Molecular Ecology

Article	Citations
Population genomics for wildlife conservation and management	316
The long‐standing significance of genetic diversity in conservation	157
A beginner's guide to low‐coverage whole genome sequencing for population genomics	149
Best practices in metabarcoding of fungi: From experimental design to results	125
Environmental adaptation is stronger for abundant rather than rare microorganisms in wetland soils from the Qinghai‐Tibet Plateau	104
Meta‐analysis shows both congruence and complementarity of DNA and eDNA metabarcoding to traditional methods for biological community assessment	103
A framework for understanding gene expression plasticity and its influence on stress tolerance	92
Contrasting heat stress response patterns of coral holobionts across the Red Sea suggest distinct mechanisms of thermal tolerance	77
Suppression gene drive in continuous space can result in unstable persistence of both drive and wild‐type alleles	75
The genetic architecture of target‐site resistance to pyrethroid insecticides in the African malaria vectors Anopheles gambiae and Anopheles coluzzii	72
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)	72
Insights into invasive species from whole‐genome resequencing	71
Diversity of gut microbiomes in marine fishes is shaped by host‐related factors	70
Fishing for fish environmental DNA: Ecological applications, methodological considerations, surveying designs, and ways forward	64
Alternative splicing and gene expression play contrasting roles in the parallel phenotypic evolution of a salmonid fish	55
Stochastic community assembly decreases soil fungal richness in arid ecosystems	54
The importance of alternative splicing in adaptive evolution	52
Environmental DNA for biomonitoring	52
Genotype–Environment mismatch of kelp forests under climate change	51
Polygenic and major‐locus contributions to sexual maturation timing in Atlantic salmon	51
Steeper spatial scaling patterns of subsoil microbiota are shaped by deterministic assembly process	50
Benefits and costs of hosting facultative symbionts in plant‐sucking insects: A meta‐analysis	50
Vertical diversity and association pattern of total, abundant and rare microbial communities in deep‐sea sediments	50
Nuclear eDNA estimates population allele frequencies and abundance in experimental mesocosms and field samples	50
Phylogenomics and species delimitation for effective conservation of manta and devil rays	49

Inversion breakpoints and the evolution of supergenes	49
Large‐scale genome sampling reveals unique immunity and metabolic adaptations in bats	48
The problem of omnivory: A synthesis on omnivory and DNA metabarcoding	47
Functional redundancy and specific taxa modulate the contribution of prokaryotic diversity and composition to multifunctionality	47
An overview of current population genomics methods for the analysis of whole‐genome resequencing data in eukaryotes	47
Runs of homozygosity in killer whale genomes provide a global record of demographic histories	46
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	46
Freshwater zooplankton microbiome composition is highly flexible and strongly influenced by the environment	45
Monitoring of spatiotemporal occupancy patterns of fish and amphibian species in a lentic aquatic system using environmental DNA	44
Integrating physiology and environmental dynamics to operationalize environmental DNA (eDNA) as a means to monitor freshwater macro‐organism abundance	44
Creating space for Indigenous perspectives on access and benefit‐sharing: Encouraging researcher use of the Local Contexts Notices	43
Population genomics in the arboviral vector Aedes aegypti reveals the genomic architecture and evolution of endogenous viral elements	43
Prevalence and polymorphism of a mussel transmissible cancer in Europe	43
Microbial generalist or specialist: Intraspecific variation and dormancy potential matter	41
Unlocking the phylogenetic diversity, primary habitats, and abundances of free‐living Symbiodiniaceae on a coral reef	41
Describing the current status of Plasmodium falciparum population structure and drug resistance within mainland Tanzania using molecular inversion probes	41
The Pleistocene species pump past its prime: Evidence from European butterfly sister species	41
Connecting tree‐ring phenotypes, genetic associations and transcriptomics to decipher the genomic architecture of drought adaptation in a widespread conifer	40
Pheromone receptor of the globally invasive quarantine pest of the palm tree, the red palm weevil (Rhynchophorus ferrugineus)	40
The use and misuse of regression models in landscape genetic analyses	40
Using replicate hybrid zones to understand the genomic basis of adaptive divergence	39
Landscape genomics of Quercus lobata reveals genes involved in local climate adaptation at multiple spatial scales	38
Intraspecific genetic variation matters when predicting seagrass distribution under climate change	38
Historical population declines prompted significant genomic erosion in the northern and southern white rhinoceros (Ceratotherium simum)	38
The impact of anthropogenic disturbances on the genetic diversity of terrestrial species: A global meta‐analysis	37
Decline in telomere length with increasing age across nonhuman vertebrates: A meta‐analysis	37
Environmental specialization and cryptic genetic divergence in two massive coral species from the Florida Keys Reef Tract	37
“Everything is not everywhere”: Time‐calibrated phylogeography of the genus Milnesium (Tardigrada)	37
Telomere length is heritable and genetically correlated with lifespan in a wild bird	36
Estimating the genetic diversity of Pacific salmon and trout using multigene eDNA metabarcoding	35
Ancient horse genomes reveal the timing and extent of dispersals across the Bering Land Bridge	35
Does getting defensive get you anywhere?—Seasonal balancing selection, temperature, and parasitoids shape real‐world, protective endosymbiont dynamics in the pea aphid	34
Spatial population genomics of a recent mosquito invasion	34
Genetic population structure constrains local adaptation in sticklebacks	34
Disturbance alters the forest soil microbiome	33
Heterogeneous genetic basis of age at maturity in salmonid fishes	32
Fungal guilds and soil functionality respond to tree community traits rather than to tree diversity in European forests	32
On the comparative biology of mammalian telomeres: Telomere length co‐evolves with body mass, lifespan and cancer risk	32
Genomic data of different resolutions reveal consistent inbreeding estimates but contrasting homozygosity landscapes for the threatened Aotearoa New Zealand hihi	32
Decision‐making and best practices for taxonomy‐free environmental DNA metabarcoding in biomonitoring using Hill numbers	32
Divergence and hybridization in sea turtles: Inferences from genome data show evidence of ancient gene flow between species	31
Anthropogenic impact on the historical phytoplankton community of Lake Constance reconstructed by multimarker analysis of sediment‐core environmental DNA	31
Application of plant metabarcoding to identify diverse honeybee pollen forage along an urban–agricultural gradient	31
How telomere dynamics are influenced by the balance between mitochondrial efficiency, reactive oxygen species production and DNA damage	30
Ancient divergence of Indian and Tibetan wolves revealed by recombination‐aware phylogenomics	30
The macroecology of extra‐pair paternity in birds	30
Reinventing the wheel? Reassessing the roles of gene flow, sorting and convergence in repeated evolution	30
The challenge and promise of estimating the de novo mutation rate from whole‐genome comparisons among closely related individuals	30
Mega‐fire in redwood tanoak forest reduces bacterial and fungal richness and selects for pyrophilous taxa that are phylogenetically conserved	29
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	29

The pace of modern life, revisited	29
Complex histories of gene flow and a mitochondrial capture event in a nonsister pair of birds	29
Using ITS2 metabarcoding and microscopy to analyse shifts in pollen diets of honey bees and bumble bees along a mass‐flowering crop gradient	29
Predator preferences shape the diets of arthropodivorous bats more than quantitative local prey abundance	29
Rapid changes in DNA methylation associated with the initiation of reproduction in a small songbird	29
The relevance of pedigrees in the conservation genomics era	29
Natural selection and the distribution of chromosomal inversion lengths	29
Preconditioning improves bleaching tolerance in the reef‐building coral Pocillopora acuta through modulations in the programmed cell death pathways	29
Expanding the conservation genomics toolbox: Incorporating structural variants to enhance genomic studies for species of conservation concern	28
The adjustment of life history strategies drives the ecological adaptations of soil microbiota to aridity	28
Supporting in situ conservation of the genetic diversity of crop wild relatives using genomic technologies	28
Two ways to be endemic. Alps and Apennines are different functional refugia during climatic cycles	28
Sex‐specific expression and DNA methylation in a species with extreme sexual dimorphism and paternal genome elimination	28
Pleiotropy facilitates parallel adaptation in sticklebacks	28
Migratory behaviour is positively associated with genetic diversity in butterflies	28
Pollinators mediate floral microbial diversity and microbial network under agrochemical disturbance	28
Towards exhaustive community ecology via DNA metabarcoding	28
Rapid bacterial and fungal successional dynamics in first year after chaparral wildfire	27
Root presence modifies the long‐term decomposition dynamics of fungal necromass and the associated microbial communities in a boreal forest	27
Connecting high‐throughput biodiversity inventories: Opportunities for a site‐based genomic framework for global integration and synthesis	27
Quantifying dispersal variability among nearshore marine populations	27
Distinct microbiota composition and fermentation products indicate functional compartmentalization in the hindgut of a marine herbivorous fish	27
Footprints of global change in marine life: Inferring past environment based on DNA methylation and gene expression marks	27
Ecological divergence of wild strawberry DNA methylation patterns at distinct spatial scales	27
Demographic history and identification of threats revealed by population genomic analysis provide insights into conservation for an endangered maple	27
RETRACTED: The genomics of mimicry: Gene expression throughout development provides insights into convergent and divergent phenotypes in a Müllerian mimicry system	27
Decreased spatial variation and deterministic processes of bacterial community assembly in the rhizosphere of Phragmites australis across the Middle–Lower Yangtze plain	27
Satellite DNA evolution in Corvoidea inferred from short and long reads	27
Environmental correlates of genetic variation in the invasive European starling in North America	26
A simulation study to examine the impact of recombination on phylogenomic inferences under the multispecies coalescent model	26
Tissue‐specific gene expression shows a cynipid wasp repurposes oak host gene networks to create a complex and novel parasite‐specific organ	26
Opportunities and challenges for high‐quality biodiversity tissue archives in the age of long‐read sequencing	26
Capabilities and limitations of using DNA metabarcoding to study plant–pollinator interactions	26
Bacterial dispersal and drift drive microbiome diversity patterns within a population of feral hindgut fermenters	26
Host species identity shapes the diversity and structure of insect microbiota	26
Telomere heritability and parental age at conception effects in a wild avian population	25
Genomic and fitness consequences of inbreeding in an endangered carnivore	25
Within‐individual repeatability in telomere length: A meta‐analysis in nonmammalian vertebrates	25
Complex reticulate evolution of speckled brush‐furred rats (Lophuromys) in the Ethiopian centre of endemism	25
Gene drives for vertebrate pest control: Realistic spatial modelling of eradication probabilities and times for island mouse populations	25
Metagenomic analysis reveals Culex mosquito virome diversity and Japanese encephalitis genotype V in the Republic of Korea	25
Phylogeography of the wide‐host range panglobal plant pathogen Phytophthora cinnamomi	25
Moving beyond assumptions: Polyploidy and environmental effects explain a geographical parthenogenesis scenario in European plants	25
Transposable elements and introgression introduce genetic variation in the invasive ant Cardiocondyla obscurior	25
Genomic variation of an endosymbiotic dinoflagellate (Symbiodinium ‘fitti’) among closely related coral hosts	25
Founder effects shape linkage disequilibrium and genomic diversity of a partially clonal invader	25
Thermal adaptation rather than demographic history drives genetic structure inferred by copy number variants in a marine fish	24
Polygenic adaptation and negative selection across traits, years and environments in a long‐lived plant species (Pinus pinaster Ait., Pinaceae)	24
An island‐hopping bird reveals how founder events shape genome‐wide divergence	24
Leech blood‐meal invertebrate‐derived DNA reveals differences in Bornean mammal diversity across habitats	24
The population genetics of urban and rural amphibians in North America	24
Diversity and abundance of soil microbial communities decline, and community compositions change with severity of post‐logging fire	24
Genetic trade‐offs underlie divergent life history strategies for local adaptation in white clover	24
DNA methylation is not a driver of gene expression reprogramming in young honey bee workers	24
Host phenotype and microbiome vary with infection status, parasite genotype, and parasite microbiome composition	24
Genomic signatures of selection in bats surviving white‐nose syndrome	24
Social isolation causes downregulation of immune and stress response genes and behavioural changes in a social insect	24
Predictable and host‐species specific humanization of the gut microbiota in captive primates	24
Genome assembly, structural variants, and genetic differentiation between lake whitefish young species pairs (Coregonus sp.) with long and short reads	24
Pan‐regional marine benthic cryptobiome biodiversity patterns revealed by metabarcoding Autonomous Reef Monitoring Structures	24
Whole genome resequencing reveals genomic regions associated with thermal adaptation in redband trout	24
Genomic analyses show extremely perilous conservation status of African and Asiatic cheetahs (Acinonyx jubatus)	23
Population genomic, olfactory, dietary, and gut microbiota analyses demonstrate the unique evolutionary trajectory of feral pigs	23
Benthic monitoring of oil and gas offshore platforms in the North Sea using environmental DNA metabarcoding	23
Host resistance to Bacillus thuringiensis is linked to altered bacterial community within a specialist insect herbivore	23
Diel pCO2 fluctuations alter the molecular response of coral reef fishes to ocean acidification conditions	23
Genetic signatures of divergent selection in European beech (Fagus sylvatica L.) are associated with the variation in temperature and precipitation across its distribution range	23
A single nucleotide polymorphism variant located in the cis‐regulatory region of the ABCG2 gene is associated with mallard egg colour	23
Recovery from hybrid breakdown reveals a complex genetic architecture of mitonuclear incompatibilities	23
Movement of transposable elements contributes to cichlid diversity	23
Zooming on dynamics of marine microbial communities in the phycosphere of Akashiwo sanguinea (Dinophyta) blooms	23
Population dynamics of caribou shaped by glacial cycles before the last glacial maximum	23
The precautionary principle and dietary DNA metabarcoding: Commonly used abundance thresholds change ecological interpretation	23
Genomic signatures of inbreeding and mutation load in a threatened rattlesnake	22
Social groups constrain the spatiotemporal dynamics of wild sifaka gut microbiomes	22
Impacts of Quaternary glaciation, geological history and geography on animal species history in continental East Asia: A phylogeographic review	22
Identification of a rapidly‐spreading triple mutant for high‐level metabolic insecticide resistance in Anopheles gambiae provides a real‐time molecular diagnostic for antimalarial intervention	22
From high masked to high realized genetic load in inbred Scandinavian wolves	22
Evolutionary dynamics of piRNA clusters in Drosophila	22
The genetic architecture and population genomic signatures of glyphosate resistance in Amaranthus tuberculatus	22

Host genetics, phenotype and geography structure the microbiome of a foundational seaweed	22
Intraspecific variation in symbiont density in an insect–microbe symbiosis	22
Characterizing environmental stress responses of aposymbioticAstrangia poculatato divergent thermal challenges	22
Technical considerations in Hi‐C scaffolding and evaluation of chromosome‐scale genome assemblies	22
Life‐history trade‐offs and the genetic basis of fitness in Arabidopsis thaliana	22
Incipiently social carpenter bees (Xylocopa) host distinctive gut bacterial communities and display geographical structure as revealed by full‐length PacBio 16S rRNA sequencing	22
A population genomic unveiling of a new cryptic mosquito taxon within the malaria‐transmitting Anopheles gambiae complex	22
Gene family amplification facilitates adaptation in freshwater unionid bivalve Megalonaias nervosa	22
Between‐population differences in constitutive and infection‐induced gene expression in threespine stickleback	21
Molecular mechanisms of local adaptation for salt‐tolerance in a treefrog	21
Early presence of Batrachochytrium dendrobatidis in Mexico with a contemporary dominance of the global panzootic lineage	21
CYP2J19 mediates carotenoid colour introgression across a natural avian hybrid zone	21
Mosquito‐bacteria interactions during larval development trigger metabolic changes with carry‐over effects on adult fitness	21
Seasonal dynamics of marine protist communities in tidally mixed coastal waters	21
Incursions of divergent genotypes, evolution of virulence and host jumps shape a continental clonal population of the stripe rust pathogen Puccinia striiformis	21
Long‐term and rapid evolution in powdery mildew fungi	21
Rapid evolution of genome‐wide gene expression and plasticity during saline to freshwater invasions by the copepod Eurytemora affinis species complex	21
Small freshwater ecosystems with dissimilar microbial communities exhibit similar temporal patterns	21
Cophylogeny and specificity between cryptic coral species (Pocillopora spp.) at Mo′orea and their symbionts (Symbiodiniaceae)	21
Historical isolation facilitates species radiation by sexual selection: Insights fromChorthippusgrasshoppers	21
Conservation genomics reveals pesticide and pathogen exposure in the declining bumble bee Bombus terricola	21
Long‐term stability of soil bacterial and fungal community structures revealed in their abundant and rare fractions	21
Microbiome assembly and maintenance across the lifespan of bumble bee workers	21
Urban forest soils harbour distinct and more diverse communities of bacteria and fungi compared to less disturbed forest soils	20
Environmental DNA metabarcoding of cow dung reveals taxonomic and functional diversity of invertebrate assemblages	20
Plants, pollinators and their interactions under global ecological change: The role of pollen DNA metabarcoding	20
Winter warming rapidly increases carbon degradation capacities of fungal communities in tundra soil: Potential consequences on carbon stability	20
Metabolic plasticity of mixotrophic algae is key for their persistence in browning environments	20
Causes and consequences of telomere lengthening in a wild vertebrate population	20
Egg corticosterone can stimulate telomerase activity and promote longer telomeres during embryo development	20
Genomic basis of the loss of diadromy inGalaxias maculatus: Insights from reciprocal transplant experiments	20
Peatland microbial community responses to plant functional group and drought are depth‐dependent	20
Floral resources shape parasite and pathogen dynamics in bees facing urbanization	20
Soil microbial diversity and community composition during conversion from conventional to organic agriculture	20
Using seasonal genomic changes to understand historical adaptation to new environments: Parallel selection on stickleback in highly‐variable estuaries	20
Sharing and reporting benefits from biodiversity research	20
Repeated sampling of individuals reveals impact of tropical and temperate habitats on microbiota of a migratory bird	20
Mechanisms of niche‐neutrality balancing can drive the assembling of microbial community	20
Genomic divergence of Stellera chamaejasme through local selection across the Qinghai–Tibet plateau and northern China	20
Extensive photobiont sharing in a rapidly radiating cyanolichen clade	20
Testing small‐scale ecological gradients and intraspecific differentiation for hundreds of kelp forest species using haplotypes from metabarcoding	20
Going with the flow: How corals in high‐flow environments can beat the heat	20
Biodiversity and vector‐borne diseases: Host dilution and vector amplification occur simultaneously for Amazonian leishmaniases	19
Of telomeres and temperature: Measuring thermal effects on telomeres in ectothermic animals	19
Of bars and stripes: A Malawi cichlid hybrid cross provides insights into genetic modularity and evolution of modifier loci underlying colour pattern diversification	19
Telomeres in ecology and evolution: A review and classification of hypotheses	19
Anthropogenic and natural barriers affect genetic connectivity in an Alpine butterfly	19
The population genetics of adaptation through copy number variation in a fungal plant pathogen	19
Drivers of change and stability in the gut microbiota of an omnivorous avian migrant exposed to artificial food supplementation	19
Extensive human‐mediated jump dispersal within and across the native and introduced ranges of the invasive termite Reticulitermes flavipes	19
Where whole‐genome duplication is most beneficial: Adaptation of mangroves to a wide salinity range between land and sea	19
Venoms for all occasions: The functional toxin profiles of different anatomical regions in sea anemones are related to their ecological function	19
Thermal sensitivity of the Spiroplasma–Drosophila hydei protective symbiosis: The best of climes, the worst of climes	19
High heritability of telomere length and low heritability of telomere shortening in wild birds	19
Plant‐bacteria associations are phylogenetically structured in the phyllosphere	19
Temperature, rainfall and wind variables underlie environmental adaptation in natural populations of Drosophila melanogaster	19
Odorant receptor orthologues in conifer‐feeding beetles display conserved responses to ecologically relevant odours	19
The masking effect of extracellular DNA and robustness of intracellular DNA in anaerobic digester NGS studies: A discriminatory study of the total DNA pool	19
Interaction between MHC diversity and constitution, gut microbiota and Astrovirus infections in a neotropical bat	19
Host plant diet affects growth and induces altered gene expression and microbiome composition in the wood white (Leptidea sinapis) butterfly	19
Distinct methylome patterns contribute to ecotypic differentiation in the growth of the storage organ of a flowering plant (sacred lotus)	19
On the use of genome‐wide data to model and date the time of anthropogenic hybridisation: An example from the Scottish wildcat	19
Elevated rates of positive selection drive the evolution of pestiferousness in the Colorado potato beetle (Leptinotarsa decemlineata, Say)	18
Antigenic variation of SARS‐CoV‐2 in response to immune pressure	18
Genomics‐informed delineation of conservation units in a desert amphibian	18
Genome‐wide transcriptomic changes reveal the genetic pathways involved in insect migration	18
A mobile sex‐determining region, male‐specific haplotypes and rearing environment influence age at maturity in Chinook salmon	18
The genomic signature of ecological divergence along the benthic‐limnetic axis in allopatric and sympatric threespine stickleback	18
Evidence for ephemeral ring species formation during the diversification history of western fence lizards (Sceloporus occidentalis)	18
Topography drives microgeographic adaptations of closely related species in two tropical tree species complexes	18
Lions and brown bears colonized North America in multiple synchronous waves of dispersal across the Bering Land Bridge	18
Intrinsic variation in the vertically transmitted core virome of the mosquito Aedes aegypti	18
Contrasting fungal responses to wildfire across different ecosystem types	18
Complex population history affects admixture analyses in nine‐spined sticklebacks	17
Allele‐specific expression and gene regulation help explain transgressive thermal tolerance in non‐native hybrids of the endangered California tiger salamander (Ambystoma californiense)	17
Multi‐omics analysis identifies a CYP9K1 haplotype conferring pyrethroid resistance in the malaria vector Anopheles funestus in East Africa	17
Decade‐scale stability and change in a marine bivalve microbiome	17
Genome‐wide single nucleotide polymorphism markers reveal population structure and dispersal direction of an expanding nuisance algal bloom species	17
Phylogenetic and geographical analysis of a retrovirus during the early stages of endogenous adaptation and exogenous spread in a new host	17
Balanced polymorphism fuels rapid selection in an invasive crab despite high gene flow and low genetic diversity	17
Host genomic influence on bacterial composition in the switchgrass rhizosphere	17
Genomic inference of contemporary effective population size in a large island population of collared flycatchers (Ficedula albicollis)	17
Seascape genomics of coastal bottlenose dolphins along strong gradients of temperature and salinity	17
Refining the genomic location of single nucleotide polymorphism variation affecting Atlantic salmon maturation timing at a key large‐effect locus	17
Comparative genome sequencing reveals insights into the dynamics of Wolbachia in native and invasive cherry fruit flies	17
Genomic differentiation and local adaptation on a microgeographic scale in a resident songbird	17
Timing strains of the marine insect Clunio marinus diverged and persist with gene flow	17
Drivers of neutral and adaptive differentiation in pike (Esox lucius) populations from contrasting environments	17
Comparable response of wild rodent gut microbiome to anthropogenic habitat contamination	17
Network analysis with either Illumina or MinION reveals that detecting vertebrate species requires metabarcoding of iDNA from a diverse fly community	17
Whole genome resequencing identifies local adaptation associated with environmental variation for redband trout	17
Whole‐genome sequencing and genome regions of special interest: Lessons from major histocompatibility complex, sex determination, and plant self‐incompatibility	17
Transposable elements mark a repeat‐rich region associated with migratory phenotypes of willow warblers (Phylloscopus trochilus)	17
Global dissemination of influenza A virus is driven by wild bird migration through arctic and subarctic zones	17
Brazilian marine phylogeography: A literature synthesis and analysis of barriers	17