Data from: Resolving a phylogenetic hypothesis for parrots: implications from systematics to conservation

Provost KL, Joseph L, Smith BT

Date Published: November 2, 2017

DOI: https://doi.org/10.5061/dryad.m6n2t

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Title Map Making Scripts
Downloaded 7 times
Description 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.
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Title Figure Making Scripts
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Description 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.
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Title GenBank Pipeline Main Scripts
Downloaded 2 times
Description 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.
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Title GenBank Pipeline Subscripts
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Description 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.
Download Genbank Pipeline Subscripts.zip (33.06 Kb)
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Title Subset_XX_Genes_100bp.fasta Alignment Files
Downloaded 3 times
Description 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.
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Title RunPartitionFinder_Subset_XX_Genes_rclusterf.cfg Config Files
Downloaded 8 times
Description 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".
Download RunPartitionFinder_Subset_XX_Genes_rclust...es.zip (21.74 Kb)
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Title best_scheme_Subset_XX_Genes_rcluserf.part Partition files
Downloaded 2 times
Description 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".
Download best_scheme_Subset_XX_Genes_rcluserf.part...es.zip (17.22 Kb)
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Title COMBINED_Parrots_XXXX.asc ASCII raster files
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Description 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.
Download COMBINED_Parrots_XXXX.asc ASCII raster files.zip (1.975 Mb)
Download README.txt (18.38 Kb)
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Title Intraspecific_Genetic_Sampling_Citations
Downloaded 2 times
Description 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 "?".
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Title ConcatenatedGbFiles_Parrots_March2017
Downloaded 5 times
Description 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.
Download README.txt (18.38 Kb)
Download ConcatenatedGbFiles_Parrots_March2017.gb (542.1 Mb)
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Title getUniqueGbAccession
Downloaded 1 time
Description This Python script is used to extract the unique GenBank accession numbers from Fasta-formatted alignment files produced by our GenBank pipeline.
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Title extractReferencesFromGenbank
Downloaded 2 times
Description 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.
Download extractReferencesFromGenbank.py (1.226 Kb)
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Title RAxML_AllSubsets_BestTrees_WithBootstraps_100bp_Partitioned
Downloaded 11 times
Description 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.
Download RAxML_AllSubsets_BestTrees_WithBootstraps_...ewick (83.63 Kb)
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Title RAxML_AllSubsets_BestTrees_WithBootstraps_100bp_NotParitioned
Downloaded 4 times
Description 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.
Download RAxML_AllSubsets_BestTrees_WithBootstraps_...ewick (114.6 Kb)
Download README.txt (18.45 Kb)
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When using this data, please cite the original publication:

Provost KL, Joseph L, Smith BT (2017) Resolving a phylogenetic hypothesis for parrots: implications from systematics to conservation. Emu – Austral Ornithology, online in advance of print. https://doi.org/10.1080/01584197.2017.1387030

Additionally, please cite the Dryad data package:

Provost KL, Joseph L, Smith BT (2017) Data from: Resolving a phylogenetic hypothesis for parrots: implications from systematics to conservation. Dryad Digital Repository. https://doi.org/10.5061/dryad.m6n2t
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