Supplementary materials: RADseq phylogenetics in two frog clades

Restriction-site associated DNA sequencing (RADseq) has become an
accessible way to obtain genome-wide data in the form of single nucleotide
polymorphisms (SNPs) for phylogenetic inference. Nonetheless, how
differences in RADseq methods influence phylogenetic estimation is poorly
understood because most comparisons have largely relied on conceptual
predictions rather than empirical tests. We examine how differences in
ddRAD and 2bRAD data influence phylogenetic estimation in two non-model
frog groups. We compare the impact of method choice on phylogenetic
information, missing data, and allelic dropout, considering different
sequencing depths. Given that researchers must balance input (funding,
time) with output (amount and quality of data), we also provide
comparisons of laboratory effort, computational time, monetary costs, and
the repeatability of library preparation and sequencing. Both 2bRAD and
ddRAD methods estimated well-supported trees, even at low sequencing
depths, and had comparable amounts of missing data, patterns of allelic
dropout, and phylogenetic signal. Compared to ddRAD, 2bRAD produced more
repeatable datasets, had simpler laboratory protocols, and an overall
faster bioinformatics assembly. However, many fewer parsimony-informative
sites per SNP were obtained from 2bRAD data when using native pipelines,
highlighting a need for further investigation into the effects of each
pipeline on resulting datasets. Our study underscores the importance of
comparing RADseq methods, such as expected results and theoretical
performance using empirical datasets, before undertaking costly
experiments.