C. Ane

Anomalous networks under the multispecies coalescent: theory and prevalence

The paper investigates anomalous networks under the multispecies coalescent model, finding that truly anomalous 4-taxon networks are rare but some appear anomalous due to limited gene sampling.

Summary tests of introgression are highly sensitive to rate variation across lineages

This study evaluates how rate variation affects three summary statistics for detecting hybridization and finds increased false positives and reduced power with rate variation.

PhyloCoalSimulations: A simulator for network multispecies coalescent models, including a new extension for the inheritance of gene flow

The paper introduces a new network coalescent model for simulating gene trees under species networks and implements it in the PhyloCoalSimulations Julia package.

Accounting for within-species variation in continuous trait evolution on a phylogenetic network

This paper introduces a phylogenetic linear model for network-based comparative methods to account for within-species variation in continuous traits, showing its effectiveness through simulations and application to Polemonium data.

Phylogenetic Comparative Methods on Phylogenetic Networks with Reticulations

This paper extends Phylogenetic Comparative Methods to phylogenetic networks with reticulations, developing algorithms and statistical tests for trait evolution and transgressive evolution in Xiphophorus fishes.

Inference of Adaptive Shifts for Multivariate Correlated Traits

This paper introduces a method to detect adaptive shifts in multivariate correlated traits across phylogenetic trees, showing improved performance over existing methods.