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

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 phylogenet...,
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 scr..., , # 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)

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