity and structure from partially clonal and selfed autopolyploid organisms	28
The great tit HapMap project: A continental‐scale analysis of genomic variation in a songbird	28
Contemporary Ne estimation using temporally spaced data with linked loci	27
Evaluating the role of reference‐genome phylogenetic distance on evolutionary inference	27
The Long and the Short of It: Nanopore‐Based eDNA Metabarcoding of Marine Vertebrates Works; Sensitivity and Species‐Level Assignment Depend on Amplicon Lengths	27
DNA methylation‐based biomarkers for ageing long‐lived cetaceans	27
pr2‐primers: An 18S rRNA primer database for protists	27
Strategies for sample labelling and library preparation in DNA metabarcoding studies	27
Issue Information	26
When barcoding fails: Genome chimerization (admixing) and reticulation obscure phylogenetic and taxonomic relationships	26
Genomic Prediction of Individual Inbreeding Levels for the Management of Genetic Diversity in Populations With Small Effective Size	26
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A Long‐Term Ecological Research Data Set From the Marine Genetic Monitoring Program ARMS‐MBON 2018–2020	26
Chromosome‐level genome of Entada phaseoloides provides insights into genome evolution and biosynthesis of triterpenoid saponins	26
Evolutionary history and seascape genomics of Harbour porpoises (Phocoena phocoena) across environmental gradients in the North Atlantic and adjacent waters	25
Coalescent‐based species delimitation meets deep learning: Insights from a highly fragmented cactus system	25

Detecting clonemate pairs in multicellular diploid clonal species based on a shared heterozygosity index	25
Non‐invasive age estimation based on faecal DNA using methylation‐sensitive high‐resolution melting for Indo‐Pacific bottlenose dolphins	25
Bee foraging preferences, microbiota and pathogens revealed by direct shotgun metagenomics of honey	25
Replicate DNA metabarcoding can discriminate seasonal and spatial abundance shifts in river macroinvertebrate assemblages	25
Do not be scared of the genome's 5th base—Explaining phenotypic variability and evolutionary dynamics through DNA methylation analysis	25
Recovering the genomes hidden in museum wet collections	25
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	24
A roadmap to robust discriminant analysis of principal components	24
Improved high‐throughput MHC typing for non‐model species using long‐read sequencing	24
COInr and mkCOInr: Building and customizing a nonredundant barcoding reference database from BOLD and NCBI using a semi‐automated pipeline	24
Enhancing metabarcoding efficiency and ecological insights through integrated taxonomy and DNA reference barcoding: A case study on beach meiofauna	23
Lessons from assembling UCEs: A comparison of common methods and the case of Clavinomia (Halictidae)	23
Allelic bias when performing in‐solution enrichment of ancient human DNA	23
A consensus protocol for the recovery of mercury methylation genes from metagenomes	23
Quantifying uncertainty in inferences of landscape genetic resistance due to choice of individual‐based genetic distance metric	23
Detection and population genomics of sea turtle species via noninvasive environmental DNA analysis of nesting beach sand tracks and oceanic water	22
Plastid Genome Assembly Using Long‐read data	22
Issue Information	22
Environmental RNA can distinguish life stages in amphibian populations	22
On‐site environmental DNA detection of species using ultrarapid mobile PCR	22
ParAquaSeq, a Database of Ecologically Annotated rRNA Sequences Covering Zoosporic Parasites Infecting Aquatic Primary Producers in Natural and Industrial Systems	22
Chromosome‐scale genome assembly of areca palm (Areca catechu)	21
Comparative genomics of a vertically transmitted thiotrophic bacterial ectosymbiont and its close free‐living relative	21
Unlocking inaccessible historical genomes preserved in formalin	21
The unknown unknown: A framework for assessing environmental DNA assay specificity against unsampled taxa	21
Phylogenomic and syntenic data demonstrate complex evolutionary processes in early radiation of the rosids	21
Leveraging an existing whole‐genome resequencing population data set to characterize toll‐like receptor gene diversity in a threatened bird	21
Metabarcoding using nanopore long‐read sequencing for the unbiased characterization of apicomplexan haemoparasites	21
SLRfinder: A method to detect candidate sex‐linked regions with linkage disequilibrium clustering	21
Testing the applicability of environmental DNA metabarcoding to landscape genetics	21
The accuracy of predicting maladaptation to new environments with genomic data	20
FreshOmics: A manually curated and standardized –omics database for investigating freshwater microbiomes	20
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A collaborative backbone resource for comparative studies of subterranean evolution: The World Asellidae database	20
Missing genotype imputation in non‐model species using self‐organizing maps	20
Beyond Presence and Absence: Using eDNA and Microsatellite Genotyping to Estimate Densities of Microscopic Life Forms in Wild Populations	20
Pseudoreplication in genomic‐scale data sets	20
New deep learning‐based methods for visualizing ecosystem properties using environmental DNA metabarcoding data	20
MOSCA 2.0: A bioinformatics framework for metagenomics, metatranscriptomics and metaproteomics data analysis and visualization	19
A dynamic ancestral graph model and GPU‐based simulation of a community based on metagenomic sampling	19
A bioinformatic toolkit to simultaneously identify sex and sex‐linked regions	19
Genome architecture used to supplement species delineation in two cryptic marine ciliates	19
Issue Information	19
Identification and quantification of chimeric sequencing reads in a highly multiplexed RAD‐seq protocol	19
Tools and applications for integrative analysis of DNA methylation in social insects	19
An exploration of assembly strategies and quality metrics on the accuracy of the rewarewa (Knightia excelsa) genome	18
Environmental DNA metabarcoding of freshwater fish in Malaysian tropical rivers using short‐read nanopore sequencing as a potential biomonitoring tool	18
Launching insectphylo.org; a new hub facilitating construction and use of synthesis molecular phylogenies of insects	18
MuDoGeR: Multi‐Domain Genome recovery from metagenomes made easy	18
Assessing the limits of local ancestry inference from small reference panels	18
SEGUL: Ultrafast, memory‐efficient and mobile‐friendly software for manipulating and summarizing phylogenomic datasets	18
High‐quality genomes reveal significant genetic divergence and cryptic speciation in the model organism Folsomia candida (collembola)	18
Using metatranscriptomics to estimate the diversity and composition of zooplankton communities	18
Detailed DNA barcoding of mayflies in a small European country proved how far we are from having comprehensive barcode reference libraries	18
Conservation in a litre of air	18
Influence of RNA‐Seq library construction, sampling methods, and tissue harvesting time on gene expression estimation	17
Prey ration, temperature, and predator species influence digestion rates of prey DNA inferred from qPCR and metabarcoding	17
The year of the tiger and the year of tiger genomes!	17
CRISPR‐Cas9 enrichment, a new strategy in microbial metagenomics to investigate complex genomic regions: The case of an environmental integron	17
A targeted amplicon sequencing panel to simultaneously identify mosquito species and Plasmodium presence across the entire Anopheles genus	16
Contemporary issues, current best practice and ways forward in soil protist ecology	16
Three Novel Spider Genomes Unveil Spidroin Diversification and Hox Cluster Architecture: Ryuthela nishihirai (Liphistiidae), Uloborus plumipes (Uloboridae) and Cheiracanthium punctori	16
Testing genome skimming for species discrimination in the large and taxonomically difficult genus Rhododendron	16
The WZA: A window‐based method for characterizing genotype–environment associations	16
Correction to “epiGBS2: Improvements and Evaluation of Highly Multiplexed, epiGBS‐Based Reduced Representation Bisulfite Sequencing”	16
TransPi—a comprehensive TRanscriptome ANalysiS PIpeline for de novo transcriptome assembly	16
Correcting for Bias in Estimates of θw$$ {\theta}_w $$ and Tajima's D$$ D $$ From Missing Data in Next‐Generation Sequencing	16
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Validating a Target‐Enrichment Design for Capturing Uniparental Haplotypes in Ancient Domesticated Animals	15
Management and conservation implications of cryptic population substructure for two commercially exploited fishes (Merluccius spp.) in southern Africa	15
Species delimitation with limited sampling: An example from rare trapdoor spider genus Cyclocosmia (Mygalomorphae, Halonoproctidae)	15
Bayesian StairwayPlot for Inferring Single Population Demographic Histories From Site Frequency Spectra	15
Genome and gene evolution of seahorse species revealed by the chromosome‐level genome of Hippocampus abdominalis	15
A Short‐Read Amplicon Sequencing Protocol and Bioinformatic Pipeline for Ecological Surveillance of Dipteran Disease Vectors	15
High quality haplotype‐resolved genome assemblies of Populus tomentosa Carr., a stabilized interspecific hybrid species widespread in Asia	15
Exhaustive reanalysis of barcode sequences from public repositories highlights ongoing misidentifications and impacts taxa diversity and distribution	15
Inferring the timing and strength of natural selection and gene migration in the evolution of chicken from ancient DNA data	14
RIDGE, a tool tailored to detect gene flow barriers across species pairs	14
Express barcoding with NextGenPCR and MinION for species‐level sorting of ecological samples	14
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Machine learning in molecular ecology	14
Efficiency of eDNA and iDNA in assessing vertebrate diversity and its abundance	14
A High‐Throughput Ancient DNA Extraction Method for Large‐Scale Sample Screening	14
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Who are you? A framework to identify and report genetic sample mix‐ups	14
RNA allows identifying the consumption of carrion prey	14
A molecular‐based identification resource for the arthropods of Finland	14
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Individual haplotyping of whale sharks from seawater environmental DNA	14
DNA barcodes highlight genetic diversity patterns in rodents from lowland desert and Andean areas in Argentina	13
Genetic variation and domestication of horses revealed by 10 chromosome‐level genomes and whole‐genome resequencing	13
The answer, my friend, is blowin’ in the wind: Blow sampling provides a new dimension to whale population monitoring	13
DROP: Molecular voucher database for identification of Drosophila parasitoids	13
Comparative genomics reveals the dynamic evolutionary history of cement protein genes of barnacles from intertidal to deep‐sea hydrothermal vents	13
Delimiting the rare, endangered and actively speciating	13
A chromosomal level genome sequence for Quasipaa spinosa (Dicroglossidae) reveals chromosomal evolution and population diversity	13
Environmental DNA phylogeography: Successful reconstruction of phylogeographic patterns of multiple fish species from cups of water	13
HMS‐S‐S: A tool for the identification of Sulphur metabolism‐related genes and analysis of operon structures in genome and metagenome assemblies	13
Chromosome‐level genome assembly of Pedicularis kansuensis illuminates genome evolution of facultative parasitic plant	13
Macrobial airborne environmental DNA analysis: A review of progress, challenges, and recommendations for an emerging application	13
A guide to avian museomics: Insights gained from resequencing hundreds of avian study skins	13
Temporal Variability in Effective Size (N̂e) Identifies Potential Sources of Discrepancies Between Mark Recapture and Close Kin Mark Recapture Estimates of Population Abundance	13
Estimation of spatial demographic maps from polymorphism data using a neural network	13
Chromosome‐level genome assembly of the mirid predator Cyrtorhinus lividipennis Reuter (Hemiptera: Miridae), an important natural enemy in the rice ecosystem	13
Issue Information	13
Scaling‐up RADseq methods for large datasets of non‐invasive samples: Lessons for library construction and data preprocessing	13
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Affordable de novo generation of fish mitogenomes using amplification‐free enrichment of mitochondrial DNA and deep sequencing of long fragments	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
Next‐generation bioinformatics: An ultrafast and user‐friendly tool for phylogenomic data exploration	13
quickLD: An efficient software for linkage disequilibrium analyses	13
An empirical test of the estimation of historical effective population size using Drosophila melanogaster	13
Quantitative assessment of reef foraminifera community from metabarcoding data	13
A Post‐Mortem Molecular Damage Profile in the Ancient Human Mitochondrial DNA	12
Chromosome‐level genome assembly of a triploid poplar Populus alba ‘Berolinensis’	12
Phylogenomic analyses of the genusDrosophilareveals genomic signals of climate adaptation	12
Chromosome‐level genomes of two armyworms, Mythimna separata and Mythimna loreyi, provide insights into the biosynthesis and reception of sex pheromones	12
Next‐Generation Snow Leopard Population Assessment Tool: Multiplex‐PCR SNP Panel for Individual Identification From Faeces	12
Application of palaeogenetic techniques to historic mollusc shells reveals phylogeographic structure in a New Zealand abalone	12
Taxon‐specific or universal? Using target capture to study the evolutionary history of rapid radiations	12
Utilizing paralogues for phylogenetic reconstruction has the potential to increase species tree support and reduce gene tree discordance in target enrichment data	12
Polly: An R package for genotyping microsatellites and detecting highly polymorphic DNA markers from short‐read data	12
Integration of De Novo Chromosome‐Level Genome and Population Resequencing of Peganum (Nitrariaceae): A Case Study of Speciation and Evolutionary Trajectories in Arid Central Asia	12
CCS‐Consensuser: A Haplotype‐Aware Consensus Generator for PacBio Amplicon Sequences	12
Simultaneous genotyping of snails and infecting trematode parasites using high‐throughput amplicon sequencing	12
Identifying loci under selection via explicit demographic models	12
The chromosome‐level genome assembly of the Japanese yellowtail jack Seriola aureovittata provides insights into genome evolution and efficient oxygen transport	11
EntoSieve: Automated Size‐Sorting of Insect Bulk Samples to Aid Accurate Megabarcoding and Metabarcoding	11
Performance of DNA Metabarcoding vs. Morphological Methods for Assessing Intertidal Turf and Foliose Algae Diversity	11
Maintenance of genetic diversity in subdivided populations using genomic coancestry matrices	11
Unrecognised DNA Degradation in Flash‐Frozen Genetic Samples in Natural History Collections	11
Morphological and taxonomic diversity of mesozooplankton is an important driver of carbon export fluxes in the ocean	11
Joint identification of sex and sex‐linked scaffolds in non‐model organisms using low depth sequencing data	11
A Molecular Survey of the Occurrence of Coffee Berry Disease Resistant Coffee Cultivars Near the Wild Gene Pool of Arabica Coffee in Its Region of Origin in Southwest Ethiopia	11
Estimating predation rates from molecular gut content analysis	11
Hi‐C scaffolded short‐ and long‐read genome assemblies of the California sea lion are broadly consistent for syntenic inference across 45 million years of evolution	11
Genomic and Methylomic Signatures Associated With the Maintenance of Genome Stability and Adaptive Evolution in Two Closely Allied Wolf Spiders	11
Environmental DNA methylation of Lymnaea stagnalis varies with age and is hypermethylated compared to tissue DNA	11
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Correction to “Quantifying Mitochondrial Heteroplasmy Diversity: A Computational Approach”	11
Integrating Pool‐seq uncertainties into demographic inference	11
A Snakemake Toolkit for the Batch Assembly, Annotation and Phylogenetic Analysis of Mitochondrial Genomes and Ribosomal Genes From Genome Skims of Museum Collections	11
A novel assembly pipeline and functional annotations for targeted sequencing: A case study on the globally threatened Margaritiferidae (Bivalvia: Unionida)	11
Transcriptome‐wide SNPs for Botrychium lunaria ferns enable fine‐grained analysis of ploidy and population structure	10
Finding the perfect pairs: A matchmaking of plant markers and primers for multi‐marker eDNA metabarcoding	10
Evolution of olfactory receptor superfamily in bats based on high throughput molecular modelling	10
Too Far From Relatives? Impact of the Genetic Distance on the Success of Exon Capture in Phylogenomics	10
CRISPR‐Cas9‐mediated host signal reduction for 18S metabarcoding of host‐associated eukaryotes	10
One metric or many? Refining the analytical framework of landscape resistance estimation in individual‐based landscape genetic analyses	10
A chromosomal assembly of the soybean cyst nematode genome	10
Spatial metabolomics reveal divergent cardenolide processing in the monarch (Danaus plexippus) and the common crow butterfly (Euploea core)	10
Guidelines for standardizing the application of discriminant analysis of principal components to genotype data	10
Effect of reduced genomic representation on using runs of homozygosity for inbreeding characterization	10
HiMAP2: Identifying phylogenetically informative genetic markers from diverse genomic resources	10
Coming of age for COI metabarcoding of whole organism community DNA: Towards bioinformatic harmonisation	10
Systematic review and meta‐analysis: Water type and temperature affect environmental DNA decay	10
Just keep it simple? Benchmarking the accuracy of taxonomy assignment software in metabarcoding studies	10
Invertebrates for vertebrate biodiversity monitoring: Comparisons using three insect taxa as iDNA samplers	10
Massive genome investigations reveal insights of prevalent introgression for environmental adaptation and triterpene biosynthesis in Ganoderma	10
Extensive sequence divergence between the reference genomes of two zebrafish strains, Tuebingen and AB	10
Toward absolute abundance for conservation applications: Estimating the number of contributors via microhaplotype genotyping of mixed‐DNA samples	10
mapmixture: An R package and web app for spatial visualisation of admixture and population structure	9
NMπ 2.0: Software update to minimize the risk of false positives among determinants of reproductive success	9
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Diet preferences based on sequence read count: The role of species interaction in tissue bias correction	9
DNA barcoding of Cymbidium by genome skimming: Call for next‐generation nuclear barcodes	9
The Impact of Whole‐Animal Fluid Preservation on the Observed Gut Microbiome of Vertebrates: Implications for the Use of Museum Specimens in Microbiome Research	9
Transposable element annotation in non‐model species: The benefits of species‐specific repeat libraries using semi‐automated EDTA and DeepTE de novo pipelines	9
Correcting for Replicated Genotypes May Introduce More Problems Than it Solves	9
Towards a better future for DNA barcoding: Evaluating monophyly‐ and distance‐based species identification using COI gene fragments of Dacini fruit flies	9
Plant DNA barcode library for native flowering plants in the arid region of northwestern China	9
High‐quality haplotype‐resolved genome assembly for ring‐cup oak (Quercus glauca) provides insight into oaks demographic dynamics	9
MrIML: Multi‐response interpretable machine learning to model genomic landscapes	9
The population genetics of partial diapause, with applications to the aestivating malaria mosquito Anopheles coluzzii	9