S. Tarasov

From museum drawer to tree: historical DNA phylogenomics clarifies the systematics of rare dung beetles (Coleoptera: Scarabaeinae) from museum collections

The paper uses low-cost DNA extraction and Ultraconserved Elements to generate a phylogenetic tree of rare dung beetles from museum specimens, revealing reclassification of a genus.

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.

New phylogenetic Markov models for inapplicable morphological characters

This paper introduces new phylogenetic Markov models for handling anatomically dependent morphological characters and provides tools for their implementation and evaluation.

To design or not to design? Comparison of beetle ultraconserved element probe set utility based on phylogenetic distance, breadth, and method of probe design

The paper evaluates UCE probe set utility for scarabaeoid beetles based on phylogenetic distance, breadth, and design method, finding that utility decreases with greater distance and narrower breadth.

Metagenomics reveals that Dung Beetles (Coleoptera: Scarabaeinae) broadly feed on Reptile dung and could feed on that of Dinosaurs

This study uses metagenomics and trapping experiments to show dung beetles feed on reptile and bird dung, suggesting sauropsid dung may have driven their evolution and insular community formation.

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.

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.

Integration of anatomy ontologies and evo-devo using structured Markov models suggests a new framework for modeling discrete phenotypic traits

This paper introduces structured Markov models with hidden states to model discrete phenotypic traits, resolving issues in ancestral character state reconstruction and phylogenetic inference.

The Invariant Nature of a Morphological Character and Character State: Insights from Gene Regulatory Networks

The paper argues that gene regulatory networks make morphological characters and states invariant, allowing flexible representation of phenotypes in phylogenetic analyses.