An integrated pathway for building regional phylogenies for ecological studies

Aims: Phylogenies are increasingly used in community ecology, biogeography and macroecology.
However, sourcing a phylogeny comprising the entire species pool for a focal region can be difficult. Typically, a bespoke phylogeny must be created requiring considerable data manipulation and the use of many standalone software. Here we present a suite of methodological tools within the popular R environment that help to build molecular phylogenies appropriate for ecological studies with a regional focus.

Innovation: Our R package regPhylo provides a pipeline to construct a Bayesian posterior distribution of time-calibrated trees suitable to address ecological questions. The novel contributions of regPhylo include options to: use prior phylogenetic knowledge through flexible topological constraints; include spatial metadata in sourcing DNA sequences; and include taxa without DNA sequences and then infer consequent phylogenetic uncertainty. Specifically, regPhylo helps researchers: retrieve DNA sequences; enhance available metadata; select DNA sequences based on their length or spatial proximity to the region of study; align sequences; and perform quality control. Output from the pipeline is a file ready to run in the Bayesian tree reconstruction software BEAST2, appropriate for estimating time-calibrated trees and including phylogenetic uncertainty for downstream analyses.

Main conclusions: Overall, regPhylo improves the integration of popular standalone phylogenetic software into the flexible R environment. It provides a novel approach to include topological constraints based on prior knowledge, include taxa without DNA sequences, and select spatially appropriate DNA sequences. When coupled with a Bayesian tree-building process, our approach provides estimates of uncertainty in both topology and branch-lengths. We demonstrate the utility of the package by constructing a posterior distribution of time-calibrated phylogenies for the New Zealand marine ray-finned fishes (Actinopterygii) providing the unprecedented opportunity to include phylogenetic information in downstream ecological analyses for marine fishes in this region.