A phylogeny of the birds of New Zealand

This repository contains supplementary sata associated with this manuscript: Estimating phylogenies for species assemblages: a complete phylogeny for the past and present native birds of New ZealandLanfear R and Bromham L (2011) Molecular Phylogenetics and Evolution 61(3):958–963http://dx.doi.org/10.1016/j.ympev.2011.07.018 There are four files in this collection: GeneFinder.pyPython script to search GenBank for sequences that match taxonIDs in a list.Instructions on use are in the script itself, open the script in a text editor to read them. SupplementaryData.xlsContains the species list, taxonomy, the TaxonIDs used for each species, whether the TaxonID is forthe NZ species or a substitute taxon, GenBank accession numbers for each sequence used in the supermatrix(a -1 indicates that a no data were available for that taxon and that gene), and full details of allcontsraints used ('1' indicates that a given taxon was included in a constraint). MrBayes_inputfile.nexAn example input file for the MrBayes analysis. Seven of these were run independently.This file also contains the alignments for each gene. MrBayes_posterior_sample_trees.nex.zipThe full posterior sample of 133,000 trees from the analysis.These trees exclude 2,000,000 generations of burnin from each run. 50percent_majorityrule_tree.nexThe 50% majorityrule tree that summarises the full posterior sample of 133,000 trees. Thiswas calculated by loading each run into MrBayes, and summarising the trees using the 'sumt' command.