Data from: 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.