Molecular Ecology

Article	Citations
Cover Image	217
Community‐wide correlations between species richness, abundance and population genomic diversity in a freshwater biodiversity hotspot	192
Issue Information	171
Clones on the run: The genomics of a recently expanded partially clonal species	124
The transcriptional state and chromatin landscape of cichlid jaw shape variation across species and environments	99
Interspecies genome divergence is predominantly due to frequent small scale rearrangements in Eucalyptus	83
Traits and tradeoffs among non‐native ectomycorrhizal fungal symbionts affect pine seedling establishment in a Hawaiian coinvasion landscape	68
Telomere dynamics in relation to experimentally increased locomotion costs and fitness in great tits	67
Adaptive cellular evolution or cellular system drift in hares	61
Hybrid enrichment of adaptive variation revealed by genotype–environment associations in montane sedges	59
Bacterial communities in a subarctic stream network: Spatial and seasonal patterns of benthic biofilm and bacterioplankton	54
Association between parasite microbiomes and caste development and colony structure in a social trematode	49
Evolutionary roles of polyploidization‐derived structural variations in the phenotypic diversification of Panax species	48
Organellar DNA continues to provide a rich source of information in the genomics era	46
Whole‐genome resequencing confirms reproductive isolation between sympatric demes of brown trout (Salmo trutta) detected with allozymes	46
Out of the Qinghai‐Tibet plateau: Genomic biogeography of the alpine monospecific genus Megadenia (Biscutelleae, Brassicaceae)	45
Host‐pathogen‐environment interactions predict survival outcomes of adult sockeye salmon (Oncorhynchus nerka) released from fisheries	44
Diversification along a benthic to pelagic gradient contributes to fish diversity in the world's largest lake (Lake Baikal, Russia)	43
Genomic analysis of a parasite invasion: Colonization of the Americas by the blood fluke Schistosoma mansoni	43
A genomic assessment of the marine‐speciation paradox within the toothed whale superfamily Delphinoidea	43
Grassland ecosystem type drives AM fungal diversity and functional guild distribution in North American grasslands	43
Effect of urbanization and parasitism on the gut microbiota of Darwin's finch nestlings	42
Acclimatory gene expression of primed clams enhances robustness to elevated pCO2	41
Brazilian marine phylogeography: A literature synthesis and analysis of barriers	40
Demographic modelling helps track the rapid and recent divergence of a conifer species pair from Central Mexico	40

Diving into the diversity of colour patterns in reef fishes	39
Positive selection in gamete interaction proteins in Carnivora	39
Ecology Not Genetic Covariance Explains Correlated Trait Divergence During Speciation	39
The effect of divergent and parallel selection on the genomic landscape of divergence	39
Understanding the role of temperature in seasonal timing: Effects on behavioural, physiological and molecular phenotypes	38
The impacts of positive selection on genomic variation in Drosophila serrata: Insights from a deep learning approach	38
Genetic and telomeric variability: Insights from a tropical avian hybrid zone	37
Genome‐wide SNP assessment of contemporary European red deer genetic structure highlights the distinction of peripheral populations and the main admixture zones in Europe	37
Extremes of snow and temperature affect patterns of genetic diversity and differentiation in the alpine butterfly Parnassius smintheus	37
DNA Methylation Dynamics Reflect Sex and Status Differences in Mortality Rates in a Polygynous Bat	36
Evolutionary History and Rhizosphere Microbial Community Composition in Domesticated Hops (Humulus lupulus L.)	36
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	36
Experimental evidence that root‐associated fungi improve plant growth at high altitude	36
Museomics Sheds Light on Evolutionary Diversity in a Critically Endangered Cockatoo Species From Wallacea	36
Decoding plant‐induced transcriptomic variability and consistency in two related polyphagous mites differing in host ranges	35
Genomic divergence and introgression between cryptic species of a widespread North American songbird	35
Genomic, morphological and physiological data support fast ecotypic differentiation and incipient speciation in an alpine diving beetle	35
Long‐read sequencing in ecology and evolution: Understanding how complex genetic and epigenetic variants shape biodiversity	35
On the origin and structure of haplotype blocks	35
Issue Information	34
More complex than you think: Taxonomic and temporal patterns of plant–pollinator networks of caraway (Carum carvi L.)	34
Hypoxia as a physiological cue and pathological stress for coral larvae	34
Issue Information	34
Regulation of host gene expression by gastrointestinal tract microbiota in Chinook Salmon (Oncorhynchus tshawytscha)	33
Primrose homostyles: A classic case of possible balancing selection revisited	33
Environmental conditions drive zooplankton community structure in the epipelagic oceanic water of the southern Gulf of Mexico: A molecular approach	33
Phylogenetic diversity only weakly mitigates climate‐change‐driven biodiversity loss in insect communities	33
Large effective population size masks population genetic structure in Hirondellea amphipods within the deepest marine ecosystem, the Mariana Trench	33
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Semi‐quantitative metabarcoding reveals how climate shapes arthropod community assembly along elevation gradients on Hawaii Island	32
Genome‐wide variant analyses reveal new patterns of admixture and population structure in Australian dingoes	32
Recent genetic exchanges and admixture shape the genome and population structure of the zoonotic pathogen Cryptosporidium parvum	32
The effect of a temperature‐sensitive prophage on the evolution of virulence in an opportunistic bacterial pathogen	32
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The first steps toward a global pandemic: Reconstructing the demographic history of parasite host switches in its native range	31
Erratum	31
When do autopolyploids need poly‐sequencing data?	31
Demographic changes in Pleistocene sea turtles were driven by past sea level fluctuations affecting feeding habitat availability	31
Genetic responses in sexual diploid and unisexual triploid goldfish (Carassius auratus) introduced into a high‐altitude environment	30
Genomic variation across Chinook salmon populations reveals effects of a duplication on migration alleles and supports fine scale structure	30
Cophylogeny and specificity between cryptic coral species (Pocillopora spp.) at Mo′orea and their symbionts (Symbiodiniaceae)	30
Reticulate and Hybrid Speciation is Promoted by Environmental Instability in an Indo‐Pacific Species Complex of Whistlers (Aves: Pachycephala)	30
Microbiomes associated with avian malaria survival differ between susceptible Hawaiian honeycreepers and sympatric malaria‐resistant introduced birds	30
Satellite DNA evolution in Corvoidea inferred from short and long reads	30
Genome‐wide phylogeography reveals cryptic speciation in the circumglobal planktonic calcifier Limacina bulimoides	30
Tidal gradients, fine‐scale homing and a potential cryptic ecotype of wild spawning pink salmon (Oncorhynchus gorbuscha)	30
Infection by the Lungworm Rhabdias pseudosphaerocephala Affects the Expression of Immune‐Related microRNAs by Its Co‐Evolved Host, the Cane Toad Rhinella marina	29
Integrative biological analyses of responses to food deprivation reveal resilience mechanisms in sea urchin larvae	29
Variation in phenotypic plasticity across age‐at‐maturity genotypes in wild Atlantic salmon	29
Characterizing feral swine movement across the contiguous United States using neural networks and genetic data	29

Genetic mixing in conservation translocations increases diversity of a keystone threatened species,Bettongia lesueur	29
An Early‐Life Disruption of Gut Microbiota Has Opposing Effects on Parasite Resistance in Two Host Species	29
Nestling sex and behaviour determine the host preference of insect vectors in avian nests	29
Heterogeneous patterns of heterozygosity loss in isolated populations of the threatened eastern barred bandicoot (Perameles gunnii)	29
Tracking population structure and phenology through time using ancient genomes from waterlogged white oak wood	28
Environmental heterogeneity structures root‐associated fungal communities in Daphne arbuscula (Thymelaeaceae), a shrub adapted to extreme rocky habitats	28
Recurrent Hybridisations During Diversification of One Rhododendron Species Complex	28
Ultraconserved Elements Reveal the Relationship Between Facultative Keratinophagy and Synanthropic Evolution in Clothes Moths	28
Historical Lead Contamination Linked to Atmospheric Deposition is Associated With Declines in Ectomycorrhizal Diversity and Shifts in Fungal Community Composition	28
Convergent Evolutionary Dead‐End and Breakdown of Hard Chorion in Parental‐Egg‐Care Fish Reproductive Strategies	28
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	27
Slow crabs ‐ fast genomes: Locomotory capacity predicts skew magnitude in crustacean mitogenomes	27
Evolutionary ecology of denitrifying methanotrophic NC10 bacteria in the deep‐sea biosphere	27
Is speciation an unrelenting march to reproductive isolation?	27
Phylogeography of the blacklegged tick (Ixodes scapularis) throughout the USA identifies candidate loci for differences in vectorial capacity	27
Telomere dysfunction is associated with dark‐induced bleaching in the reef coral Stylophora pistillata	27
Larger, more connected societies of ants have a higher prevalence of viruses	27
Limited introgression from non‐native commercial strains and signatures of adaptation in the key pollinator Bombus terrestris	27
Issue Information	26
Combined genome and transcriptome provides insight into the genetic evolution of an edible halophyte Suaeda salsa adaptation to high salinity	26
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Issue Information	26
Wild sunflower goes viral: Citizen science and comparative genomics allow tracking the origin and establishment of invasive sunflower in the Levant	25
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Molecular mechanisms underlying plasticity in a thermally varying environment	25
Lineage and role in integrative taxonomy of a heterotrophic orchid complex	24
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Immune genotypes, immune responses, and survival in a wild bird population	24
Inferring the ecological and evolutionary determinants of community genetic diversity	24
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Genetic analysis reveals the putative native range and widespread double‐clonal reproduction in the invasive longhorn crazy ant	24
Brettanomyces bruxellensis: Overview of the genetic and phenotypic diversity of an anthropized yeast	24
The challenge of demonstrating contemporary natural selection on polygenic quantitative traits in the wild	24
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Sex chromosome heteromorphism and the Fast‐X effect in poeciliids	24
The genomic basis of reproductive and migratory behaviour in a polymorphic salmonid	24
Shuffling between Cladocopium and Durusdinium extensively modifies the physiology of each symbiont without stressing the coral host	23
Metagenomic analysis reveals Culex mosquito virome diversity and Japanese encephalitis genotype V in the Republic of Korea	23
Parental breeding decisions and genetic quality predict social structure of independent offspring	23
Long‐term biogeographical processes dominate patterns of genetic diversity in a wingless grasshopper despite substantial recent habitat fragmentation	23
Omics to Study and Manage Aquatic Environments: A Snapshot From the AquaEcOmics Meeting (Evian‐les‐Bains, 2025)	23
Cryptic hybridization between the ancient lineages of Natterer's bat (Myotis nattereri)	23
DNA methylation markers of age(ing) in non‐model animals	23
Genomic health is dependent on long‐term population demographic history	23
Parentage influence on gene expression under acidification revealed through single‐embryo sequencing	23
Phenotypic cross‐species conservation and cross‐generation directionality switching in epigenetic inheritance	23
Investigating the genetic basis of vertebrate dispersal combining RNA‐seq, RAD‐seq and quantitative genetics	23
Relic DNA obscures DNA‐based profiling of multiple microbial taxonomic groups in a river‐reservoir ecosystem	23
Whole‐genome sequencing illuminates multifaceted targets of selection to humic substances in Eurasian perch	23
Ectoparasite presence and brood size manipulation interact to accelerate telomere shortening in nestling jackdaws	23
Defence by duplication: The relation between phenotypic glyphosate resistance and EPSPS gene copy number variation in Amaranthus palmeri	23
Seascape genomics of coastal bottlenose dolphins along strong gradients of temperature and salinity	23
Geographical distance, host evolutionary history and diet drive gut microbiome diversity of fish across the Yellow River	23
Genetic adaptation despite high gene flow in a range‐expanding population	22
The Genetic Architecture of Local Adaptation and Reproductive Character Displacement in Scutiger boulengeri Complex (Anura: Megophryidae)	22
Combining GWAS and population genomic analyses to characterize coevolution in a legume‐rhizobia symbiosis	22
Phylogenomics and phylogeographic model testing using convolutional neural networks reveal a history of recent admixture in the Canarian Kleinia neriifolia	22
Plasticity for the win: Flexible transcriptional response to host plant switches in the comma butterfly (Polygonia c‐album)	22
Ephemeral Speciation in a New Guinean Honeyeater Complex (Aves: Melidectes)	22
Host preference explains the high endemism of ectomycorrhizal fungi in a dipterocarp rainforest	22
Population genomic structure of a widespread, urban‐dwelling mammal: The eastern grey squirrel (Sciurus carolinensis)	22
Seasonal dynamics of the wild rodent faecal virome	22
Issue Information	21
Heat‐stress memory enhances the acclimation of a migratory insect pest to global warming	21
Molecular ecology of microbiomes in the wild: Common pitfalls, methodological advances and future directions	21
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Sexy fingers: Pheromones in the glands of male dendrobatid frogs	21
Evolved and Plastic Gene Expression in Adaptation of a Specialist Fly to a Novel Niche	21
Revisiting old truths: The evolution of male coloration in guppies as a function of predation	21
Evolutionary variation in gene conversion at the avian MHC is explained by fluctuating selection, gene copy numbers and life history	21
Approximate Bayesian Computation applied to time series of population genetic data disentangles rapid genetic changes and demographic variations in a pathogen population	21
Longitudinal gut microbiome dynamics in relation to age and senescence in a wild animal population	21
Comparative population genomics of manta rays has global implications for management	21
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Fire shapes fungal guild diversity and composition through direct and indirect pathways	20
The faecal metabolome of black howler monkeys (Alouatta pigra) varies in response to seasonal dietary changes	20
It is time for ancient DNA to sweat the small stuff	20
Genomic architecture underlying morphological and physiological adaptation to high elevation in a songbird	20

Adaptive divergence in bill morphology and other thermoregulatory traits is facilitated by restricted gene flow in song sparrows on the California Channel Islands	20
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Long live the host! Proteomic analysis reveals possible strategies for parasitic manipulation of its social host	20
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Parental effects in a filamentous fungus: Phenotype, fitness and mechanism	20
Rhizobium nodule diversity and composition are influenced by clover host selection and local growth conditions	20
Population genomics and sexual signals support reproductive character displacement in Uperoleia (Anura: Myobatrachidae) in a contact zone	20
Issue Information	20
Divergence of alternative sugar preferences through modulation of the expression and activity of the Gal3 sensor in yeast	20
Responses of pea plants to multiple antagonists are mediated by order of attack and phytohormone crosstalk	20
Genomic investigation of colour polymorphism and phylogeographic variation among populations of black‐headed bulbul (Brachypodius atriceps) in insular southeast Asia	20
Metabarcoding for biodiversity inventory blind spots: A test case using the beetle fauna of an insular cloud forest	20
Age‐ and caste‐independent piRNAs in the germline and miRNA profiles linked to caste and fecundity in the ant Temnothorax rugatulus	19
Genomic, Phenotypic and Environmental Correlates of Speciation in the Midwife Toads (Alytes)	19
The structure of tropical bat–plant interaction networks during an extreme El Niño‐Southern Oscillation event	19
Complex dynamics of coral gene expression responses to low pH across species	19
Pleistocene parades of carnivores into North America	19
Correction to “The Opposed Forces of Differentiation and Admixture Across Glacial Cycles in the Butterfly Aglais urticae”	19
Whole‐genome sequencing reveals fine‐scale environment‐associated divergence near the range limits of a temperate reef fish	19
Repeatome evolution across space and time: Unravelling repeats dynamics in the plant genus Erythrostemon Klotzsch (Leguminosae Juss)	19
Genetic legacies of mega‐landslides: Cycles of isolation and contact across flank collapses in an oceanic island	19
Speciation patterns of related species under the hybrid zone: A case study of three sclerophyllous oaks in the east Himalaya–Hengduan Mountains	19
Brain and antennal transcriptomes of host ants reveal potential links between behaviour and the functioning of socially parasitic colonies	19
Synthesizing environmental, epidemiological and vector and parasite genetic data to assist decision making for disease elimination	19
Complex adaptive architecture underlies adaptation to quantitative host resistance in a fungal plant pathogen	19
Social Complexity During Early Development has Long‐Term Effects on Neuroplasticity in the Social Decision‐Making Network	19
Different trematode parasites in the same snail host: Species‐specific or shared microbiota?	19
Genomics reveal population structure, evolutionary history, and signatures of selection in the northern bottlenose whale, Hyperoodon ampullatus	19
Expression of Elongase‐ and Desaturase‐Encoding Genes Shapes the Cuticular Hydrocarbon Profiles of Honey Bees	19
Genomic‐based epidemiology reveals independent origins and gene flow of glyphosate resistance in Bassia scoparia populations across North America	19
Gene expression differentiation in the reproductive tissues of Drosophila willistoni subspecies and their hybrids	19
Repeated Mitochondrial Capture With Limited Genomic Introgression in a Lizard Group	19
Different molecular changes underlie the same phenotypic transition: Origins and consequences of independent shifts to homostyly within species	19
Multiple genomic solutions for local adaptation in two closely related species (sheep and goats) facing the same climatic constraints	19
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	19
Strategies to identify and dissect trade‐offs in plants	19
Genomic and phenotypic changes associated with alterations of migratory behaviour in a songbird	19
High promiscuity among females of the invasive pest species Drosophila suzukii	19
Environmental DNA unveils deep phylogeographic structure of a freshwater fish	19
Global flyway evolution in red knots Calidris canutus and genetic evidence for a Nearctic refugium	18
Issue Information	18
Domestication and evolutionary histories of specialized gut symbionts across cephalotine ants	18
Diet in phenotypically divergent sympatric species of African weakly electric fish (genus: Campylomormyrus)—A hybrid capture/HTS metabarcoding approach	18
No Evidence That Life History Strategies Shape Within‐Body Mosaics of Ageing	18
Genome assembly, structural variants, and genetic differentiation between lake whitefish young species pairs (Coregonus sp.) with long and short reads	18
Microbiota composition and diversity of multiple body sites vary according to reproductive performance in a seabird	18
Population Genetics and Invasion History of the European Starling Across Aotearoa New Zealand	18
Whole genome population structure of North Atlantic kelp confirms high‐latitude glacial refugia	18
Phylogeography of horseshoe bat sarbecoviruses in Vietnam and neighbouring countries. Implications for the origins of SARS‐CoV and SARS‐CoV‐2	18
Defence‐relevant gene expression differences in hatchlings among wild Newfoundland and farmed European and North American Atlantic salmon and their hybrids	18
Capabilities and limitations of using DNA metabarcoding to study plant–pollinator interactions	18
Natural selection and the distribution of chromosomal inversion lengths	18
Host genotype and microbiome associations in co‐occurring clonal and non‐clonal kelp, Ecklonia radiata	18
Epigenomic Changes in Ostrinia Moths Under Elevated Pupal and Adult Temperature	18
Fitness consequences of population bottlenecks in an invasive blowfly	18
A Test of the Long‐Term Efficiency of Genetic Rescue With Drosophila melanogaster	18
Selection for Tameness in Red Junglefowl Recapitulates Genetic Loci Associated With Domestication‐Related Brain Composition	18
Issue Information	18
Evaluating the persistence and utility of five wild Vitis species in the context of climate change	18
Differential temperature effects on photoperiodism in female voles: A possible explanation for declines in vole populations	17
Understanding Dynamic Molecular Responses Is Key to Designing Environmental Stress Experiments: A Review of Gene and Protein Expression in Cnidaria Under Stress	17
Demography‐driven and adaptive introgression in a hybrid zone of the Armeria syngameon	17
Fifty Years of Conservation Genetics: A Personal Perspective	17
Living with chronic infection: Persistent immunomodulation during avirulent haemoparasitic infection in a wild rodent	17
Limited dispersal and local adaptation promote allopatric speciation in a biodiversity hotspot	17
Transcriptional response of the calcification and stress response toolkits in an octocoral under heat and pH stress	17
Plant invasion reconstructs soil microbial assembly and functionality in coastal salt marshes	17
Of bars and stripes: A Malawi cichlid hybrid cross provides insights into genetic modularity and evolution of modifier loci underlying colour pattern diversification	17
Escalation by duplication: Milkweed bug trumps Monarch butterfly	17
Hybrid‐derived weedy rice maintains adaptive combinations of alleles associated with seed dormancy	17
Impact of disturbance and dietary shift on gastrointestinal bacterial community and its invertebrate host system	17
Frequent Hybridisation Between Parapatric Lekking Bird‐of‐Paradise Species	17
Issue Information	17
Distinct patterns of inheritance shape life‐history traits in steelhead trout	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
Understanding stochastic and deterministic assembly processes in microbial communities along temporal, spatial and environmental scales	17
Expression–environment associations in transcriptomic heat stress responses for a global plant lineage	17
Domestication obscures genomic estimates of population history	17
Amazonian colonization from the Atlantic Forest: New perspectives on the connections of South American tropical forests	17
Biodiversity Genomics Research Practices Require Harmonising to Meet Stakeholder Needs in Conservation	17
Habitat‐linked genetic variation supports microgeographic adaptive divergence in an island‐endemic bird species	17
Variable hybridization between two Lake Tanganyikan cichlid species in recent secondary contact	17
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Parallel duplication and loss of aquaporin‐coding genes during the “out of the sea” transition as potential key drivers of animal terrestrialization	17
Tissue‐specific transcriptional patterns underlie seasonal phenotypes in honey bees (Apis mellifera)	17
Linking large‐scale genetic structure of three Argynnini butterfly species to geography and environment	17
DNA methylation is not a driver of gene expression reprogramming in young honey bee workers	17
Strong Bottlenecks Constrain Adaptive Coevolution in a Host–Parasite Metapopulation	17
Genomic associations with poxvirus across divergent island populations in Berthelot's pipit	17
Transgressive gene expression and expression plasticity under thermal stress in a stable hybrid zone	17
Odorant receptor orthologues in conifer‐feeding beetles display conserved responses to ecologically relevant odours	16
Discordant Pleistocene population size histories in a guild of hymenopteran parasitoids	16
Awaking the dormant virome in the rhizosphere	16