Molecular Ecology

Article	Citations
Cover Image	209
Issue Information	202
Museomics Sheds Light on Evolutionary Diversity in a Critically Endangered Cockatoo Species From Wallacea	180
Discovery of XY Sex Chromosomes in Mauremys mutica Provides Insights Into the Role of KDM6B Gene in Coexistence of Temperature‐Dependent and Genetic Sex Determination	151
Evolutionary History and Rhizosphere Microbial Community Composition in Domesticated Hops (Humulus lupulus L.)	112
Genomic divergence and introgression between cryptic species of a widespread North American songbird	96
Telomere dynamics in relation to experimentally increased locomotion costs and fitness in great tits	93
Genomic data support multiple introductions and explosive demographic expansions in a highly invasive aquatic insect	78
More complex than you think: Taxonomic and temporal patterns of plant–pollinator networks of caraway (Carum carvi L.)	76
The transcriptional state and chromatin landscape of cichlid jaw shape variation across species and environments	68
Adaptive cellular evolution or cellular system drift in hares	65
Genomic, morphological and physiological data support fast ecotypic differentiation and incipient speciation in an alpine diving beetle	64
Decoding plant‐induced transcriptomic variability and consistency in two related polyphagous mites differing in host ranges	64
The impacts of positive selection on genomic variation in Drosophila serrata: Insights from a deep learning approach	64
Traits and tradeoffs among non‐native ectomycorrhizal fungal symbionts affect pine seedling establishment in a Hawaiian coinvasion landscape	62
Hybrid enrichment of adaptive variation revealed by genotype–environment associations in montane sedges	60
Interspecies genome divergence is predominantly due to frequent small scale rearrangements in Eucalyptus	57
Bacterial communities in a subarctic stream network: Spatial and seasonal patterns of benthic biofilm and bacterioplankton	55
Demographic modelling helps track the rapid and recent divergence of a conifer species pair from Central Mexico	53
Association between parasite microbiomes and caste development and colony structure in a social trematode	52
Grassland ecosystem type drives AM fungal diversity and functional guild distribution in North American grasslands	50
Organellar DNA continues to provide a rich source of information in the genomics era	48
Out of the Qinghai‐Tibet plateau: Genomic biogeography of the alpine monospecific genus Megadenia (Biscutelleae, Brassicaceae)	47
Diving into the diversity of colour patterns in reef fishes	46
Host‐pathogen‐environment interactions predict survival outcomes of adult sockeye salmon (Oncorhynchus nerka) released from fisheries	45

Understanding the role of temperature in seasonal timing: Effects on behavioural, physiological and molecular phenotypes	45
Whole‐genome resequencing confirms reproductive isolation between sympatric demes of brown trout (Salmo trutta) detected with allozymes	45
Experimental evidence that root‐associated fungi improve plant growth at high altitude	44
Genome‐wide SNP assessment of contemporary European red deer genetic structure highlights the distinction of peripheral populations and the main admixture zones in Europe	44
Effect of urbanization and parasitism on the gut microbiota of Darwin's finch nestlings	42
Brazilian marine phylogeography: A literature synthesis and analysis of barriers	41
Hypoxia as a physiological cue and pathological stress for coral larvae	41
DNA Methylation Dynamics Reflect Sex and Status Differences in Mortality Rates in a Polygynous Bat	40
On the origin and structure of haplotype blocks	40
A genomic assessment of the marine‐speciation paradox within the toothed whale superfamily Delphinoidea	39
Community‐wide correlations between species richness, abundance and population genomic diversity in a freshwater biodiversity hotspot	39
Clones on the run: The genomics of a recently expanded partially clonal species	39
Acclimatory gene expression of primed clams enhances robustness to elevated pCO2	39
Genetic and telomeric variability: Insights from a tropical avian hybrid zone	39
Diversification along a benthic to pelagic gradient contributes to fish diversity in the world's largest lake (Lake Baikal, Russia)	39
Intraspecific genetic variation matters when predicting seagrass distribution under climate change	37
Positive selection in gamete interaction proteins in Carnivora	37
Evolutionary roles of polyploidization‐derived structural variations in the phenotypic diversification of Panax species	36
Genomic analysis of a parasite invasion: Colonization of the Americas by the blood fluke Schistosoma mansoni	36
Extremes of snow and temperature affect patterns of genetic diversity and differentiation in the alpine butterfly Parnassius smintheus	36
Long‐read sequencing in ecology and evolution: Understanding how complex genetic and epigenetic variants shape biodiversity	35
Ecology Not Genetic Covariance Explains Correlated Trait Divergence During Speciation	35
The effect of divergent and parallel selection on the genomic landscape of divergence	35
Issue Information	34
Infection by the Lungworm Rhabdias pseudosphaerocephala Affects the Expression of Immune‐Related microRNAs by Its Co‐Evolved Host, the Cane Toad Rhinella marina	33
Issue Information	33
Historical Lead Contamination Linked to Atmospheric Deposition is Associated With Declines in Ectomycorrhizal Diversity and Shifts in Fungal Community Composition	33
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Early‐life seasonal, weather and social effects on telomere length in a wild mammal	32
Nestling sex and behaviour determine the host preference of insect vectors in avian nests	32
Erratum	32
Arbuscular mycorrhizal fungi and plant diversity drive restoration of nitrogen‐cycling microbial communities	32
Preconditioning improves bleaching tolerance in the reef‐building coral Pocillopora acuta through modulations in the programmed cell death pathways	32
Primrose homostyles: A classic case of possible balancing selection revisited	32
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Environmental heterogeneity structures root‐associated fungal communities in Daphne arbuscula (Thymelaeaceae), a shrub adapted to extreme rocky habitats	31
Demographic changes in Pleistocene sea turtles were driven by past sea level fluctuations affecting feeding habitat availability	31
Habitat restoration weakens negative environmental effects on telomere dynamics	31
Genetic responses in sexual diploid and unisexual triploid goldfish (Carassius auratus) introduced into a high‐altitude environment	31
Phylogeography of the blacklegged tick (Ixodes scapularis) throughout the USA identifies candidate loci for differences in vectorial capacity	31
When do autopolyploids need poly‐sequencing data?	31
An Early‐Life Disruption of Gut Microbiota Has Opposing Effects on Parasite Resistance in Two Host Species	31
Genome‐wide phylogeography reveals cryptic speciation in the circumglobal planktonic calcifier Limacina bulimoides	31
Evolutionary ecology of denitrifying methanotrophic NC10 bacteria in the deep‐sea biosphere	31
Regulation of host gene expression by gastrointestinal tract microbiota in Chinook Salmon (Oncorhynchus tshawytscha)	31
The effect of a temperature‐sensitive prophage on the evolution of virulence in an opportunistic bacterial pathogen	31
Characterizing feral swine movement across the contiguous United States using neural networks and genetic data	31
Genome‐wide variant analyses reveal new patterns of admixture and population structure in Australian dingoes	30
Larger, more connected societies of ants have a higher prevalence of viruses	30
Is speciation an unrelenting march to reproductive isolation?	30

Telomere dysfunction is associated with dark‐induced bleaching in the reef coral Stylophora pistillata	30
Genomic variation across Chinook salmon populations reveals effects of a duplication on migration alleles and supports fine scale structure	30
Large effective population size masks population genetic structure in Hirondellea amphipods within the deepest marine ecosystem, the Mariana Trench	29
Recent genetic exchanges and admixture shape the genome and population structure of the zoonotic pathogen Cryptosporidium parvum	29
Slow crabs ‐ fast genomes: Locomotory capacity predicts skew magnitude in crustacean mitogenomes	29
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The first steps toward a global pandemic: Reconstructing the demographic history of parasite host switches in its native range	29
Limited introgression from non‐native commercial strains and signatures of adaptation in the key pollinator Bombus terrestris	29
Semi‐quantitative metabarcoding reveals how climate shapes arthropod community assembly along elevation gradients on Hawaii Island	29
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	29
Environmental conditions drive zooplankton community structure in the epipelagic oceanic water of the southern Gulf of Mexico: A molecular approach	29
Integrative biological analyses of responses to food deprivation reveal resilience mechanisms in sea urchin larvae	29
Satellite DNA evolution in Corvoidea inferred from short and long reads	28
Ultraconserved Elements Reveal the Relationship Between Facultative Keratinophagy and Synanthropic Evolution in Clothes Moths	28
Genetic mixing in conservation translocations increases diversity of a keystone threatened species,Bettongia lesueur	28
Tracking population structure and phenology through time using ancient genomes from waterlogged white oak wood	28
Tidal gradients, fine‐scale homing and a potential cryptic ecotype of wild spawning pink salmon (Oncorhynchus gorbuscha)	28
Variation in phenotypic plasticity across age‐at‐maturity genotypes in wild Atlantic salmon	28
Genotype–Environment mismatch of kelp forests under climate change	28
Combined genome and transcriptome provides insight into the genetic evolution of an edible halophyte Suaeda salsa adaptation to high salinity	28
Heterogeneous patterns of heterozygosity loss in isolated populations of the threatened eastern barred bandicoot (Perameles gunnii)	28
Cophylogeny and specificity between cryptic coral species (Pocillopora spp.) at Mo′orea and their symbionts (Symbiodiniaceae)	28
Microbiomes associated with avian malaria survival differ between susceptible Hawaiian honeycreepers and sympatric malaria‐resistant introduced birds	28
Issue Information	27
Ephemeral Speciation in a New Guinean Honeyeater Complex (Aves: Melidectes)	27
Phylogenetic diversity only weakly mitigates climate‐change‐driven biodiversity loss in insect communities	27
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Issue Information	27
Comparative population genomics of manta rays has global implications for management	27
Genomic health is dependent on long‐term population demographic history	26
Geographical distance, host evolutionary history and diet drive gut microbiome diversity of fish across the Yellow River	26
Phylogeographic analysis of shrubby beardtongues reveals range expansions during the Last Glacial Maximum and implicates the Klamath Mountains as a hotspot for hybridization	26
The Pleistocene species pump past its prime: Evidence from European butterfly sister species	26
Genetic analysis reveals the putative native range and widespread double‐clonal reproduction in the invasive longhorn crazy ant	26
Host preference explains the high endemism of ectomycorrhizal fungi in a dipterocarp rainforest	26
The genomic basis of reproductive and migratory behaviour in a polymorphic salmonid	26
The challenge of demonstrating contemporary natural selection on polygenic quantitative traits in the wild	26
Phylogenomics and phylogeographic model testing using convolutional neural networks reveal a history of recent admixture in the Canarian Kleinia neriifolia	25
Longitudinal gut microbiome dynamics in relation to age and senescence in a wild animal population	25
Molecular mechanisms underlying plasticity in a thermally varying environment	25
Genetic adaptation despite high gene flow in a range‐expanding population	25
Cryptic hybridization between the ancient lineages of Natterer's bat (Myotis nattereri)	24
Lineage and role in integrative taxonomy of a heterotrophic orchid complex	24
Whole‐genome sequencing illuminates multifaceted targets of selection to humic substances in Eurasian perch	24
Wild sunflower goes viral: Citizen science and comparative genomics allow tracking the origin and establishment of invasive sunflower in the Levant	24
Plasticity for the win: Flexible transcriptional response to host plant switches in the comma butterfly (Polygonia c‐album)	24
Brettanomyces bruxellensis: Overview of the genetic and phenotypic diversity of an anthropized yeast	23
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Parental breeding decisions and genetic quality predict social structure of independent offspring	23
Evolved and Plastic Gene Expression in Adaptation of a Specialist Fly to a Novel Niche	23
Sexy fingers: Pheromones in the glands of male dendrobatid frogs	23
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Evolutionary variation in gene conversion at the avian MHC is explained by fluctuating selection, gene copy numbers and life history	23
Relic DNA obscures DNA‐based profiling of multiple microbial taxonomic groups in a river‐reservoir ecosystem	23
Shuffling between Cladocopium and Durusdinium extensively modifies the physiology of each symbiont without stressing the coral host	23
Issue Information	23
DNA methylation markers of age(ing) in non‐model animals	23
Ectoparasite presence and brood size manipulation interact to accelerate telomere shortening in nestling jackdaws	23
Population genomic structure of a widespread, urban‐dwelling mammal: The eastern grey squirrel (Sciurus carolinensis)	22
Male meiotic recombination rate varies with seasonal temperature fluctuations in wild populations of autotetraploid Arabidopsis arenosa	22
Parentage influence on gene expression under acidification revealed through single‐embryo sequencing	22
Sex chromosome heteromorphism and the Fast‐X effect in poeciliids	22
Seasonal dynamics of the wild rodent faecal virome	22
The Genetic Architecture of Local Adaptation and Reproductive Character Displacement in Scutiger boulengeri Complex (Anura: Megophryidae)	22
Metagenomic analysis reveals Culex mosquito virome diversity and Japanese encephalitis genotype V in the Republic of Korea	22
Long‐term biogeographical processes dominate patterns of genetic diversity in a wingless grasshopper despite substantial recent habitat fragmentation	22
Combining GWAS and population genomic analyses to characterize coevolution in a legume‐rhizobia symbiosis	22
Heat‐stress memory enhances the acclimation of a migratory insect pest to global warming	22
Defence by duplication: The relation between phenotypic glyphosate resistance and EPSPS gene copy number variation in Amaranthus palmeri	22
Investigating the genetic basis of vertebrate dispersal combining RNA‐seq, RAD‐seq and quantitative genetics	22
Approximate Bayesian Computation applied to time series of population genetic data disentangles rapid genetic changes and demographic variations in a pathogen population	22
Phenotypic cross‐species conservation and cross‐generation directionality switching in epigenetic inheritance	22
The challenge and promise of estimating the de novo mutation rate from whole‐genome comparisons among closely related individuals	22
Immune genotypes, immune responses, and survival in a wild bird population	21
Seascape genomics of coastal bottlenose dolphins along strong gradients of temperature and salinity	21
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Inferring the ecological and evolutionary determinants of community genetic diversity	21
Revisiting old truths: The evolution of male coloration in guppies as a function of predation	21
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Molecular ecology of microbiomes in the wild: Common pitfalls, methodological advances and future directions	21
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Long live the host! Proteomic analysis reveals possible strategies for parasitic manipulation of its social host	20
Genomic investigation of colour polymorphism and phylogeographic variation among populations of black‐headed bulbul (Brachypodius atriceps) in insular southeast Asia	20
Responses of pea plants to multiple antagonists are mediated by order of attack and phytohormone crosstalk	20
Repeated Mitochondrial Capture With Limited Genomic Introgression in a Lizard Group	20
A Test of the Long‐Term Efficiency of Genetic Rescue With Drosophila melanogaster	20
Correction to “The Opposed Forces of Differentiation and Admixture Across Glacial Cycles in the Butterfly Aglais urticae”	20
Speciation patterns of related species under the hybrid zone: A case study of three sclerophyllous oaks in the east Himalaya–Hengduan Mountains	20
High promiscuity among females of the invasive pest species Drosophila suzukii	20
Quality of phytoplankton deposition structures bacterial communities at the water‐sediment interface	20
Rhizobium nodule diversity and composition are influenced by clover host selection and local growth conditions	20
Parental effects in a filamentous fungus: Phenotype, fitness and mechanism	20
Social Complexity During Early Development has Long‐Term Effects on Neuroplasticity in the Social Decision‐Making Network	20
Genomic, Phenotypic and Environmental Correlates of Speciation in the Midwife Toads (Alytes)	20
Fire shapes fungal guild diversity and composition through direct and indirect pathways	20
Genomic architecture underlying morphological and physiological adaptation to high elevation in a songbird	20
Age‐ and caste‐independent piRNAs in the germline and miRNA profiles linked to caste and fecundity in the ant Temnothorax rugatulus	20
Tackling the challenges of evolutionary forest research with multidata approaches	20
Diet in phenotypically divergent sympatric species of African weakly electric fish (genus: Campylomormyrus)—A hybrid capture/HTS metabarcoding approach	20
It is time for ancient DNA to sweat the small stuff	20
Expression of Elongase‐ and Desaturase‐Encoding Genes Shapes the Cuticular Hydrocarbon Profiles of Honey Bees	20
Issue Information	20
Defence‐relevant gene expression differences in hatchlings among wild Newfoundland and farmed European and North American Atlantic salmon and their hybrids	19
Synthesizing environmental, epidemiological and vector and parasite genetic data to assist decision making for disease elimination	19
Genomic‐based epidemiology reveals independent origins and gene flow of glyphosate resistance in Bassia scoparia populations across North America	19
Whole genome population structure of North Atlantic kelp confirms high‐latitude glacial refugia	19
Metabarcoding for biodiversity inventory blind spots: A test case using the beetle fauna of an insular cloud forest	19
Adaptive divergence in bill morphology and other thermoregulatory traits is facilitated by restricted gene flow in song sparrows on the California Channel Islands	19
Fitness consequences of population bottlenecks in an invasive blowfly	19
Complex adaptive architecture underlies adaptation to quantitative host resistance in a fungal plant pathogen	19
The structure of tropical bat–plant interaction networks during an extreme El Niño‐Southern Oscillation event	19
Capabilities and limitations of using DNA metabarcoding to study plant–pollinator interactions	19
Gene expression differentiation in the reproductive tissues of Drosophila willistoni subspecies and their hybrids	19
Genomic and phenotypic changes associated with alterations of migratory behaviour in a songbird	19
The faecal metabolome of black howler monkeys (Alouatta pigra) varies in response to seasonal dietary changes	19
Population genomics and sexual signals support reproductive character displacement in Uperoleia (Anura: Myobatrachidae) in a contact zone	19
Genetic legacies of mega‐landslides: Cycles of isolation and contact across flank collapses in an oceanic island	19
Repeatome evolution across space and time: Unravelling repeats dynamics in the plant genus Erythrostemon Klotzsch (Leguminosae Juss)	19
Different trematode parasites in the same snail host: Species‐specific or shared microbiota?	19
Whole‐genome sequencing reveals fine‐scale environment‐associated divergence near the range limits of a temperate reef fish	19
Phylogeography of horseshoe bat sarbecoviruses in Vietnam and neighbouring countries. Implications for the origins of SARS‐CoV and SARS‐CoV‐2	19
Domestication and evolutionary histories of specialized gut symbionts across cephalotine ants	19
Pleistocene parades of carnivores into North America	18
Brain and antennal transcriptomes of host ants reveal potential links between behaviour and the functioning of socially parasitic colonies	18
Human activity strongly influences genetic dynamics of the most widespread invasive plant in the sub‐Antarctic	18
Issue Information	18
High Quality Diet Enhances Immune Response and Affects Gene Expression During Viral Infection in an Insect Herbivore	18
Divergent island hybrids mixed waves of ancient gene flow	18
Issue Information	18
Complex dynamics of coral gene expression responses to low pH across species	18
Multiple genomic solutions for local adaptation in two closely related species (sheep and goats) facing the same climatic constraints	18
Seq’ and ARMS shall find: DNA (meta)barcoding of Autonomous Reef Monitoring Structures across the tree of life uncovers hidden cryptobiome of tropical urban coral reefs	18
Different molecular changes underlie the same phenotypic transition: Origins and consequences of independent shifts to homostyly within species	18
Divergence of alternative sugar preferences through modulation of the expression and activity of the Gal3 sensor in yeast	18
Fifty Years of Conservation Genetics: A Personal Perspective	18
Issue Information	18
Environmental DNA unveils deep phylogeographic structure of a freshwater fish	18
Selection for Tameness in Red Junglefowl Recapitulates Genetic Loci Associated With Domestication‐Related Brain Composition	18
Strategies to identify and dissect trade‐offs in plants	18
Genomics reveal population structure, evolutionary history, and signatures of selection in the northern bottlenose whale, Hyperoodon ampullatus	18
Not All Bark Beetles Smell the Same: Population‐Level Functional Olfactory Polymorphisms in Ips typographus Pheromone Receptor ItypOR33	18
Robust Sensory Traits Across Light Habitats: Visual Signals but Not Receptors Vary in Centrarchids Inhabiting Distinct Photic Environments	18
Issue Information	18
A globally ubiquitous symbiont can drive experimental host evolution	17
Impact of disturbance and dietary shift on gastrointestinal bacterial community and its invertebrate host system	17
Pathogen invasion increases the abundance of predatory protists and their prey associations in the plant microbiome	17
Understanding Dynamic Molecular Responses Is Key to Designing Environmental Stress Experiments: A Review of Gene and Protein Expression in Cnidaria Under Stress	17
Genome‐wide molecular phylogenetic analyses and mating experiments which reveal the evolutionary history and an intermediate stage of speciation of a giant water bug	17
Do chromosome rearrangements fix by genetic drift or natural selection? Insights from Brenthis butterflies	17
Natural selection and the distribution of chromosomal inversion lengths	17
Hybrid‐derived weedy rice maintains adaptive combinations of alleles associated with seed dormancy	17
Escalation by duplication: Milkweed bug trumps Monarch butterfly	17
Tissue‐specific transcriptional patterns underlie seasonal phenotypes in honey bees (Apis mellifera)	17
Variable hybridization between two Lake Tanganyikan cichlid species in recent secondary contact	17
Microbiota composition and diversity of multiple body sites vary according to reproductive performance in a seabird	17
Habitat‐linked genetic variation supports microgeographic adaptive divergence in an island‐endemic bird species	17
Global flyway evolution in red knots Calidris canutus and genetic evidence for a Nearctic refugium	17
DNA methylation is not a driver of gene expression reprogramming in young honey bee workers	17
Living with chronic infection: Persistent immunomodulation during avirulent haemoparasitic infection in a wild rodent	17
Differential temperature effects on photoperiodism in female voles: A possible explanation for declines in vole populations	17
Expression patterns of melanin‐related genes are linked to crypsis and conspicuousness in a pumpkin toadlet	17
Linking large‐scale genetic structure of three Argynnini butterfly species to geography and environment	17
Population Genetics and Invasion History of the European Starling Across Aotearoa New Zealand	17
Social and paternal female choice for male MHC genes in golden snub‐nosed monkeys (Rhinopithecus roxellana)	17
Genomic associations with poxvirus across divergent island populations in Berthelot's pipit	17
Host genotype and microbiome associations in co‐occurring clonal and non‐clonal kelp, Ecklonia radiata	17
Parallel duplication and loss of aquaporin‐coding genes during the “out of the sea” transition as potential key drivers of animal terrestrialization	17
Genomic inference of contemporary effective population size in a large island population of collared flycatchers (Ficedula albicollis)	17
Expression–environment associations in transcriptomic heat stress responses for a global plant lineage	17