Molecular Ecology

Article	Citations
Issue Information	167
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	87
Decoding plant‐induced transcriptomic variability and consistency in two related polyphagous mites differing in host ranges	82
Genetic and telomeric variability: Insights from a tropical avian hybrid zone	71
Genomic divergence and introgression between cryptic species of a widespread North American songbird	71
Genetic Adaptation to Brackish Water and Spawning Season in European Cisco	70
Hybrid enrichment of adaptive variation revealed by genotype–environment associations in montane sedges	64
Extremes of snow and temperature affect patterns of genetic diversity and differentiation in the alpine butterfly Parnassius smintheus	60
Adaptive cellular evolution or cellular system drift in hares	59
Genomic, morphological and physiological data support fast ecotypic differentiation and incipient speciation in an alpine diving beetle	58
Acclimatory gene expression of primed clams enhances robustness to elevated pCO2	57
Organellar DNA continues to provide a rich source of information in the genomics era	56
Diving into the diversity of colour patterns in reef fishes	56
Community‐wide correlations between species richness, abundance and population genomic diversity in a freshwater biodiversity hotspot	55
Understanding the role of temperature in seasonal timing: Effects on behavioural, physiological and molecular phenotypes	53
Association between parasite microbiomes and caste development and colony structure in a social trematode	47
Interspecies genome divergence is predominantly due to frequent small scale rearrangements in Eucalyptus	46
Grassland ecosystem type drives AM fungal diversity and functional guild distribution in North American grasslands	44
Ecology Not Genetic Covariance Explains Correlated Trait Divergence During Speciation	44
Long‐read sequencing in ecology and evolution: Understanding how complex genetic and epigenetic variants shape biodiversity	44
Traits and tradeoffs among non‐native ectomycorrhizal fungal symbionts affect pine seedling establishment in a Hawaiian coinvasion landscape	43
Genome‐wide SNP assessment of contemporary European red deer genetic structure highlights the distinction of peripheral populations and the main admixture zones in Europe	43
Bacterial communities in a subarctic stream network: Spatial and seasonal patterns of benthic biofilm and bacterioplankton	42
Cryptic Barriers to Gene Flow Driven by Deep‐Sea Reproductive Strategy in Direct‐Developing Pandalid Shrimp	41
Evolutionary roles of polyploidization‐derived structural variations in the phenotypic diversification of Panax species	41

Massive Genomic and Transcriptomic Changes Within a Young Inversion Polymorphism in the Absence of Degeneration	41
Issue Information	41
DNA Methylation Dynamics Reflect Sex and Status Differences in Mortality Rates in a Polygynous Bat	41
Museomics Sheds Light on Evolutionary Diversity in a Critically Endangered Cockatoo Species From Wallacea	40
On the origin and structure of haplotype blocks	40
The transcriptional state and chromatin landscape of cichlid jaw shape variation across species and environments	40
Experimental evidence that root‐associated fungi improve plant growth at high altitude	39
Clones on the run: The genomics of a recently expanded partially clonal species	38
Positive selection in gamete interaction proteins in Carnivora	38
The impacts of positive selection on genomic variation in Drosophila serrata: Insights from a deep learning approach	37
Demographic modelling helps track the rapid and recent divergence of a conifer species pair from Central Mexico	36
Brazilian marine phylogeography: A literature synthesis and analysis of barriers	35
Combined Evidence Reveals the Origin of a Rapid Range Expansion Despite Retained Genetic Diversity and a Weak Founder Effect	35
The effect of divergent and parallel selection on the genomic landscape of divergence	34
More complex than you think: Taxonomic and temporal patterns of plant–pollinator networks of caraway (Carum carvi L.)	34
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Evolutionary History and Rhizosphere Microbial Community Composition in Domesticated Hops ( Humulus lupulus L .	33
A genomic assessment of the marine‐speciation paradox within the toothed whale superfamily Delphinoidea	33
Out of the Qinghai‐Tibet plateau: Genomic biogeography of the alpine monospecific genus Megadenia (Biscutelleae, Brassicaceae)	33
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Effect of urbanization and parasitism on the gut microbiota of Darwin's finch nestlings	33
Infection by the Lungworm Rhabdias pseudosphaerocephala Affects the Expression of Immune‐Related microRNAs by Its Co‐Evolved Host, the Cane Toad Rhinella marina	31
Integrative biological analyses of responses to food deprivation reveal resilience mechanisms in sea urchin larvae	31
Microbiomes associated with avian malaria survival differ between susceptible Hawaiian honeycreepers and sympatric malaria‐resistant introduced birds	31
A Comparative Analysis of Long‐Term Effective Population Sizes Across Eukaryotes	31
The effect of a temperature‐sensitive prophage on the evolution of virulence in an opportunistic bacterial pathogen	31
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Recent genetic exchanges and admixture shape the genome and population structure of the zoonotic pathogen Cryptosporidium parvum	31
Genomic variation across Chinook salmon populations reveals effects of a duplication on migration alleles and supports fine scale structure	31
Ultraconserved Elements Reveal the Relationship Between Facultative Keratinophagy and Synanthropic Evolution in Clothes Moths	31
Issue Information	31
Combined genome and transcriptome provides insight into the genetic evolution of an edible halophyte Suaeda salsa adaptation to high salinity	31
Primrose homostyles: A classic case of possible balancing selection revisited	31
Differential Bottom‐Up Control of Planktonic and Sedimentary Bacterial Communities by Phytoplankton and Extracellular Enzymes in an Asymmetric River Confluence	30
Large effective population size masks population genetic structure in Hirondellea amphipods within the deepest marine ecosystem, the Mariana Trench	30
Highly Expressed Odorant Receptor Orthologs Detect the Aggregation Pheromone Lineatin in Trypodendron Ambrosia Beetles	30
Genome‐wide phylogeography reveals cryptic speciation in the circumglobal planktonic calcifier Limacina bulimoides	30
Genetic responses in sexual diploid and unisexual triploid goldfish (Carassius auratus) introduced into a high‐altitude environment	30
Issue Information	30
Social Structure and Interactions Differentially Shape Aerotolerant and Anaerobic Gut Microbiomes in a Cooperative Breeding Species	30
Dissolved Organic Carbon Shapes Sediment Bacterial Diversity in Continental Lakes	30
Phylogenetic diversity only weakly mitigates climate‐change‐driven biodiversity loss in insect communities	30
Evolutionary ecology of denitrifying methanotrophic NC10 bacteria in the deep‐sea biosphere	30
Historical Lead Contamination Linked to Atmospheric Deposition is Associated With Declines in Ectomycorrhizal Diversity and Shifts in Fungal Community Composition	30
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
An Early‐Life Disruption of Gut Microbiota Has Opposing Effects on Parasite Resistance in Two Host Species	29
Expansion and Temporal Expression Regulation of Cuticle‐Associated Gene Families: Molecular Basis of Adaptive Evolution of Moulting in Decapods	29
Tracking population structure and phenology through time using ancient genomes from waterlogged white oak wood	28
Cophylogeny and specificity between cryptic coral species ( Pocillopora spp.) at Mo′orea and their symbionts (Symbiodiniaceae)	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
Environmental heterogeneity structures root‐associated fungal communities in Daphne arbuscula (Thymelaeaceae), a shrub adapted to extreme rocky habitats	28
Variation in phenotypic plasticity across age‐at‐maturity genotypes in wild Atlantic salmon	28
Limited introgression from non‐native commercial strains and signatures of adaptation in the key pollinator Bombus terrestris	28
Genome‐wide variant analyses reveal new patterns of admixture and population structure in Australian dingoes	28
Recurrent Hybridisations During Diversification of One Rhododendron Species Complex	28
Tidal gradients, fine‐scale homing and a potential cryptic ecotype of wild spawning pink salmon ( Oncorhynchus gorbuscha )	28
Phylogeography of the blacklegged tick (Ixodes scapularis) throughout the USA identifies candidate loci for differences in vectorial capacity	27
Regulation of host gene expression by gastrointestinal tract microbiota in Chinook Salmon (Oncorhynchus tshawytscha)	27
Characterizing feral swine movement across the contiguous United States using neural networks and genetic data	26
Gene Expression Associated With Behaviour Manipulation in Wood Ants Infected With Larval Lancet Fluke, Dicrocoelium dendriticum	26
Geographic Divergence and the Genomic Basis of Reproductive Diapause in Drosophila triauraria	26
Reticulate and Hybrid Speciation is Promoted by Environmental Instability in an Indo‐Pacific Species Complex of Whistlers (Aves: Pachycephala )	26
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The Genetic Architecture of Local Adaptation and Reproductive Character Displacement in Scutiger boulengeri Complex (Anura: Megophryidae)	25
Genetic analysis reveals the putative native range and widespread double‐clonal reproduction in the invasive longhorn crazy ant	25
Genetic mixing in conservation translocations increases diversity of a keystone threatened species, Bettongia lesueur	25
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Host preference explains the high endemism of ectomycorrhizal fungi in a dipterocarp rainforest	25
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Convergent Evolutionary Dead‐End and Breakdown of Hard Chorion in Parental‐Egg‐Care Fish Reproductive Strategies	25
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Ephemeral Speciation in a New Guinean Honeyeater Complex ( Aves : Melidectes )	24
Evolved and Plastic Gene Expression in Adaptation of a Specialist Fly to a Novel Niche	24
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Long‐term biogeographical processes dominate patterns of genetic diversity in a wingless grasshopper despite substantial recent habitat fragmentation	24
Phylogenomics and phylogeographic model testing using convolutional neural networks reveal a history of recent admixture in the Canarian Kleinia neriifolia	24
Parentage influence on gene expression under acidification revealed through single‐embryo sequencing	23
Evolutionary variation in gene conversion at the avian MHC is explained by fluctuating selection, gene copy numbers and life history	23
Approximate Bayesian Computation applied to time series of population genetic data disentangles rapid genetic changes and demographic variations in a pathogen population	23
Plastic Responses and Standing Genetic Variation in Salinity‐Responsive Genes Under Projected Salinisation in Freshwater Fish	23
Do Snow‐Adapted Prey Facilitate Coexistence of the Sierra Nevada Red Fox With Sympatric Carnivores?	23
Ectoparasite presence and brood size manipulation interact to accelerate telomere shortening in nestling jackdaws	23
Relic DNA obscures DNA‐based profiling of multiple microbial taxonomic groups in a river‐reservoir ecosystem	23
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Omics to Study and Manage Aquatic Environments: A Snapshot From the AquaEcOmics Meeting (Evian‐les‐Bains, 2025)	23
Population genomic structure of a widespread, urban‐dwelling mammal: The eastern grey squirrel (Sciurus carolinensis)	23
Immune genotypes, immune responses, and survival in a wild bird population	23
Seasonal dynamics of the wild rodent faecal virome	22
Molecular ecology of microbiomes in the wild: Common pitfalls, methodological advances and future directions	22
Indirect Environmental Effects on the Gut‐Brain Axis in a Wild Mammal	22
Lineage and role in integrative taxonomy of a heterotrophic orchid complex	22
Inferring the ecological and evolutionary determinants of community genetic diversity	22
Geographical distance, host evolutionary history and diet drive gut microbiome diversity of fish across the Yellow River	22
Parental breeding decisions and genetic quality predict social structure of independent offspring	22
The challenge of demonstrating contemporary natural selection on polygenic quantitative traits in the wild	22
Sexy fingers: Pheromones in the glands of male dendrobatid frogs	22
Genomic health is dependent on long‐term population demographic history	22
Longitudinal gut microbiome dynamics in relation to age and senescence in a wild animal population	22
Integrating Population Genomics and Historical Occurrence Data to Assess the Impact of Land‐Use Changes on Centris Oil Bees in the Brazilian Cerrado	22
Phenotypic cross‐species conservation and cross‐generation directionality switching in epigenetic inheritance	22
DNA methylation markers of age(ing) in non‐model animals	22
Sex chromosome heteromorphism and the Fast‐X effect in poeciliids	21
Heat‐stress memory enhances the acclimation of a migratory insect pest to global warming	21
Genetic adaptation despite high gene flow in a range‐expanding population	21
Genetic and Environmental Similarities Drive Repeated Genomic Evolution in Island Lizards	21
Comparative population genomics of manta rays has global implications for management	21
Plasticity for the win: Flexible transcriptional response to host plant switches in the comma butterfly (Polygonia c‐album)	21
Cryptic hybridization between the ancient lineages of Natterer's bat (Myotis nattereri)	21
Balancing Selection on a Single Locus Controls Colour Polymorphism in a Reptile via Tubulin Modification	21
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The genomic basis of reproductive and migratory behaviour in a polymorphic salmonid	20
Investigating the genetic basis of vertebrate dispersal combining RNA‐seq, RAD‐seq and quantitative genetics	20
Genomic architecture underlying morphological and physiological adaptation to high elevation in a songbird	20
Genomic and phenotypic changes associated with alterations of migratory behaviour in a songbird	20
Pleistocene parades of carnivores into North America	20
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Combining GWAS and population genomic analyses to characterize coevolution in a legume‐rhizobia symbiosis	20
Issue Information	20
Defence‐relevant gene expression differences in hatchlings among wild Newfoundland and farmed European and North American Atlantic salmon and their hybrids	20
Parental effects in a filamentous fungus: Phenotype, fitness and mechanism	20
It is time for ancient DNA to sweat the small stuff	20
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Synthesizing environmental, epidemiological and vector and parasite genetic data to assist decision making for disease elimination	20
Correction to “The Opposed Forces of Differentiation and Admixture Across Glacial Cycles in the Butterfly Aglais urticae ”	20
Fitness consequences of population bottlenecks in an invasive blowfly	20

PoolSeq Genome‐Wide Association Studies and Microbial Signature Analyses Identify Novel Candidates Associated With Pyrethroid Resistance Evolution in Anopheles funestus	19
Genetic Mapping of Resistance: ddRADseq ‐Based QTL and Associated Polymorphism Conferring Resistan	19
Turnip Mosaic Virus Infection in a Perennial Arabidopsis Reduces Aphid Fecundity in the Natural Environment	19
Genomic Introgressions May Affect Hybridogenetic Reproduction in Water Frog Hybrids	19
Genomic, Phenotypic and Environmental Correlates of Speciation in the Midwife Toads ( Alytes )	19
Age‐ and caste‐independent piRNAs in the germline and miRNA profiles linked to caste and fecundity in the ant Temnothorax rugatulus	19
Connectivity and Age of Restored Atlantic Forest Fragments Drives Composition and Functionality of the Fungal Community in the Leaf Litter Layer	19
The faecal metabolome of black howler monkeys (Alouatta pigra) varies in response to seasonal dietary changes	19
Complex dynamics of coral gene expression responses to low pH across species	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
Genetic legacies of mega‐landslides: Cycles of isolation and contact across flank collapses in an oceanic island	19
Domestication and evolutionary histories of specialized gut symbionts across cephalotine ants	19
Selection for Tameness in Red Junglefowl Recapitulates Genetic Loci Associated With Domestication‐Related Brain Composition	19
Pigments, Chromatophore Structure, and Gene Expression Underlying Colour Polytypy of a Panamanian Poison Frog	19
Genetic Diversity of Polymyxin Resistance Genes in Klebsiella pneumoniae Clinical Isolates	19
Rhizobium nodule diversity and composition are influenced by clover host selection and local growth conditions	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
Gene expression differentiation in the reproductive tissues of Drosophila willistoni subspecies and their hybrids	18
Diet in phenotypically divergent sympatric species of African weakly electric fish (genus: Campylomormyrus)—A hybrid capture/HTS metabarcoding approach	18
Repeated Mitochondrial Capture With Limited Genomic Introgression in a Lizard Group	18
Different trematode parasites in the same snail host: Species‐specific or shared microbiota?	18
Fire shapes fungal guild diversity and composition through direct and indirect pathways	18
Repeatome evolution across space and time: Unravelling repeats dynamics in the plant genus Erythrostemon Klotzsch (Leguminosae Juss)	18
Strategies to identify and dissect trade‐offs in plants	18
High promiscuity among females of the invasive pest species Drosophila suzukii	18
Brain and antennal transcriptomes of host ants reveal potential links between behaviour and the functioning of socially parasitic colonies	18
Divergence of alternative sugar preferences through modulation of the expression and activity of the Gal3 sensor in yeast	18
Whole genome population structure of North Atlantic kelp confirms high‐latitude glacial refugia	18
Long live the host! Proteomic analysis reveals possible strategies for parasitic manipulation of its social host	18
Kinship Analysis Confirms Tolerant Galapagos Mockingbirds Are a Source of Nest Flies That Threaten Darwin's Finches	18
Speciation patterns of related species under the hybrid zone: A case study of three sclerophyllous oaks in the east Himalaya–Hengduan Mountains	18
Social Complexity During Early Development has Long‐Term Effects on Neuroplasticity in the Social Decision‐Making Network	18
Phylogeography of horseshoe bat sarbecoviruses in Vietnam and neighbouring countries. Implications for the origins of SARS ‐	18
Genomics reveal population structure, evolutionary history, and signatures of selection in the northern bottlenose whale, Hyperoodon ampullatus	18
Repeatable Genomic Outcomes Along the Speciation Continuum: Insights From Pine Hybrid Zones (Genus Pinus )	18
Expression of Elongase‐ and Desaturase‐Encoding Genes Shapes the Cuticular Hydrocarbon Profiles of Honey Bees	18
Watershed Fingerprints in Reservoir Sediments: Microeukaryotic Sedimentary DNA Tracks Decades of Anthropogenic Disturbance	18
No Evidence That Life History Strategies Shape Within‐Body Mosaics of Ageing	18
Environmental DNA unveils deep phylogeographic structure of a freshwater fish	18
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A Test of the Long‐Term Efficiency of Genetic Rescue With Drosophila melanogaster	17
Environmental Gradients Decouple Demographic and Adaptive Connectivity in a Highly Mobile Coastal Marine Species	17
Multiple genomic solutions for local adaptation in two closely related species (sheep and goats) facing the same climatic constraints	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	17
Extensive Multi‐Species Hybridization Between Leuciscidae Minnow Species	17
Living with chronic infection: Persistent immunomodulation during avirulent haemoparasitic infection in a wild rodent	17
Preserving Wild Pears: Using Genomic Data to Assess Species Boundaries, Interspecific Hybridization, and Genetic Diversity to Inform Conservation	17
Genomic Prediction of Disease Resistance Provides a Path to Marker Assisted Restoration in a Wetland Foundation Tree Species	17
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Urbanization Shapes Dietary Composition and Snout Morphology of Salamanders	17
Population genomics and sexual signals support reproductive character displacement in Uperoleia (Anura: Myobatrachidae) in a contact zone	17
Neutral Additivity Dominates the Outcome of Soil Microbial Community Coalescence	17
Mind the Gaps: Shortfalls in Studies of the Intraspecific Genetic Diversity of Plants Across the Gran Chaco	17
Genomic Evidence for Dual Introductions, Limited Gene Flow and Niche Preferences in the Invasive Wasp Vespula germanica in South Africa	17
Linking large‐scale genetic structure of three Argynnini butterfly species to geography and environment	17
Do chromosome rearrangements fix by genetic drift or natural selection? Insights from Brenthis butterflies	17
Escalation by duplication: Milkweed bug trumps Monarch butterfly	17
Genetic Diversity and Population Structure in Cities Is Not Consistent Among Cosmopolitan Plant Species	17
Robust Sensory Traits Across Light Habitats: Visual Signals but Not Receptors Vary in Centrarchids Inhabiting Distinct Photic Environments	17
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Sporecasting Biogeography Across Scales: Continental Patterns and Local Constraints on Macrofungal Dispersal	17
Metabarcoding for biodiversity inventory blind spots: A test case using the beetle fauna of an insular cloud forest	17
Genomic and Morphological Divergence Under Extreme Environments: Insights Into the Adaptation and Speciation of Lepus yarkandensis and	17
High Quality Diet Enhances Immune Response and Affects Gene Expression During Viral Infection in an Insect Herbivore	17
Spatiotemporal Dynamics of Blood Parasite Infections and Impacts on Avian Health and Reproduction	17
Functional Shifts in the Gut DNA Virome in a Long‐Distance Migratory Shorebird During the Pre‐Migratory Fattening	17
Host genotype and microbiome associations in co‐occurring clonal and non‐clonal kelp, Ecklonia radiata	17
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Frequent Hybridisation Between Parapatric Lekking Bird‐of‐Paradise Species	17
Social and paternal female choice for male MHC genes in golden snub‐nosed monkeys (Rhinopithecus roxellana)	16
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Population Genetics and Invasion History of the European Starling Across Aotearoa New Zealand	16
Divergent island hybrids mixed waves of ancient gene flow	16
Genetic Architecture of Immune Cell DNA Methylation in the Rhesus Macaque	16
Amazonian colonization from the Atlantic Forest: New perspectives on the connections of South American tropical forests	16
Variable hybridization between two Lake Tanganyikan cichlid species in recent secondary contact	16
When South Meets North: A Joint Contact Zone Coinciding With Environmental Gradients in Three Boreal Tree Species	16
Temporal dynamics of soil fungi in a pyrodiverse dry‐sclerophyll forest	16
Strong Bottlenecks Constrain Adaptive Coevolution in a Host–Parasite Metapopulation	16
Pathogen invasion increases the abundance of predatory protists and their prey associations in the plant microbiome	16
Demography‐driven and adaptive introgression in a hybrid zone of the Armeria syngameon	16
Understanding stochastic and deterministic assembly processes in microbial communities along temporal, spatial and environmental scales	16
Transgressive gene expression and expression plasticity under thermal stress in a stable hybrid zone	16
Parallel duplication and loss of aquaporin‐coding genes during the “out of the sea” transition as potential key drivers of animal terrestrialization	16
Not All Bark Beetles Smell the Same : Population‐Level Functional Olfactory Polymorphisms in Ips typographus Pheromone Recepto	16
Distinct patterns of inheritance shape life‐history traits in steelhead trout	16
Evaluating the persistence and utility of five wild Vitis species in the context of climate change	16
Differential Regulation of Apoptosis and Symbiodiniaceae Energy Transfer Mediate the Link Between Bleaching and Disease in Exaiptasia diaphana	16
Admixture Affects the Rate and Repeatability of Experimental Adaptation to a Stressful Environment in Callosobruchus maculatus	16
Plant invasion reconstructs soil microbial assembly and functionality in coastal salt marshes	16
Fifty Years of Conservation Genetics: A Personal Perspective	16
Hybrid‐derived weedy rice maintains adaptive combinations of alleles associated with seed dormancy	16
Deciphering the Patterns and Drivers of Tardigrade Diversity Along Altitudinal Gradients	16