Molecular Ecology Resources

Article	Citations
Issue Information	305
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Average nucleotide diversity should be weighted by per‐site sample size	81
Current stewardship practices in invasion biology limit the value and secondary use of genomic data	66
CPGView: A package for visualizing detailed chloroplast genome structures	56
Leveraging genomic load estimates to optimize captive breeding programmes	54
Improved recovery and annotation of genes in metagenomes through the prediction of fungal introns	53
eDNAssay: A machine learning tool that accurately predicts qPCR cross‐amplification	53
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The endangered White Sands pupfish (Cyprinodon tularosa) genome reveals low diversity and heterogenous patterns of differentiation	53
Target enrichment of long open reading frames and ultraconserved elements to link microevolution and macroevolution in non‐model organisms	53
Genetic landscape clustering of a large DNA barcoding data set reveals shared patterns of genetic divergence among freshwater fishes of the Maroni Basin	52
Fast‐tracking bespoke DNA reference database generation from museum collections for biomonitoring and conservation	51
The role of oceanic currents in the dispersal and connectivity of the mangrove Rhizophora mangle on the Southwest Atlantic region	50
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Cover Image	48
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Chromosome‐level genome assembly of Welwitschia mirabilis, a unique Namib Desert species	46
Genomic insights into evolution and control of Wohlfahrtia magnifica, a widely distributed myiasis‐causing fly of warm‐blooded vertebrates	46
Good from far, but far from good: The impact of a reference genome on evolutionary inference	45
A chromosome‐level genome of Antechinus flavipes provides a reference for an Australian marsupial genus with male death after mating	45
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Who are you? A framework to identify and report genetic sample mix‐ups	43
Issue Information	43
Chromosome‐level assembly of the mangrove plant Aegiceras corniculatum genome generated through Illumina, PacBio and Hi‐C sequencing technologies	43

Machine learning in molecular ecology	40
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The promise and challenges of characterizing genome‐wide structural variants: A case study in a critically endangered parrot	39
Leveraging whole‐genome sequencing to estimate telomere length in plants	37
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	37
Issue Information	37
Genomic and machine learning‐based screening of aquaculture‐associated introgression into at‐risk wild North American Atlantic salmon (Salmo salar) populations	36
Does clustering of DNA barcodes agree with botanical classification directly at high taxonomic levels? Trees in French Guiana as a case study	36
That's Not a Hybrid: How to Distinguish Patterns of Admixture and Isolation By Distance	35
The voice of the little giants: Arcellinida testate amoebae in environmental DNA‐based bioindication, from taxonomy free to haplotypic level	34
A high‐quality functional genome assembly of Delia radicum L. (Diptera: Anthomyiidae) annotated from egg to adult	34
Crimp: An efficient tool for summarizing multiple clusterings in population structure analysis and beyond	34
The Ocean barcode atlas: A web service to explore the biodiversity and biogeography of marine organisms	33
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Genome and gene evolution of seahorse species revealed by the chromosome‐level genome of Hippocampus abdominalis	32
The topological nature of tag jumping in environmental DNA metabarcoding studies	32
Management and conservation implications of cryptic population substructure for two commercially exploited fishes (Merluccius spp.) in southern Africa	31
Genotyping single nucleotide polymorphisms and inferring ploidy by amplicon sequencing for polyploid, ploidy‐variable organisms	31
The complete and closed genome of the facultative generalist Candidatus Endoriftia persephone from deep‐sea hydrothermal vents	31
A road map for in vivo evolution experiments with blood‐borne parasitic microbes	31
The practice and promise of temporal genomics for measuring evolutionary responses to global change	31
A chromosome‐level genome of Portunus trituberculatus provides insights into its evolution, salinity adaptation and sex determination	30
Inferring the timing and strength of natural selection and gene migration in the evolution of chicken from ancient DNA data	30
A multispecies amplicon sequencing approach for genetic diversity assessments in grassland plant species	30
RNA allows identifying the consumption of carrion prey	29
A second unveiling: Haplotig masking of the eastern oyster genome improves population‐level inference	29
epiGBS2: Improvements and evaluation of highly multiplexed, epiGBS‐based reduced representation bisulfite sequencing	29
Assessing genome assembly quality prior to downstream analysis: N50 versus BUSCO	29
Optimizing ddRAD sequencing for population genomic studies with ddgRADer	28
Revisiting the Briggs Ancient DNA Damage Model: A Fast Maximum Likelihood Method to Estimate Post‐Mortem Damage	28
Use of 16S rRNA gene sequences to identify cyanobacteria that can grow in far‐red light	28
Individual haplotyping of whale sharks from seawater environmental DNA	28
The Ribosomal Operon Database: A Full‐Length rDNA Operon Database Derived From Genome Assemblies	28
Using target capture to address conservation challenges: Population‐level tracking of a globally‐traded herbal medicine	28
Allometric scaling improves the characterization of complex community transcriptomes	28
Detecting Assembly Errors With Klumpy: Building Confidence in Your Daily Genomic Analysis	28
Sequence coverage required for accurate genotyping by sequencing in polyploid species	28
Particle size influences decay rates of environmental DNA in aquatic systems	27
A molecular‐based identification resource for the arthropods of Finland	26
Hybridization capture of larch (Larix Mill.) chloroplast genomes from sedimentary ancient DNA reveals past changes of Siberian forest	26
Development of epigenetic biomarkers for the identification of sex and thermal stress in fish using DNA methylation analysis and machine learning procedures	26
CRISPR‐based diagnostics detects invasive insect pests	25
Alignment‐free methods for polyploid genomes: Quick and reliable genetic distance estimation	25
A library preparation optimized for metagenomics of RNA viruses	25
Tracing the geographic origin of endangered plant species using transcriptome‐derived SNPs: An example of Cathaya argyrophylla	25
DNA barcoding of Chinese snakes reveals hidden diversity and conservation needs	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
Mini reviews: A new manuscript category for summarizing emerging topics	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
A high‐quality carabid genome assembly provides insights into beetle genome evolution and cold adaptation	24

Bayesian tests for random mating in polyploids	24
A chromosome‐scale genome assembly and annotation of the spring orchid (Cymbidium goeringii)	24
A reference‐free approach to analyse RADseq data using standard next generation sequencing toolkits	24
Successes and limitations of quantitative diet metabarcoding in a small, herbivorous mammal	24
Predicting sample success for large‐scale ancient DNA studies on marine mammals	24
Design and implementation of multiplexed amplicon sequencing panels to serve genomic epidemiology of infectious disease: A malaria case study	24
Novel quality metrics allow identifying and generating high‐quality assemblies of piRNA clusters	24
Reconstructing queen genotypes by pool sequencing colonies in eusocial insects: Statistical Methods and their application to honeybee	24
A setback into a success: What can batch effects tell us about best practices in genomics?	24
Chromosome‐scale assembly and whole‐genome sequencing of 266 giant panda roundworms provide insights into their evolution, adaptation and potential drug targets	24
A chromosome‐level genome assembly for the tertiary relict plant Tetracentron sinense oliv. (trochodendraceae)	23
SPdel: A pipeline to compare and visualize species delimitation methods for single‐locus datasets	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
Landscape transcriptomics as a tool for addressing global change effects across diverse species	22
Collecting baleen whale blow samples by drone: A minimally intrusive tool for conservation genetics	22
Ichthyoplankton metabarcoding: An efficient tool for early detection of invasive species establishment	22
HMicroDB: A Comprehensive Database of Herpetofaunal Microbiota With a Focus on Host Phylogeny, Physiological Traits, and Environment Factors	22
Genomic and transcriptomic analyses of a social hemipteran provide new insights into insect sociality	22
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Benchmarking the Mantel test and derived methods for testing association between distance matrices	20
Evaluating the use of lake sedimentary DNA in palaeolimnology: A comparison with long‐term microscopy‐based monitoring of the phytoplankton community	20
Exhaustive reanalysis of barcode sequences from public repositories highlights ongoing misidentifications and impacts taxa diversity and distribution	20
Mind the Gap: A Neural Network Framework for Imputing Genotypes in Non‐Model Species	20
Nonlethal age estimation of three threatened fish species using DNA methylation: Australian lungfish, Murray cod and Mary River cod	20
Journeying towards best practice data management in biodiversity genomics	20
Recovery of 197 eukaryotic bins reveals major challenges for eukaryote genome reconstruction from terrestrial metagenomes	20
f‐Statistics estimation and admixture graph construction with Pool‐Seq or allele count data using the R package poolfstat	20
Monitoring environmental microbiomes: Alignment of microbiology and computational biology competencies within a culturally integrated curriculum and research framework	20
Hīkina te mānuka: Advancing Indigenous Leadership in Molecular Ecology	20
Pan‐genome analysis highlights the role of structural variation in the evolution and environmental adaptation of Asian honeybees	20
Long‐ and short‐read metabarcoding technologies reveal similar spatiotemporal structures in fungal communities	20
metaPR2: A database of eukaryotic 18S rRNA metabarcodes with an emphasis on protists	19
A step towards the validation of bacteria biotic indices using DNA metabarcoding for benthic monitoring	19
Efficiency of eDNA and iDNA in assessing vertebrate diversity and its abundance	19
Airborne environmental DNA captures terrestrial vertebrate diversity in nature	19
Analysing landscape effects on dispersal networks and gene flow with genetic graphs	19
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	19
Labile sex chromosomes in the Australian freshwater fish family Percichthyidae	18
Molecular diet analysis in mussels and other metazoan filter feeders and an assessment of their utility as natural eDNA samplers	18
Complex interactions between environmental DNA (eDNA) state and water chemistries on eDNA persistence suggested by meta‐analyses	18
Why eDNA fractions need consideration in biomonitoring	18
High quality haplotype‐resolved genome assemblies of Populus tomentosa Carr., a stabilized interspecific hybrid species widespread in Asia	18
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	18
eDNAFlow, an automated, reproducible and scalable workflow for analysis of environmental DNA sequences exploiting Nextflow and Singularity	18
ModEst: Accurate estimation of genome size from next generation sequencing data	18
Optimal sequence similarity thresholds for clustering of molecular operational taxonomic units inDNAmetabarcoding studies	18
Environmental RNA degrades more rapidly than environmental DNA across a broad range of pH conditions	18
A chromosome‐level assembly of the black tiger shrimp (Penaeus monodon) genome facilitates the identification of growth‐associated genes	18
GeneMiner: A tool for extracting phylogenetic markers from next‐generation sequencing data	17
Metazoa‐level USCOs as markers in species delimitation and classification	17
Seq2Sat and SatAnalyzer toolkit: Towards comprehensive microsatellite genotyping from sequencing data	17
Integrating eDNA metabarcoding and simultaneous underwater visual surveys to describe complex fish communities in a marine biodiversity hotspot	17
Species delimitation with limited sampling: An example from rare trapdoor spider genus Cyclocosmia (Mygalomorphae, Halonoproctidae)	17
A cost‐effective blood DNA methylation‐based age estimation method in domestic cats, Tsushima leopard cats (Prionailurus bengalensis euptilurus) and Panthera species, using ta	17
Improving the reliability of eDNA data interpretation	17
RIDGE, a tool tailored to detect gene flow barriers across species pairs	17
Chromosome‐level genome assembly of Sichuan pepper provides insights into apomixis, drought tolerance, and alkaloid biosynthesis	17
slimr: An R package for tailor‐made integrations of data in population genomic simulations over space and time	16
DNA methylation as a tool to explore ageing in wild roe deer populations	16
Pedigree‐based assessment of recent population connectivity in a threatened rattlesnake	16
Sampling effect in predicting the evolutionary response of populations to climate change	16
A comprehensive analysis comparing linear and generalized linear models in detecting adaptive SNPs	16
gscramble: Simulation of Admixed Individuals Without Reuse of Genetic Material	16
DNA barcodes highlight genetic diversity patterns in rodents from lowland desert and Andean areas in Argentina	16
Scaling‐up RADseq methods for large datasets of non‐invasive samples: Lessons for library construction and data preprocessing	16
quickLD: An efficient software for linkage disequilibrium analyses	16
Regarding the F‐word: The effects of data filtering on inferred genotype‐environment associations	16
Filtration extraction method using a microfluidic channel for measuring environmental DNA	16
Genome of the butterfly hillstream loach provides insights into adaptations to torrential mountain stream life	16
Chromosome‐level assembly of Culex pipiens molestus and improved reference genome of Culex pipiens pallens (Culicidae, Diptera)	16
Time to get real with qPCR controls: The frequency of sample contamination and the informative power of negative controls in environmental DNA studies	15
HMS‐S‐S: A tool for the identification of Sulphur metabolism‐related genes and analysis of operon structures in genome and metagenome assemblies	15
Arthropods are kin: Operationalizing Indigenous data sovereignty to respectfully utilize genomic data from Indigenous lands	15
Comparing iDNA from mosquitoes and flies to survey mammals in a semi‐controlled Neotropical area	15
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	15
Development of SNP Panels from Low‐Coverage Whole Genome Sequencing (lcWGS) to Support Indigenous Fisheries for Three Salmonid Species in Northern Canada	15
Issue Information	15
Benchmarking long‐read sequencing strategies for obtaining ASV‐resolved rRNA operons from environmental microeukaryotes	15
A rodent anchored hybrid enrichment probe set for a range of phylogenetic utility: From order to species	15

SPEDE‐sampler: An R Shiny application to assess how methodological choices and taxon sampling can affect Generalized Mixed Yule Coalescent output and interpretation	15
Cover Image	15
Roof of the world: Home and border in the genomic era	15
Barcoding and traditional health practitioner perspectives are informative to monitor and conserve frogs and reptiles traded for traditional medicine in urban South Africa	15
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DROP: Molecular voucher database for identification of Drosophila parasitoids	14
Genetic variation and domestication of horses revealed by 10 chromosome‐level genomes and whole‐genome resequencing	14
More than dirt: Sedimentary ancient DNA and Indigenous Australia	14
Express barcoding with NextGenPCR and MinION for species‐level sorting of ecological samples	14
Culture‐enriched community profiling improves resolution of the vertebrate gut microbiota	14
Reframing Formalin: A Molecular Opportunity Enabling Historical Epigenomics and Retrospective Gene Expression Studies	14
Individual genotypes from environmental DNA: Fingerprinting snow tracks of three large carnivore species	14
Multiplexing PCR allows the identification of within‐species genetic diversity in ancient eDNA	14
Improved genome assembly of Chinese shrimp (Fenneropenaeus chinensis) suggests adaptation to the environment during evolution and domestication	13
Metagenomic‐based discovery and comparison of the lignin degrading potential of microbiomes in aquatic and terrestrial ecosystems via the LCdb database	13
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Lysis‐Hi‐C as a method to study polymicrobial communities and eDNA	13
Variance effective population size is affected by census size in sub‐structured populations	13
Simulating plasticity as a framework for understanding habitat selection and its role in adaptive capacity and extinction risk through an expansion of CDMetaPOP	13
An empirical test of the estimation of historical effective population size using Drosophila melanogaster	13
Chromosome‐level genome assembly of Pedicularis kansuensis illuminates genome evolution of facultative parasitic plant	13
Issue Information	13
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Demogenomic inference from spatially and temporally heterogeneous samples	13
Single‐molecule long‐read sequencing reveals extensive genomic and transcriptomic variation between maize and its wild relative teosinte (Zea mays ssp. parviglumis)	13
Comparative genomics reveals the dynamic evolutionary history of cement protein genes of barnacles from intertidal to deep‐sea hydrothermal vents	13
Evaluating restriction enzyme selection for reduced representation sequencing in conservation genomics	13
Inference of the distribution of fitness effects of mutations is affected by single nucleotide polymorphism filtering methods, sample size and population structure	13
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Chromosome‐level genome assembly of an agricultural pest, the rice leaffolder Cnaphalocrocis exigua (Crambidae, Lepidoptera)	12
Environmental DNA phylogeography: Successful reconstruction of phylogeographic patterns of multiple fish species from cups of water	12
Assembly‐free quantification of vagrant DNA inserts	12
Chromosome‐level genome and population genomic analysis provide insights into the evolution and environmental adaptation of Jinjiang oysterCrassostrea ariakensis	12
Chromosome‐level genome assembly of the mirid predator Cyrtorhinus lividipennis Reuter (Hemiptera: Miridae), an important natural enemy in the rice ecosystem	12
Exploring Environmental Microfungal Diversity Through Serial Single Cell Screening	12
Affordable de novo generation of fish mitogenomes using amplification‐free enrichment of mitochondrial DNA and deep sequencing of long fragments	12
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Genomic analysis of Medicago ruthenica provides insights into its tolerance to abiotic stress and demographic history	12
Chromosome‐level de novo genome assembly of Telopea speciosissima (New South Wales waratah) using long‐reads, linked‐reads and Hi‐C	12
MaxTemp: A Method to Maximise Precision of the Temporal Method for Estimating Ne in Genetic Monitoring Programs	12
A target capture approach for phylogenomic analyses at multiple evolutionary timescales in rosewoods (Dalbergia spp.) and the legume family (Fabaceae)	12
Chromosome‐level genome assembly reveals genomic architecture of northern range expansion in the mountain pine beetle, Dendroctonus ponderosae Hopkins (Coleoptera: Curculionidae)	12
SambaR: An R package for fast, easy and reproducible population‐genetic analyses of biallelic SNP data sets	12
Insect Cytochrome P450 Database: An Integrated Resource of Genetic Diversity, Evolution and Function	12