DOI: 10.5061/dryad.m6n2t
title: Data from: Resolving a phylogenetic hypothesis for parrots: implications from systematics to conservation

description: Advances in sequencing technology and phylogenetics have revolutionised
 avian biology by providing an evolutionary framework for studying natural
 groupings. In the parrots (Psittaciformes), DNA-based studies have led to
 a reclassification of clades, yet substantial gaps remain in the data
 gleaned from genetic information. Here we provide an overview of published
 genetic data of parrots, characterise sampling depth across the phylogeny,
 and evaluate support for existing systematic treatments. We inferred a
 concatenated tree with 307 species from a 30-gene supermatrix. We
 recovered well-supported relationships among recently proposed clades.
 Taxonomic groups were more stable towards the base of the tree and
 increased sampling will be required to clarify relationships at the tips,
 particularly below the generic level. Only a third of species have been
 sampled intraspecifically in population genetic or phylogeographic
 surveys. Intraspecific sampling has not been geographically or
 phylogenetically even across Psittaciformes, especially poor in the
 cockatoos, Southeast Asia, and parts of Australo-Papua. Threatened species
 are poorly sampled in the Neotropics. We highlight where effort should be
 focused to improve sampling based on geography and conservation status. In
 sum, phylogenetic relationships among the major parrot clades are robust,
 but relationships within and between genera and species provide
 opportunities for future investigations.
description: Map Making
 Scripts This zip file contains
 within it three R scripts which are used to make the ASCII-formatted
 Raster files used in our manuscript. For the purposes of our research,
 these are used to describe IUCN status, within-species sampling, GenBank
 sampling, and species richness of parrot species per spatial grid
 cell. Figure Making
 Scripts This zip file contains
 five R scripts which are used to create the figures in the main text and
 supplementary materials. Script names indicate which figures are made by
 which scripts. GenBank Pipeline Main
 Scripts This zip file contains
 three bash/shell scripts which are used to download files from GenBank,
 filter out unwanted loci or individuals, and construct alignments for use
 in phylogenetic analyses. These three shell scripts call many subscripts
 which are located in the GenBank Pipeline Subscripts zip file.
 Genbank Pipeline Main
 Scripts.zip GenBank Pipeline
 Subscripts This zip file contains
 multiple Python scripts called by the scripts in the GenBank Main Scripts
 file. These execute the specific functions to download sequences from
 GenBank and convert them into an aligned supermatrix of genes for use in
 phylogenetics. For details on individual scripts, see
 README.txt. Genbank Pipeline
 Subscripts.zip Subset_XX_Genes_100bp.fasta Alignment Files This zip file contains 15 fasta-formatted alignment files. These are supermatrices produced from GenBank sequence data. They are subsets of the main supermatrix (a.k.a. Subset_01) where each subset requires that all individual species retained in the supermatrix have at least XX genes, with XX ranging from 01 to 15. RunPartitionFinder_Subset_XX_Genes_rclusterf.cfg Config Files This zip file contains config files for the program PartitionFinder2. They are associated with the gene subsets found in "Subset_XX_Genes_100bp.fasta Alignment Files.zip". best_scheme_Subset_XX_Genes_rcluserf.part Partition files This zip file contains our results from PartitionFinder2. It gives the nucleotide partitions for use in later phylogenetic analyses such as RAxML. Each file is associated with one of the gene subsets from "Subset_XX_Genes_100bp.fasta Alignment Files.zip". COMBINED_Parrots_XXXX.asc ASCII raster files This zip file contains multiple raster files in ASCII format. They are worldwide summaries of parrot species diversity, IUCN status, within-species sampling, GenBank sampling, and combinations of the above. Four of these files were used to make Figure 4 in the main manuscript, while the remainder were not used. Intraspecific_Genetic_Sampling_Citations This CSV file represents our dataset used to determine whether parrot species had intraspecific within-species genetic sampling done. If within-species sampling was found, we cite the reference. We also note situations in which we are aware of ongoing but unpublished work on this subject. In some cases due to taxonomic uncertainty, whether a species has been sampled is unclear, indicated by a "?". ConcatenatedGbFiles_Parrots_March2017 This large file is the concatenated, GenBank-formatted sequences downloaded from GenBank for use in this publication, dating to March 2017. This file forms the basis for creating the aligned supermatrix for use in our phylogeny. getUniqueGbAccession This Python script is used to extract the unique GenBank accession numbers from Fasta-formatted alignment files produced by our GenBank pipeline. extractReferencesFromGenbank This Python script is used to extract all of the reference information from a large GenBank-formatted (.gb) file and place it into a CSV for ease of access later on. This was used to create Supplementary Table 1. RAxML_AllSubsets_BestTrees_WithBootstraps_100bp_Partitioned This newick-formatted file contains 15 maximum-likelihood phylogenies produced in RAxML, one for each of the 15 gene subsets. These contain bootstrap values as well. This file incorporates nucleotide partitioning into the RAxML runs, and forms the basis for all of the trees in the manuscript. RAxML_AllSubsets_BestTrees_WithBootstraps_100bp_NotParitioned This newick-formatted file contains 15 maximum-likelihood phylogenies produced in RAxML, one for each of the 15 gene subsets. These contain bootstrap values as well. This file does not use any nucleotide partitioning. None of the trees were used in the main manuscript, but are provided for comparison with the partitioned trees.
description: # Data from: Resolving a phylogenetic hypothesis for parrots: implications
 from systematics to conservation
 [https://doi.org/10.5061/dryad.m6n2t](https://doi.org/10.5061/dryad.m6n2t)
 See individual READMEs