Molecular Ecology Resources

Papers
(The median citation count of Molecular Ecology Resources is 3. 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 2021-11-01 to 2025-11-01.)
ArticleCitations
An Innovative Binding‐Protein‐Based dsRNA Extraction Method: Comparison of Cost‐Effectiveness of Virus Detection Methods Using High‐Throughput Sequencing401
The voice of the little giants: Arcellinida testate amoebae in environmental DNA‐based bioindication, from taxonomy free to haplotypic level107
Collecting baleen whale blow samples by drone: A minimally intrusive tool for conservation genetics77
Particle size influences decay rates of environmental DNA in aquatic systems70
metaPR2: A database of eukaryotic 18S rRNA metabarcodes with an emphasis on protists65
The topological nature of tag jumping in environmental DNA metabarcoding studies64
Use of 16S rRNA gene sequences to identify cyanobacteria that can grow in far‐red light63
Chromosome‐Level Genome Assembly of the Loach Goby Rhyacichthys aspro Offers Insights Into Gobioidei Evolution61
Evaluating the use of lake sedimentary DNA in palaeolimnology: A comparison with long‐term microscopy‐based monitoring of the phytoplankton community57
Stomach Content DNA (scDNA) Detection and Quantification for Predator Diet Assessment Using High‐Throughput Nanofluidic Chip Technology: Species‐Specific qPCR Assay Pa57
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 bats55
Fast‐tracking bespoke DNA reference database generation from museum collections for biomonitoring and conservation54
detectEVE: Fast, Sensitive and Precise Detection of Endogenous Viral Elements in Genomic Data49
Issue Information47
A road map for in vivo evolution experiments with blood‐borne parasitic microbes47
Bayesian tests for random mating in polyploids44
A chromosome‐scale genome assembly and annotation of the spring orchid (Cymbidium goeringii)44
Revisiting the Briggs Ancient DNA Damage Model: A Fast Maximum Likelihood Method to Estimate Post‐Mortem Damage44
DNA barcoding of Chinese snakes reveals hidden diversity and conservation needs42
Characterising Soil Eukaryotic Diversity From NEON Metagenomics Datasets42
Molecular diet analysis in mussels and other metazoan filter feeders and an assessment of their utility as natural eDNA samplers42
A second unveiling: Haplotig masking of the eastern oyster genome improves population‐level inference41
An Accessible Metagenomic Strategy Allows for Better Characterisation of Invertebrate Bulk Samples41
Benchmarking the Mantel test and derived methods for testing association between distance matrices41
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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 structure39
Simulating plasticity as a framework for understanding habitat selection and its role in adaptive capacity and extinction risk through an expansion of CDMetaPOP37
Monitoring of multiple fish species by quantitative environmental DNA metabarcoding surveys over two summer seasons36
Beware of Plant DNA in Animal Dietary Metabarcoding: Lessons From a Strictly Insectivorous Bat36
Potential PCR amplification bias in identifying complex ecological patterns: Higher species compositional homogeneity revealed in smaller‐size coral reef zooplankton by metatranscriptomics36
SPEDE‐sampler: An R Shiny application to assess how methodological choices and taxon sampling can affect Generalized Mixed Yule Coalescent output and interpretation36
RETRACTION: Age Prediction of Green Turtles With an Epigenetic Clock35
Towards Large‐Scale Museomics Projects: A Cost‐Effective and High‐Throughput Extraction Method for Obtaining Historical DNA From Museum Insect Specimens34
MaxTemp: A Method to Maximise Precision of the Temporal Method for Estimating Ne in Genetic Monitoring Programs34
Demogenomic inference from spatially and temporally heterogeneous samples34
Saprotrophic Arachnopeziza Species as New Resources to Study the Obligate Biotrophic Lifestyle of Powdery Mildew Fungi34
A needle in a haystack: A new metabarcoding approach to survey diversity at the species level of Arcellinida (Amoebozoa: Tubulinea)33
Independent Avian Epigenetic Clocks for Ageing and Development33
Cover Image33
Fishing for DNA? Designing baits for population genetics in target enrichment experiments: Guidelines, considerations and the new tool supeRbaits33
Comparing eDNA and Transect Methods for Aquatic Biodiversity Assessment in Lakes and Ponds32
Assessing the impact of USER‐treatment on hyRAD capture applied to ancient DNA32
Scaling Up Species Delimitation From DNA Barcodes to Whole Organelle Genomes: Strong Evidence for Discordance Among Genes and Methods for the Red Alga Dasyclonium32
The great tit HapMap project: A continental‐scale analysis of genomic variation in a songbird31
Proteomic fingerprinting enables quantitative biodiversity assessments of species and ontogenetic stages in Calanus congeners (Copepoda, Crustacea) from the Arctic Ocean31
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 infection31
GenAPoPop 1.0: A user‐friendly software to analyse genetic diversity and structure from partially clonal and selfed autopolyploid organisms31
Chromosome‐level genome of Entada phaseoloides provides insights into genome evolution and biosynthesis of triterpenoid saponins30
Methylome Profiling of a Deuterostome Invertebrate Using Oxford Nanopore Technology ( ONT )29
When barcoding fails: Genome chimerization (admixing) and reticulation obscure phylogenetic and taxonomic relationships29
DNA methylation‐based biomarkers for ageing long‐lived cetaceans28
Evaluating the Benefits and Limits of Multiple Displacement Amplification With Whole‐Genome Oxford Nanopore Sequencing28
A comprehensive framework for detecting copy number variants from single nucleotide polymorphism data: ‘rCNV’, a versatile r package for paralogue and CNV detection28
MycoAI: Fast and accurate taxonomic classification for fungal ITS sequences28
The Long and the Short of It: Nanopore‐Based eDNA Metabarcoding of Marine Vertebrates Works; Sensitivity and Species‐Level Assignment Depend on Amplicon Lengths27
Performance of DNA metabarcoding, standard barcoding and morphological approaches in the identification of insect biodiversity27
Species discrimination in Schima (Theaceae): Next‐generation super‐barcodes meet evolutionary complexity27
Batch effects in population genomic studies with low‐coverage whole genome sequencing data: Causes, detection and mitigation27
Issue Information27
Recovering the genomes hidden in museum wet collections26
Replicate DNA metabarcoding can discriminate seasonal and spatial abundance shifts in river macroinvertebrate assemblages26
Evolutionary history and seascape genomics of Harbour porpoises (Phocoena phocoena) across environmental gradients in the North Atlantic and adjacent waters26
A roadmap to robust discriminant analysis of principal components26
Do not be scared of the genome's 5th base—Explaining phenotypic variability and evolutionary dynamics through DNA methylation analysis26
ParAquaSeq, a Database of Ecologically Annotated rRNA Sequences Covering Zoosporic Parasites Infecting Aquatic Primary Producers in Natural and Industrial Systems25
Allelic bias when performing in‐solution enrichment of ancient human DNA25
Lessons from assembling UCEs: A comparison of common methods and the case of Clavinomia (Halictidae)25
Detecting clonemate pairs in multicellular diploid clonal species based on a shared heterozygosity index25
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 meiofauna23
A consensus protocol for the recovery of mercury methylation genes from metagenomes23
Quantifying uncertainty in inferences of landscape genetic resistance due to choice of individual‐based genetic distance metric23
Bee foraging preferences, microbiota and pathogens revealed by direct shotgun metagenomics of honey23
COInr and mkCOInr: Building and customizing a nonredundant barcoding reference database from BOLD and NCBI using a semi‐automated pipeline22
Non‐invasive age estimation based on faecal DNA using methylation‐sensitive high‐resolution melting for Indo‐Pacific bottlenose dolphins22
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
A Long‐Term Ecological Research Data Set From the Marine Genetic Monitoring Program ARMSMBON 2018–202022
Detection and population genomics of sea turtle species via noninvasive environmental DNA analysis of nesting beach sand tracks and oceanic water22
Quaternary Habitat Fluctuations and Demographic Dynamics in Turtles Inferred From Environmental Niche Modelling and Whole Genome Data22
Plastid Genome Assembly Using Long‐read data22
Environmental RNA can distinguish life stages in amphibian populations22
SLRfinder: A method to detect candidate sex‐linked regions with linkage disequilibrium clustering22
Robust, Open‐Source and Automation‐Friendly DNA Extraction Protocol for Hologenomic Research22
Comparative genomics of a vertically transmitted thiotrophic bacterial ectosymbiont and its close free‐living relative21
Missing genotype imputation in non‐model species using self‐organizing maps21
A collaborative backbone resource for comparative studies of subterranean evolution: The World Asellidae database21
Leveraging an existing whole‐genome resequencing population data set to characterize toll‐like receptor gene diversity in a threatened bird21
The unknown unknown: A framework for assessing environmental DNA assay specificity against unsampled taxa21
Phylogenomic and syntenic data demonstrate complex evolutionary processes in early radiation of the rosids20
FreshOmics: A manually curated and standardized –omics database for investigating freshwater microbiomes20
Unravelling the Web of Life: Incomplete Lineage Sorting and Hybridisation as Primary Mechanisms Over Polyploidisation in the Evolutionary Dynamics of Pear Species20
The accuracy of predicting maladaptation to new environments with genomic data20
New deep learning‐based methods for visualizing ecosystem properties using environmental DNA metabarcoding data20
Ultraconserved Elements and Machine Learning Classifiers Enable Robust Phylogenetics and Taxonomy in Model and Non‐Model Nematodes20
Testing the applicability of environmental DNA metabarcoding to landscape genetics20
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Metabarcoding using nanopore long‐read sequencing for the unbiased characterization of apicomplexan haemoparasites19
Prey ration, temperature, and predator species influence digestion rates of prey DNA inferred from qPCR and metabarcoding19
Issue Information19
Three Novel Spider Genomes Unveil Spidroin Diversification and Hox Cluster Architecture: Ryuthela nishihirai (Liphistiidae), Uloborus plumipes (Uloboridae) and Cheiracanthium punctori18
MuDoGeR: Multi‐Domain Genome recovery from metagenomes made easy18
Influence of RNA‐Seq library construction, sampling methods, and tissue harvesting time on gene expression estimation18
A dynamic ancestral graph model and GPU‐based simulation of a community based on metagenomic sampling18
Accelerating Moss Identification Through the Development of Specific DNA Barcodes Based on the Whole Chloroplast Genome18
High‐quality genomes reveal significant genetic divergence and cryptic speciation in the model organism Folsomia candida (collembola)18
Tools and applications for integrative analysis of DNA methylation in social insects18
CRISPR‐Cas9 enrichment, a new strategy in microbial metagenomics to investigate complex genomic regions: The case of an environmental integron17
Conservation in a litre of air17
Assessing the limits of local ancestry inference from small reference panels17
Detailed DNA barcoding of mayflies in a small European country proved how far we are from having comprehensive barcode reference libraries17
The year of the tiger and the year of tiger genomes!17
Contemporary issues, current best practice and ways forward in soil protist ecology17
MOSCA 2.0: A bioinformatics framework for metagenomics, metatranscriptomics and metaproteomics data analysis and visualization17
TransPi—a comprehensive TRanscriptome ANalysiS PIpeline for de novo transcriptome assembly16
The WZA: A window‐based method for characterizing genotype–environment associations16
RDAforest: Identifying Environmental Drivers of Polygenic Adaptation16
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Identification and quantification of chimeric sequencing reads in a highly multiplexed RAD‐seq protocol16
Correcting for Bias in Estimates of θw and Tajima's D From Missing Data in Next‐Generation Sequencing16
Correction to “epiGBS2: Improvements and Evaluation of Highly Multiplexed, epiGBS‐Based Reduced Representation Bisulfite Sequencing”16
SEGUL: Ultrafast, memory‐efficient and mobile‐friendly software for manipulating and summarizing phylogenomic datasets16
Genome architecture used to supplement species delineation in two cryptic marine ciliates16
Issue Information16
Launching insectphylo.org; a new hub facilitating construction and use of synthesis molecular phylogenies of insects16
Beyond Presence and Absence: Using eDNA and Microsatellite Genotyping to Estimate Densities of Microscopic Life Forms in Wild Populations16
Environmental DNA metabarcoding of freshwater fish in Malaysian tropical rivers using short‐read nanopore sequencing as a potential biomonitoring tool16
RNA allows identifying the consumption of carrion prey15
Who are you? A framework to identify and report genetic sample mix‐ups15
RIDGE, a tool tailored to detect gene flow barriers across species pairs15
Genome and gene evolution of seahorse species revealed by the chromosome‐level genome of Hippocampus abdominalis15
Inferring the timing and strength of natural selection and gene migration in the evolution of chicken from ancient DNA data15
Validating a Target‐Enrichment Design for Capturing Uniparental Haplotypes in Ancient Domesticated Animals15
A High‐Throughput Ancient DNA Extraction Method for Large‐Scale Sample Screening15
Bayesian StairwayPlot for Inferring Single Population Demographic Histories From Site Frequency Spectra14
Efficiency of eDNA and iDNA in assessing vertebrate diversity and its abundance14
Machine Learning Enables Alignment‐Free Distance Calculation and Phylogenetic Placement Using k ‐Mer Frequencies14
Affordable de novo generation of fish mitogenomes using amplification‐free enrichment of mitochondrial DNA and deep sequencing of long fragments14
The answer, my friend, is blowin’ in the wind: Blow sampling provides a new dimension to whale population monitoring14
Species delimitation with limited sampling: An example from rare trapdoor spider genus Cyclocosmia (Mygalomorphae, Halonoproctidae)14
A Short‐Read Amplicon Sequencing Protocol and Bioinformatic Pipeline for Ecological Surveillance of Dipteran Disease Vectors14
Machine learning in molecular ecology14
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A chromosome‐level genome assembly enables the identification of the follicule stimulating hormone receptor as the master sex‐determining gene in the flatfish Solea senegalensis14
Management and conservation implications of cryptic population substructure for two commercially exploited fishes (Merluccius spp.) in southern Africa14
A molecular‐based identification resource for the arthropods of Finland14
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DNA barcodes highlight genetic diversity patterns in rodents from lowland desert and Andean areas in Argentina14
Express barcoding with NextGenPCR and MinION for species‐level sorting of ecological samples13
Genomes of Two Monophagous Weevils and Their Host Plant Provide Insights Into Evolution of Plant Defence and Insect Counter‐Defence13
Next‐generation bioinformatics: An ultrafast and user‐friendly tool for phylogenomic data exploration13
Comparative genomics reveals the dynamic evolutionary history of cement protein genes of barnacles from intertidal to deep‐sea hydrothermal vents13
Temporal Variability in Effective Size (N̂e) Identifies Potential Sources of Discrepancies Between Mark Recapture and Close Kin Mark Recapture Estimates of Population Abundance13
Chromosome‐level genome assembly of Pedicularis kansuensis illuminates genome evolution of facultative parasitic plant13
An empirical test of the estimation of historical effective population size using Drosophila melanogaster13
Macrobial airborne environmental DNA analysis: A review of progress, challenges, and recommendations for an emerging application13
Quantifying Soil Microbiome Abundance by Metatranscriptomics and Complementary Molecular Techniques—Cross‐Validation and Perspectives13
Environmental DNA phylogeography: Successful reconstruction of phylogeographic patterns of multiple fish species from cups of water13
Quantitative assessment of reef foraminifera community from metabarcoding data13
A chromosomal level genome sequence for Quasipaa spinosa (Dicroglossidae) reveals chromosomal evolution and population diversity12
Delimiting the rare, endangered and actively speciating12
Next‐Generation Snow Leopard Population Assessment Tool: Multiplex‐PCR SNP Panel for Individual Identification From Faeces12
HMS‐S‐S: A tool for the identification of Sulphur metabolism‐related genes and analysis of operon structures in genome and metagenome assemblies12
CCS‐Consensuser: A Haplotype‐Aware Consensus Generator for PacBio Amplicon Sequences12
Estimation of spatial demographic maps from polymorphism data using a neural network12
Utilizing paralogues for phylogenetic reconstruction has the potential to increase species tree support and reduce gene tree discordance in target enrichment data12
Polly: An R package for genotyping microsatellites and detecting highly polymorphic DNA markers from short‐read data12
Issue Information12
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Genetic variation and domestication of horses revealed by 10 chromosome‐level genomes and whole‐genome resequencing12
Scaling‐up RADseq methods for large datasets of non‐invasive samples: Lessons for library construction and data preprocessing12
A Novel Protistan Trait Database Reveals Functional Redundancy and Complementarity in Terrestrial Protists (Amoebozoa and Rhizaria)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 Asia12
Issue Information12
Chromosome‐level genome assembly of a triploid poplar Populus albaBerolinensis12
A guide to avian museomics: Insights gained from resequencing hundreds of avian study skins12
Application of palaeogenetic techniques to historic mollusc shells reveals phylogeographic structure in a New Zealand abalone11
Unrecognised DNA Degradation in Flash‐Frozen Genetic Samples in Natural History Collections11
Morphological and taxonomic diversity of mesozooplankton is an important driver of carbon export fluxes in the ocean11
Chromosome‐level genomes of two armyworms, Mythimna separata and Mythimna loreyi, provide insights into the biosynthesis and reception of sex pheromones11
A Post‐Mortem Molecular Damage Profile in the Ancient Human Mitochondrial DNA11
Environmental DNA methylation of Lymnaea stagnalis varies with age and is hypermethylated compared to tissue DNA11
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Phylogenomic analyses of the genusDrosophilareveals genomic signals of climate adaptation11
A novel assembly pipeline and functional annotations for targeted sequencing: A case study on the globally threatened Margaritiferidae (Bivalvia: Unionida)11
Pan‐Genome of Jasminum sambac Reveals the Genetic Diversity of Different Petal Morphology and Aroma‐Related Genes11
A Snakemake Toolkit for the Batch Assembly, Annotation and Phylogenetic Analysis of Mitochondrial Genomes and Ribosomal Genes From Genome Skims of Museum Collections10
The chromosome‐level genome assembly of the Japanese yellowtail jack Seriola aureovittata provides insights into genome evolution and efficient oxygen transport10
Arthropod: A Tool for Phylogenomic Research in Arthropods10
EntoSieve: Automated Size‐Sorting of Insect Bulk Samples to Aid Accurate Megabarcoding and Metabarcoding10
Spatial metabolomics reveal divergent cardenolide processing in the monarch (Danaus plexippus) and the common crow butterfly (Euploea core)10
Non‐Invasive Underwater DNA Sampling Illuminates Red Sea Echinoderm Diversity10
Genomic and Methylomic Signatures Associated With the Maintenance of Genome Stability and Adaptive Evolution in Two Closely Allied Wolf Spiders10
Integrating Pool‐seq uncertainties into demographic inference10
Evolution of olfactory receptor superfamily in bats based on high throughput molecular modelling9
The Impact of Whole‐Animal Fluid Preservation on the Observed Gut Microbiome of Vertebrates: Implications for the Use of Museum Specimens in Microbiome Research9
One metric or many? Refining the analytical framework of landscape resistance estimation in individual‐based landscape genetic analyses9
HiMAP2: Identifying phylogenetically informative genetic markers from diverse genomic resources9
Performance of DNA Metabarcoding vs. Morphological Methods for Assessing Intertidal Turf and Foliose Algae Diversity9
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 Ethiopia9
Linkage Mapping vs. Association: A Comparison of Two RADseq‐Based Approaches to Identify Markers for Homomorphic Sex Chromosomes in Large Genomes9
Finding the perfect pairs: A matchmaking of plant markers and primers for multi‐marker eDNA metabarcoding9
Chromosome‐scale genomes reveal genomic consequences of inbreeding in the South China tiger: A comparative study with the Amur tiger9
Diet preferences based on sequence read count: The role of species interaction in tissue bias correction9
Parent‐offspring inference in inbred populations9
Correction to “Quantifying Mitochondrial Heteroplasmy Diversity: A Computational Approach”9
Maintenance of genetic diversity in subdivided populations using genomic coancestry matrices9
An Optimised Method to Identify Reintroduced Swift Foxes (Vulpes velox) Through SNP Genotyping of Non‐Invasively Collected Scat Samples Using In‐Solution Hybridisation Capture9
Guidelines for standardizing the application of discriminant analysis of principal components to genotype data9
Toward absolute abundance for conservation applications: Estimating the number of contributors via microhaplotype genotyping of mixed‐DNA samples9
The population genetics of partial diapause, with applications to the aestivating malaria mosquito Anopheles coluzzii9
Comparing genome‐based estimates of relatedness for use in pedigree‐based conservation management9
Estimating predation rates from molecular gut content analysis9
Systematic review and meta‐analysis: Water type and temperature affect environmental DNA decay9
EggLib 3: A python package for population genetics and genomics8
Revisiting Genetic Data Stewardship Practices in Aotearoa New Zealand: A Call to Action on Integrating Māori Data Sovereignty8
Effect of reduced genomic representation on using runs of homozygosity for inbreeding characterization8
High‐quality haplotype‐resolved genome assembly for ring‐cup oak (Quercus glauca) provides insight into oaks demographic dynamics8
Correcting for Replicated Genotypes May Introduce More Problems Than it Solves8
Plant DNA barcode library for native flowering plants in the arid region of northwestern China8
Too Far From Relatives? Impact of the Genetic Distance on the Success of Exon Capture in Phylogenomics8
NMπ 2.0: Software update to minimize the risk of false positives among determinants of reproductive success8
mapmixture: An R package and web app for spatial visualisation of admixture and population structure8
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Towards a better future for DNA barcoding: Evaluating monophyly‐ and distance‐based species identification using COI gene fragments of Dacini fruit flies8
CRISPR‐Cas9‐mediated host signal reduction for 18S metabarcoding of host‐associated eukaryotes8
DNA barcoding of Cymbidium by genome skimming: Call for next‐generation nuclear barcodes8
Extensive sequence divergence between the reference genomes of two zebrafish strains, Tuebingen and AB8
Massive genome investigations reveal insights of prevalent introgression for environmental adaptation and triterpene biosynthesis in Ganoderma8
Current stewardship practices in invasion biology limit the value and secondary use of genomic data7
CRISPR‐based diagnostics detects invasive insect pests7
Improved recovery and annotation of genes in metagenomes through the prediction of fungal introns7
Issue Information7
A multispecies amplicon sequencing approach for genetic diversity assessments in grassland plant species7
A setback into a success: What can batch effects tell us about best practices in genomics?7
Host Traits Impact the Outcome of Metagenomic Library Preparation From Dental Calculus Samples Across Diverse Mammals7
Comparative Decay Dynamics and Detectability of eDNA and eRNA in Connected and Isolated Freshwater7
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Advancing Species Conservation and Management Through Omics Tools7
Metazoa‐level USCOs as markers in species delimitation and classification7
Genomic and machine learning‐based screening of aquaculture‐associated introgression into at‐risk wild North American Atlantic salmon (Salmo salar) populations7
A chromosome‐level genome of Portunus trituberculatus provides insights into its evolution, salinity adaptation and sex determination7
Pan‐genome analysis highlights the role of structural variation in the evolution and environmental adaptation of Asian honeybees7
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 sets7
HMicroDB: A Comprehensive Database of Herpetofaunal Microbiota With a Focus on Host Phylogeny, Physiological Traits, and Environment Factors7
The practice and promise of temporal genomics for measuring evolutionary responses to global change7
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