Molecular Ecology Resources

Papers
(The median citation count of Molecular Ecology Resources is 4. 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 2021-08-01 to 2025-08-01.)
ArticleCitations
Chromosome‐scale assembly and whole‐genome sequencing of 266 giant panda roundworms provide insights into their evolution, adaptation and potential drug targets372
A chromosome‐scale genome assembly and annotation of the spring orchid (Cymbidium goeringii)82
Alignment‐free methods for polyploid genomes: Quick and reliable genetic distance estimation71
Good from far, but far from good: The impact of a reference genome on evolutionary inference69
A road map for in vivo evolution experiments with blood‐borne parasitic microbes65
Bayesian tests for random mating in polyploids58
DNA barcoding of Chinese snakes reveals hidden diversity and conservation needs57
Use of 16S rRNA gene sequences to identify cyanobacteria that can grow in far‐red light57
A second unveiling: Haplotig masking of the eastern oyster genome improves population‐level inference55
Collecting baleen whale blow samples by drone: A minimally intrusive tool for conservation genetics52
detectEVE: Fast, Sensitive and Precise Detection of Endogenous Viral Elements in Genomic Data50
An Accessible Metagenomic Strategy Allows for Better Characterisation of Invertebrate Bulk Samples50
Fast‐tracking bespoke DNA reference database generation from museum collections for biomonitoring and conservation46
Issue Information44
Chromosome‐Level Genome Assembly of the Loach Goby Rhyacichthys aspro Offers Insights Into Gobioidei Evolution43
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 bats42
Benchmarking the Mantel test and derived methods for testing association between distance matrices42
Stomach Content DNA (scDNA) Detection and Quantification for Predator Diet Assessment Using High‐Throughput Nanofluidic Chip Technology: Species‐Specific qPCR Assay Pa39
An Innovative Binding‐Protein‐Based dsRNA Extraction Method: Comparison of Cost‐Effectiveness of Virus Detection Methods Using High‐Throughput Sequencing39
Revisiting the Briggs Ancient DNA Damage Model: A Fast Maximum Likelihood Method to Estimate Post‐Mortem Damage39
metaPR2: A database of eukaryotic 18S rRNA metabarcodes with an emphasis on protists38
Molecular diet analysis in mussels and other metazoan filter feeders and an assessment of their utility as natural eDNA samplers38
Evaluating the use of lake sedimentary DNA in palaeolimnology: A comparison with long‐term microscopy‐based monitoring of the phytoplankton community38
Particle size influences decay rates of environmental DNA in aquatic systems38
The voice of the little giants: Arcellinida testate amoebae in environmental DNA‐based bioindication, from taxonomy free to haplotypic level38
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The topological nature of tag jumping in environmental DNA metabarcoding studies37
Deciphering the molecular signal from past and alive bacterial communities in aquatic sedimentary archives37
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Chromosome‐level genome assembly reveals genomic architecture of northern range expansion in the mountain pine beetle, Dendroctonus ponderosae Hopkins (Coleoptera: Curculionidae)36
Simulating plasticity as a framework for understanding habitat selection and its role in adaptive capacity and extinction risk through an expansion of CDMetaPOP35
A needle in a haystack: A new metabarcoding approach to survey diversity at the species level of Arcellinida (Amoebozoa: Tubulinea)35
Inference of the distribution of fitness effects of mutations is affected by single nucleotide polymorphism filtering methods, sample size and population structure35
SPEDE‐sampler: An R Shiny application to assess how methodological choices and taxon sampling can affect Generalized Mixed Yule Coalescent output and interpretation35
Beware of Plant DNA in Animal Dietary Metabarcoding: Lessons From a Strictly Insectivorous Bat34
Monitoring of multiple fish species by quantitative environmental DNA metabarcoding surveys over two summer seasons34
Independent Avian Epigenetic Clocks for Ageing and Development34
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 chelicer34
MaxTemp: A Method to Maximise Precision of the Temporal Method for Estimating Ne in Genetic Monitoring Programs34
Potential PCR amplification bias in identifying complex ecological patterns: Higher species compositional homogeneity revealed in smaller‐size coral reef zooplankton by metatranscriptomics34
Demogenomic inference from spatially and temporally heterogeneous samples33
Towards Large‐Scale Museomics Projects: A Cost‐Effective and High‐Throughput Extraction Method for Obtaining Historical DNA From Museum Insect Specimens33
Fishing for DNA? Designing baits for population genetics in target enrichment experiments: Guidelines, considerations and the new tool supeRbaits32
Cover Image31
Comparative analysis of fish environmental DNA reveals higher sensitivity achieved through targeted sequence‐based metabarcoding31
The proof is in the poo: Non‐invasive method to detect endoparasitic infection30
DNA methylation‐based biomarkers for ageing long‐lived cetaceans30
A comprehensive framework for detecting copy number variants from single nucleotide polymorphism data: ‘rCNV’, a versatile r package for paralogue and CNV detection30
Batch effects in population genomic studies with low‐coverage whole genome sequencing data: Causes, detection and mitigation29
Proteomic fingerprinting enables quantitative biodiversity assessments of species and ontogenetic stages in Calanus congeners (Copepoda, Crustacea) from the Arctic Ocean29
Species discrimination in Schima (Theaceae): Next‐generation super‐barcodes meet evolutionary complexity29
Assessing the impact of USER‐treatment on hyRAD capture applied to ancient DNA29
Chromosome‐level genome of Entada phaseoloides provides insights into genome evolution and biosynthesis of triterpenoid saponins29
MycoAI: Fast and accurate taxonomic classification for fungal ITS sequences28
When barcoding fails: Genome chimerization (admixing) and reticulation obscure phylogenetic and taxonomic relationships28
The great tit HapMap project: A continental‐scale analysis of genomic variation in a songbird28
Performance of DNA metabarcoding, standard barcoding and morphological approaches in the identification of insect biodiversity28
The Long and the Short of It: Nanopore‐Based eDNA Metabarcoding of Marine Vertebrates Works; Sensitivity and Species‐Level Assignment Depend on Amplicon Lengths28
Evaluating the Benefits and Limits of Multiple Displacement Amplification With Whole‐Genome Oxford Nanopore Sequencing27
Scaling Up Species Delimitation From DNA Barcodes to Whole Organelle Genomes: Strong Evidence for Discordance Among Genes and Methods for the Red Alga Dasyclonium27
Comparing eDNA and Transect Methods for Aquatic Biodiversity Assessment in Lakes and Ponds27
Strategies for sample labelling and library preparation in DNA metabarcoding studies27
GenAPoPop 1.0: A user‐friendly software to analyse genetic diversity and structure from partially clonal and selfed autopolyploid organisms27
A roadmap to robust discriminant analysis of principal components26
Detection and population genomics of sea turtle species via noninvasive environmental DNA analysis of nesting beach sand tracks and oceanic water26
Issue Information26
Replicate DNA metabarcoding can discriminate seasonal and spatial abundance shifts in river macroinvertebrate assemblages26
Coalescent‐based species delimitation meets deep learning: Insights from a highly fragmented cactus system26
Bee foraging preferences, microbiota and pathogens revealed by direct shotgun metagenomics of honey25
A consensus protocol for the recovery of mercury methylation genes from metagenomes25
Cover Image25
Recovering the genomes hidden in museum wet collections25
Detecting clonemate pairs in multicellular diploid clonal species based on a shared heterozygosity index25
Do not be scared of the genome's 5th base—Explaining phenotypic variability and evolutionary dynamics through DNA methylation analysis25
Genomic Prediction of Individual Inbreeding Levels for the Management of Genetic Diversity in Populations With Small Effective Size24
Enhancing metabarcoding efficiency and ecological insights through integrated taxonomy and DNA reference barcoding: A case study on beach meiofauna24
Environmental RNA can distinguish life stages in amphibian populations24
Improved high‐throughput MHC typing for non‐model species using long‐read sequencing24
ParAquaSeq, a Database of Ecologically Annotated rRNA Sequences Covering Zoosporic Parasites Infecting Aquatic Primary Producers in Natural and Industrial Systems24
Non‐invasive age estimation based on faecal DNA using methylation‐sensitive high‐resolution melting for Indo‐Pacific bottlenose dolphins24
Lessons from assembling UCEs: A comparison of common methods and the case of Clavinomia (Halictidae)24
Evolutionary history and seascape genomics of Harbour porpoises (Phocoena phocoena) across environmental gradients in the North Atlantic and adjacent waters23
Allelic bias when performing in‐solution enrichment of ancient human DNA23
Quantifying uncertainty in inferences of landscape genetic resistance due to choice of individual‐based genetic distance metric23
A Long‐Term Ecological Research Data Set From the Marine Genetic Monitoring Program ARMSMBON 2018–202023
Unlocking inaccessible historical genomes preserved in formalin22
COInr and mkCOInr: Building and customizing a nonredundant barcoding reference database from BOLD and NCBI using a semi‐automated pipeline22
Missing genotype imputation in non‐model species using self‐organizing maps22
Phylogenomic and syntenic data demonstrate complex evolutionary processes in early radiation of the rosids22
Genotyping‐in‐thousands by sequencing (GT‐seq) of noninvasive faecal and degraded samples: A new panel to enable ongoing monitoring of Canadian polar bear populations22
FreshOmics: A manually curated and standardized –omics database for investigating freshwater microbiomes22
New deep learning‐based methods for visualizing ecosystem properties using environmental DNA metabarcoding data22
Plastid Genome Assembly Using Long‐read data22
Comparative genomics of a vertically transmitted thiotrophic bacterial ectosymbiont and its close free‐living relative22
Leveraging an existing whole‐genome resequencing population data set to characterize toll‐like receptor gene diversity in a threatened bird22
SLRfinder: A method to detect candidate sex‐linked regions with linkage disequilibrium clustering21
The unknown unknown: A framework for assessing environmental DNA assay specificity against unsampled taxa21
Issue Information21
Identification and quantification of chimeric sequencing reads in a highly multiplexed RAD‐seq protocol20
Metabarcoding using nanopore long‐read sequencing for the unbiased characterization of apicomplexan haemoparasites20
Pseudoreplication in genomic‐scale data sets20
A bioinformatic toolkit to simultaneously identify sex and sex‐linked regions20
A collaborative backbone resource for comparative studies of subterranean evolution: The World Asellidae database20
The accuracy of predicting maladaptation to new environments with genomic data20
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Testing the applicability of environmental DNA metabarcoding to landscape genetics20
A dynamic ancestral graph model and GPU‐based simulation of a community based on metagenomic sampling19
High‐quality genomes reveal significant genetic divergence and cryptic speciation in the model organism Folsomia candida (collembola)19
Tools and applications for integrative analysis of DNA methylation in social insects19
Using metatranscriptomics to estimate the diversity and composition of zooplankton communities19
Testing genome skimming for species discrimination in the large and taxonomically difficult genus Rhododendron18
TransPi—a comprehensive TRanscriptome ANalysiS PIpeline for de novo transcriptome assembly18
CRISPR‐Cas9 enrichment, a new strategy in microbial metagenomics to investigate complex genomic regions: The case of an environmental integron18
RDAforest: Identifying Environmental Drivers of Polygenic Adaptation18
Contemporary issues, current best practice and ways forward in soil protist ecology18
The year of the tiger and the year of tiger genomes!18
Influence of RNA‐Seq library construction, sampling methods, and tissue harvesting time on gene expression estimation18
Conservation in a litre of air17
Beyond Presence and Absence: Using eDNA and Microsatellite Genotyping to Estimate Densities of Microscopic Life Forms in Wild Populations17
Assessing the limits of local ancestry inference from small reference panels17
Three Novel Spider Genomes Unveil Spidroin Diversification and Hox Cluster Architecture: Ryuthela nishihirai (Liphistiidae), Uloborus plumipes (Uloboridae) and Cheiracanthium punctori17
SEGUL: Ultrafast, memory‐efficient and mobile‐friendly software for manipulating and summarizing phylogenomic datasets17
Correction to “epiGBS2: Improvements and Evaluation of Highly Multiplexed, epiGBS‐Based Reduced Representation Bisulfite Sequencing”17
MOSCA 2.0: A bioinformatics framework for metagenomics, metatranscriptomics and metaproteomics data analysis and visualization17
Prey ration, temperature, and predator species influence digestion rates of prey DNA inferred from qPCR and metabarcoding17
Issue Information17
The WZA: A window‐based method for characterizing genotype–environment associations17
Detailed DNA barcoding of mayflies in a small European country proved how far we are from having comprehensive barcode reference libraries16
Accelerating Moss Identification Through the Development of Specific DNA Barcodes Based on the Whole Chloroplast Genome16
Environmental DNA metabarcoding of freshwater fish in Malaysian tropical rivers using short‐read nanopore sequencing as a potential biomonitoring tool16
MuDoGeR: Multi‐Domain Genome recovery from metagenomes made easy16
Genome architecture used to supplement species delineation in two cryptic marine ciliates16
Correcting for Bias in Estimates of θw and Tajima's D From Missing Data in Next‐Generation Sequencing16
Launching insectphylo.org; a new hub facilitating construction and use of synthesis molecular phylogenies of insects16
Validating a Target‐Enrichment Design for Capturing Uniparental Haplotypes in Ancient Domesticated Animals15
Machine learning in molecular ecology15
Inferring the timing and strength of natural selection and gene migration in the evolution of chicken from ancient DNA data15
Efficiency of eDNA and iDNA in assessing vertebrate diversity and its abundance15
A High‐Throughput Ancient DNA Extraction Method for Large‐Scale Sample Screening15
High quality haplotype‐resolved genome assemblies of Populus tomentosa Carr., a stabilized interspecific hybrid species widespread in Asia15
Genome and gene evolution of seahorse species revealed by the chromosome‐level genome of Hippocampus abdominalis15
Bayesian StairwayPlot for Inferring Single Population Demographic Histories From Site Frequency Spectra15
RNA allows identifying the consumption of carrion prey15
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Who are you? A framework to identify and report genetic sample mix‐ups15
A Short‐Read Amplicon Sequencing Protocol and Bioinformatic Pipeline for Ecological Surveillance of Dipteran Disease Vectors15
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RIDGE, a tool tailored to detect gene flow barriers across species pairs14
An empirical test of the estimation of historical effective population size using Drosophila melanogaster14
HMS‐S‐S: A tool for the identification of Sulphur metabolism‐related genes and analysis of operon structures in genome and metagenome assemblies14
Environmental DNA phylogeography: Successful reconstruction of phylogeographic patterns of multiple fish species from cups of water14
The answer, my friend, is blowin’ in the wind: Blow sampling provides a new dimension to whale population monitoring14
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Management and conservation implications of cryptic population substructure for two commercially exploited fishes (Merluccius spp.) in southern Africa14
Genetic variation and domestication of horses revealed by 10 chromosome‐level genomes and whole‐genome resequencing14
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Affordable de novo generation of fish mitogenomes using amplification‐free enrichment of mitochondrial DNA and deep sequencing of long fragments14
DNA barcodes highlight genetic diversity patterns in rodents from lowland desert and Andean areas in Argentina14
Genomes of Two Monophagous Weevils and Their Host Plant Provide Insights Into Evolution of Plant Defence and Insect Counter‐Defence14
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Species delimitation with limited sampling: An example from rare trapdoor spider genus Cyclocosmia (Mygalomorphae, Halonoproctidae)14
A molecular‐based identification resource for the arthropods of Finland14
A chromosomal level genome sequence for Quasipaa spinosa (Dicroglossidae) reveals chromosomal evolution and population diversity14
Chromosome‐level genome assembly of the mirid predator Cyrtorhinus lividipennis Reuter (Hemiptera: Miridae), an important natural enemy in the rice ecosystem14
Chromosome‐level genome assembly of Pedicularis kansuensis illuminates genome evolution of facultative parasitic plant14
A guide to avian museomics: Insights gained from resequencing hundreds of avian study skins13
Scaling‐up RADseq methods for large datasets of non‐invasive samples: Lessons for library construction and data preprocessing13
Comparative genomics reveals the dynamic evolutionary history of cement protein genes of barnacles from intertidal to deep‐sea hydrothermal vents13
Next‐generation bioinformatics: An ultrafast and user‐friendly tool for phylogenomic data exploration13
Utilizing paralogues for phylogenetic reconstruction has the potential to increase species tree support and reduce gene tree discordance in target enrichment data13
Simultaneous genotyping of snails and infecting trematode parasites using high‐throughput amplicon sequencing13
Phylogenomic analyses of the genusDrosophilareveals genomic signals of climate adaptation13
Macrobial airborne environmental DNA analysis: A review of progress, challenges, and recommendations for an emerging application13
Temporal Variability in Effective Size (N̂e) Identifies Potential Sources of Discrepancies Between Mark Recapture and Close Kin Mark Recapture Estimates of Population Abundance13
Estimation of spatial demographic maps from polymorphism data using a neural network13
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Chromosome‐level genome assembly of a triploid poplar Populus albaBerolinensis13
A Post‐Mortem Molecular Damage Profile in the Ancient Human Mitochondrial DNA13
Express barcoding with NextGenPCR and MinION for species‐level sorting of ecological samples13
Quantifying Soil Microbiome Abundance by Metatranscriptomics and Complementary Molecular Techniques—Cross‐Validation and Perspectives13
Quantitative assessment of reef foraminifera community from metabarcoding data13
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
Application of palaeogenetic techniques to historic mollusc shells reveals phylogeographic structure in a New Zealand abalone13
Issue Information12
Integration of De Novo Chromosome‐Level Genome and Population Resequencing of Peganum (Nitrariaceae): A Case Study of Speciation and Evolutionary Trajectories in Arid Central Asia12
Chromosome‐level genomes of two armyworms, Mythimna separata and Mythimna loreyi, provide insights into the biosynthesis and reception of sex pheromones12
CCS‐Consensuser: A Haplotype‐Aware Consensus Generator for PacBio Amplicon Sequences12
Next‐Generation Snow Leopard Population Assessment Tool: Multiplex‐PCR SNP Panel for Individual Identification From Faeces12
Delimiting the rare, endangered and actively speciating12
Polly: An R package for genotyping microsatellites and detecting highly polymorphic DNA markers from short‐read data12
Taxon‐specific or universal? Using target capture to study the evolutionary history of rapid radiations12
Coming of age for COI metabarcoding of whole organism community DNA: Towards bioinformatic harmonisation11
Maintenance of genetic diversity in subdivided populations using genomic coancestry matrices11
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Environmental DNA methylation of Lymnaea stagnalis varies with age and is hypermethylated compared to tissue DNA11
EntoSieve: Automated Size‐Sorting of Insect Bulk Samples to Aid Accurate Megabarcoding and Metabarcoding11
A Snakemake Toolkit for the Batch Assembly, Annotation and Phylogenetic Analysis of Mitochondrial Genomes and Ribosomal Genes From Genome Skims of Museum Collections11
Spatial metabolomics reveal divergent cardenolide processing in the monarch (Danaus plexippus) and the common crow butterfly (Euploea core)11
Invertebrates for vertebrate biodiversity monitoring: Comparisons using three insect taxa as iDNA samplers11
Finding the perfect pairs: A matchmaking of plant markers and primers for multi‐marker eDNA metabarcoding11
The chromosome‐level genome assembly of the Japanese yellowtail jack Seriola aureovittata provides insights into genome evolution and efficient oxygen transport11
Pan‐Genome of Jasminum sambac Reveals the Genetic Diversity of Different Petal Morphology and Aroma‐Related Genes11
Unrecognised DNA Degradation in Flash‐Frozen Genetic Samples in Natural History Collections11
A novel assembly pipeline and functional annotations for targeted sequencing: A case study on the globally threatened Margaritiferidae (Bivalvia: Unionida)11
Just keep it simple? Benchmarking the accuracy of taxonomy assignment software in metabarcoding studies11
Linkage Mapping vs. Association: A Comparison of Two RADseq‐Based Approaches to Identify Markers for Homomorphic Sex Chromosomes in Large Genomes11
Integrating Pool‐seq uncertainties into demographic inference11
Joint identification of sex and sex‐linked scaffolds in non‐model organisms using low depth sequencing data11
Genomic and Methylomic Signatures Associated With the Maintenance of Genome Stability and Adaptive Evolution in Two Closely Allied Wolf Spiders11
Morphological and taxonomic diversity of mesozooplankton is an important driver of carbon export fluxes in the ocean11
Transcriptome‐wide SNPs for Botrychium lunaria ferns enable fine‐grained analysis of ploidy and population structure11
Arthropod: A Tool for Phylogenomic Research in Arthropods10
Performance of DNA Metabarcoding vs. Morphological Methods for Assessing Intertidal Turf and Foliose Algae Diversity10
Systematic review and meta‐analysis: Water type and temperature affect environmental DNA decay10
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Estimating predation rates from molecular gut content analysis10
Evolution of olfactory receptor superfamily in bats based on high throughput molecular modelling10
An Optimised Method to Identify Reintroduced Swift Foxes (Vulpes velox) Through SNP Genotyping of Non‐Invasively Collected Scat Samples Using In‐Solution Hybridisation Capture10
HiMAP2: Identifying phylogenetically informative genetic markers from diverse genomic resources10
NMπ 2.0: Software update to minimize the risk of false positives among determinants of reproductive success10
Correction to “Quantifying Mitochondrial Heteroplasmy Diversity: A Computational Approach”10
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 Ethiopia10
Diet preferences based on sequence read count: The role of species interaction in tissue bias correction10
Parent‐offspring inference in inbred populations10
Guidelines for standardizing the application of discriminant analysis of principal components to genotype data10
Towards a better future for DNA barcoding: Evaluating monophyly‐ and distance‐based species identification using COI gene fragments of Dacini fruit flies9
One metric or many? Refining the analytical framework of landscape resistance estimation in individual‐based landscape genetic analyses9
Comparing genome‐based estimates of relatedness for use in pedigree‐based conservation management9
DNA barcoding of Cymbidium by genome skimming: Call for next‐generation nuclear barcodes9
The Impact of Whole‐Animal Fluid Preservation on the Observed Gut Microbiome of Vertebrates: Implications for the Use of Museum Specimens in Microbiome Research9
CRISPR‐Cas9‐mediated host signal reduction for 18S metabarcoding of host‐associated eukaryotes9
Chromosome‐scale genomes reveal genomic consequences of inbreeding in the South China tiger: A comparative study with the Amur tiger9
MrIML: Multi‐response interpretable machine learning to model genomic landscapes9
Correcting for Replicated Genotypes May Introduce More Problems Than it Solves9
Plant DNA barcode library for native flowering plants in the arid region of northwestern China9
The population genetics of partial diapause, with applications to the aestivating malaria mosquito Anopheles coluzzii9
Too Far From Relatives? Impact of the Genetic Distance on the Success of Exon Capture in Phylogenomics9
High‐quality haplotype‐resolved genome assembly for ring‐cup oak (Quercus glauca) provides insight into oaks demographic dynamics9
mapmixture: An R package and web app for spatial visualisation of admixture and population structure9
EggLib 3: A python package for population genetics and genomics9
Massive genome investigations reveal insights of prevalent introgression for environmental adaptation and triterpene biosynthesis in Ganoderma9
Extensive sequence divergence between the reference genomes of two zebrafish strains, Tuebingen and AB9
Toward absolute abundance for conservation applications: Estimating the number of contributors via microhaplotype genotyping of mixed‐DNA samples9
CRISPR‐based diagnostics detects invasive insect pests8
The impact of estimator choice: Disagreement in clustering solutions across K estimators for Bayesian analysis of population genetic structure across a wide range of empirical data sets8
Using target capture to address conservation challenges: Population‐level tracking of a globally‐traded herbal medicine8
A chromosome‐level genome of Portunus trituberculatus provides insights into its evolution, salinity adaptation and sex determination8
Genomic and machine learning‐based screening of aquaculture‐associated introgression into at‐risk wild North American Atlantic salmon (Salmo salar) populations8
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Recovery of 197 eukaryotic bins reveals major challenges for eukaryote genome reconstruction from terrestrial metagenomes8
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