DOI: 10.5061/dryad.r6b87
title: Data from: Building the avian tree of life using a large-scale, sparse supermatrix

description: Birds are the most diverse tetrapod class, with about 10,000 extant
 species that represent a remarkable evolutionary radiation in which most
 taxa arose during a short period of time. There has been a tremendous
 increase in the amount of molecular data available from birds, and more
 than two-thirds of these species have some sequence data available. Here
 we assembled these available sequence data from birds to estimate a
 large-scale avian phylogeny. We performed an unconstrained maximum
 likelihood analysis of a sparse supermatrix comprising 22 nuclear loci and
 seven mitochondrial regions from 6714 species. We inferred a phylogeny
 with a backbone remarkably similar to that obtained by detailed analyses
 of multigene datasets, yet with the addition of thousands of more taxa.
 All orders were monophyletic with generally high support. While most
 families and genera were well supported, a number of them, especially
 within the oscine passerines, had little or no support. This likely
 reflects problems with the circumscription of these genera and families.
 Our results indicate that the amount of sequence data currently available
 is sufficient to produce a robust estimate of the avian tree of life using
 current methods of inference. The availability of a tree that is
 unconstrained by prior information, with branch lengths that have a direct
 connection to the underlying data, should be useful for comparative
 methods, taxonomic revisions, and prioritizing taxa that should be
 targeted for additional data collection.
description: SupplementalFigure1PDF figure describing relationships among Passeriformes families. Each clade that contained species from a single family was collapsed to a single terminal. Italics indicate families that were not monophyletic. The number in parentheses after the family names indicates the number of species in the full tree represented by the lineage. ML bootstrap support values are presented above branches; “*” indicates 100% bootstrap support. Support values on terminal branches indicate the support for monophyly of specific families.AllBird.NewNames.7000Taxa.phyAlignment of the entire 7000-taxon supermatrix in Phylip Format. This alignment uses the revised Clements names instead of the original GenBank names, and taxon names include the orders and families.GeneBordersThis file indicates the starting and ending alignment positions for each gene in the supermatrix.TotalAccessionTableTab-delimited text file that includes the Genbank ID numbers for all of the sequences in the supermatrix. The first column has the Clements names and the second has the original GenBank names. The other columns have the accession numbers for a specified gene.BigBird.All.NewNames.7000Taxa.treNewick strings of the maximum likelihood (ML) and ML bootstrap trees built from the original supermatrix. The first tree in the file is the ML tree, and the other 100 trees are ML bootstrap trees. The numbers represent molecular branch lengths.BigBird.All.NewNames.6714Taxa.treNeiwck strings of the maximum likelihood (ML) and ML bootstrap trees built from the original supermatrix, trimmed to only have one representative taxon per species and edited to correspond to the Clements taxonomy. These are subtrees of “BigBird.All.NewNames.7000Taxa.tre”. The first tree in the file is the ML tree, and the other 100 trees are ML bootstrap trees. The numbers represent molecular branch lengths.