DOI: 10.5061/dryad.t4b8gtjbc
title: Data from: Introgressed variants obscure phylogenetic relationships but are not subject to positive selection in Australasian long-tailed parrots

description: Gene flow often obscures phylogenetic relationships, but the evolutionary
 significance of introgressed variants is unclear. Here, we examine the
 Australasian long-tailed parrots (Psittaculinae: Polytelini), in which an
 unexpected sister relationship between Polytelis alexandrae and the genus
 Aprosmictus, and not the other Polytelis species, has been observed. We
 tested whether this relationship was due to ancient introgression in whole
 genomes and found that the majority of gene trees had Ap. erythropterus
 and P. alexandrae as sister taxa, whereas network analysis indicated
 monophyly of Polytelis, and 48% of gene trees were in phylogenetic
 conflict due to introgression from Ap. erythropterus into P. alexandrae.
 Some 4–8% of the genome of P. alexandrae was introgressed from Ap.
 erythropterus, with signals of gene flow occurring throughout the genome.
 These findings indicate that topologies with P. alexandrae and the genus
 Ap. erythropterus as sister taxa were biased by gene flow and affirm that
 Polytelis is monophyletic. Next, we assessed the evolutionary outcomes for
 introgressed variants and found that, among introgressed protein-coding
 genes, only two (0.8%) were under positive selection, in comparison to 99
 (1.7%) of non-introgressed genes. Our results indicate that, despite the
 ubiquity of genetic introgression across a given phylogeny, many genetic
 variants flowing between species may play a small role in molecular
 adaptations, with selection most frequently acting on existing variation.
description: The data was generated using the methods described herein and in
 the manuscript Smith et al. "Introgressed variants obscure
 phylogenetic relationships but are not subject to positive selection in
 Australasian long-tailed parrots."
description: README.md file was updated on Oct 24, 2024 (edited May 1, 2025; Oct 29
 2025) by Brian T. Smith & Agusto Luzuriaga-Neira.\ Contacts:
 [bsmith1@amnh.org](mailto:bsmith1@amnh.org),
 [aluzuriaganeira@amnh.org](mailto:aluzuriaganeira@amnh.org). Scripts,
 lists of commands, and complementary files used in data analyses related
 to: # **“Introgressed variants obscure phylogenetic relationships but are
 not subject to positive selection in Australasian long-tailed parrots.”**
 --- # Authors: ``` Brian Tilston Smith Department of Ornithology, American
 Museum of Natural History, Central Park West at 79th Street, New York, NY
 10024, USA Agusto Luzuriaga-Neira Department of Ornithology, American
 Museum of Natural History, Central Park West at 79th Street, New York, NY
 10024, USA David Alvarez-Ponce Biology Department, University of Nevada,
 Reno, Reno, NV 89557, USA Kaiya L. Provost Biology Department, Adelphi
 University, Garden City, NY 11530, USA Gregory Thom Museum of Natural
 Science and Department of Biological Sciences, Louisiana State University,
 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 the dataset** These data were collected to infer
 phylogenetic relationships among a group of Australian long tailed
 parrots. This submission includes files, scripts and commands to reproduce
 the results presented in the study. Additional files to reproduce the
 results can be found in the NCBI bioproject **PRJNA1157411** or provided
 by the authors upon request. The dataset is organized in hierarchical
 structure. ├── Data.tar.gz: Contains input files and some of the output
 files, we avoid uplaodig large input and output files. They are available
 upon request. │   ├── abba-baba-test: Input files for abba-baba-test using
 Dsuite, including a bed file for the gaped analysis. │   │   ├──
 concatenatedtree.nwk │   │   └── sets.txt │   ├── aphid-analysis: Contains
 input files and output files from aphid introgression analysis. │   │  
 ├── aphid_out.csv │   │   ├── aphid_out.log │   │   ├── gaped-loci.bed │  
 │   ├── ltailed_parrots.in │   │   ├── ltailed_parrots.opt │   │   ├──
 ltailed_parrots.tax │   │   └── ltailed_parrots.trees │   ├──
 astral-tree-est: Contains the list of trees used as astral input and the
 output files. │  │   ├── 295503loci.trees │   │   └──
 polytelis_295503_GT.astral.tre │   ├── bpp-introg-analysis: Contains the
 ima and input control files used for BPP introgression analyses, input
 alignments are available under request. │   │   ├── A00-ale-Apr_bpp.ctl
 │   │   ├── imap-ale-apr.txt │   │   ├── imap.txt │   │   └──
 polytelis-bpp-msci-100.ctl │   ├── busco-whole-genome: Contain the image
 summarizing the BUSCO scores for all read mapping genomes used in this
 study. │   │   ├── busco_figure.png │   │   └── fastas.list │   ├──
 cds-prediction: Contains fast file of read mapping genomes and the list of
 the NCBI genome accesions of genomes used as reference. │   │   ├──
 ncbi_acc_ref_geno.list │   │   └── reaad-mapped-based-genomes │   │   ├──
 ale_PRS4773.fas │   │   ├── ali_ANWCB3182.fas │   │   ├──
 ant_ANWCB31719.fas │   │   ├── apr_ANWCB43803.fas │   │   └──
 swa_ANWCB53967.fas │   ├── genome-processing: Contains vcf file resulting
 of GATK haplotype calling and the list of ncbi SRA accesions of the
 sequences generated and used in this study. Also includes the bed file
 used to split whole genome alignment in 50 SNPs windows │   │   ├──
 1_50SNPs_windows.bed │   │   ├── SNP-only_filtered_no_MD.recode_ren.vcf.gz
 │   │   └── wgs_ncbi_acces.txt │   ├── genome-stats: Contains the *.geno
 and the pop set file used to calculate genome statistics, including bed
 files for gaped and non-gaped analysis. │   │   ├── 295kregions.sort.bed
 │   │   ├── gaped_loci.bed │   │   ├── input.geno.gz │   │   └── pops.txt
 │   ├── paml-sel-test: Contains the CDS's, alignments and the control
 files used for positive selection in paml. │   │   ├──
 06-outFilteredPhy.tar.gz │   │   ├── ale_PRS4773_filt.codingseq │   │  
 ├── ali_ANWCB3182_filt.codingseq │   │   ├── ant_ANWCB31719_filt.codingseq
 │   │   ├── apr_ANWCB43803_filt.codingseq │   │   ├── M1a.ctl │   │   ├──
 M2a.ctl │   │   ├── M7.ctl │   │   ├── M8.ctl │   │   ├── MA.ctl │   │  
 ├── mel_GCF_012275295.1_filt.codingseq │   │   ├── nullMA.ctl │   │   ├──
 swa_ANWCB53967_filt.codingseq │   │   ├── tree1.trees │   │   └──
 tree2.trees │   ├── SNaQ-analysis: Contains the list of trees used for
 SNaQ analysis. │   │   ├── allpolytrees.unroot.txt │   │   ├──
 gaped_loci.bed │   │   └── species_tree.nwk │   ├── snpeff-variant-an:
 Contains annotated vcf file from GF and non-GF snps as well their summary
 in html format. The annotation was performed using snpeEffect software.
 │   │   ├── ale-apr-gf-annon.vcf.gz │   │   ├── gf_ale-apr_summary.html
 │   │   ├── nointro_only_ale-apr.annon.vcf.gz │   │   └──
 non-intro-ale-apr_snpEff.html │   └── uces-processing: Contains the list
 of UCE's SRA accessions, input and output files used in this study.
 │   ├── mafft-nexus-clean-75p.charsets │   ├──
 mafft-nexus-clean-75p.phylip │   ├── mafft-nexus-clean-75p.phylip.contree
 │   └── uces_ncbi_sra_acc.tsv ├── README.md: Describe the files in the
 repository. ├── Scripts.tar.gz: Contains the list of scripts and command
 lines used in this study, bash scripts need to be adapted to the local
 configuration to run directly from command line. Any doubts contact the
 authors. Scripts are organized by analysis in their respective folder. │  
 ├── abba-baba-test │   │   └── run_dsuite.sh │   ├── aphid-analysis │  
 │   └── runAphid.sh │   ├── astral-tree-est │   │   └──
 astral_tree_est_cmd.sh │   ├── bpp-introg-analysis │   │   └──
 run_bpp_cmd.sh │   ├── busco-whole-genome │   │   └── run_busco_loop.sh
 │   ├── cds-prediction │   │   └── run_gmoma.sh │   ├──
 gene-tree-estimation │   │   ├── 1_50SNPs_windows.bed │   │   ├──
 1_producing_50SNP_window \_alignments.sh │   │   ├── loop2.sh │   ├──
 genome-processing │   │   ├── 1_producing_50SNP_window \_alignments.sh │  
 │   ├── A1.reheader_bams.sh │   │   ├── fix_vcf_headers.py │   │   ├──
 loop2.sh │   │   ├── split_genetrees_directories.sh │   │   ├──
 STEP01-BWA_alignment_filtZF_Parrots_combined.job │   │   ├──
 STEP02.1-GATK_SNP_calling_parrots.job │   │   ├──
 STEP02-GATK_SNP_calling_parrots.job │   │   ├──
 STEP03-1-GATK_SNP_GVCF_parrots.job │   │   ├──
 STEP03.1-Validade_Variants_parrots.job │   │   ├──
 STEP04.1-GATK_Variant_Quality_parrots.job │   │   ├──
 STEP04-GATK_SNP_GVCF_combine_parrots.job │   │   ├──
 STEP05.0-GATK_SNP_filter_parrots.job │   │   ├──
 STEP06-GATK_SNP_BQSR_parrots.job │   │   └──
 STEP8.0-GATK_SNP_select_variants.job │   ├── genome-stats │   │   └──
 run_popgen_stats.sh │   ├── paml-sel-test │   │   └── run_paml_sel_test.sh
 │   ├── SNaQ-analysis │   │   ├── launch_snaq.job │   │   ├──
 network_est_cmd.jl │   │   └── snaq_boot.jl │   ├── snpeff-variant-an │  
 │   └── run_Snpeff.sh │   └── uces-processing │   │   ├── uces_proc_cmd.sh
 │   │   └── uces_tree_cmd.sh └── SupplementaryTablesAndFigures.tar.gz:
 Contains supplementary tables and figures mentioned in the main text of
 the aritcle. ├── Supplementary-Figures.pdf └── Supplementary-Tables.xlsx
 ``` 29 directories, 91 files ```