An integrated pathway for building regional phylogenies for ecological studies

Abstract

Aim 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 packages. 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.

Phylogenetic measures reveal eco‐evolutionary drivers of biodiversity along a depth gradient

“…The MCCT showed general agreement with the tree published by Eme et al () (Supplementary material Appendix 2 Fig. A9).…”

“…We built a Bayesian posterior distribution of time‐calibrated molecular phylogenies for New Zealand marine ray‐finned fishes (class Actinopterygii) following the procedure of Eme et al (). We used their same 15 gene supermatrix, adding DNA sequences for 14 species never sequenced before, and also added 6 taxa that lacked sequence data.…”

Disentangling thermal from alternative drivers of reflectance in jewel beetles: A macroecological study

“…Of our 81 focal taxa, 48 had no molecular data, hence they were incorporated a priori based on taxonomic affiliation, using a combination of two subfamily‐, seven tribe‐ and 13 genus‐level topological constraints (Supporting Information Table S9; Figure S3). This method is very similar to many others (e.g., Eme et al, 2019; Thomas et al, 2013) where taxa are grafted onto backbone trees within predefined lineages via a birth–death model, and is essentially the same as done by Eme et al (2019), where this is done simultaneously with whole tree inference (i.e., by using hard topology constraints in BEAST). Further details of phylogenetic supermatrix assembly and inference are provided in the Supporting Information (Supplementary Information S3).…”

“…This method is very similar to many others (e.g., Eme et al, 2019;Thomas et al, 2013) where taxa are grafted onto backbone trees within predefined lineages via a birth-death model, and is essentially the same as done by Eme et al (2019), where this is done simultaneously with whole tree inference (i.e., by using hard topology constraints in BEAST). Further details of phylogenetic supermatrix assembly and inference are provided in the Supporting Information (Supplementary Information S3).…”

Launching insectphylo.org; a new hub facilitating construction and use of synthesis molecular phylogenies of insects

“…Thus, the constraints may be applied only to the overlapping species (Frandsen et al, 2016), or by considering backbone terminals as taxon representatives and thus including barcodes for close relatives (Fouquier et al, 2016), which requires an attempt to reconcile taxonomic overlap between the two (Chesters, 2017(Chesters, , 2020. Furthermore, the delineation of soft and hard topological constraints can provide increased flexibility, as it enables inclusion of a much wider sample of the barcode set into the constraint process, giving more nuanced application across the set of potential constraints, and allows a more diverse number of backbone sources (Chesters, 2020;Eme et al, 2019).…”