Molecular Ecology

Article	Citations
Community‐wide correlations between species richness, abundance and population genomic diversity in a freshwater biodiversity hotspot	196
Issue Information	174
Clones on the run: The genomics of a recently expanded partially clonal species	129
The transcriptional state and chromatin landscape of cichlid jaw shape variation across species and environments	84
Interspecies genome divergence is predominantly due to frequent small scale rearrangements in Eucalyptus	69
Telomere dynamics in relation to experimentally increased locomotion costs and fitness in great tits	68
Adaptive cellular evolution or cellular system drift in hares	62
Hybrid enrichment of adaptive variation revealed by genotype–environment associations in montane sedges	61
Bacterial communities in a subarctic stream network: Spatial and seasonal patterns of benthic biofilm and bacterioplankton	57
Association between parasite microbiomes and caste development and colony structure in a social trematode	52
Evolutionary roles of polyploidization‐derived structural variations in the phenotypic diversification of Panax species	51
Whole‐genome resequencing confirms reproductive isolation between sympatric demes of brown trout (Salmo trutta) detected with allozymes	48
Grassland ecosystem type drives AM fungal diversity and functional guild distribution in North American grasslands	47
Effect of urbanization and parasitism on the gut microbiota of Darwin's finch nestlings	46
On the origin and structure of haplotype blocks	46
Hypoxia as a physiological cue and pathological stress for coral larvae	45
Genomic, morphological and physiological data support fast ecotypic differentiation and incipient speciation in an alpine diving beetle	45
More complex than you think: Taxonomic and temporal patterns of plant–pollinator networks of caraway (Carum carvi L.)	43
Positive selection in gamete interaction proteins in Carnivora	43
The effect of divergent and parallel selection on the genomic landscape of divergence	43
Diving into the diversity of colour patterns in reef fishes	42
The impacts of positive selection on genomic variation in Drosophila serrata: Insights from a deep learning approach	42
Ecology Not Genetic Covariance Explains Correlated Trait Divergence During Speciation	42
Genetic and telomeric variability: Insights from a tropical avian hybrid zone	41
Museomics Sheds Light on Evolutionary Diversity in a Critically Endangered Cockatoo Species From Wallacea	40

Genome‐wide SNP assessment of contemporary European red deer genetic structure highlights the distinction of peripheral populations and the main admixture zones in Europe	40
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	40
Extremes of snow and temperature affect patterns of genetic diversity and differentiation in the alpine butterfly Parnassius smintheus	40
A genomic assessment of the marine‐speciation paradox within the toothed whale superfamily Delphinoidea	39
Evolutionary History and Rhizosphere Microbial Community Composition in Domesticated Hops (Humulus lupulus L.)	39
Long‐read sequencing in ecology and evolution: Understanding how complex genetic and epigenetic variants shape biodiversity	39
Understanding the role of temperature in seasonal timing: Effects on behavioural, physiological and molecular phenotypes	38
Decoding plant‐induced transcriptomic variability and consistency in two related polyphagous mites differing in host ranges	37
Experimental evidence that root‐associated fungi improve plant growth at high altitude	36
Organellar DNA continues to provide a rich source of information in the genomics era	36
Demographic modelling helps track the rapid and recent divergence of a conifer species pair from Central Mexico	36
Genomic analysis of a parasite invasion: Colonization of the Americas by the blood fluke Schistosoma mansoni	36
Traits and tradeoffs among non‐native ectomycorrhizal fungal symbionts affect pine seedling establishment in a Hawaiian coinvasion landscape	36
Host‐pathogen‐environment interactions predict survival outcomes of adult sockeye salmon (Oncorhynchus nerka) released from fisheries	36
Combined Evidence Reveals the Origin of a Rapid Range Expansion Despite Retained Genetic Diversity and a Weak Founder Effect	36
DNA Methylation Dynamics Reflect Sex and Status Differences in Mortality Rates in a Polygynous Bat	35
Acclimatory gene expression of primed clams enhances robustness to elevated pCO2	35
Genomic divergence and introgression between cryptic species of a widespread North American songbird	35
Diversification along a benthic to pelagic gradient contributes to fish diversity in the world's largest lake (Lake Baikal, Russia)	34
Out of the Qinghai‐Tibet plateau: Genomic biogeography of the alpine monospecific genus Megadenia (Biscutelleae, Brassicaceae)	34
Brazilian marine phylogeography: A literature synthesis and analysis of barriers	34
Issue Information	34
Phylogenetic diversity only weakly mitigates climate‐change‐driven biodiversity loss in insect communities	34
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Primrose homostyles: A classic case of possible balancing selection revisited	33
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	32
Environmental conditions drive zooplankton community structure in the epipelagic oceanic water of the southern Gulf of Mexico: A molecular approach	32
Semi‐quantitative metabarcoding reveals how climate shapes arthropod community assembly along elevation gradients on Hawaii Island	32
Large effective population size masks population genetic structure in Hirondellea amphipods within the deepest marine ecosystem, the Mariana Trench	32
The effect of a temperature‐sensitive prophage on the evolution of virulence in an opportunistic bacterial pathogen	32
Erratum	31
Satellite DNA evolution in Corvoidea inferred from short and long reads	31
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Genome‐wide phylogeography reveals cryptic speciation in the circumglobal planktonic calcifier Limacina bulimoides	31
Tidal gradients, fine‐scale homing and a potential cryptic ecotype of wild spawning pink salmon (Oncorhynchus gorbuscha)	31
Combined genome and transcriptome provides insight into the genetic evolution of an edible halophyte Suaeda salsa adaptation to high salinity	31
Larger, more connected societies of ants have a higher prevalence of viruses	31
Highly Expressed Odorant Receptor Orthologs Detect the Aggregation Pheromone Lineatin in Trypodendron Ambrosia Beetles	30
Characterizing feral swine movement across the contiguous United States using neural networks and genetic data	30
Slow crabs ‐ fast genomes: Locomotory capacity predicts skew magnitude in crustacean mitogenomes	30
Cophylogeny and specificity between cryptic coral species (Pocillopora spp.) at Mo′orea and their symbionts (Symbiodiniaceae)	30
Telomere dysfunction is associated with dark‐induced bleaching in the reef coral Stylophora pistillata	30
Demographic changes in Pleistocene sea turtles were driven by past sea level fluctuations affecting feeding habitat availability	30
Recurrent Hybridisations During Diversification of One Rhododendron Species Complex	30
Phylogeography of the blacklegged tick (Ixodes scapularis) throughout the USA identifies candidate loci for differences in vectorial capacity	30
When do autopolyploids need poly‐sequencing data?	29
Genomic variation across Chinook salmon populations reveals effects of a duplication on migration alleles and supports fine scale structure	29
The first steps toward a global pandemic: Reconstructing the demographic history of parasite host switches in its native range	29
Reticulate and Hybrid Speciation is Promoted by Environmental Instability in an Indo‐Pacific Species Complex of Whistlers (Aves: Pachycephala)	29

Microbiomes associated with avian malaria survival differ between susceptible Hawaiian honeycreepers and sympatric malaria‐resistant introduced birds	29
An Early‐Life Disruption of Gut Microbiota Has Opposing Effects on Parasite Resistance in Two Host Species	28
Variation in phenotypic plasticity across age‐at‐maturity genotypes in wild Atlantic salmon	28
Heterogeneous patterns of heterozygosity loss in isolated populations of the threatened eastern barred bandicoot (Perameles gunnii)	28
Integrative biological analyses of responses to food deprivation reveal resilience mechanisms in sea urchin larvae	28
Genetic responses in sexual diploid and unisexual triploid goldfish (Carassius auratus) introduced into a high‐altitude environment	28
Convergent Evolutionary Dead‐End and Breakdown of Hard Chorion in Parental‐Egg‐Care Fish Reproductive Strategies	27
Nestling sex and behaviour determine the host preference of insect vectors in avian nests	27
Environmental heterogeneity structures root‐associated fungal communities in Daphne arbuscula (Thymelaeaceae), a shrub adapted to extreme rocky habitats	27
Infection by the Lungworm Rhabdias pseudosphaerocephala Affects the Expression of Immune‐Related microRNAs by Its Co‐Evolved Host, the Cane Toad Rhinella marina	27
Historical Lead Contamination Linked to Atmospheric Deposition is Associated With Declines in Ectomycorrhizal Diversity and Shifts in Fungal Community Composition	26
Tracking population structure and phenology through time using ancient genomes from waterlogged white oak wood	26
Regulation of host gene expression by gastrointestinal tract microbiota in Chinook Salmon (Oncorhynchus tshawytscha)	26
Recent genetic exchanges and admixture shape the genome and population structure of the zoonotic pathogen Cryptosporidium parvum	26
Ultraconserved Elements Reveal the Relationship Between Facultative Keratinophagy and Synanthropic Evolution in Clothes Moths	26
Limited introgression from non‐native commercial strains and signatures of adaptation in the key pollinator Bombus terrestris	25
Issue Information	25
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Evolutionary ecology of denitrifying methanotrophic NC10 bacteria in the deep‐sea biosphere	25
Genetic mixing in conservation translocations increases diversity of a keystone threatened species, Bettongia lesueur	25
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Genome‐wide variant analyses reveal new patterns of admixture and population structure in Australian dingoes	25
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Wild sunflower goes viral: Citizen science and comparative genomics allow tracking the origin and establishment of invasive sunflower in the Levant	24
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Parentage influence on gene expression under acidification revealed through single‐embryo sequencing	24
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Molecular mechanisms underlying plasticity in a thermally varying environment	24
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Investigating the genetic basis of vertebrate dispersal combining RNA‐seq, RAD‐seq and quantitative genetics	24
Issue Information	24
The challenge of demonstrating contemporary natural selection on polygenic quantitative traits in the wild	24
Lineage and role in integrative taxonomy of a heterotrophic orchid complex	24
Parental breeding decisions and genetic quality predict social structure of independent offspring	24
Geographical distance, host evolutionary history and diet drive gut microbiome diversity of fish across the Yellow River	24
Long‐term biogeographical processes dominate patterns of genetic diversity in a wingless grasshopper despite substantial recent habitat fragmentation	23
Sex chromosome heteromorphism and the Fast‐X effect in poeciliids	23
Issue Information	23
Sexy fingers: Pheromones in the glands of male dendrobatid frogs	23
Phenotypic cross‐species conservation and cross‐generation directionality switching in epigenetic inheritance	23
Plasticity for the win: Flexible transcriptional response to host plant switches in the comma butterfly (Polygonia c‐album)	23
Host preference explains the high endemism of ectomycorrhizal fungi in a dipterocarp rainforest	23
Evolutionary variation in gene conversion at the avian MHC is explained by fluctuating selection, gene copy numbers and life history	23
Defence by duplication: The relation between phenotypic glyphosate resistance and EPSPS gene copy number variation in Amaranthus palmeri	23
Evolved and Plastic Gene Expression in Adaptation of a Specialist Fly to a Novel Niche	23
Phylogenomics and phylogeographic model testing using convolutional neural networks reveal a history of recent admixture in the Canarian Kleinia neriifolia	23
Seasonal dynamics of the wild rodent faecal virome	22
Cryptic hybridization between the ancient lineages of Natterer's bat (Myotis nattereri)	22
The Genetic Architecture of Local Adaptation and Reproductive Character Displacement in Scutiger boulengeri Complex (Anura: Megophryidae)	22
Comparative population genomics of manta rays has global implications for management	22
Combining GWAS and population genomic analyses to characterize coevolution in a legume‐rhizobia symbiosis	22
Inferring the ecological and evolutionary determinants of community genetic diversity	22
Approximate Bayesian Computation applied to time series of population genetic data disentangles rapid genetic changes and demographic variations in a pathogen population	22
Molecular ecology of microbiomes in the wild: Common pitfalls, methodological advances and future directions	22
DNA methylation markers of age(ing) in non‐model animals	22
Immune genotypes, immune responses, and survival in a wild bird population	22
Ephemeral Speciation in a New Guinean Honeyeater Complex (Aves: Melidectes)	22
Whole‐genome sequencing illuminates multifaceted targets of selection to humic substances in Eurasian perch	21
The genomic basis of reproductive and migratory behaviour in a polymorphic salmonid	21
Population genomic structure of a widespread, urban‐dwelling mammal: The eastern grey squirrel (Sciurus carolinensis)	21
Genetic analysis reveals the putative native range and widespread double‐clonal reproduction in the invasive longhorn crazy ant	21
Genomic health is dependent on long‐term population demographic history	21
Genetic adaptation despite high gene flow in a range‐expanding population	21
Omics to Study and Manage Aquatic Environments: A Snapshot From the AquaEcOmics Meeting (Evian‐les‐Bains, 2025)	21
Relic DNA obscures DNA‐based profiling of multiple microbial taxonomic groups in a river‐reservoir ecosystem	21
Seascape genomics of coastal bottlenose dolphins along strong gradients of temperature and salinity	21
Heat‐stress memory enhances the acclimation of a migratory insect pest to global warming	21
Shuffling between Cladocopium and Durusdinium extensively modifies the physiology of each symbiont without stressing the coral host	21
Do Snow‐Adapted Prey Facilitate Coexistence of the Sierra Nevada Red Fox With Sympatric Carnivores?	21
Brettanomyces bruxellensis: Overview of the genetic and phenotypic diversity of an anthropized yeast	20
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Longitudinal gut microbiome dynamics in relation to age and senescence in a wild animal population	20
Long live the host! Proteomic analysis reveals possible strategies for parasitic manipulation of its social host	20
Repeated Mitochondrial Capture With Limited Genomic Introgression in a Lizard Group	20
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Revisiting old truths: The evolution of male coloration in guppies as a function of predation	20
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Whole‐genome sequencing reveals fine‐scale environment‐associated divergence near the range limits of a temperate reef fish	20
Multiple genomic solutions for local adaptation in two closely related species (sheep and goats) facing the same climatic constraints	20
A Test of the Long‐Term Efficiency of Genetic Rescue With Drosophila melanogaster	20

Ectoparasite presence and brood size manipulation interact to accelerate telomere shortening in nestling jackdaws	20
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The faecal metabolome of black howler monkeys (Alouatta pigra) varies in response to seasonal dietary changes	20
Correction to “The Opposed Forces of Differentiation and Admixture Across Glacial Cycles in the Butterfly Aglais urticae”	20
Issue Information	20
Selection for Tameness in Red Junglefowl Recapitulates Genetic Loci Associated With Domestication‐Related Brain Composition	19
It is time for ancient DNA to sweat the small stuff	19
Parental effects in a filamentous fungus: Phenotype, fitness and mechanism	19
The structure of tropical bat–plant interaction networks during an extreme El Niño‐Southern Oscillation event	19
Divergence of alternative sugar preferences through modulation of the expression and activity of the Gal3 sensor in yeast	19
Whole genome population structure of North Atlantic kelp confirms high‐latitude glacial refugia	19
Defence‐relevant gene expression differences in hatchlings among wild Newfoundland and farmed European and North American Atlantic salmon and their hybrids	19
Metabarcoding for biodiversity inventory blind spots: A test case using the beetle fauna of an insular cloud forest	19
Fitness consequences of population bottlenecks in an invasive blowfly	19
Population genomics and sexual signals support reproductive character displacement in Uperoleia (Anura: Myobatrachidae) in a contact zone	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
Speciation patterns of related species under the hybrid zone: A case study of three sclerophyllous oaks in the east Himalaya–Hengduan Mountains	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
Expression of Elongase‐ and Desaturase‐Encoding Genes Shapes the Cuticular Hydrocarbon Profiles of Honey Bees	19
Complex adaptive architecture underlies adaptation to quantitative host resistance in a fungal plant pathogen	19
Synthesizing environmental, epidemiological and vector and parasite genetic data to assist decision making for disease elimination	19
Rhizobium nodule diversity and composition are influenced by clover host selection and local growth conditions	19
Phylogeography of horseshoe bat sarbecoviruses in Vietnam and neighbouring countries. Implications for the origins of SARS‐CoV and SARS‐CoV‐2	19
Social Complexity During Early Development has Long‐Term Effects on Neuroplasticity in the Social Decision‐Making Network	19
Genomic architecture underlying morphological and physiological adaptation to high elevation in a songbird	19
Genomics reveal population structure, evolutionary history, and signatures of selection in the northern bottlenose whale, Hyperoodon ampullatus	19
Genetic legacies of mega‐landslides: Cycles of isolation and contact across flank collapses in an oceanic island	19
Pleistocene parades of carnivores into North America	19
High promiscuity among females of the invasive pest species Drosophila suzukii	19
Genomic and phenotypic changes associated with alterations of migratory behaviour in a songbird	19
Complex dynamics of coral gene expression responses to low pH across species	19
Different trematode parasites in the same snail host: Species‐specific or shared microbiota?	19
Repeatome evolution across space and time: Unravelling repeats dynamics in the plant genus Erythrostemon Klotzsch (Leguminosae Juss)	19
Genomic, Phenotypic and Environmental Correlates of Speciation in the Midwife Toads (Alytes)	18
Brain and antennal transcriptomes of host ants reveal potential links between behaviour and the functioning of socially parasitic colonies	18
Different molecular changes underlie the same phenotypic transition: Origins and consequences of independent shifts to homostyly within species	18
Issue Information	18
Pathogen invasion increases the abundance of predatory protists and their prey associations in the plant microbiome	18
Biodiversity Genomics Research Practices Require Harmonising to Meet Stakeholder Needs in Conservation	18
Global flyway evolution in red knots Calidris canutus and genetic evidence for a Nearctic refugium	18
Domestication and evolutionary histories of specialized gut symbionts across cephalotine ants	18
Age‐ and caste‐independent piRNAs in the germline and miRNA profiles linked to caste and fecundity in the ant Temnothorax rugatulus	18
Gene expression differentiation in the reproductive tissues of Drosophila willistoni subspecies and their hybrids	18
Strategies to identify and dissect trade‐offs in plants	18
Escalation by duplication: Milkweed bug trumps Monarch butterfly	18
Population Genetics and Invasion History of the European Starling Across Aotearoa New Zealand	18
Issue Information	18
Demography‐driven and adaptive introgression in a hybrid zone of the Armeria syngameon	18
Genomic‐based epidemiology reveals independent origins and gene flow of glyphosate resistance in Bassia scoparia populations across North America	18
Environmental DNA unveils deep phylogeographic structure of a freshwater fish	18
No Evidence That Life History Strategies Shape Within‐Body Mosaics of Ageing	18
Diet in phenotypically divergent sympatric species of African weakly electric fish (genus: Campylomormyrus)—A hybrid capture/HTS metabarcoding approach	18
Issue Information	18
Frequent Hybridisation Between Parapatric Lekking Bird‐of‐Paradise Species	18
Social and paternal female choice for male MHC genes in golden snub‐nosed monkeys (Rhinopithecus roxellana)	18
Do chromosome rearrangements fix by genetic drift or natural selection? Insights from Brenthis butterflies	18
Fire shapes fungal guild diversity and composition through direct and indirect pathways	18
Expression patterns of melanin‐related genes are linked to crypsis and conspicuousness in a pumpkin toadlet	17
Understanding Dynamic Molecular Responses Is Key to Designing Environmental Stress Experiments: A Review of Gene and Protein Expression in Cnidaria Under Stress	17
Preserving Wild Pears: Using Genomic Data to Assess Species Boundaries, Interspecific Hybridization, and Genetic Diversity to Inform Conservation	17
Robust Sensory Traits Across Light Habitats: Visual Signals but Not Receptors Vary in Centrarchids Inhabiting Distinct Photic Environments	17
Differential temperature effects on photoperiodism in female voles: A possible explanation for declines in vole populations	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
Distinct patterns of inheritance shape life‐history traits in steelhead trout	17
Understanding stochastic and deterministic assembly processes in microbial communities along temporal, spatial and environmental scales	17
Tissue‐specific transcriptional patterns underlie seasonal phenotypes in honey bees (Apis mellifera)	17
Genomic associations with poxvirus across divergent island populations in Berthelot's pipit	17
Genome assembly, structural variants, and genetic differentiation between lake whitefish young species pairs (Coregonus sp.) with long and short reads	17
Hybrid‐derived weedy rice maintains adaptive combinations of alleles associated with seed dormancy	17
Divergent island hybrids mixed waves of ancient gene flow	17
Linking large‐scale genetic structure of three Argynnini butterfly species to geography and environment	17
Expression–environment associations in transcriptomic heat stress responses for a global plant lineage	17
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Living with chronic infection: Persistent immunomodulation during avirulent haemoparasitic infection in a wild rodent	17
Impact of disturbance and dietary shift on gastrointestinal bacterial community and its invertebrate host system	17
Domestication obscures genomic estimates of population history	17
Transcriptional response of the calcification and stress response toolkits in an octocoral under heat and pH stress	17
High Quality Diet Enhances Immune Response and Affects Gene Expression During Viral Infection in an Insect Herbivore	17
Plant invasion reconstructs soil microbial assembly and functionality in coastal salt marshes	17
Issue Information	17
Fifty Years of Conservation Genetics: A Personal Perspective	17
Amazonian colonization from the Atlantic Forest: New perspectives on the connections of South American tropical forests	17
Immune gene regulation is associated with age and environmental adversity in a nonhuman primate	17
Limited dispersal and local adaptation promote allopatric speciation in a biodiversity hotspot	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
Variable hybridization between two Lake Tanganyikan cichlid species in recent secondary contact	17
Strong Bottlenecks Constrain Adaptive Coevolution in a Host–Parasite Metapopulation	17
Habitat‐linked genetic variation supports microgeographic adaptive divergence in an island‐endemic bird species	17
‘Re‐Wilding’ an Animal Model With Microbiota Shifts Immunity and Stress Gene Expression During Infection	16
Evolution of Hybrid Inviability Associated With Chromosome Fusions	16
Introgressive hybridization in the west Pacific pen shells (genus Atrina): Restricted interspecies gene flow within the genome	16
Genetic differentiation across a steep and narrow environmental gradient: Quantitative genetic and genomic insights into Lake Superior populations of Quercus rubra	16
Geographical isolation versus dispersal: Relictual alpine grasshoppers support a model of interglacial diversification with limited hybridization	16