Molecular Ecology Resources

Article	Citations
Issue Information	328
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Current stewardship practices in invasion biology limit the value and secondary use of genomic data	62
Average nucleotide diversity should be weighted by per‐site sample size	62
Leveraging genomic load estimates to optimize captive breeding programmes	60
Bayesian StairwayPlot for Inferring Single Population Demographic Histories From Site Frequency Spectra	59
Navigating Past Oceans: Comparing Metabarcoding and Metagenomics of Marine Ancient Sediment Environmental DNA	59
Landscape transcriptomics as a tool for addressing global change effects across diverse species	58
A second unveiling: Haplotig masking of the eastern oyster genome improves population‐level inference	56
Pan‐genome analysis highlights the role of structural variation in the evolution and environmental adaptation of Asian honeybees	56
Target enrichment of long open reading frames and ultraconserved elements to link microevolution and macroevolution in non‐model organisms	55
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Improved recovery and annotation of genes in metagenomes through the prediction of fungal introns	50
Genetic landscape clustering of a large DNA barcoding data set reveals shared patterns of genetic divergence among freshwater fishes of the Maroni Basin	49
The endangered White Sands pupfish (Cyprinodon tularosa) genome reveals low diversity and heterogenous patterns of differentiation	49
Issue Information	43
The role of oceanic currents in the dispersal and connectivity of the mangrove Rhizophora mangle on the Southwest Atlantic region	42
Machine learning in molecular ecology	42
A High‐Throughput Ancient DNA Extraction Method for Large‐Scale Sample Screening	41
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Genomic insights into evolution and control of Wohlfahrtia magnifica, a widely distributed myiasis‐causing fly of warm‐blooded vertebrates	39
Good from far, but far from good: The impact of a reference genome on evolutionary inference	38
Chromosome‐level genome assembly of Welwitschia mirabilis, a unique Namib Desert species	38

Who are you? A framework to identify and report genetic sample mix‐ups	37
A chromosome‐level genome of Antechinus flavipes provides a reference for an Australian marsupial genus with male death after mating	37
A high‐quality carabid genome assembly provides insights into beetle genome evolution and cold adaptation	35
Chromosome‐scale assembly and whole‐genome sequencing of 266 giant panda roundworms provide insights into their evolution, adaptation and potential drug targets	35
The promise and challenges of characterizing genome‐wide structural variants: A case study in a critically endangered parrot	34
DNA barcoding of Chinese snakes reveals hidden diversity and conservation needs	34
A road map for in vivo evolution experiments with blood‐borne parasitic microbes	34
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Issue Information	33
Leveraging whole‐genome sequencing to estimate telomere length in plants	33
Crimp: An efficient tool for summarizing multiple clusterings in population structure analysis and beyond	32
Does clustering of DNA barcodes agree with botanical classification directly at high taxonomic levels? Trees in French Guiana as a case study	32
The voice of the little giants: Arcellinida testate amoebae in environmental DNA‐based bioindication, from taxonomy free to haplotypic level	32
SPdel: A pipeline to compare and visualize species delimitation methods for single‐locus datasets	31
A high‐quality functional genome assembly of Delia radicum L. (Diptera: Anthomyiidae) annotated from egg to adult	31
Individual haplotyping of whale sharks from seawater environmental DNA	31
Genome and gene evolution of seahorse species revealed by the chromosome‐level genome of Hippocampus abdominalis	31
detectEVE: Fast, Sensitive and Precise Detection of Endogenous Viral Elements in Genomic Data	30
Fast‐tracking bespoke DNA reference database generation from museum collections for biomonitoring and conservation	30
The practice and promise of temporal genomics for measuring evolutionary responses to global change	29
A multispecies amplicon sequencing approach for genetic diversity assessments in grassland plant species	29
Nonlethal age estimation of three threatened fish species using DNA methylation: Australian lungfish, Murray cod and Mary River cod	29
gscramble: Simulation of Admixed Individuals Without Reuse of Genetic Material	29
Management and conservation implications of cryptic population substructure for two commercially exploited fishes (Merluccius spp.) in southern Africa	29
Inferring the timing and strength of natural selection and gene migration in the evolution of chicken from ancient DNA data	29
Genotyping single nucleotide polymorphisms and inferring ploidy by amplicon sequencing for polyploid, ploidy‐variable organisms	29
The complete and closed genome of the facultative generalist Candidatus Endoriftia persephone from deep‐sea hydrothermal vents	29
A chromosome‐level genome of Portunus trituberculatus provides insights into its evolution, salinity adaptation and sex determination	29
epiGBS2: Improvements and evaluation of highly multiplexed, epiGBS‐based reduced representation bisulfite sequencing	28
Journeying towards best practice data management in biodiversity genomics	28
Sequence coverage required for accurate genotyping by sequencing in polyploid species	28
RNA allows identifying the consumption of carrion prey	28
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Use of 16S rRNA gene sequences to identify cyanobacteria that can grow in far‐red light	28
Hīkina te mānuka: Advancing Indigenous Leadership in Molecular Ecology	28
Monitoring environmental microbiomes: Alignment of microbiology and computational biology competencies within a culturally integrated curriculum and research framework	28
The Ribosomal Operon Database: A Full‐Length rDNA Operon Database Derived From Genome Assemblies	27
A step towards the validation of bacteria biotic indices using DNA metabarcoding for benthic monitoring	26
Detecting Assembly Errors With Klumpy: Building Confidence in Your Daily Genomic Analysis	26
Stomach Content DNA (scDNA) Detection and Quantification for Predator Diet Assessment Using High‐Throughput Nanofluidic Chip Technology: Species‐Specific qPCR Assay Pa	26
Revisiting the Briggs Ancient DNA Damage Model: A Fast Maximum Likelihood Method to Estimate Post‐Mortem Damage	26
A library preparation optimized for metagenomics of RNA viruses	25
Allometric scaling improves the characterization of complex community transcriptomes	25
Alignment‐free methods for polyploid genomes: Quick and reliable genetic distance estimation	25
Optimizing ddRAD sequencing for population genomic studies with ddgRADer	25
Particle size influences decay rates of environmental DNA in aquatic systems	25
A chromosome‐scale genome assembly and annotation of the spring orchid (Cymbidium goeringii)	24
A setback into a success: What can batch effects tell us about best practices in genomics?	24
Reconstructing queen genotypes by pool sequencing colonies in eusocial insects: Statistical Methods and their application to honeybee	24
Mini reviews: A new manuscript category for summarizing emerging topics	24

Successes and limitations of quantitative diet metabarcoding in a small, herbivorous mammal	24
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 sets	24
CRISPR‐based diagnostics detects invasive insect pests	24
Genomic library preparation and hybridization capture of formalin‐fixed tissues and allozyme supernatant for population genomics and considerations for combining capture‐ and RADseq‐based single nucle	24
Genomic and transcriptomic analyses of a social hemipteran provide new insights into insect sociality	23
Bayesian tests for random mating in polyploids	23
Recovered microbiome of an oviparous lizard differs across gut and reproductive tissues, cloacal swabs, and faeces	23
Molecular assays of pollen use consistently reflect pollinator visitation patterns in a system of flowering plants	23
A cost‐effective blood DNA methylation‐based age estimation method in domestic cats, Tsushima leopard cats (Prionailurus bengalensis euptilurus) and Panthera species, using ta	22
Exhaustive reanalysis of barcode sequences from public repositories highlights ongoing misidentifications and impacts taxa diversity and distribution	22
Ichthyoplankton metabarcoding: An efficient tool for early detection of invasive species establishment	22
Metazoa‐level USCOs as markers in species delimitation and classification	22
Collecting baleen whale blow samples by drone: A minimally intrusive tool for conservation genetics	22
Efficiency of eDNA and iDNA in assessing vertebrate diversity and its abundance	22
Species delimitation with limited sampling: An example from rare trapdoor spider genus Cyclocosmia (Mygalomorphae, Halonoproctidae)	22
RIDGE, a tool tailored to detect gene flow barriers across species pairs	22
Recovery of 197 eukaryotic bins reveals major challenges for eukaryote genome reconstruction from terrestrial metagenomes	22
Molecular diet analysis in mussels and other metazoan filter feeders and an assessment of their utility as natural eDNA samplers	22
Seq2Sat and SatAnalyzer toolkit: Towards comprehensive microsatellite genotyping from sequencing data	22
Using target capture to address conservation challenges: Population‐level tracking of a globally‐traded herbal medicine	21
slimr: An R package for tailor‐made integrations of data in population genomic simulations over space and time	21
Chromosome‐level de novo genome assembly and whole‐genome resequencing of the threatened species Acanthochlamys bracteata (Velloziaceae) provide insights into alpine plant divergence in a biodi	21
High quality haplotype‐resolved genome assemblies of Populus tomentosa Carr., a stabilized interspecific hybrid species widespread in Asia	20
Mind the Gap: A Neural Network Framework for Imputing Genotypes in Non‐Model Species	20
ModEst: Accurate estimation of genome size from next generation sequencing data	20
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	20
Genome and Metagenome Skimming: Future Sequencing Methods for Environmental DNA (eDNA) Studies	20
HMicroDB: A Comprehensive Database of Herpetofaunal Microbiota With a Focus on Host Phylogeny, Physiological Traits, and Environment Factors	20
A Possible More Precise Management Unit Delineation Based on Epigenomic Differentiation of a Long‐Distance‐Migratory Marine Fish Scomberomorus niphonius	20
Airborne environmental DNA captures terrestrial vertebrate diversity in nature	20
A Short‐Read Amplicon Sequencing Protocol and Bioinformatic Pipeline for Ecological Surveillance of Dipteran Disease Vectors	20
That's Not a Hybrid: How to Distinguish Patterns of Admixture and Isolation By Distance	20
metaPR2: A database of eukaryotic 18S rRNA metabarcodes with an emphasis on protists	19
eDNAssay: A machine learning tool that accurately predicts qPCR cross‐amplification	19
GeneMiner: A tool for extracting phylogenetic markers from next‐generation sequencing data	19
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A molecular‐based identification resource for the arthropods of Finland	19
Novel quality metrics allow identifying and generating high‐quality assemblies of piRNA clusters	19
Evaluating the use of lake sedimentary DNA in palaeolimnology: A comparison with long‐term microscopy‐based monitoring of the phytoplankton community	18
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Strong Signatures of Selection on Candidate Genes Underlying Core Speciation Mechanisms in Desert Tortoises	18
Development of epigenetic biomarkers for the identification of sex and thermal stress in fish using DNA methylation analysis and machine learning procedures	18
The topological nature of tag jumping in environmental DNA metabarcoding studies	18
Genomic and machine learning‐based screening of aquaculture‐associated introgression into at‐risk wild North American Atlantic salmon (Salmo salar) populations	17
CPGView: A package for visualizing detailed chloroplast genome structures	17
Long‐ and short‐read metabarcoding technologies reveal similar spatiotemporal structures in fungal communities	17
Labile sex chromosomes in the Australian freshwater fish family Percichthyidae	17
Tracing the geographic origin of endangered plant species using transcriptome‐derived SNPs: An example of Cathaya argyrophylla	17
Optimal sequence similarity thresholds for clustering of molecular operational taxonomic units inDNAmetabarcoding studies	17
Design and implementation of multiplexed amplicon sequencing panels to serve genomic epidemiology of infectious disease: A malaria case study	17
What can optimized cost distances based on genetic distances offer? A simulation study on the use and misuse of ResistanceGA	16
Scaling‐up RADseq methods for large datasets of non‐invasive samples: Lessons for library construction and data preprocessing	16
Benchmarking the Mantel test and derived methods for testing association between distance matrices	16
Environmental RNA degrades more rapidly than environmental DNA across a broad range of pH conditions	16
Population genomics provides insights into lineage divergence and local adaptation within the cotton bollworm	16
DNA barcodes highlight genetic diversity patterns in rodents from lowland desert and Andean areas in Argentina	16
Improved de novo chromosome‐level genome assembly of the vulnerable walnut tree Juglans mandshurica reveals gene family evolution and possible genome basis of resistance to lesion nematode	16
f‐Statistics estimation and admixture graph construction with Pool‐Seq or allele count data using the R package poolfstat	16
DNA methylation as a tool to explore ageing in wild roe deer populations	16
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Filtration extraction method using a microfluidic channel for measuring environmental DNA	16
Chromosome‐level genome assembly of Sichuan pepper provides insights into apomixis, drought tolerance, and alkaloid biosynthesis	16
Why eDNA fractions need consideration in biomonitoring	16
A high‐quality reference genome forFraxinus pennsylvanicafor ash species restoration and research	16
Genome of the butterfly hillstream loach provides insights into adaptations to torrential mountain stream life	15
A rodent anchored hybrid enrichment probe set for a range of phylogenetic utility: From order to species	15
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Beware of Plant DNA in Animal Dietary Metabarcoding: Lessons From a Strictly Insectivorous Bat	15
Sampling effect in predicting the evolutionary response of populations to climate change	15
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Reframing Formalin: A Molecular Opportunity Enabling Historical Epigenomics and Retrospective Gene Expression Studies	15
quickLD: An efficient software for linkage disequilibrium analyses	15
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Development of SNP Panels from Low‐Coverage Whole Genome Sequencing (lcWGS) to Support Indigenous Fisheries for Three Salmonid Species in Northern Canada	15
A Pipeline and Recommendations for Population and Individual Diagnostic SNP Selection in Non‐Model Species	14
SPEDE‐sampler: An R Shiny application to assess how methodological choices and taxon sampling can affect Generalized Mixed Yule Coalescent output and interpretation	14
Exploring Environmental Microfungal Diversity Through Serial Single Cell Screening	14
Comparing iDNA from mosquitoes and flies to survey mammals in a semi‐controlled Neotropical area	14
Temporal Variability in Effective Size (N̂e) Identifies Potential Sources of Discrepancies Between Mark Recapture and Close Kin Mark Recapture Estimates of Population Abundance	14
Monitoring of multiple fish species by quantitative environmental DNA metabarcoding surveys over two summer seasons	14

Issue Information	13
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Benchmarking long‐read sequencing strategies for obtaining ASV‐resolved rRNA operons from environmental microeukaryotes	13
Barcoding and traditional health practitioner perspectives are informative to monitor and conserve frogs and reptiles traded for traditional medicine in urban South Africa	13
Comparative genomics reveals the dynamic evolutionary history of cement protein genes of barnacles from intertidal to deep‐sea hydrothermal vents	13
Metagenomic‐based discovery and comparison of the lignin degrading potential of microbiomes in aquatic and terrestrial ecosystems via the LCdb database	13
Culture‐enriched community profiling improves resolution of the vertebrate gut microbiota	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
Roof of the world: Home and border in the genomic era	13
More than dirt: Sedimentary ancient DNA and Indigenous Australia	13
Individual genotypes from environmental DNA: Fingerprinting snow tracks of three large carnivore species	13
Chromosome‐level genome assembly of Pedicularis kansuensis illuminates genome evolution of facultative parasitic plant	13
Multiplexing PCR allows the identification of within‐species genetic diversity in ancient eDNA	13
Issue Information	13
Arthropods are kin: Operationalizing Indigenous data sovereignty to respectfully utilize genomic data from Indigenous lands	13
Express barcoding with NextGenPCR and MinION for species‐level sorting of ecological samples	13
Single‐molecule long‐read sequencing reveals extensive genomic and transcriptomic variation between maize and its wild relative teosinte (Zea mays ssp. parviglumis)	12
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Lysis‐Hi‐C as a method to study polymicrobial communities and eDNA	12
Chromosome‐level genome and population genomic analysis provide insights into the evolution and environmental adaptation of Jinjiang oysterCrassostrea ariakensis	12
Simulating plasticity as a framework for understanding habitat selection and its role in adaptive capacity and extinction risk through an expansion of CDMetaPOP	12
Inference of the distribution of fitness effects of mutations is affected by single nucleotide polymorphism filtering methods, sample size and population structure	12
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Assembly‐free quantification of vagrant DNA inserts	12
Demogenomic inference from spatially and temporally heterogeneous samples	12
Evaluating restriction enzyme selection for reduced representation sequencing in conservation genomics	12
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High‐quality genome of a pioneer mangrove Laguncularia racemosa explains its advantages for intertidal zone reforestation	11
Chromosome‐level genome assembly of an agricultural pest, the rice leaffolder Cnaphalocrocis exigua (Crambidae, Lepidoptera)	11
Enhancing amphibian biomonitoring through eDNA metabarcoding	11
Assessing candidate DNA barcodes for Chinese and internationally traded timber species	11
Chromosome‐level genome assembly of the mirid predator Cyrtorhinus lividipennis Reuter (Hemiptera: Miridae), an important natural enemy in the rice ecosystem	11
MaxTemp: A Method to Maximise Precision of the Temporal Method for Estimating Ne in Genetic Monitoring Programs	11
Fishing for DNA? Designing baits for population genetics in target enrichment experiments: Guidelines, considerations and the new tool supeRbaits	11
Affordable de novo generation of fish mitogenomes using amplification‐free enrichment of mitochondrial DNA and deep sequencing of long fragments	11
Issue Information	11
Cochlear Cell Atlas of Two Laryngeal Echolocating Bats—New Evidence for the Adaptive Nervous Physiology in Constant Frequency Bat	11
Chromosomal‐level assembly of Bactericera cockerelli reveals rampant gene family expansions impacting genome structure, function and insect‐microbe‐plant‐interactions	11
To bee, or not to bee? One leg is the question	11
A target capture approach for phylogenomic analyses at multiple evolutionary timescales in rosewoods (Dalbergia spp.) and the legume family (Fabaceae)	11
Revealing population demographics with environmental RNA	11
Chromosome‐level de novo genome assembly of Telopea speciosissima (New South Wales waratah) using long‐reads, linked‐reads and Hi‐C	11
Insect Cytochrome P450 Database: An Integrated Resource of Genetic Diversity, Evolution and Function	11