Molecular Ecology

Article	Citations
Population genomics for wildlife conservation and management	255
Ecosystems monitoring powered by environmental genomics: A review of current strategies with an implementation roadmap	140
Environmental DNA: What's behind the term? Clarifying the terminology and recommendations for its future use in biomonitoring	137
The long‐standing significance of genetic diversity in conservation	129
A beginner's guide to low‐coverage whole genome sequencing for population genomics	117
Multiple chromosomal inversions contribute to adaptive divergence of a dune sunflower ecotype	98
Biases in bulk: DNA metabarcoding of marine communities and the methodology involved	89
Best practices in metabarcoding of fungi: From experimental design to results	88
Environmental adaptation is stronger for abundant rather than rare microorganisms in wetland soils from the Qinghai‐Tibet Plateau	86
Meta‐analysis shows both congruence and complementarity of DNA and eDNA metabarcoding to traditional methods for biological community assessment	75
A framework for understanding gene expression plasticity and its influence on stress tolerance	72
The phylogenetic range of bacterial and viral pathogens of vertebrates	71
Diverse groups of fungi are associated with plastics in the surface waters of the Western South Atlantic and the Antarctic Peninsula	68
Contrasting heat stress response patterns of coral holobionts across the Red Sea suggest distinct mechanisms of thermal tolerance	68
The relationship between eDNA particle concentration and organism abundance in nature is strengthened by allometric scaling	67
Suppression gene drive in continuous space can result in unstable persistence of both drive and wild‐type alleles	65
Copy number variants outperform SNPs to reveal genotype–temperature association in a marine species	64
Meta‐analysis of the coral environmental stress response: Acropora corals show opposing responses depending on stress intensity	61
Trade‐offs between reducing complex terminology and producing accurate interpretations from environmental DNA: Comment on “Environmental DNA: What's behind the term?” by Pawlowski et al., (2020)	60
Insights into invasive species from whole‐genome resequencing	59
Diversity of gut microbiomes in marine fishes is shaped by host‐related factors	58
Beyond DNA barcoding: The unrealized potential of genome skim data in sample identification	57
The genetic architecture of target‐site resistance to pyrethroid insecticides in the African malaria vectors Anopheles gambiae and Anopheles coluzzii	56
Thermal stratification and fish thermal preference explain vertical eDNA distributions in lakes	54
Variation in recombination rate affects detection of outliers in genome scans under neutrality	54

Global patterns of population genetic differentiation in seed plants	51
Environmental DNA effectively captures functional diversity of coastal fish communities	51
Estimating fish population abundance by integrating quantitative data on environmental DNA and hydrodynamic modelling	50
Environmental DNA surveys detect distinct metazoan communities across abyssal plains and seamounts in the western Clarion Clipperton Zone	49
Gene flow creates a mirage of cryptic species in a Southeast Asian spotted stream frog complex	48
The limited spatial scale of dispersal in soil arthropods revealed with whole‐community haplotype‐level metabarcoding	48
Alternative splicing and gene expression play contrasting roles in the parallel phenotypic evolution of a salmonid fish	47
Marine biomonitoring with eDNA: Can metabarcoding of water samples cut it as a tool for surveying benthic communities?	46
Genome‐wide SNP analysis reveals an increase in adaptive genetic variation through selective breeding of coral	46
Evolutionary trade‐offs of insecticide resistance — The fitness costs associated with target‐site mutations in the nAChR of Drosophila melanogaster	46
Stochastic community assembly decreases soil fungal richness in arid ecosystems	45
Shared ancestral polymorphisms and chromosomal rearrangements as potential drivers of local adaptation in a marine fish	45
Phylogenomics and species delimitation for effective conservation of manta and devil rays	44
Nuclear eDNA estimates population allele frequencies and abundance in experimental mesocosms and field samples	44
The problem of omnivory: A synthesis on omnivory and DNA metabarcoding	43
Genetic evidence for the origin of Aedes aegypti, the yellow fever mosquito, in the southwestern Indian Ocean	43
Steeper spatial scaling patterns of subsoil microbiota are shaped by deterministic assembly process	43
Polygenic and major‐locus contributions to sexual maturation timing in Atlantic salmon	43
The balance between deterministic and stochastic processes in structuring lake bacterioplankton community over time	43
Supervised machine learning is superior to indicator value inference in monitoring the environmental impacts of salmon aquaculture using eDNA metabarcodes	42
Reconstructing marine plankton food web interactions using DNA metabarcoding	42
Benefits and costs of hosting facultative symbionts in plant‐sucking insects: A meta‐analysis	42
Fishing for fish environmental DNA: Ecological applications, methodological considerations, surveying designs, and ways forward	42
Capturing open ocean biodiversity: Comparing environmental DNA metabarcoding to the continuous plankton recorder	41
Prevalence and polymorphism of a mussel transmissible cancer in Europe	41
Vertical diversity and association pattern of total, abundant and rare microbial communities in deep‐sea sediments	40
Runs of homozygosity in killer whale genomes provide a global record of demographic histories	40
Large‐scale genome sampling reveals unique immunity and metabolic adaptations in bats	40
Monitoring of spatiotemporal occupancy patterns of fish and amphibian species in a lentic aquatic system using environmental DNA	40
Freshwater zooplankton microbiome composition is highly flexible and strongly influenced by the environment	40
Genotype–Environment mismatch of kelp forests under climate change	40
The importance of alternative splicing in adaptive evolution	39
Creating space for Indigenous perspectives on access and benefit‐sharing: Encouraging researcher use of the Local Contexts Notices	39
Functional redundancy and specific taxa modulate the contribution of prokaryotic diversity and composition to multifunctionality	39
Major imprint of surface plankton on deep ocean prokaryotic structure and activity	39
Fungal communities differentially respond to warming and drought in tropical grassland soil	39
Integrative species delimitation reveals cryptic diversity in the southern Appalachian Antrodiaetus unicolor (Araneae: Antrodiaetidae) species complex	39
Gut microbiota degrades toxic isothiocyanates in a flea beetle pest	39
Population genomics in the arboviral vector Aedes aegypti reveals the genomic architecture and evolution of endogenous viral elements	38
An overview of current population genomics methods for the analysis of whole‐genome resequencing data in eukaryotes	38
Integrating physiology and environmental dynamics to operationalize environmental DNA (eDNA) as a means to monitor freshwater macro‐organism abundance	37
Assessment of stream macroinvertebrate communities with eDNA is not congruent with tissue‐based metabarcoding	37
Monitoring the ecological status of rivers with diatom eDNA metabarcoding: A comparison of taxonomic markers and analytical approaches for the inference of a molecular diatom index	37
Connecting tree‐ring phenotypes, genetic associations and transcriptomics to decipher the genomic architecture of drought adaptation in a widespread conifer	37
Environmental DNA for biomonitoring	37
Thermotolerant coral symbionts modulate heat stress‐responsive genes in their hosts	37
Inversion breakpoints and the evolution of supergenes	36
Historical population declines prompted significant genomic erosion in the northern and southern white rhinoceros (Ceratotherium simum)	36
The use and misuse of regression models in landscape genetic analyses	35
Using replicate hybrid zones to understand the genomic basis of adaptive divergence	35

The Pleistocene species pump past its prime: Evidence from European butterfly sister species	35
Community assembly of bacteria and archaea in coastal waters governed by contrasting mechanisms: A seasonal perspective	35
Genomic evidence for gene flow between monarchs with divergent migratory phenotypes and flight performance	35
Regional differences in the abiotic environment contribute to genomic divergence within a wild tomato species	34
Telomere length is heritable and genetically correlated with lifespan in a wild bird	33
Unlocking the phylogenetic diversity, primary habitats, and abundances of free‐living Symbiodiniaceae on a coral reef	33
Movement ecology and sex are linked to barn owl microbial community composition	33
Homogeneous environmental selection dominates microbial community assembly in the oligotrophic South Pacific Gyre	33
Estimating the genetic diversity of Pacific salmon and trout using multigene eDNA metabarcoding	32
Comparison of markers for the monitoring of freshwater benthic biodiversity through DNA metabarcoding	32
Phylogenomics unravels Quaternary vicariance and allopatric speciation patterns in temperate‐montane plant species: A case study on the Ranunculus auricomus species complex	32
Spatial population genomics of a recent mosquito invasion	32
Molecular adaptation and convergent evolution of frugivory in Old World and neotropical fruit bats	32
Heterogeneous genetic invasions of three insecticide resistance mutations in Indo‐Pacific populations of Aedes aegypti (L.)	32
New insights into the population genetics of partially clonal organisms: When seagrass data meet theoretical expectations	32
Intraspecific genetic variation matters when predicting seagrass distribution under climate change	31
Fungal guilds and soil functionality respond to tree community traits rather than to tree diversity in European forests	31
Genetic population structure constrains local adaptation in sticklebacks	31
The role of introgression and ecotypic parallelism in delineating intraspecific conservation units	31
Landscape genomics of Quercus lobata reveals genes involved in local climate adaptation at multiple spatial scales	30
Decline in telomere length with increasing age across nonhuman vertebrates: A meta‐analysis	30
Ancient horse genomes reveal the timing and extent of dispersals across the Bering Land Bridge	30
Decision‐making and best practices for taxonomy‐free environmental DNA metabarcoding in biomonitoring using Hill numbers	30
Genes acting in synapses and neuron projections are early targets of selection during urban colonization	30
Multispecies models reveal that eDNA metabarcoding is more sensitive than backpack electrofishing for conducting fish surveys in freshwater streams	29
Accounting for environmental variation in co‐occurrence modelling reveals the importance of positive interactions in root‐associated fungal communities	29
Disturbance alters the forest soil microbiome	29
Environmental enrichment induces intergenerational behavioural and epigenetic effects on fish	29
Pheromone receptor of the globally invasive quarantine pest of the palm tree, the red palm weevil (Rhynchophorus ferrugineus)	29
The impact of anthropogenic disturbances on the genetic diversity of terrestrial species: A global meta‐analysis	29
The gut microbiota and Bergmann’s rule in wild house mice	29
Genetic monitoring of translocated plant populations in practice	29
Finding complexity in complexes: Assessing the causes of mitonuclear discordance in a problematic species complex of Mesoamerican toads	29
Heterogeneous genetic basis of age at maturity in salmonid fishes	29
“Everything is not everywhere”: Time‐calibrated phylogeography of the genus Milnesium (Tardigrada)	29
Genomic data reveal international lineages of critical priority Escherichia coli harbouring wide resistome in Andean condors (Vultur gryphus Linnaeus, 1758)	29
Novel genetic sex markers reveal high frequency of sex reversal in wild populations of the agile frog (Rana dalmatina) associated with anthropogenic land use	28
Ancient divergence of Indian and Tibetan wolves revealed by recombination‐aware phylogenomics	28
Application of plant metabarcoding to identify diverse honeybee pollen forage along an urban–agricultural gradient	28
Interactions among Triatoma sanguisuga blood feeding sources, gut microbiota and Trypanosoma cruzi diversity in southern Louisiana	28
How do microbiota associated with an invasive seaweed vary across scales?	28
Modelling technical and biological biases in macroinvertebrate community assessment from bulk preservative using multiple metabarcoding markers	28
Describing the current status of Plasmodium falciparum population structure and drug resistance within mainland Tanzania using molecular inversion probes	28
The macroecology of extra‐pair paternity in birds	27
Microbial generalist or specialist: Intraspecific variation and dormancy potential matter	27
Environmental specialization and cryptic genetic divergence in two massive coral species from the Florida Keys Reef Tract	27
Increased diversity and concordant shifts in community structure of coral‐associated Symbiodiniaceae and bacteria subjected to chronic human disturbance	27
Sex‐specific expression and DNA methylation in a species with extreme sexual dimorphism and paternal genome elimination	27
Dual RNA‐sequencing analyses of a coral and its native symbiont during the establishment of symbiosis	27
Natural selection and the distribution of chromosomal inversion lengths	26
Lost and found: Frogs in a biodiversity hotspot rediscovered with environmental DNA	26
Two ways to be endemic. Alps and Apennines are different functional refugia during climatic cycles	26
Cryptic lineages respond differently to coral bleaching	26
Ultraconserved yet informative for species delimitation: Ultraconserved elements resolve long‐standing systematic enigma in Central European bees	26
Morphological vs. DNA metabarcoding approaches for the evaluation of stream ecological status with benthic invertebrates: Testing different combinations of markers and strategies of data filtering	26
High genomic diversity in the bank vole at the northern apex of a range expansion: The role of multiple colonizations and end‐glacial refugia	26
Rapid repeatable phenotypic and genomic adaptation following multiple introductions	26
Ecological and evolutionary drivers of haemoplasma infection and bacterial genotype sharing in a Neotropical bat community	26
Anthropogenic impact on the historical phytoplankton community of Lake Constance reconstructed by multimarker analysis of sediment‐core environmental DNA	26
Reinventing the wheel? Reassessing the roles of gene flow, sorting and convergence in repeated evolution	26
The challenge and promise of estimating the de novo mutation rate from whole‐genome comparisons among closely related individuals	26
Connecting high‐throughput biodiversity inventories: Opportunities for a site‐based genomic framework for global integration and synthesis	26
Does getting defensive get you anywhere?—Seasonal balancing selection, temperature, and parasitoids shape real‐world, protective endosymbiont dynamics in the pea aphid	26
Rapid evolutionary changes in gene expression in response to climate fluctuations	25
Genomic islands of divergence infer a phenotypic landscape in Pacific lamprey	25
Migration, pathogens and the avian microbiome: A comparative study in sympatric migrants and residents	25
Genomic data of different resolutions reveal consistent inbreeding estimates but contrasting homozygosity landscapes for the threatened Aotearoa New Zealand hihi	25
Host functional and phylogenetic composition rather than host diversity structure plant–herbivore networks	25
The pace of modern life, revisited	25
Complex histories of gene flow and a mitochondrial capture event in a nonsister pair of birds	25
Expanding the conservation genomics toolbox: Incorporating structural variants to enhance genomic studies for species of conservation concern	25
Preconditioning improves bleaching tolerance in the reef‐building coral Pocillopora acuta through modulations in the programmed cell death pathways	25
Using ITS2 metabarcoding and microscopy to analyse shifts in pollen diets of honey bees and bumble bees along a mass‐flowering crop gradient	24
Bonds of bros and brothers: Kinship and social bonding in postdispersal male macaques	24
Within‐individual repeatability in telomere length: A meta‐analysis in nonmammalian vertebrates	24
Fungal heavy metal adaptation through single nucleotide polymorphisms and copy‐number variation	24
Predictable and host‐species specific humanization of the gut microbiota in captive primates	24
Predator preferences shape the diets of arthropodivorous bats more than quantitative local prey abundance	24
Sustained immune activation is associated with susceptibility to the amphibian chytrid fungus	24
Whole genome resequencing reveals genomic regions associated with thermal adaptation in redband trout	24

Newly discovered cichlid fish biodiversity threatened by hybridization with non‐native species	24
A microbial mandala for environmental monitoring: Predicting multiple impacts on estuarine prokaryote communities of the Bay of Biscay	24
How telomere dynamics are influenced by the balance between mitochondrial efficiency, reactive oxygen species production and DNA damage	24
Quantifying dispersal variability among nearshore marine populations	24
Unraveling hierarchical genetic structure in a marine metapopulation: A comparison of three high‐throughput genotyping approaches	24
The relevance of pedigrees in the conservation genomics era	23
Telomere heritability and parental age at conception effects in a wild avian population	23
Footprints of global change in marine life: Inferring past environment based on DNA methylation and gene expression marks	23
Ecological divergence of wild strawberry DNA methylation patterns at distinct spatial scales	23
Paternal effects in a wild‐type zebrafish implicate a role of sperm‐derived small RNAs	23
Signatures of selection in a recent invasion reveal adaptive divergence in a highly vagile invasive species	23
Root presence modifies the long‐term decomposition dynamics of fungal necromass and the associated microbial communities in a boreal forest	23
Leech blood‐meal invertebrate‐derived DNA reveals differences in Bornean mammal diversity across habitats	23
Gut microbiota of invasive bullfrog tadpoles responds more rapidly to temperature than a noninvasive congener	23
On the comparative biology of mammalian telomeres: Telomere length co‐evolves with body mass, lifespan and cancer risk	23
Age, tissue, genotype and virus infection regulate Wolbachia levels in Drosophila	23
Host resistance to Bacillus thuringiensis is linked to altered bacterial community within a specialist insect herbivore	23
Genomic variation of an endosymbiotic dinoflagellate (Symbiodinium ‘fitti’) among closely related coral hosts	23
Rapid changes in DNA methylation associated with the initiation of reproduction in a small songbird	23
Environmental correlates of genetic variation in the invasive European starling in North America	23
Spatial, climate and ploidy factors drive genomic diversity and resilience in the widespread grass Themeda triandra	22
Divergence and hybridization in sea turtles: Inferences from genome data show evidence of ancient gene flow between species	22
Decreased spatial variation and deterministic processes of bacterial community assembly in the rhizosphere of Phragmites australis across the Middle–Lower Yangtze plain	22
Bacterial dispersal and drift drive microbiome diversity patterns within a population of feral hindgut fermenters	22
Supporting in situ conservation of the genetic diversity of crop wild relatives using genomic technologies	22
Capabilities and limitations of using DNA metabarcoding to study plant–pollinator interactions	22
Pollinators mediate floral microbial diversity and microbial network under agrochemical disturbance	22
Founder effects shape linkage disequilibrium and genomic diversity of a partially clonal invader	22
Social isolation causes downregulation of immune and stress response genes and behavioural changes in a social insect	22
Multifunctionality of biocrusts is positively predicted by network topologies consistent with interspecies facilitation	22
A ketocarotenoid‐based colour polymorphism in the Sira poison frog Ranitomeya sirensis indicates novel gene interactions underlying aposematic signal variation	22
Host species identity shapes the diversity and structure of insect microbiota	22
Intraspecific variation in symbiont density in an insect–microbe symbiosis	22
Multiple glacial refugia and contemporary dispersal shape the genetic structure of an endemic amphibian from the Pyrenees	21
Regulation of ion transport and energy metabolism enables certain coral genotypes to maintain calcification under experimental ocean acidification	21
Odorant binding proteins promote flight activity in the migratory insect, Helicoverpa armigera	21
Incorporating interspecific interactions into phylogeographic models: A case study with Californian oaks	21
Demographic history and identification of threats revealed by population genomic analysis provide insights into conservation for an endangered maple	21
Hurricanes overcome migration lag and shape intraspecific genetic variation beyond a poleward mangrove range limit	21
A single nucleotide polymorphism variant located in the cis‐regulatory region of the ABCG2 gene is associated with mallard egg colour	21
Host phenotype and microbiome vary with infection status, parasite genotype, and parasite microbiome composition	21
Effects of soil preservation for biodiversity monitoring using environmental DNA	21
Parentage analyses identify local dispersal events and sibling aggregations in a natural population of Millepora hydrocorals, a free‐spawning marine invertebrate	21
Complex reticulate evolution of speckled brush‐furred rats (Lophuromys) in the Ethiopian centre of endemism	21
Recovery from hybrid breakdown reveals a complex genetic architecture of mitonuclear incompatibilities	21
The molecular basis of venom resistance in a rattlesnake‐squirrel predator‐prey system	21
Mega‐fire in redwood tanoak forest reduces bacterial and fungal richness and selects for pyrophilous taxa that are phylogenetically conserved	20
Egg corticosterone can stimulate telomerase activity and promote longer telomeres during embryo development	20
Distinct microbiota composition and fermentation products indicate functional compartmentalization in the hindgut of a marine herbivorous fish	20
Migratory behaviour is positively associated with genetic diversity in butterflies	20
The genetic architecture and population genomic signatures of glyphosate resistance in Amaranthus tuberculatus	20
Transposable elements and introgression introduce genetic variation in the invasive ant Cardiocondyla obscurior	20
Genomic and fitness consequences of inbreeding in an endangered carnivore	20
Incapacitating effects of fungal coinfection in a novel pathogen system	20
Phylogeography of the wide‐host range panglobal plant pathogen Phytophthora cinnamomi	20
Evolutionary dynamics of piRNA clusters in Drosophila	20
Technical considerations in Hi‐C scaffolding and evaluation of chromosome‐scale genome assemblies	20
Gene drives for vertebrate pest control: Realistic spatial modelling of eradication probabilities and times for island mouse populations	20
RETRACTED: The genomics of mimicry: Gene expression throughout development provides insights into convergent and divergent phenotypes in a Müllerian mimicry system	20
Fungal communities living within leaves of native Hawaiian dicots are structured by landscape‐scale variables as well as by host plants	20
Cladocopium community divergence in two Acropora coral hosts across multiple spatial scales	20
Genomic signatures of selection in bats surviving white‐nose syndrome	20
Disentangling the effects of geographic peripherality and habitat suitability on neutral and adaptive genetic variation in Swiss stone pine	20
Opportunities and challenges for high‐quality biodiversity tissue archives in the age of long‐read sequencing	20
Polygenic adaptation and negative selection across traits, years and environments in a long‐lived plant species (Pinus pinaster Ait., Pinaceae)	20
Moving beyond assumptions: Polyploidy and environmental effects explain a geographical parthenogenesis scenario in European plants	20
DNA methylation is not a driver of gene expression reprogramming in young honey bee workers	20
Genomic basis of the loss of diadromy in Galaxias maculatus: Insights from reciprocal transplant experiments	20
The roles of climate, geography and natural selection as drivers of genetic and phenotypic differentiation in a widespread amphibian Hyla annectans (Anura: Hylidae)	20
On the way to specificity ‐ Microbiome reflects sponge genetic cluster primarily in highly structured populations	20
The precautionary principle and dietary DNA metabarcoding: Commonly used abundance thresholds change ecological interpretation	20
Characterizing environmental stress responses of aposymbiotic Astrangia poculata to divergent thermal challenges	20
Introgression across evolutionary scales suggests reticulation contributes to Amazonian tree diversity	20
Diel pCO2 fluctuations alter the molecular response of coral reef fishes to ocean acidification conditions	19
Thermal adaptation rather than demographic history drives genetic structure inferred by copy number variants in a marine fish	19
Divergent and linked selection shape patterns of genomic differentiation between European and North American Atlantic salmon (Salmo salar)	19
Gene flow and climate‐associated genetic variation in a vagile habitat specialist	19
Pan‐regional marine benthic cryptobiome biodiversity patterns revealed by metabarcoding Autonomous Reef Monitoring Structures	19
Genomic and phenotypic divergence unveil microgeographic adaptation in the Amazonian hyperdominant tree Eperua falcata Aubl. (Fabaceae)	19
Restoring ancestral phenotypes is a general pattern in gene expression evolution during adaptation to new environments in Tribolium castaneum	19
Tissue‐specific gene expression shows a cynipid wasp repurposes oak host gene networks to create a complex and novel parasite‐specific organ	19
Genomic signatures of inbreeding and mutation load in a threatened rattlesnake	19
Using seasonal genomic changes to understand historical adaptation to new environments: Parallel selection on stickleback in highly‐variable estuaries	19
Early presence of Batrachochytrium dendrobatidis in Mexico with a contemporary dominance of the global panzootic lineage	19
Rapid evolution of genome‐wide gene expression and plasticity during saline to freshwater invasions by the copepod Eurytemora affinis species complex	19
Plasma proteomic profiles differ between European and North American myotid bats colonized by Pseudogymnoascus destructans	19
Detoxification of plant defensive glucosinolates by an herbivorous caterpillar is beneficial to its endoparasitic wasp	19
Metagenomic analysis reveals Culex mosquito virome diversity and Japanese encephalitis genotype V in the Republic of Korea	19
Genomic analyses show extremely perilous conservation status of African and Asiatic cheetahs (Acinonyx jubatus)	19
A simulation study to examine the impact of recombination on phylogenomic inferences under the multispecies coalescent model	19
Conservation genomics reveals pesticide and pathogen exposure in the declining bumble bee Bombus terricola	19
Ciliate diversity and distribution across horizontal and vertical scales in the open ocean	19
Benthic monitoring of oil and gas offshore platforms in the North Sea using environmental DNA metabarcoding	19
Foraging shifts and visual preadaptation in ecologically diverse bats	19
High heritability of telomere length and low heritability of telomere shortening in wild birds	19