Jeet Sukumaran

The effects of post-divergence gene flow on simultaneous divergence time (SDT) testing

This study evaluates how post-divergence gene flow affects the accuracy of simultaneous divergence time estimates using simulations and Bayesian methods.

Thermal Dynamics of Ectotherm Behavioral Strategies: Insights from Agent-Based Simulations

This paper uses agent-based simulations to analyze thermoregulatory strategies in ectotherms, finding minimal differences between strategies and highlighting environmental factors' role in thermal refugia occupancy.

Information theoretic inference of magnitude and direction of gene flow in metapopulation networks using nyemtaay, with potential for applications in metastasizing cancer clonal cell origin analysis

AutoPhy: Automated phylogenetic identification of novel protein subfamilies

AutoPhy automatically clusters protein sequences into monophyletic subfamilies without pre-defined thresholds, resolving misannotations and identifying novel functional groups and viral strains.

An assembly-free method of phylogeny reconstruction using short-read sequences from pooled samples without barcodes

AFPhyloMix reconstructs haplotype phylogenies from pooled short-read sequences without barcoding, achieving 80% accuracy for up to 15 haplotypes in simulations and real data.

SPART, a versatile and standardized data exchange format for species partition information

The paper introduces SPART, a standardized format for exchanging species partition information, to improve interoperability among species delimitation tools.

Machine Learning Biogeographic Processes from Biotic Patterns: A New Trait-Dependent Dispersal and Diversification Model with Model-Choice By Simulation-Trained Discriminant Analysis

The paper introduces a new trait-dependent dispersal and diversification model and applies it to study taxon cycles in Wallacean avifauna using simulation-trained discriminant analysis.