Current statistical biogeographical analysis methods are limited in the ways ecology can be related to the processes of diversification and geographical range evolution, requiring conflation of geography and ecology, and/or assuming ecologies that ar...
The reality of larger and larger molecular databases and the need to integrate data scalably have presented a major challenge for the use of phenotypic data. Morphology is currently primarily described in discrete publications, entrenched in noncompu...
Analysis of phylogenetic trees has become an essential tool in epidemiology. Likelihood-based methods fit models to phylogenies to draw inferences about the phylodynamics and history of viral transmission. However, these methods are often computation...
Birth-death (BD) models are widely used in combination with species phylogenies to study past diversification dynamics. Current inference approaches typically rely on likelihood-based methods. These methods are not generalizable, as a new likelihood ...
Resolving phylogenetic relationships among taxa remains a challenge in the era of big data due to the presence of genetic admixture in a wide range of organisms. Rapidly developing sequencing technologies and statistical tests enable evolutionary rel...
Placing new sequences onto reference phylogenies is increasingly used for analyzing environmental samples, especially microbiomes. Existing placement methods assume that query sequences have evolved under specific models directly on the reference phy...
Reconstructing the phylogenetic relationships between species is one of the most formidable tasks in evolutionary biology. Multiple methods exist to reconstruct phylogenetic trees, each with their own strengths and weaknesses. Both simulation and emp...
Rapid and reliable identification of insects is important in many contexts, from the detection of disease vectors and invasive species to the sorting of material from biodiversity inventories. Because of the shortage of adequate expertise, there has ...
Modeling discrete phenotypic traits for either ancestral character state reconstruction or morphology-based phylogenetic inference suffers from ambiguities of character coding, homology assessment, dependencies, and selection of adequate models. Thes...