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Parallel changes in gut microbiome composition and function in parallel local adaptation and speciation

https://doi.org/10.1101/736843
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Outgoing claims: the papers this work cites, builds on, or argues with.

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Evolutionary history of an adaptive radiation in species pairs of threespine sticklebacks (Gasterosteus): insights from mitochondrial DNA
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Microbiota Regulate Intestinal Absorption and Metabolism of Fatty Acids in the Zebrafish
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Ecological Impacts of Reverse Speciation in Threespine Stickleback
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Divergence across diet, time and populations rules out parallel evolution in the gut microbiomes of Trinidadian guppies
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Dietary input of microbes and host genetic variation shape among-population differences in stickleback gut microbiota
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An obesity-associated gut microbiome with increased capacity for energy harvest
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Evolutionary diversification in stickleback affects ecosystem functioning
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Functional interactions between the gut microbiota and host metabolism
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Diet rapidly and reproducibly alters the human gut microbiome
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Genetics of ecological divergence during speciation
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Environment dominates over host genetics in shaping human gut microbiota
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Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences
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Individual diet has sex-dependent effects on vertebrate gut microbiota
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QIIME allows analysis of high-throughput community sequencing data
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Unravelling the effects of the environment and host genotype on the gut microbiome
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High taxonomic variability despite stable functional structure across microbial communities
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Contrasting effects of environment and genetics generate a continuum of parallel evolution
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Low temperature and low salinity drive putatively adaptive growth differences in populations of threespine stickleback
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Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample
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Commensal bacteria play a role in mating preference of Drosophila melanogaster
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Animals in a bacterial world, a new imperative for the life sciences
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Evolution of stickleback in 50 years on earthquake-uplifted islands
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Microbiome interactions shape host fitness
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Microbiome composition shapes rapid genomic adaptation of Drosophila melanogaster
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ggplot2: Elegant Graphics for Data Analysis (2nd ed.)
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Ecological Character Displacement and Speciation in Sticklebacks
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Life-History Evolution in Guppies (Poecilia reticulata: Poeciliidae). IV. Parallelism in Life-History Phenotypes
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Constraints on Adaptive Evolution: The Functional Trade‐Off between Reproduction and Fast‐Start Swimming Performance in the Trinidadian Guppy (Poecilia reticulata)
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The Evolutionary Biology of the Threespine Stickleback
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Adaptive genetic variation mediates bottom-up and top-down control in an aquatic ecosystem
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The microbiota influences the Drosophila melanogaster life history strategy
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Gut microbial communities of American pikas ( O chotona princeps): Evidence for phylosymbiosis and adaptations to novel diets
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Individuals' diet diversity influences gut microbial diversity in two freshwater fish (threespine stickleback and Eurasian perch)
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EXPERIMENTAL CONFIRMATION THAT BODY SIZE DETERMINES MATE PREFERENCE VIA PHENOTYPE MATCHING IN A STICKLEBACK SPECIES PAIR
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Swimming capacity and energetics of migrating and non‐migrating morphs of three‐spined sticklebackGasterosteus aculeatusL. and their ecological implications
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Fine-scale local adaptation in life histories along a continuous environmental gradient in Trinidadian guppies
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Speciation in reverse: morphological and genetic evidence of the collapse of a three‐spined stickleback ( Gasterosteus aculeatus ) species pair
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LIFE‐HISTORY EVOLUTION IN GUPPIES ( POECILIA RETICULATA ): 1. PHENOTYPIC AND GENETIC CHANGES IN AN INTRODUCTION EXPERIMENT
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THE GENETICS OF ADAPTIVE SHAPE SHIFT IN STICKLEBACK: PLEIOTROPY AND EFFECT SIZE
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A GENERAL FRAMEWORK FOR THE ANALYSIS OF PHENOTYPIC TRAJECTORIES IN EVOLUTIONARY STUDIES
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VARIABLE PROGRESS TOWARD ECOLOGICAL SPECIATION IN PARAPATRY: STICKLEBACK ACROSS EIGHT LAKE-STREAM TRANSITIONS
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Microbiome investigation in the ecological speciation context of lake whitefish (Coregonus clupeaformis) using next‐generation sequencing
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Responses to simulated winter conditions differ between threespine stickleback ecotypes
inferredcites →https://doi.org/10.1111/mec.15344openalex-snapshot
The microbiota influences the Drosophila melanogaster life history strategy
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Widespread Parallel Evolution in Sticklebacks by Repeated Fixation of Ectodysplasin Alleles
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Evolution of Mammals and Their Gut Microbes
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The Newest Synthesis: Understanding the Interplay of Evolutionary and Ecological Dynamics
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Diet Drives Convergence in Gut Microbiome Functions Across Mammalian Phylogeny and Within Humans
inferredcites →https://doi.org/10.1126/science.1240659openalex-snapshot
The Hologenomic Basis of Speciation: Gut Bacteria Cause Hybrid Lethality in the Genus Nasonia
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Stick Insect Genomes Reveal Natural Selection’s Role in Parallel Speciation
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Contingency and Determinism in Replicated Adaptive Radiations of Island Lizards
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The Effect of Diet on the Human Gut Microbiome: A Metagenomic Analysis in Humanized Gnotobiotic Mice
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Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB
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Host Genetic Control of the Microbiota Mediates the Drosophila Nutritional Phenotype
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UniFrac: a New Phylogenetic Method for Comparing Microbial Communities
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Microbes Drive Evolution of Animals and Plants: the Hologenome Concept
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Ecological predictions lead to the discovery of a benthic–limnetic sympatric species pair of threespine stickleback in Little Quarry Lake, British Columbia
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Social behavior and feeding ability of two phenotypes of Gasterosteus aculeatus in relation to their spatial and trophic segregation in a temperate lake
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Holobionts and ecological speciation: the intestinal microbiota of lake whitefish species pairs
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Mechanisms underlying parallel reductions in aerobic capacity in non-migratory threespine stickleback ( Gasterosteus aculeatus ) populations
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Phylosymbiosis: Relationships and Functional Effects of Microbial Communities across Host Evolutionary History
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Ecological and Evolutionary Effects of Stickleback on Community Structure
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INTRASPECIFIC VARIATION IN A PREDATOR AFFECTS COMMUNITY STRUCTURE AND CASCADING TROPHIC INTERACTIONS
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Specialization of trophic position and habitat use by sticklebacks in an adaptive radiation
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Parasites and pathogens lag behind their host during periods of host range advance
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Adaptive Radiation in Sticklebacks: Trade‐Offs in Feeding Performance and Growth
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Life-History Evolution in Guppies (Poecilia reticulata): 1. Phenotypic and Genetic Changes in an Introduction Experiment
inferredcites →https://doi.org/10.2307/5902openalex-snapshot
The Evolutionary Biology of the Threespine Stickleback
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vegan: Community Ecology Package

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Incoming claims: where this work appears in other papers’ reference lists and arguments.

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The Role of Tree-Insect-Microbiome Interactions in Herbivory and Applications in Pest Management
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Gene expression remodelling and immune response during adaptive divergence in an African cichlid fish
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Dynamics of Insect–Microbiome Interaction Influence Host and Microbial Symbiont
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The Microbiome of Neotropical Water Striders and Its Potential Role in Codiversification
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