Data from: Resolving a phylogenetic hypothesis for parrots: implications from systematics to conservation
Data files
Sep 14, 2018 version files 548.54 MB
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best_scheme_Subset_XX_Genes_rcluserf.part Partition files.zip
17.22 KB
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COMBINED_Parrots_XXXX.asc ASCII raster files.zip
1.98 MB
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ConcatenatedGbFiles_Parrots_March2017.gb
542.14 MB
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extractReferencesFromGenbank.py
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Figure Making Scripts.zip
18.62 KB
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Genbank Pipeline Main Scripts.zip
6.71 KB
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Genbank Pipeline Subscripts.zip
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getUniqueGbAccession.py
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Intraspecific_Genetic_Sampling_Citations.csv
46.18 KB
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Map Making Scripts.zip
3.96 KB
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RAxML_AllSubsets_BestTrees_WithBootstraps_100bp_NotParitioned.newick
114.70 KB
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RAxML_AllSubsets_BestTrees_WithBootstraps_100bp_Partitioned.newick
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README_for_best_scheme_Subset_XX_Genes_rcluserf.part Partition files.txt
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README_for_COMBINED_Parrots_XXXX.asc ASCII raster files.txt
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README_for_ConcatenatedGbFiles_Parrots_March2017.txt
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README_for_extractReferencesFromGenbank.txt
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README_for_Figure Making Scripts.txt
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README_for_Genbank Pipeline Main Scripts.txt
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README_for_Genbank Pipeline Subscripts.txt
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README_for_Intraspecific_Genetic_Sampling_Citations.txt
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README_for_Map Making Scripts.txt
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README_for_RAxML_AllSubsets_BestTrees_WithBootstraps_100bp_NotParitioned.txt
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README_for_RAxML_AllSubsets_BestTrees_WithBootstraps_100bp_Partitioned.txt
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README_for_RunPartitionFinder_Subset_XX_Genes_rclusterf.cfg Config Files.txt
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README_for_Subset_XX_Genes_100bp.fasta Alignment Files.txt
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RunPartitionFinder_Subset_XX_Genes_rclusterf.cfg Config Files.zip
21.74 KB
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Subset_XX_Genes_100bp.fasta Alignment Files.zip
3.84 MB
Sep 14, 2018 version files 548.54 MB
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best_scheme_Subset_XX_Genes_rcluserf.part Partition files.zip
17.22 KB
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COMBINED_Parrots_XXXX.asc ASCII raster files.zip
1.98 MB
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ConcatenatedGbFiles_Parrots_March2017.gb
542.14 MB
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extractReferencesFromGenbank.py
1.23 KB
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Figure Making Scripts.zip
18.62 KB
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Genbank Pipeline Main Scripts.zip
6.71 KB
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Genbank Pipeline Subscripts.zip
33.07 KB
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getUniqueGbAccession.py
1.25 KB
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Intraspecific_Genetic_Sampling_Citations.csv
46.18 KB
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Map Making Scripts.zip
3.96 KB
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RAxML_AllSubsets_BestTrees_WithBootstraps_100bp_NotParitioned.newick
114.70 KB
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RAxML_AllSubsets_BestTrees_WithBootstraps_100bp_Partitioned.newick
83.64 KB
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README_for_best_scheme_Subset_XX_Genes_rcluserf.part Partition files.txt
18.38 KB
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README_for_COMBINED_Parrots_XXXX.asc ASCII raster files.txt
18.38 KB
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README_for_ConcatenatedGbFiles_Parrots_March2017.txt
18.38 KB
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README_for_extractReferencesFromGenbank.txt
18.38 KB
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README_for_Figure Making Scripts.txt
18.38 KB
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README_for_Genbank Pipeline Main Scripts.txt
18.38 KB
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README_for_Genbank Pipeline Subscripts.txt
18.38 KB
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README_for_Intraspecific_Genetic_Sampling_Citations.txt
18.38 KB
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README_for_Map Making Scripts.txt
18.38 KB
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README_for_RAxML_AllSubsets_BestTrees_WithBootstraps_100bp_NotParitioned.txt
18.45 KB
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README_for_RAxML_AllSubsets_BestTrees_WithBootstraps_100bp_Partitioned.txt
18.45 KB
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README_for_RunPartitionFinder_Subset_XX_Genes_rclusterf.cfg Config Files.txt
18.38 KB
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README_for_Subset_XX_Genes_100bp.fasta Alignment Files.txt
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README.md
208 B
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RunPartitionFinder_Subset_XX_Genes_rclusterf.cfg Config Files.zip
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Subset_XX_Genes_100bp.fasta Alignment Files.zip
3.84 MB
Abstract
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.
https://doi.org/10.5061/dryad.m6n2t
See individual READMEs