Data from: Revised evolutionary and taxonomic synthesis for parrots (order: Psittaciformes) guided by phylogenomic analysis
Data files
Mar 24, 2024 version files 101.70 MB
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Alignment.zip
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README.md
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Time_calibrated_tree.zip
Abstract
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.
README: 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
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
Number of variables: 13
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)
Methods
Please see Methods section of the main text.