Data from: Short tree, long tree, right tree, wrong tree: new acquisition bias corrections for inferring SNP phylogenies

Single nucleotide polymorphisms (SNPs) are useful markers for phylogenetic
studies owing in part to their ubiquity throughout the genome and ease of
collection. Restriction site associated DNA sequencing (RADseq) methods
are becoming increasingly popular for SNP data collection, but an
assessment of the best practises for using these data in phylogenetics is
lacking. We use computer simulations, and new double digest RADseq
(ddRADseq) data for the lizard family Phrynosomatidae, to investigate the
accuracy of RAD loci for phylogenetic inference. We compare the two
primary ways RAD loci are used during phylogenetic analysis, including the
analysis of full sequences (i.e., SNPs together with invariant sites), or
the analysis of SNPs on their own after excluding invariant sites. We find
that using full sequences rather than just SNPs is preferable from the
perspectives of branch length and topological accuracy, but not of
computational time. We introduce two new acquisition bias corrections for
dealing with alignments composed exclusively of SNPs, a conditional
likelihood method and a reconstituted DNA approach. The conditional
likelihood method conditions on the presence of variable characters only
(the number of invariant sites that are unsampled but known to exist is
not considered), while the reconstituted DNA approach requires the user to
specify the exact number of unsampled invariant sites prior to the
analysis. Under simulation, branch length biases increase with the amount
of missing data for both acquisition bias correction methods, but branch
length accuracy is much improved in the reconstituted DNA approach
compared to the conditional likelihood approach. Phylogenetic analyses of
the empirical data using concatenation or a coalescent-based species tree
approach provide strong support for many of the accepted relationships
among phrynosomatid lizards, suggesting that RAD loci contain useful
phylogenetic signal across a range of divergence times despite the
presence of missing data. Phylogenetic analysis of RAD loci requires
careful attention to model assumptions, especially if downstream analyses
depend on branch lengths.