J. R. Stinchcombe

Predicting fitness related traits using gene expression and machine learning

This study uses machine learning to analyze gene expression data from Ipomoea hederacea, finding that photosynthesis and stress-related genes are under selection and important for predicting fitness.

Genetic architecture of heritable leaf microbes

The paper investigates how host genetic variation affects the assembly of leaf-associated microbiomes in Ipomoea hederacea, finding contributions from both Mendelian and quantitative genetic factors.

Resistance and resilience of soil microbiomes under climate change

This study examines how soil microbiomes respond to climate change treatments and their legacy effects on microbial community composition and plant performance.

Genome size and repeat content contribute to a complex architecture of flowering time in Amaranthus tuberculatus

This study examines genome size and repeat content variation in Amaranthus tuberculatus, finding that larger genomes correlate with slower flowering times, but polygenic and gene copy number variants have greater impact on flowering time adaptation.

Is there a latitudinal diversity gradient for symbiotic microbes? A case study with sensitive partridge peas

This study investigates whether a latitudinal diversity gradient exists in symbiotic microbes of Chamaecrista nictitans, finding increased non-rhizobial species richness at lower latitudes.

Strong selection is poorly aligned with genetic variation in Ipomoea hederacea: implications for divergence and constraint

The study examines selection and genetic variation in Ipomoea hederacea, finding poor alignment between selection and genetic covariance structure and divergence patterns.

G-matrix stability of clinally diverging populations of an annual weed.

The paper examines genetic (co)variances of clinally varying traits in Ipomoea hederacea populations to assess how genetic architecture influences divergence across its range.

Symbiosis with rhizobia limits range expansion only in polyploid legumes

The paper examines how symbiosis with rhizobia and polyploidy affect range expansion in legumes, finding that rhizobia symbiosis limits expansion only in polyploids.

Rapid weed adaptation and range expansion in response to agriculture over the last two centuries

The paper studies how modern agriculture has driven the evolution and range expansion of common waterhemp over the last two centuries through genome analysis of historical and present-day samples.

Selective ancestral sorting and de novo evolution in the agricultural invasion of Amaranthus tuberculatus

This study investigates how A. tuberculatus adapts to agricultural environments through ancestral sorting and de novo evolution, finding both preadaptation and new adaptations.

Repeated origins, gene flow, and allelic interactions of herbicide resistance mutations in a widespread agricultural weed

This study investigates the evolutionary history of herbicide resistance mutations in common waterhemp, finding parallel origins, gene flow, and allelic interactions shaping their spread and persistence.

Multiple Mutualist Effects generate synergistic selection and strengthen fitness alignment in a tripartite interaction between legumes, rhizobia, and mycorrhizal fungi

The paper shows that multiple mutualists in legumes, rhizobia, and mycorrhizal fungi synergistically affect selection, heritability, and fitness alignment in their host plant.

Phenotypic plasticity, population structure and adaptation in a young weed species with a worldwide distribution

This study investigates the roles of phenotypic plasticity and genetic adaptation in the rapid global spread of the weed Capsella bursa-pastoris through common garden experiments.

Priority effects alter interaction outcomes in a legume-rhizobium mutualism

The paper shows that the order of microbial inoculation affects legume-rhizobium mutualism outcomes, with early arrival of effective microbes improving plant growth and symbiont persistence.

The genetic architecture and genomic context of glyphosate resistance in Amaranthus tuberculatus

This study identifies the genetic architecture of glyphosate resistance in Amaranthus tuberculatus, revealing polygenic resistance mechanisms beyond target-site mutations.

Assessing the remarkable morphological diversity and transcriptomic basis of leaf shape in Ipomoea batatas (sweetpotato)

The paper analyzes leaf shape variation in sweetpotato using morphometric and transcriptomic approaches, finding that genetics largely drive shape variation but environment plays a significant role with quantitative measures.

Multiple modes of convergent adaptation in the spread of glyphosate-resistant Amaranthus tuberculatus

This study investigates the genetic mechanisms of glyphosate resistance in Amaranthus tuberculatus, finding multiple modes of convergent adaptation through gene flow and de novo mutations in different populations.

Transposable elements are important contributors to standing variation in gene expression in Capsella grandiflora

This study shows that transposable elements (TEs) significantly contribute to gene expression variation in Capsella grandiflora, with rare TE variants predominantly causing downregulation, more so than rare SNPs.

More partners, more ranges: generalist legumes spread more easily around the globe

The paper investigates how generalist legumes spread more easily than specialist legumes by analyzing their rhizobial partners and introduced ranges.

A note on measuring natural selection on principal component scores

The paper describes a method to transform selection gradients from principal component scores back to original traits, addressing multicollinearity and improving biological interpretation.