Molecular Ecology

Article	Citations
Telomere dynamics in relation to experimentally increased locomotion costs and fitness in great tits	203
Long‐read sequencing in ecology and evolution: Understanding how complex genetic and epigenetic variants shape biodiversity	198
Organellar DNA continues to provide a rich source of information in the genomics era	177
Hybrid enrichment of adaptive variation revealed by genotype–environment associations in montane sedges	145
Positive selection in gamete interaction proteins in Carnivora	107
Out of the Qinghai‐Tibet plateau: Genomic biogeography of the alpine monospecific genus Megadenia (Biscutelleae, Brassicaceae)	96
Genomic analysis of a parasite invasion: Colonization of the Americas by the blood fluke Schistosoma mansoni	91
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Genomic divergence and introgression between cryptic species of a widespread North American songbird	73
The impacts of positive selection on genomic variation in Drosophila serrata: Insights from a deep learning approach	72
Diving into the diversity of colour patterns in reef fishes	66
Extremes of snow and temperature affect patterns of genetic diversity and differentiation in the alpine butterfly Parnassius smintheus	63
Genetic and telomeric variability: Insights from a tropical avian hybrid zone	63
Adaptive cellular evolution or cellular system drift in hares	62
Demographic modelling helps track the rapid and recent divergence of a conifer species pair from Central Mexico	61
Issue Information	60
Genomic data support multiple introductions and explosive demographic expansions in a highly invasive aquatic insect	59
Museomics Sheds Light on Evolutionary Diversity in a Critically Endangered Cockatoo Species From Wallacea	59
Genomic, morphological and physiological data support fast ecotypic differentiation and incipient speciation in an alpine diving beetle	57
Traits and tradeoffs among non‐native ectomycorrhizal fungal symbionts affect pine seedling establishment in a Hawaiian coinvasion landscape	56
Decoding plant‐induced transcriptomic variability and consistency in two related polyphagous mites differing in host ranges	55
Bacterial communities in a subarctic stream network: Spatial and seasonal patterns of benthic biofilm and bacterioplankton	53
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	52
Association between parasite microbiomes and caste development and colony structure in a social trematode	51
A genomic assessment of the marine‐speciation paradox within the toothed whale superfamily Delphinoidea	50

Acclimatory gene expression of primed clams enhances robustness to elevated pCO2	48
The transcriptional state and chromatin landscape of cichlid jaw shape variation across species and environments	46
Experimental evidence that root‐associated fungi improve plant growth at high altitude	45
More complex than you think: Taxonomic and temporal patterns of plant–pollinator networks of caraway (Carum carvi L.)	45
Whole‐genome resequencing confirms reproductive isolation between sympatric demes of brown trout (Salmo trutta) detected with allozymes	45
DNA Methylation Dynamics Reflect Sex and Status Differences in Mortality Rates in a Polygynous Bat	44
Interspecies genome divergence is predominantly due to frequent small scale rearrangements in Eucalyptus	43
The effect of divergent and parallel selection on the genomic landscape of divergence	40
Brazilian marine phylogeography: A literature synthesis and analysis of barriers	40
Host‐pathogen‐environment interactions predict survival outcomes of adult sockeye salmon (Oncorhynchus nerka) released from fisheries	39
Community‐wide correlations between species richness, abundance and population genomic diversity in a freshwater biodiversity hotspot	39
Evolutionary roles of polyploidization‐derived structural variations in the phenotypic diversification of Panax species	38
Effect of urbanization and parasitism on the gut microbiota of Darwin's finch nestlings	38
Diversification along a benthic to pelagic gradient contributes to fish diversity in the world's largest lake (Lake Baikal, Russia)	38
Analysing indoor mycobiomes through a large‐scale citizen science study in Norway	38
Evolutionary History and Rhizosphere Microbial Community Composition in Domesticated Hops (Humulus lupulus L.)	38
Genome‐wide SNP assessment of contemporary European red deer genetic structure highlights the distinction of peripheral populations and the main admixture zones in Europe	38
Understanding the role of temperature in seasonal timing: Effects on behavioural, physiological and molecular phenotypes	38
On the origin and structure of haplotype blocks	37
Grassland ecosystem type drives AM fungal diversity and functional guild distribution in North American grasslands	37
Hypoxia as a physiological cue and pathological stress for coral larvae	36
Clones on the run: The genomics of a recently expanded partially clonal species	36
Telomere dysfunction is associated with dark‐induced bleaching in the reef coral Stylophora pistillata	35
Intraspecific genetic variation matters when predicting seagrass distribution under climate change	35
Infection by the Lungworm Rhabdias pseudosphaerocephala Affects the Expression of Immune‐Related microRNAs by Its Co‐Evolved Host, the Cane Toad Rhinella marina	34
Issue Information	34
Environmental heterogeneity structures root‐associated fungal communities in Daphne arbuscula (Thymelaeaceae), a shrub adapted to extreme rocky habitats	33
Is speciation an unrelenting march to reproductive isolation?	33
Evolutionary ecology of denitrifying methanotrophic NC10 bacteria in the deep‐sea biosphere	32
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Issue Information	32
Regulation of host gene expression by gastrointestinal tract microbiota in Chinook Salmon (Oncorhynchus tshawytscha)	31
Arbuscular mycorrhizal fungi and plant diversity drive restoration of nitrogen‐cycling microbial communities	31
Genotype–Environment mismatch of kelp forests under climate change	31
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	31
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Larger, more connected societies of ants have a higher prevalence of viruses	30
Slow crabs ‐ fast genomes: Locomotory capacity predicts skew magnitude in crustacean mitogenomes	30
Combined genome and transcriptome provides insight into the genetic evolution of an edible halophyte Suaeda salsa adaptation to high salinity	30
Historical Lead Contamination Linked to Atmospheric Deposition is Associated With Declines in Ectomycorrhizal Diversity and Shifts in Fungal Community Composition	30
Tidal gradients, fine‐scale homing and a potential cryptic ecotype of wild spawning pink salmon (Oncorhynchus gorbuscha)	30
Genetic mixing in conservation translocations increases diversity of a keystone threatened species,Bettongia lesueur	30
Phylogeography of the blacklegged tick (Ixodes scapularis) throughout the USA identifies candidate loci for differences in vectorial capacity	30
The effect of a temperature‐sensitive prophage on the evolution of virulence in an opportunistic bacterial pathogen	30
Tracking population structure and phenology through time using ancient genomes from waterlogged white oak wood	30
Limited introgression from non‐native commercial strains and signatures of adaptation in the key pollinator Bombus terrestris	30
Demographic changes in Pleistocene sea turtles were driven by past sea level fluctuations affecting feeding habitat availability	30
Variation in phenotypic plasticity across age‐at‐maturity genotypes in wild Atlantic salmon	30
Genome‐wide phylogeography reveals cryptic speciation in the circumglobal planktonic calcifier Limacina bulimoides	30
Environmental conditions drive zooplankton community structure in the epipelagic oceanic water of the southern Gulf of Mexico: A molecular approach	30

Semi‐quantitative metabarcoding reveals how climate shapes arthropod community assembly along elevation gradients on Hawaii Island	29
An Early‐Life Disruption of Gut Microbiota Has Opposing Effects on Parasite Resistance in Two Host Species	29
Habitat restoration weakens negative environmental effects on telomere dynamics	29
Characterizing feral swine movement across the contiguous United States using neural networks and genetic data	29
Nestling sex and behaviour determine the host preference of insect vectors in avian nests	29
The first steps toward a global pandemic: Reconstructing the demographic history of parasite host switches in its native range	29
Erratum	29
Genomic variation across Chinook salmon populations reveals effects of a duplication on migration alleles and supports fine scale structure	29
Recent genetic exchanges and admixture shape the genome and population structure of the zoonotic pathogen Cryptosporidium parvum	28
When do autopolyploids need poly‐sequencing data?	28
Microbiomes associated with avian malaria survival differ between susceptible Hawaiian honeycreepers and sympatric malaria‐resistant introduced birds	28
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Phylogenetic diversity only weakly mitigates climate‐change‐driven biodiversity loss in insect communities	28
Cophylogeny and specificity between cryptic coral species (Pocillopora spp.) at Mo′orea and their symbionts (Symbiodiniaceae)	28
Genetic responses in sexual diploid and unisexual triploid goldfish (Carassius auratus) introduced into a high‐altitude environment	28
Primrose homostyles: A classic case of possible balancing selection revisited	28
Integrative biological analyses of responses to food deprivation reveal resilience mechanisms in sea urchin larvae	28
Social dominance and rainfall predict telomere dynamics in a cooperative arid‐zone bird	28
Satellite DNA evolution in Corvoidea inferred from short and long reads	28
Heterogeneous patterns of heterozygosity loss in isolated populations of the threatened eastern barred bandicoot (Perameles gunnii)	28
Early‐life seasonal, weather and social effects on telomere length in a wild mammal	28
Large effective population size masks population genetic structure in Hirondellea amphipods within the deepest marine ecosystem, the Mariana Trench	27
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Plasticity for the win: Flexible transcriptional response to host plant switches in the comma butterfly (Polygonia c‐album)	27
Preconditioning improves bleaching tolerance in the reef‐building coral Pocillopora acuta through modulations in the programmed cell death pathways	27
Phenotypic cross‐species conservation and cross‐generation directionality switching in epigenetic inheritance	27
Issue Information	27
Comparative population genomics of manta rays has global implications for management	27
Molecular ecology of microbiomes in the wild: Common pitfalls, methodological advances and future directions	27
Genome‐wide variant analyses reveal new patterns of admixture and population structure in Australian dingoes	27
Lineage and role in integrative taxonomy of a heterotrophic orchid complex	27
Parental breeding decisions and genetic quality predict social structure of independent offspring	27
Ephemeral Speciation in a New Guinean Honeyeater Complex (Aves: Melidectes)	27
Issue Information	27
Phylogeographic analysis of shrubby beardtongues reveals range expansions during the Last Glacial Maximum and implicates the Klamath Mountains as a hotspot for hybridization	26
Shuffling between Cladocopium and Durusdinium extensively modifies the physiology of each symbiont without stressing the coral host	26
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Genomic health is dependent on long‐term population demographic history	26
Whole‐genome sequencing illuminates multifaceted targets of selection to humic substances in Eurasian perch	26
Genetic analysis reveals the putative native range and widespread double‐clonal reproduction in the invasive longhorn crazy ant	26
Brettanomyces bruxellensis: Overview of the genetic and phenotypic diversity of an anthropized yeast	26
Relic DNA obscures DNA‐based profiling of multiple microbial taxonomic groups in a river‐reservoir ecosystem	26
Metagenomic analysis reveals Culex mosquito virome diversity and Japanese encephalitis genotype V in the Republic of Korea	26
The genomic basis of reproductive and migratory behaviour in a polymorphic salmonid	25
Molecular mechanisms underlying plasticity in a thermally varying environment	25
Wild sunflower goes viral: Citizen science and comparative genomics allow tracking the origin and establishment of invasive sunflower in the Levant	25
Combining GWAS and population genomic analyses to characterize coevolution in a legume‐rhizobia symbiosis	25
DNA methylation markers of age(ing) in non‐model animals	25
Sex chromosome heteromorphism and the Fast‐X effect in poeciliids	24
Approximate Bayesian Computation applied to time series of population genetic data disentangles rapid genetic changes and demographic variations in a pathogen population	24
Long‐term biogeographical processes dominate patterns of genetic diversity in a wingless grasshopper despite substantial recent habitat fragmentation	24
The challenge of demonstrating contemporary natural selection on polygenic quantitative traits in the wild	24
Genetic adaptation despite high gene flow in a range‐expanding population	24
Defence by duplication: The relation between phenotypic glyphosate resistance and EPSPS gene copy number variation in Amaranthus palmeri	23
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Longitudinal gut microbiome dynamics in relation to age and senescence in a wild animal population	23
Host preference explains the high endemism of ectomycorrhizal fungi in a dipterocarp rainforest	23
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Cryptic hybridization between the ancient lineages of Natterer's bat (Myotis nattereri)	23
Sexy fingers: Pheromones in the glands of male dendrobatid frogs	23
Parentage influence on gene expression under acidification revealed through single‐embryo sequencing	23
Population genomic structure of a widespread, urban‐dwelling mammal: The eastern grey squirrel (Sciurus carolinensis)	23
Male meiotic recombination rate varies with seasonal temperature fluctuations in wild populations of autotetraploid Arabidopsis arenosa	23
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Ectoparasite presence and brood size manipulation interact to accelerate telomere shortening in nestling jackdaws	22
Heat‐stress memory enhances the acclimation of a migratory insect pest to global warming	22
Seascape genomics of coastal bottlenose dolphins along strong gradients of temperature and salinity	22
Evolved and Plastic Gene Expression in Adaptation of a Specialist Fly to a Novel Niche	22
Phylogenomics and phylogeographic model testing using convolutional neural networks reveal a history of recent admixture in the Canarian Kleinia neriifolia	22
Inferring the ecological and evolutionary determinants of community genetic diversity	22
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Investigating the genetic basis of vertebrate dispersal combining RNA‐seq, RAD‐seq and quantitative genetics	22
The faecal metabolome of black howler monkeys (Alouatta pigra) varies in response to seasonal dietary changes	21
Geographical distance, host evolutionary history and diet drive gut microbiome diversity of fish across the Yellow River	21
The Genetic Architecture of Local Adaptation and Reproductive Character Displacement in Scutiger boulengeri Complex (Anura: Megophryidae)	21
Evolutionary variation in gene conversion at the avian MHC is explained by fluctuating selection, gene copy numbers and life history	21
Parental effects in a filamentous fungus: Phenotype, fitness and mechanism	21
Immune genotypes, immune responses, and survival in a wild bird population	21

The challenge and promise of estimating the de novo mutation rate from whole‐genome comparisons among closely related individuals	21
Complex adaptive architecture underlies adaptation to quantitative host resistance in a fungal plant pathogen	21
Seasonal dynamics of the wild rodent faecal virome	21
The Pleistocene species pump past its prime: Evidence from European butterfly sister species	21
Revisiting old truths: The evolution of male coloration in guppies as a function of predation	20
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Synthesizing environmental, epidemiological and vector and parasite genetic data to assist decision making for disease elimination	20
Tackling the challenges of evolutionary forest research with multidata approaches	20
Genomic investigation of colour polymorphism and phylogeographic variation among populations of black‐headed bulbul (Brachypodius atriceps) in insular southeast Asia	20
High promiscuity among females of the invasive pest species Drosophila suzukii	20
Pleistocene parades of carnivores into North America	20
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
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Speciation patterns of related species under the hybrid zone: A case study of three sclerophyllous oaks in the east Himalaya–Hengduan Mountains	19
Issue Information	19
A Test of the Long‐Term Efficiency of Genetic Rescue With Drosophila melanogaster	19
Genomic architecture underlying morphological and physiological adaptation to high elevation in a songbird	19
Whole‐genome sequencing reveals fine‐scale environment‐associated divergence near the range limits of a temperate reef fish	19
Diet in phenotypically divergent sympatric species of African weakly electric fish (genus: Campylomormyrus)—A hybrid capture/HTS metabarcoding approach	19
Responses of pea plants to multiple antagonists are mediated by order of attack and phytohormone crosstalk	19
Divergence of alternative sugar preferences through modulation of the expression and activity of the Gal3 sensor in yeast	19
It is time for ancient DNA to sweat the small stuff	19
Expression of Elongase‐ and Desaturase‐Encoding Genes Shapes the Cuticular Hydrocarbon Profiles of Honey Bees	19
Multiple genomic solutions for local adaptation in two closely related species (sheep and goats) facing the same climatic constraints	19
Genomic, Phenotypic and Environmental Correlates of Speciation in the Midwife Toads (Alytes)	19
Fire shapes fungal guild diversity and composition through direct and indirect pathways	19
Genetic legacies of mega‐landslides: Cycles of isolation and contact across flank collapses in an oceanic island	19
Effect of social structure and introduction history on genetic diversity and differentiation	19
Defence‐relevant gene expression differences in hatchlings among wild Newfoundland and farmed European and North American Atlantic salmon and their hybrids	19
Long live the host! Proteomic analysis reveals possible strategies for parasitic manipulation of its social host	19
Genomics reveal population structure, evolutionary history, and signatures of selection in the northern bottlenose whale, Hyperoodon ampullatus	19
Domestication and evolutionary histories of specialized gut symbionts across cephalotine ants	19
Quality of phytoplankton deposition structures bacterial communities at the water‐sediment interface	19
Correction to “The Opposed Forces of Differentiation and Admixture Across Glacial Cycles in the Butterfly Aglais urticae”	19
Gene expression differentiation in the reproductive tissues of Drosophila willistoni subspecies and their hybrids	19
Different molecular changes underlie the same phenotypic transition: Origins and consequences of independent shifts to homostyly within species	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
Age‐ and caste‐independent piRNAs in the germline and miRNA profiles linked to caste and fecundity in the ant Temnothorax rugatulus	18
Adaptive divergence in bill morphology and other thermoregulatory traits is facilitated by restricted gene flow in song sparrows on the California Channel Islands	18
Population genomics and sexual signals support reproductive character displacement in Uperoleia (Anura: Myobatrachidae) in a contact zone	18
Complex dynamics of coral gene expression responses to low pH across species	18
Rhizobium nodule diversity and composition are influenced by clover host selection and local growth conditions	18
Expression patterns of melanin‐related genes are linked to crypsis and conspicuousness in a pumpkin toadlet	18
Genome‐wide molecular phylogenetic analyses and mating experiments which reveal the evolutionary history and an intermediate stage of speciation of a giant water bug	18
Capabilities and limitations of using DNA metabarcoding to study plant–pollinator interactions	18
Genomic and phenotypic changes associated with alterations of migratory behaviour in a songbird	18
Brain and antennal transcriptomes of host ants reveal potential links between behaviour and the functioning of socially parasitic colonies	18
Repeated Mitochondrial Capture With Limited Genomic Introgression in a Lizard Group	18
Strategies to identify and dissect trade‐offs in plants	18
Phylogeography of horseshoe bat sarbecoviruses in Vietnam and neighbouring countries. Implications for the origins of SARS‐CoV and SARS‐CoV‐2	18
Issue Information	18
Impact of disturbance and dietary shift on gastrointestinal bacterial community and its invertebrate host system	18
Whole genome population structure of North Atlantic kelp confirms high‐latitude glacial refugia	18
Metabarcoding for biodiversity inventory blind spots: A test case using the beetle fauna of an insular cloud forest	18
Genomic‐based epidemiology reveals independent origins and gene flow of glyphosate resistance in Bassia scoparia populations across North America	18
The structure of tropical bat–plant interaction networks during an extreme El Niño‐Southern Oscillation event	18
Fitness consequences of population bottlenecks in an invasive blowfly	18
Social Complexity During Early Development has Long‐Term Effects on Neuroplasticity in the Social Decision‐Making Network	18
Transgressive gene expression and expression plasticity under thermal stress in a stable hybrid zone	18
Differential temperature effects on photoperiodism in female voles: A possible explanation for declines in vole populations	18
A globally ubiquitous symbiont can drive experimental host evolution	18
Environmental DNA unveils deep phylogeographic structure of a freshwater fish	18
Human activity strongly influences genetic dynamics of the most widespread invasive plant in the sub‐Antarctic	18
Habitat‐linked genetic variation supports microgeographic adaptive divergence in an island‐endemic bird species	17
Living with chronic infection: Persistent immunomodulation during avirulent haemoparasitic infection in a wild rodent	17
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Immune gene regulation is associated with age and environmental adversity in a nonhuman primate	17
Social and paternal female choice for male MHC genes in golden snub‐nosed monkeys (Rhinopithecus roxellana)	17
Issue Information	17
Fifty Years of Conservation Genetics: A Personal Perspective	17
Parallel duplication and loss of aquaporin‐coding genes during the “out of the sea” transition as potential key drivers of animal terrestrialization	17
Linking large‐scale genetic structure of three Argynnini butterfly species to geography and environment	17
Epigenomic Changes in Ostrinia Moths Under Elevated Pupal and Adult Temperature	17
Escalation by duplication: Milkweed bug trumps Monarch butterfly	17
Divergent island hybrids mixed waves of ancient gene flow	17
Microbiota composition and diversity of multiple body sites vary according to reproductive performance in a seabird	17
Variable hybridization between two Lake Tanganyikan cichlid species in recent secondary contact	17
Evaluating the persistence and utility of five wild Vitis species in the context of climate change	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
Issue Information	17
Population Genetics and Invasion History of the European Starling Across Aotearoa New Zealand	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
Host genotype and microbiome associations in co‐occurring clonal and non‐clonal kelp, Ecklonia radiata	17
High Quality Diet Enhances Immune Response and Affects Gene Expression During Viral Infection in an Insect Herbivore	17
Tissue‐specific transcriptional patterns underlie seasonal phenotypes in honey bees (Apis mellifera)	17
Demography‐driven and adaptive introgression in a hybrid zone of the Armeria syngameon	17
Frequent Hybridisation Between Parapatric Lekking Bird‐of‐Paradise Species	16
Environmental versus extra‐organismal DNA	16
Understanding stochastic and deterministic assembly processes in microbial communities along temporal, spatial and environmental scales	16