Data from: Effects of phylogenetic reconstruction method on the robustness of species delimitation using single-locus data

1. Coalescent-based species delimitation methods combine population
genetic and phylogenetic theory to provide an objective means for
delineating evolutionarily significant units of diversity. The Generalized
Mixed Yule Coalescent (GMYC) and the Poisson Tree Process (PTP) are
methods that use ultrametric (GMYC or PTP) or non-ultrametric (PTP) gene
trees as input, intended for use mostly with single-locus data such as DNA
barcodes. 2. Here we assess how robust the GMYC and PTP are to different
phylogenetic reconstruction and branch smoothing methods. We reconstruct
over 400 ultrametric trees using up to 30 different combinations of
phylogenetic and smoothing methods and perform over 2,000 separate species
delimitation analyses across 16 empirical datasets. We then assess how
variable diversity estimates are, in terms of richness and identity, with
respect to species delimitation, phylogenetic and smoothing methods. 3.
The PTP method generally generates diversity estimates that are more
robust to different phylogenetic methods. The GMYC is more sensitive, but
provides consistent estimates for BEAST trees. The lower consistency of
GMYC estimates is likely a result of differences among gene trees
introduced by the smoothing step. Unresolved nodes (real anomalies or
methodological artefacts) affect both GMYC and PTP estimates, but have a
greater effect on GMYC estimates. Branch smoothing is a difficult step and
perhaps an underappreciated source of bias that may be widespread among
studies of diversity and diversification. 4. Nevertheless, careful choice
of phylogenetic method does produce equivalent PTP and GMYC diversity
estimates. We recommend simultaneous use of the PTP model with any
model-based gene tree (e.g. RAxML) and GMYC approaches with BEAST trees
for obtaining species hypotheses.