J. Uyeda

Fundamental constraints on the evolution of vertebrate life histories

This study compares aquatic and terrestrial vertebrates to identify shifts in demographic and evolutionary constraints affecting life-history evolution, finding reduced diversification potential on land and differences in viviparity transitions.

ontophylo: Reconstructing the evolutionary dynamics of phenomes using new ontology-informed phylogenetic methods

Ontophylo reconstructs phenome evolution using ontology-informed phylogenetic methods, showing accurate rate estimation and morphospace dynamics in Hymenoptera.

rphenoscate: An R package for semantic-aware evolutionary analyses of anatomical traits

The paper introduces an R package, rphenoscate, that integrates ontological knowledge into evolutionary analyses of morphological traits and demonstrates its utility with data from bees and fishes.

Assessing Bayesian Phylogenetic Information Content of Morphological Data Using Knowledge from Anatomy Ontologies

This paper evaluates how anatomical ontologies structure phylogenetic information in morphological data using Bayesian phylogenetic information metrics across two animal groups.

The Hidden Model Space of Phylogenetic State-Dependent Diversification Models (SSEs): Congruence, Challenges, and Opportunities

The paper identifies universal model congruence in state-dependent speciation and extinction models, showing trait-independent models are congruent with trait-dependent ones, and proposes a solution to mitigate unidentifiability issues.

Exploring Taxonomic and Functional Microbiome of Hawaiian Stream and Spring Irrigation Water Systems Using Illumina and Oxford Nanopore Sequencing Platforms

This study analyzes bacterial communities and their functions in irrigation water from Hawaiian farms using Illumina and Oxford Nanopore sequencing, identifying key taxa and antibiotic resistance genes.

Causal modeling refutes Hockett's hypothesis that bite configuration affects human sound evolution

The paper reanalyzes data from Blasi et al. and finds no support for Hockett's hypothesis that bite configuration affects human sound evolution, attributing the observed association to a general trend of phoneme decline with distance from Africa.

PARAMO pipeline: reconstructing ancestral anatomies using ontologies and stochastic mapping

PARAMO reconstructs ancestral anatomies using ontologies and stochastic mapping to model anatomical dependencies and track phenotypic evolution.