From: Why Do Phylogenomic Data Sets Yield Conflicting Trees? Data Type Influences the Avian Tree of Life more than Taxon Sampling Syst Biol. Analysis using the complete taxon sets (Supplementary Fig. (2015) so analyses of those data set more comparable to the data described by Jarvis et al. We used the JAR taxon sets for EB2 and Prum et al. The identity of three outliers in the EB2 data is noted next to the relevant data points. We limited GC-content calculations to parsimony-informative sites from regions with $\geqslant $50 parsimony-informative sites. Colors indicate support values (dark green: $\geqslant $95% light green: $\geqslant $70% yellow: $\geqslant $50% uncolored: $$ 1.5-fold were designated outliers. Heat map showing support for the Jarvis indicator clades for different analyses and taxon samples. The “Early Bird II” (EB2) ML tree of 235 birds using 54 lociĦ Figure 5. 2017 66(5): doi: /sysbio/syx041 Syst Biol | © The Author(s) Published by Oxford University Press, on behalf of the Society of Systematic Biologists. We obtained similar trees using a variety of partitioning schemes in ML analyses (Supplementary File S7) and in Bayesian analyses (although support values were much higher with the latter). We have indicated the data derived from draft genome sequences by adding a “G” after the taxon name. Filled circles indicate $\geqslant $95% support and open circles indicate $\geqslant $70% support. This cladogram is based on a RAxML analysis with the maximum number of partitions. The “Early Bird II” (EB2) ML tree of 235 birds using 54 loci. The “Early Bird II” (EB2) ML tree of 235 birds using 54 lociįigure 3. (2014) intron tree, with the “Jarvis non-coding indicator clade” (J3$_$ predicts that trees with similar taxon sampling will cluster. (2015) tree, based on 0.4 Mbp (82.5% exonic) obtained by sequence capture with the “Prum indicator clades” (P1 and P2) indicated. The “magnificent seven” (clades i–vii) and the “Jarvis indicator clades” (J1 and J2) are highlighted. (2014) TENT, based on 42 Mbp (46% intron, 32% exon, 22% non-coding UCEs) extracted from complete genomes. a) The Jarvis et al"- Presentation transcript:ġ Figure 1.
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