title: Short Tree, Long Tree, Right Tree, Wrong Tree: New Acquisition Bias Corrections for Inferring SNP Phylogenies.
abstract: 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.
authors.affiliation: Department of Biology, University of Washington, Seattle, WA 98195, USA; Burke Museum of Natural History and Culture, University of Washington, Seattle, WA 98195, USA; leache@uw.edu.
authors.forename: Adam D
authors.initials: AD
authors.lastname: Leaché
authors.affiliation: Department of Biology, University of Washington, Seattle, WA 98195, USA;
authors.forename: Barbara L
authors.initials: BL
authors.lastname: Banbury
authors.affiliation: Department of Biology, University of Washington, Seattle, WA 98195, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA;
authors.forename: Joseph
authors.initials: J
authors.lastname: Felsenstein
authors.affiliation: Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad Universitaria, México 04510, Distrito Federal, México;
authors.forename: Adrián Nieto-Montes
authors.initials: AN
authors.lastname: de Oca
authors.affiliation: Exelixis Laboratory, Scientific Computing Group, Heidelberg Institute for Theoretical Studies (HITS gGmbH), Schloss-Wolfsbrunnenweg 35, D-69118 Heidelberg, Germany; and Department of Informatics, Institute for Theoretical Informatics, Karlsruhe Institute of Technology, Am Fasanengarten 5, 76131 Karlsruhe, Germany.
authors.forename: Alexandros
authors.initials: A
authors.lastname: Stamatakis
mesh_terms: D000818:Animals; D002965:Classification / Q000379:methods*; D003198:Computer Simulation; D008116:Lizards / Q000145:classification / Q000235:genetics; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*
keywords: Conditional likelihood; Phrynosoma; Phrynosomatidae; SVDquartets; ddRADseq; maximum likelihood; reconstituted DNA