L. Kubatko

A Likelihood Ratio Test for Hybridization Under the Multispecies Coalescent

This paper introduces a likelihood ratio test for detecting hybridization using genomic data under the multispecies coalescent, showing improved power over existing methods.

Implications of gene tree heterogeneity on downstream phylogenetic analyses: A case study employing the Fair Proportion index

The paper examines how gene tree heterogeneity affects phylogenetic diversity indices, showing that species rankings vary significantly depending on whether gene trees or species trees are used.

Inference of Phylogenetic Networks from Sequence Data using Composite Likelihood

This paper introduces PhyNEST, a method for estimating phylogenetic networks from sequence data using composite likelihood, showing improved efficiency and accuracy compared to existing methods.

Estimation of Speciation Times Under the Multispecies Coalescent

The paper introduces a method to estimate speciation times under the multispecies coalescent model using a maximum a posteriori estimator and evaluates its performance through simulations and an empirical dataset.

Site Pattern Probabilities Under the Multispecies Coalescent and a Relaxed Molecular Clock: Theory and Applications

This paper generalizes site pattern probabilities under the multispecies coalescent to a relaxed molecular clock model, improving phylogenetic inference when mutation rates vary across species.

Phylogenetics of a Rapid, Continental Radiation: Diversification, Biogeography, and Circumscription of the Beardtongues (Penstemon; Plantaginaceae)

This study investigates the diversification, biogeography, and taxonomic circumscription of Penstemon using phylogenetic analysis, finding that the genus originated in the Pliocene/Pleistocene and requires taxonomic revision.

Identifiability of speciation times under the multispecies coalescent

This paper shows that branch lengths in fixed species trees with three or four taxa are identifiable and develops estimators and a hypothesis test for delimiting species under the coalescent model.

Consistency of SVDQuartets and Maximum Likelihood for Coalescent-based Species Tree Estimation

This paper shows that SVDQuartets is statistically consistent for species tree estimation under the coalescent model, and demonstrates ML consistency for CIS data under JC69, while highlighting challenges in the multilocus case.

A Phylogenetic Approach to Inferring the Order in Which Mutations Arise during Cancer Progression

This paper introduces a method to infer the order of somatic mutations in cancer progression using noisy single-cell sequencing data and demonstrates its effectiveness through simulations and empirical data.

Evolutionary insights into Bean common mosaic necrosis virus and Cowpea aphid borne mosaic virus using global isolates and thirteen new near complete genomes from Kenya

The paper analyzes BCMNV and CABMV genomes from Kenya to understand their evolutionary relationships and selection pressures, finding strong purifying selection and distinct clades.

Cassava brown streak virus has a rapidly evolving genome: implications for virus speciation, variability, diagnosis and host resistance

The paper compares the evolutionary rates of Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV) using whole genome sequences, finding CBSV evolves faster and has more nonsynonymous substitutions.