Data Accessibility:
All supporting files are available on Dryad:
https://datadryad.org/stash/share/XD_kUFpRIek8qAngIa3OIEclxC0JePCDmZAyCx1ClyI
(temporary link)
- Dryad file S1 . ‘Script 1’ – custom python script for
concatenating FASTA sequences into BPP-style files using a “.fasta”
file of the RAD-Seq data, a “.txt” file with the names of the
partitions of interest, and the “.txt” partition file itself. Those
three files are used to output a .phy file of the RAD-Seq data
partitions of interest to make them compatible with BPP. Further, it
creates a .txt file with the names of candidate species from the
“.phy” file.
- Dryad file S2 . ‘Script 2’ – control file for the A10-type
analysis in BPP.
- Dryad file S3 . ‘Script 3’ – custom python script to extractτ and θ values from the BPP analyses to calculategdi scores directly from BPP ‘A00’-type analysis output.
- Dryad file S4 . Results of the SNAPP+BFD* analyses. Page 1 –
the five different species delimitation models for ‘clade 1’, ranging
from 3 to 16 species assessed; the 16-species model was selected using
Bayes factors (BF). Page 2 – the three different species delimitation
models for ‘clade 2’ and ‘clade 3’; in ‘clade 2’, the 5-species model
was selected over the 2- and 13-species models; in ‘clade 3’, the
7-species model was selected over the 2- and 3-species models. Page 3
– BF scores and rankings from the clade specific SNAPP+BFD*
analyses
- Dryad file S5 . Side-by-side comparison of the ML topology
inferred using IQtree and the species tree inferred using
PAUP+SVDquartets (summarized in Fig. 2). Values at nodes indicate
bootstrap support when less than 100%.
- Dryad file S6 . gdi scores & MCMC runs from the ‘A10’
species delimitation analyses using different subsets of RADseq loci.
- Dryad file S7 . Results from the BPP +gdi “ tip-down”
species delimitation approach.
All RADseq reads are deposited in NCBI Short Read Archive under project
# pending.