DOI: 10.5061/dryad.5vd2560f
title: Data from: Ratite non-monophyly: independent evidence from 40 novel loci

description: Large-scale multi-locus studies have become common in the field of
 molecular phylogenetics, but the best way to interpret these studies when
 their results strongly conflict with prior information about phylogeny
 remains unclear. An example of such a conflict is provided by the ratites
 (the large flightless birds of southern land masses, including ostriches,
 emus, and rheas). Ratite monophyly is strongly supported by both
 morphological data and many earlier molecular studies and is used as a
 textbook example of vicariance biogeography. However, recent studies have
 indicated that ratites are not monophyletic; instead, the volant tinamous
 nest inside the ratites rather than forming their sister group within the
 avian superorder Palaeognathae. Large-scale studies can exhibit biases
 that reflect a number of factors, including limitations in the fit of the
 evolutionary models used for analyses and problems with sequence
 alignment, so the unexpected conclusion that ratites are not monophyletic
 needs to be rigorously evaluated when considered in light of prior
 evidence to the contrary. A rigorous approach to testing novel hypotheses
 generated by large-scale studies is to collect independent evidence (i.e.,
 excluding the loci and/or traits used to generate the hypotheses). This is
 likely to be particularly important when the novel hypothesis is
 controversial. Here we used 40 nuclear loci not used in previous studies
 of the Palaeognathae to investigate the relationship between the ratites
 and their lesser-known relatives the tinamous. Our results strongly
 support the recent molecular studies, revealing that the deepest branch
 within Palaeognathae separates the ostrich from the other members of the
 clade, rather than the traditional hypothesis that separates the tinamous
 from the ratites. To ensure these results reflected evolutionary history
 rather than artifacts, we examined potential biases in types of loci used,
 heterotachy, alignment biases, and discordance between gene trees and the
 species tree. All analyses of our data consistently supported
 non-monophyly of the ratites and no confounding biases could be
 identified. Given this confirmation that ratites are not monophyletic
 using independent evidence, we hope that this study stimulates further
 comparative research focused on paleognath development and genetics that
 might reveal the basis of the morphological convergence evident in these
 large, flightless birds.
description: Total Evidence Alignment
 Plus TreesIncludes data for all 61
 loci. For mtDNA, 3rd coding positions are RY coded. Trees estimated from
 this dataset (Figure 4a, b, and c) are also included.Smithetal.TotalEvidenceDataset.nexSupplementary Tables and FigureFour supplementary tables describing samples used in this study, gene regions and primer sequences, model information and topology for loci and joint posteriors on gene trees. One supplementary figure describing gene tree expectations.Smith_etal_Supplementary_Information.pdfSmithetal.Novel40_LocusDatasetThis is a nexus file including sequence data and tree files for the 40 novel loci sequenced for this study. Charsets for each locus are provided.