Molecular Ecology

Article	Citations
Issue Information	237
The transcriptional state and chromatin landscape of cichlid jaw shape variation across species and environments	201
Genetic Adaptation to Brackish Water and Spawning Season in European Cisco	145
The effect of divergent and parallel selection on the genomic landscape of divergence	98
Evolutionary roles of polyploidization‐derived structural variations in the phenotypic diversification of Panax species	73
The impacts of positive selection on genomic variation in Drosophila serrata: Insights from a deep learning approach	63
Positive selection in gamete interaction proteins in Carnivora	62
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	62
Combined Evidence Reveals the Origin of a Rapid Range Expansion Despite Retained Genetic Diversity and a Weak Founder Effect	60
Grassland ecosystem type drives AM fungal diversity and functional guild distribution in North American grasslands	59
Interspecies genome divergence is predominantly due to frequent small scale rearrangements in Eucalyptus	52
More complex than you think: Taxonomic and temporal patterns of plant–pollinator networks of caraway (Carum carvi L.)	52
Adaptive cellular evolution or cellular system drift in hares	50
Experimental evidence that root‐associated fungi improve plant growth at high altitude	48
Hybrid enrichment of adaptive variation revealed by genotype–environment associations in montane sedges	48
Demographic modelling helps track the rapid and recent divergence of a conifer species pair from Central Mexico	48
Extremes of snow and temperature affect patterns of genetic diversity and differentiation in the alpine butterfly Parnassius smintheus	47
Bacterial communities in a subarctic stream network: Spatial and seasonal patterns of benthic biofilm and bacterioplankton	45
Ecology Not Genetic Covariance Explains Correlated Trait Divergence During Speciation	45
Traits and tradeoffs among non‐native ectomycorrhizal fungal symbionts affect pine seedling establishment in a Hawaiian coinvasion landscape	44
Museomics Sheds Light on Evolutionary Diversity in a Critically Endangered Cockatoo Species From Wallacea	43
Effect of urbanization and parasitism on the gut microbiota of Darwin's finch nestlings	42
On the origin and structure of haplotype blocks	42
Clones on the run: The genomics of a recently expanded partially clonal species	42
A genomic assessment of the marine‐speciation paradox within the toothed whale superfamily Delphinoidea	41

DNA Methylation Dynamics Reflect Sex and Status Differences in Mortality Rates in a Polygynous Bat	41
Organellar DNA continues to provide a rich source of information in the genomics era	41
Genomic divergence and introgression between cryptic species of a widespread North American songbird	41
Long‐read sequencing in ecology and evolution: Understanding how complex genetic and epigenetic variants shape biodiversity	40
Genomic, morphological and physiological data support fast ecotypic differentiation and incipient speciation in an alpine diving beetle	40
Acclimatory gene expression of primed clams enhances robustness to elevated pCO2	39
Evolutionary History and Rhizosphere Microbial Community Composition in Domesticated Hops ( Humulus lupulus L .	39
Out of the Qinghai‐Tibet plateau: Genomic biogeography of the alpine monospecific genus Megadenia (Biscutelleae, Brassicaceae)	39
Community‐wide correlations between species richness, abundance and population genomic diversity in a freshwater biodiversity hotspot	38
Association between parasite microbiomes and caste development and colony structure in a social trematode	38
Understanding the role of temperature in seasonal timing: Effects on behavioural, physiological and molecular phenotypes	37
Diving into the diversity of colour patterns in reef fishes	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
Decoding plant‐induced transcriptomic variability and consistency in two related polyphagous mites differing in host ranges	37
Brazilian marine phylogeography: A literature synthesis and analysis of barriers	37
Genetic and telomeric variability: Insights from a tropical avian hybrid zone	36
Issue Information	36
Genomic analysis of a parasite invasion: Colonization of the Americas by the blood fluke Schistosoma mansoni	36
Convergent Evolutionary Dead‐End and Breakdown of Hard Chorion in Parental‐Egg‐Care Fish Reproductive Strategies	35
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Environmental heterogeneity structures root‐associated fungal communities in Daphne arbuscula (Thymelaeaceae), a shrub adapted to extreme rocky habitats	34
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Infection by the Lungworm Rhabdias pseudosphaerocephala Affects the Expression of Immune‐Related microRNAs by Its Co‐Evolved Host, the Cane Toad Rhinella marina	34
Ultraconserved Elements Reveal the Relationship Between Facultative Keratinophagy and Synanthropic Evolution in Clothes Moths	34
Primrose homostyles: A classic case of possible balancing selection revisited	34
Issue Information	33
Tracking population structure and phenology through time using ancient genomes from waterlogged white oak wood	33
An Early‐Life Disruption of Gut Microbiota Has Opposing Effects on Parasite Resistance in Two Host Species	32
Genomic variation across Chinook salmon populations reveals effects of a duplication on migration alleles and supports fine scale structure	32
Evolutionary ecology of denitrifying methanotrophic NC10 bacteria in the deep‐sea biosphere	32
Reticulate and Hybrid Speciation is Promoted by Environmental Instability in an Indo‐Pacific Species Complex of Whistlers (Aves: Pachycephala )	32
Phylogeography of the blacklegged tick (Ixodes scapularis) throughout the USA identifies candidate loci for differences in vectorial capacity	32
Historical Lead Contamination Linked to Atmospheric Deposition is Associated With Declines in Ectomycorrhizal Diversity and Shifts in Fungal Community Composition	32
The effect of a temperature‐sensitive prophage on the evolution of virulence in an opportunistic bacterial pathogen	31
Heterogeneous patterns of heterozygosity loss in isolated populations of the threatened eastern barred bandicoot (Perameles gunnii)	31
Large effective population size masks population genetic structure in Hirondellea amphipods within the deepest marine ecosystem, the Mariana Trench	30
Cophylogeny and specificity between cryptic coral species ( Pocillopora spp.) at Mo′orea and their symbionts (Symbiodiniaceae)	30
Phylogenetic diversity only weakly mitigates climate‐change‐driven biodiversity loss in insect communities	30
Genome‐wide variant analyses reveal new patterns of admixture and population structure in Australian dingoes	29
Genome‐wide phylogeography reveals cryptic speciation in the circumglobal planktonic calcifier Limacina bulimoides	29
Genetic mixing in conservation translocations increases diversity of a keystone threatened species, Bettongia lesueur	29
Integrative biological analyses of responses to food deprivation reveal resilience mechanisms in sea urchin larvae	28
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Recent genetic exchanges and admixture shape the genome and population structure of the zoonotic pathogen Cryptosporidium parvum	28
Nestling sex and behaviour determine the host preference of insect vectors in avian nests	28
Variation in phenotypic plasticity across age‐at‐maturity genotypes in wild Atlantic salmon	28
Tidal gradients, fine‐scale homing and a potential cryptic ecotype of wild spawning pink salmon (Oncorhynchus gorbuscha)	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	28
Satellite DNA evolution in Corvoidea inferred from short and long reads	27
Expansion and Temporal Expression Regulation of Cuticle‐Associated Gene Families: Molecular Basis of Adaptive Evolution of Moulting in Decapods	27

Regulation of host gene expression by gastrointestinal tract microbiota in Chinook Salmon (Oncorhynchus tshawytscha)	27
Combined genome and transcriptome provides insight into the genetic evolution of an edible halophyte Suaeda salsa adaptation to high salinity	27
Highly Expressed Odorant Receptor Orthologs Detect the Aggregation Pheromone Lineatin in Trypodendron Ambrosia Beetles	27
Recurrent Hybridisations During Diversification of One Rhododendron Species Complex	27
Issue Information	26
Characterizing feral swine movement across the contiguous United States using neural networks and genetic data	26
Microbiomes associated with avian malaria survival differ between susceptible Hawaiian honeycreepers and sympatric malaria‐resistant introduced birds	26
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Genetic responses in sexual diploid and unisexual triploid goldfish (Carassius auratus) introduced into a high‐altitude environment	26
Gene Expression Associated With Behaviour Manipulation in Wood Ants Infected With Larval Lancet Fluke, Dicrocoelium dendriticum	26
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Molecular mechanisms underlying plasticity in a thermally varying environment	26
Limited introgression from non‐native commercial strains and signatures of adaptation in the key pollinator Bombus terrestris	26
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Host preference explains the high endemism of ectomycorrhizal fungi in a dipterocarp rainforest	25
Issue Information	25
Do Snow‐Adapted Prey Facilitate Coexistence of the Sierra Nevada Red Fox With Sympatric Carnivores?	25
Issue Information	25
The Genetic Architecture of Local Adaptation and Reproductive Character Displacement in Scutiger boulengeri Complex (Anura: Megophryidae)	25
Investigating the genetic basis of vertebrate dispersal combining RNA‐seq, RAD‐seq and quantitative genetics	25
Lineage and role in integrative taxonomy of a heterotrophic orchid complex	24
Seascape genomics of coastal bottlenose dolphins along strong gradients of temperature and salinity	24
Wild sunflower goes viral: Citizen science and comparative genomics allow tracking the origin and establishment of invasive sunflower in the Levant	24
Whole‐genome sequencing illuminates multifaceted targets of selection to humic substances in Eurasian perch	24
Issue Information	24
Parentage influence on gene expression under acidification revealed through single‐embryo sequencing	24
Cryptic hybridization between the ancient lineages of Natterer's bat (Myotis nattereri)	24
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Geographical distance, host evolutionary history and diet drive gut microbiome diversity of fish across the Yellow River	24
Indirect Environmental Effects on the Gut‐Brain Axis in a Wild Mammal	24
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Combining GWAS and population genomic analyses to characterize coevolution in a legume‐rhizobia symbiosis	24
Evolved and Plastic Gene Expression in Adaptation of a Specialist Fly to a Novel Niche	24
Population genomic structure of a widespread, urban‐dwelling mammal: The eastern grey squirrel (Sciurus carolinensis)	24
Integrating Population Genomics and Historical Occurrence Data to Assess the Impact of Land‐Use Changes on Centris Oil Bees in the Brazilian Cerrado	24
Parental breeding decisions and genetic quality predict social structure of independent offspring	24
Ephemeral Speciation in a New Guinean Honeyeater Complex ( Aves : Melidectes )	23
Sexy fingers: Pheromones in the glands of male dendrobatid frogs	23
Ectoparasite presence and brood size manipulation interact to accelerate telomere shortening in nestling jackdaws	23
Sex chromosome heteromorphism and the Fast‐X effect in poeciliids	23
Genetic analysis reveals the putative native range and widespread double‐clonal reproduction in the invasive longhorn crazy ant	23
Approximate Bayesian Computation applied to time series of population genetic data disentangles rapid genetic changes and demographic variations in a pathogen population	23
Longitudinal gut microbiome dynamics in relation to age and senescence in a wild animal population	22
Genomic health is dependent on long‐term population demographic history	22
DNA methylation markers of age(ing) in non‐model animals	22
The challenge of demonstrating contemporary natural selection on polygenic quantitative traits in the wild	22
Phylogenomics and phylogeographic model testing using convolutional neural networks reveal a history of recent admixture in the Canarian Kleinia neriifolia	22
Molecular ecology of microbiomes in the wild: Common pitfalls, methodological advances and future directions	22
Phenotypic cross‐species conservation and cross‐generation directionality switching in epigenetic inheritance	22
Comparative population genomics of manta rays has global implications for management	22
Evolutionary variation in gene conversion at the avian MHC is explained by fluctuating selection, gene copy numbers and life history	22
Long‐term biogeographical processes dominate patterns of genetic diversity in a wingless grasshopper despite substantial recent habitat fragmentation	22
Omics to Study and Manage Aquatic Environments: A Snapshot From the AquaEcOmics Meeting (Evian‐les‐Bains, 2025)	21
Inferring the ecological and evolutionary determinants of community genetic diversity	21
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Immune genotypes, immune responses, and survival in a wild bird population	21
Relic DNA obscures DNA‐based profiling of multiple microbial taxonomic groups in a river‐reservoir ecosystem	21
Plasticity for the win: Flexible transcriptional response to host plant switches in the comma butterfly (Polygonia c‐album)	21
Revisiting old truths: The evolution of male coloration in guppies as a function of predation	21
Seasonal dynamics of the wild rodent faecal virome	21
Genetic adaptation despite high gene flow in a range‐expanding population	21
Brettanomyces bruxellensis: Overview of the genetic and phenotypic diversity of an anthropized yeast	21
Genetic and Environmental Similarities Drive Repeated Genomic Evolution in Island Lizards	21
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Heat‐stress memory enhances the acclimation of a migratory insect pest to global warming	21
The genomic basis of reproductive and migratory behaviour in a polymorphic salmonid	21
It is time for ancient DNA to sweat the small stuff	20
Repeated Mitochondrial Capture With Limited Genomic Introgression in a Lizard Group	20
Genomic architecture underlying morphological and physiological adaptation to high elevation in a songbird	20
Different trematode parasites in the same snail host: Species‐specific or shared microbiota?	20
Domestication and evolutionary histories of specialized gut symbionts across cephalotine ants	20
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Issue Information	20
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Genomics reveal population structure, evolutionary history, and signatures of selection in the northern bottlenose whale, Hyperoodon ampullatus	20
Synthesizing environmental, epidemiological and vector and parasite genetic data to assist decision making for disease elimination	20
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Brain and antennal transcriptomes of host ants reveal potential links between behaviour and the functioning of socially parasitic colonies	20
No Evidence That Life History Strategies Shape Within‐Body Mosaics of Ageing	20
Rhizobium nodule diversity and composition are influenced by clover host selection and local growth conditions	20

Correction to “The Opposed Forces of Differentiation and Admixture Across Glacial Cycles in the Butterfly Aglais urticae”	19
Repeatome evolution across space and time: Unravelling repeats dynamics in the plant genus Erythrostemon Klotzsch (Leguminosae Juss)	19
Repeatable Genomic Outcomes Along the Speciation Continuum: Insights From Pine Hybrid Zones (Genus Pinus )	19
Divergence of alternative sugar preferences through modulation of the expression and activity of the Gal3 sensor in yeast	19
High promiscuity among females of the invasive pest species Drosophila suzukii	19
Pleistocene parades of carnivores into North America	19
Whole‐genome sequencing reveals fine‐scale environment‐associated divergence near the range limits of a temperate reef fish	19
High‐Throughput Absolute Quantification Sequencing Advances Characterisation of Microbial Community Ecology	19
Expression of Elongase‐ and Desaturase‐Encoding Genes Shapes the Cuticular Hydrocarbon Profiles of Honey Bees	19
Complex dynamics of coral gene expression responses to low pH across species	19
Multiple genomic solutions for local adaptation in two closely related species (sheep and goats) facing the same climatic constraints	19
Parental effects in a filamentous fungus: Phenotype, fitness and mechanism	19
Defence‐relevant gene expression differences in hatchlings among wild Newfoundland and farmed European and North American Atlantic salmon and their hybrids	19
Speciation patterns of related species under the hybrid zone: A case study of three sclerophyllous oaks in the east Himalaya–Hengduan Mountains	19
Diet in phenotypically divergent sympatric species of African weakly electric fish (genus: Campylomormyrus)—A hybrid capture/HTS metabarcoding approach	19
Long live the host! Proteomic analysis reveals possible strategies for parasitic manipulation of its social host	19
Genomic, Phenotypic and Environmental Correlates of Speciation in the Midwife Toads ( Alytes )	19
A Test of the Long‐Term Efficiency of Genetic Rescue With Drosophila melanogaster	19
Fitness consequences of population bottlenecks in an invasive blowfly	19
The structure of tropical bat–plant interaction networks during an extreme El Niño‐Southern Oscillation event	19
Social Complexity During Early Development has Long‐Term Effects on Neuroplasticity in the Social Decision‐Making Network	19
The faecal metabolome of black howler monkeys (Alouatta pigra) varies in response to seasonal dietary changes	19
Genomic and phenotypic changes associated with alterations of migratory behaviour in a songbird	19
Turnip Mosaic Virus Infection in a Perennial Arabidopsis Reduces Aphid Fecundity in the Natural Environment	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	18
Robust Sensory Traits Across Light Habitats: Visual Signals but Not Receptors Vary in Centrarchids Inhabiting Distinct Photic Environments	18
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Whole genome population structure of North Atlantic kelp confirms high‐latitude glacial refugia	18
Population genomics and sexual signals support reproductive character displacement in Uperoleia (Anura: Myobatrachidae) in a contact zone	18
Genomic Introgressions May Affect Hybridogenetic Reproduction in Water Frog Hybrids	18
Strategies to identify and dissect trade‐offs in plants	18
Pigments, Chromatophore Structure, and Gene Expression Underlying Colour Polytypy of a Panamanian Poison Frog	18
Environmental DNA unveils deep phylogeographic structure of a freshwater fish	18
Frequent Hybridisation Between Parapatric Lekking Bird‐of‐Paradise Species	18
Issue Information	18
Metabarcoding for biodiversity inventory blind spots: A test case using the beetle fauna of an insular cloud forest	18
Genetic Mapping of Resistance: ddRADseq ‐Based QTL and Associated Polymorphism Conferring Resistan	18
Phylogeography of horseshoe bat sarbecoviruses in Vietnam and neighbouring countries. Implications for the origins of SARS‐CoV and SARS‐CoV‐2	18
Fire shapes fungal guild diversity and composition through direct and indirect pathways	18
Plant invasion reconstructs soil microbial assembly and functionality in coastal salt marshes	18
Age‐ and caste‐independent piRNAs in the germline and miRNA profiles linked to caste and fecundity in the ant Temnothorax rugatulus	18
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Genetic legacies of mega‐landslides: Cycles of isolation and contact across flank collapses in an oceanic island	18
Gene expression differentiation in the reproductive tissues of Drosophila willistoni subspecies and their hybrids	18
Selection for Tameness in Red Junglefowl Recapitulates Genetic Loci Associated With Domestication‐Related Brain Composition	18
Escalation by duplication: Milkweed bug trumps Monarch butterfly	17
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Global flyway evolution in red knots Calidris canutus and genetic evidence for a Nearctic refugium	17
Deciphering the Patterns and Drivers of Tardigrade Diversity Along Altitudinal Gradients	17
Do chromosome rearrangements fix by genetic drift or natural selection? Insights from Brenthis butterflies	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
Temporal dynamics of soil fungi in a pyrodiverse dry‐sclerophyll forest	17
Genomic associations with poxvirus across divergent island populations in Berthelot's pipit	17
Distinct patterns of inheritance shape life‐history traits in steelhead trout	17
Evaluating the persistence and utility of five wild Vitis species in the context of climate change	17
Preserving Wild Pears: Using Genomic Data to Assess Species Boundaries, Interspecific Hybridization, and Genetic Diversity to Inform Conservation	17
Spatiotemporal Dynamics of Blood Parasite Infections and Impacts on Avian Health and Reproduction	17
Demography‐driven and adaptive introgression in a hybrid zone of the Armeria syngameon	17
Variable hybridization between two Lake Tanganyikan cichlid species in recent secondary contact	17
Population Genetics and Invasion History of the European Starling Across Aotearoa New Zealand	17
Pathogen invasion increases the abundance of predatory protists and their prey associations in the plant microbiome	17
Impact of disturbance and dietary shift on gastrointestinal bacterial community and its invertebrate host system	17
Strong Bottlenecks Constrain Adaptive Coevolution in a Host–Parasite Metapopulation	17
Microbiota composition and diversity of multiple body sites vary according to reproductive performance in a seabird	17
Epigenomic Changes in Ostrinia Moths Under Elevated Pupal and Adult Temperature	17
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Mind the Gaps: Shortfalls in Studies of the Intraspecific Genetic Diversity of Plants Across the Gran Chaco	17
Genomic and Morphological Divergence Under Extreme Environments: Insights Into the Adaptation and Speciation of Lepus yarkandensis and	17
Living with chronic infection: Persistent immunomodulation during avirulent haemoparasitic infection in a wild rodent	17
Host genotype and microbiome associations in co‐occurring clonal and non‐clonal kelp, Ecklonia radiata	17
Transgressive gene expression and expression plasticity under thermal stress in a stable hybrid zone	17
Social and paternal female choice for male MHC genes in golden snub‐nosed monkeys (Rhinopithecus roxellana)	17
Differential temperature effects on photoperiodism in female voles: A possible explanation for declines in vole populations	17
Biodiversity Genomics Research Practices Require Harmonising to Meet Stakeholder Needs in Conservation	17
Immune gene regulation is associated with age and environmental adversity in a nonhuman primate	16
Amazonian colonization from the Atlantic Forest: New perspectives on the connections of South American tropical forests	16
Adaptive variation in homologue number within transcript families promotes expression divergence in reef‐building coral	16
Holocentric repeat landscapes: From micro‐evolutionary patterns to macro‐evolutionary associations with karyotype evolution	16
Genomic Vulnerability of a Sentinel Mammal Under Climate Change	16
Coping with antagonistic predation risks: Predator‐dependent unique responses are dominant in Ceriodaphnia cornuta	16
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Hybrid‐derived weedy rice maintains adaptive combinations of alleles associated with seed dormancy	16
Admixture Affects the Rate and Repeatability of Experimental Adaptation to a Stressful Environment in Callosobruchus maculatus	16
From Mud to Meat: Comparative Metabarcoding Reveals Two Different Evolutionary Paths to Carnivory in a Group of Meiofaunal Annelids	16
‘Re‐Wilding’ an Animal Model With Microbiota Shifts Immunity and Stress Gene Expression During Infection	16
Awaking the dormant virome in the rhizosphere	16
Distinct routes to parallel adaptation in a mountain plant	16
Species' attributes predict the relative magnitude of ecological and genetic recovery following mass mortality	16
Genetic Architecture of Immune Cell DNA Methylation in the Rhesus Macaque	16
Understanding stochastic and deterministic assembly processes in microbial communities along temporal, spatial and environmental scales	16
Genetic differentiation across a steep and narrow environmental gradient: Quantitative genetic and genomic insights into Lake Superior populations of Quercus rubra	16
A memorial to Professor Louis Bernatchez (1960–2023)	16
Land‐use type temporarily affects active pond community structure but not gene expression patterns	16
Large X‐effects are absent in torrent frogs with nascent sex chromosomes	16