DOI: 10.5061/dryad.h70rxwdrx
title: Data from: Revised evolutionary and taxonomic synthesis for parrots (order: Psittaciformes) guided by phylogenomic analysis

description: Parrots (Order: Psittaciformes) are a diverse clade that are easily
 distinguishable from other birds. Despite the clear characters that define
 the Psittaciformes (hooked bills, zygodactylous feet, and plumage that is
 often predominantly green or red), relative morphological uniformity among
 parrots has made taxonomic classification a fraught endeavor for over a
 century. Parrot systematics were propelled forward when DNA sequencing
 data shed insights into higher- and species-level relationships. However,
 despite these significant advances, major gaps in taxon sampling and
 uncertainty in relationships remained due to inferring phylogenetic
 relationships with short fragments of DNA. Recent work using genome-wide
 molecular markers with nearly complete parrot species-level sampling has
 brought clarity to many of the remaining outstanding questions on
 taxonomic relationships. Here, we build on this work by including four
 additional species to present a taxonomic revision of Psittaciformes
 better aligned with its evolutionary tree. We infer maximum likelihood and
 time-calibrated phylogenies for parrots, present accounts for 106 genera,
 compare how our findings relate to previous work, and highlight future
 areas of research. The family-group nomenclature we propose reflects deep
 evolutionary divergences with diagnosable synapomorphies that are
 commensurate across comparable ranks in psittaciform clades. We erect
 three new family-group names at the rank of tribe (Brotogerini Smith, Thom
 and Joseph, 2024; Neophemini Schodde, Smith, Thom and Joseph, 2024;
 Bolbopsittacini Smith, Thom and Joseph, 2024). We elevate one tribe to
 subfamily rank for the cacatuid genus Probosciger and we restrict usage of
 the recently introduced tribe Touitini to its type-genus Touit. At
 shallower taxonomic scales, recognition of more rather than fewer genera
 addresses issues of paraphyly or high discordance in morphological and
 genomic characters at those levels. We support many reinstatements of
 older generic names advocated in recent decades and we further reinstate
 five valid, available generic names not widely used in recent literature
 if at all (Licmetis, Gymnopsittacus, Clarkona, Suavipsitta, Cardeos). We
 advocate the retention of Vini Lesson, 1833 over Coriphilus Wagler, 1832
 based on preliminary examination showing substantially more frequent usage
 of the former. We redraw generic limits in some other cases (e.g.,
 Bolborhynchus parrotlets and allies) and this includes recognizing fewer
 genera than recently proposed for the Psittacula sensu lato ringneck
 parakeets. Our revised classification of parrots addresses many
 longstanding taxonomic questions including those that have arisen through
 the acquisition of genetic data. It provides context for the temporal
 origins of psittaciform clades and the taxonomic and phenotypic
 diversification throughout their evolutionary history. We hope that it
 will be a benchmark guiding further taxonomic study as well as for
 downstream analyses in many other fields.
description: Please see Methods section of the main
 text.
description: # Revised evolutionary and taxonomic synthesis for parrots (order:
 Psittaciformes) guided by phylogenomic analysis README file was updated on
 18-March-2024 by Brian T. Smith Supplementary files and data from: Revised
 evolutionary and taxonomic synthesis for parrots (order: Psittaciformes)
 guided by phylogenomic analysis Authors: Brian Tilston Smith Department of
 Ornithology, American Museum of Natural History, Central Park West at 79th
 Street, New York, NY 10024, USA Gregory Thom Museum of Natural Science,
 Louisiana State University, 119 Foster Hall, Baton Rouge, LA 70803, USA
 Department of Biological Sciences, Louisiana State University, 202 Life
 Science Bldg, Baton Rouge, LA 70803, USA Leo Joseph Australian National
 Wildlife Collection, National Research Collections Australia, CSIRO, GPO
 Box 1700, Canberra, ACT, 2601, Australia DATA & FILE OVERVIEW
 Description of dataset These data were collected to infer phylogenetic
 relationships among parrots. This submission includes the data and files
 to reproduce the results. The scripts/commands to reproduce the results
 presented in the study are available in Smith, Brian Tilston (2022).
 Dataset for: Smith et al., Phylogenomic analysis of the parrots of the
 world distinguishes artifactual from biological sources of gene tree
 discordance [Dataset]. Dryad.
 [https://doi.org/10.5061/dryad.b5mkkwhfm](https://doi.org/10.5061/dryad.b5mkkwhfm) List of Directories Name: Supplementary_table Description: Supplementary Table S1 Name: full-locus-alignments Description: FASTA alignments for the full datasets Name: Time_calibrated_tree Description: Input and output for molecular dating in treePL List of files and subdirectories within main directories: Directory: Supplementary_table Name: Supplementary_Table_S1.csv Description: Table summarizing samples used in this study with locality data and accession numbers. Directory: Alignment Name: mafft-nexus-clean-75p.phylip Description: 1142292 bp concatnetated alignmnet of ultraconserved loci (UCEs) that contains 388 species Name: mafft-nexus-clean-75p.charsets Description: Partition file showing the start and end point of each UCE locus in the concatenated alignment (mafft-nexus-clean-75p.phylip) Name: rename_tips.sh Description: Script to convert species ids to full names Directory: Time_calibrated_tree Name: MCC-CMA-9-Oct-2023-root-mafft-nexus-clean-75p.charsets-100-rooted-smooth-1-revised-names.tre Description: MMC tree with common ancestor heights specified Name: 9-Oct-2023-385-ingroup-bootstrap-trees-treePL.100.conf Description: treePL configuratiuon file Name: 9-Oct-2023-pxrr-root-mafft-nexus-clean-75p.charsets-100-rooted.ufboot Description: Dated, rooted bootstrap trees DATA-SPECIFIC INFORMATION FOR: ~/Supplementary_table/Supplementary_Table_S1.csv 1. Number of variables: 13 2. Variable List: SAMN Accession Number: Short Read Archive accession number Sample Name on Tree: Name of sample on the tree Organism: Genus and species name Genus: Genus the sample belongs to Species: Species epithet of sample Country: Coutry where sample was collected. Some samples come from captivity Locality: Specific locality of samples Date: When the sample was collected Lat: Latitude of where the sample was collected Long: Longitude of where the sample was collected Sex: Sex of the sample Institution Code: Code of the institution that provided the sample Sample Type: Samples were assigned to eithe historical (skin) or modern material (tissue)