Lessons learned from organizing and teaching virtual phylogenetics workshops

No abstract available

Dataset for "Exploring the distribution of phylogenetic networks generated under a birth-death-hybridization process"

Contains all simulation scripts, simulated data, and supplemental material

SiPhyNetwork: An R package for simulating phylogenetic networks

Abstract Gene flow is increasingly recognized as an important macroevolutionary process. The many mechanisms that contribute to gene flow (e.g. introgression, hybridization, lateral gene transfer) uniquely affect the diversification of dynamics of species, making it important to be able to account for these idiosyncrasies when constructing phylogenetic models. Existing phylogenetic‐network simulators for macroevolution are limited in the ways they model gene flow. We present SiPhyNetwork, an R package for simulating phylogenetic networks under a birth–death‐hybridization process. Our package unifies the existing birth–death‐hybridization models while also extending the toolkit for modelling gene flow. This tool can create patterns of reticulation such as hybridization, lateral gene transfer, and introgression. Specifically, we model different reticulate events by allowing events to either add, remove or keep constant the number of lineages. Additionally, we allow reticulation events to be trait dependent, creating the ability to model the expanse of isolating mechanisms that prevent gene flow. This tool makes it possible for researchers to model many of the complex biological factors associated with gene flow in a phylogenetic context

Lessons learned from organizing and teaching virtual phylogenetics workshops

In 2020 and 2021, the COVID-19 pandemic led to an abrupt overhaul of many academic practices, including the transition of scientific events, such as workshops, to a fully virtual format. We describe our experiences organizing and teaching online-only statistical phylogenetics workshops and the lessons we learned along the way. We found that online workshops present some specific challenges, but format choices and rigorous planning can alleviate many of the concerns typically associated with a virtual medium. In addition, online workshops have unique advantages such as the flexibility they offer to participants and instructors and their accessibility to non-traditional and underprivileged audiences. We hope that our experience will encourage workshop organizers to consider online-only events as an integral part of potential training opportunities rather than simply a stop-gap solution for unusual circumstances. In addition, we hope to prompt broader discussion about integrating aspects of online workshops into traditional in-person courses to make training opportunities more flexible and inclusive.This preprint is made available through EcoEvoRxiv Preprints at doi:10.32942/osf.io/kp8sz. Posted with permission. CC-By Attribution-ShareAlike 4.0 Internationa