DOI: 10.5061/dryad.rn8pk0pnt
title: Phylogenetic tree data for: Frequent hybridisation between parapatric lekking bird-of-paradise species

description: Hybridisation is known to occur between a wide range of taxa, including
 species for which strong sexual selection has led to markedly different
 sexual phenotypes and lek-mating behaviours. To what extent occasional
 hybridisation can overcome the reproductive barriers in such systems, and,
 for example, lead to the establishment of hybrid zones, is poorly known.
 In this study, we address this question by focusing on one of the most
 well-known avian radiations in which sexual selection has resulted in an
 extraordinary assemblage of phenotypic diversity and lek-mating
 behaviours; the birds-of-paradise (Paradisaeidae). We quantify the
 genome-wide distribution of introgression and find multiple signals of
 recent and historical gene flow between and within two genera of
 birds-of-paradise, Astrapia and Paradigalla. In addition, we present the
 first empirical genomic evidence of a putative hybrid zone between two
 lekking bird-of-paradise species that differ substantially in their
 sexually selected traits and behaviours. Our findings are consistent with
 the idea that behavioural and phenotypic traits may constitute weaker pre-
 and post-zygotic barriers to gene flow than generally thought in
 lek-mating species.
description: This project contains autosomal phylogentic tree files and
 concatenated phylogenetic tree files generated with https://github.com/MozesBlom/nf-phylo for window sizes 1000bp, 5000bp, 10000bp and 20000bp and mitochondria phylogenetic trees and alignments for seven species of birds-of-paradise (genera; <em>Astrapia </em>and <em>Paradigalla</em>) including individuals from the genera <em>Lycocorax, </em><em>Manucodia</em> and <em>Phonygammus </em>as an outgroup.  All raw reads generated for this study have been deposited at the European Nucleotide Archive (ENA), accession number PRJEB73831.
description: # Phylogenetic tree data for: Frequent hybridisation between parapatric
 lekking bird-of-paradise species
 [https://doi.org/10.5061/dryad.rn8pk0pnt](https://doi.org/10.5061/dryad.rn8pk0pnt) ## Description of the data and file structure Descriptions of methods from related paper. **Autosomal phylogenetic trees** The autosomal phylogenetic tree was constructed using a whole genome phylogenetic inference pipeline; nf-phylo ([https://github.com/MozesBlom/nf-phylo](https://github.com/MozesBlom/nf-phylo)). Consensus sequences were constructed for each individual, based on hard called variants per individual using freebayes (v.1.3.1; Garrison & Marth, 2012); heterozygous sites, low depth sites (3x), extreme high depth sites (100x) were masked, Multiple Nucleotide Polymorphisms (MNPs) were decomposed, and indels were removed. Four different window sizes (1kb, 5kb, 10kb and 20kb) were sampled every 100kb, a phylogeny inferred for each window trees using IQtree2 (v.2.0.3; Minh, Schmidt, et al., 2020), and a summary-coalescent species tree inferred using ASTRAL3 (v5.7.8; Zhang et al., 2018). Each window was filtered and assessed for a range of criteria. Alignment columns were removed if more than 40% individuals were missing for that position, individuals were removed with more than 50% missing data and windows were entirely filtered out if the length of the resulting window was below 50% of the original window length or if more than 20% of the individuals were missing. If windows were filtered out, the adjacent window was selected and evaluated for the same criteria. A gene tree was inferred for each filtered window using IQtree’s and ModelFinderPlus to determine the best substitution model on a per-windows basis (Kalyaanamoorthy et al., 2017). We also used IQtree2 to reconstruct maximum likelihood phylogenetic trees by concatenating all autosomal windows for each different window size (1kb, 5kb, 10kb and 20kb), using the general time reversible model allowing for a proportion of invariable sites with a discrete gamma distribution with four categories (GTR+I+G). Finally, site and window concordance factors were calculated (Minh, Hahn, et al., 2020) and added for branch support in the resulting phylogenetic tree. **Mitochondrial phylogenetic trees** An alignment of the assembled mitochondria was constructed with MAFFT using the Needleman-Wunsch algorithm to align pairs (--globalpair) within 1000 iterations (v.7.407; Katoh et al., 2002). A maximum likelihood phylogenetic tree was constructed from the alignment using RaxML-NG with the GTR-G substitution model and 100 bootstrap replicates(v.0.1.1; Kozlov et al., 2019). The mitochondrial phylogenetic tree was plotted with R (4.3.0) using the packages ggplot2 (v.3.4.2 ) and ggtree (v3.7.2; Yu et al., 2017). ### Files and variables #### File: 20000_bp_autosomal_windows_ASTRAL_wCF_sCF.cf.tree.nex **Description:** nf-phylo output for 20000bp autosomal summary coalescent phylogenetic tree. #### File: 20000_bp_autosomal_windows_ASTRAL_wCF_sCF.cf.tree **Description:** nf-phylo output for 20000bp autosomal summary coalescent phylogenetic tree. #### File: 20000_bp_autosomal_windows_ASTRAL_wCF_sCF.cf.stat **Description:** nf-phylo output for 20000bp autosomal summary coalescent phylogenetic tree. #### File: 20000_bp_autosomal_windows_ASTRAL_wCF_sCF.cf.branch **Description:** nf-phylo output for 20000bp autosomal summary coalescent phylogenetic tree. #### File: 20000_bp_autosomal_windows_ASTRAL.tree **Description:** nf-phylo output for 20000bp autosomal summary coalescent phylogenetic tree. #### File: 10000_bp_autosomal_windows_ASTRAL_wCF_sCF.cf.tree.nex **Description:** nf-phylo output for 10000bp autosomal summary coalescent phylogenetic tree. #### File: 10000_bp_autosomal_windows_ASTRAL_wCF_sCF.cf.tree **Description:** nf-phylo output for 10000bp autosomal summary coalescent phylogenetic tree. #### File: 10000_bp_autosomal_windows_ASTRAL_wCF_sCF.cf.stat **Description:** nf-phylo output for 10000bp autosomal summary coalescent phylogenetic tree. #### File: 10000_bp_autosomal_windows_ASTRAL_wCF_sCF.cf.branch **Description:** nf-phylo output for 10000bp autosomal summary coalescent phylogenetic tree. #### File: 10000_bp_autosomal_windows_ASTRAL.tree **Description:** nf-phylo output for 10000bp autosomal summary coalescent phylogenetic tree. #### File: 5000_bp_autosomal_windows_ASTRAL_wCF_sCF.cf.stat **Description:** nf-phylo output for 5000bp autosomal summary coalescent phylogenetic tree. #### File: 5000_bp_autosomal_windows_ASTRAL_wCF_sCF.cf.tree.nex **Description:** nf-phylo output for 5000bp autosomal summary coalescent phylogenetic tree. #### File: 5000_bp_autosomal_windows_ASTRAL_wCF_sCF.cf.tree **Description:** nf-phylo output for 5000bp autosomal summary coalescent phylogenetic tree. #### File: 5000_bp_autosomal_windows_ASTRAL_wCF_sCF.cf.branch **Description:** nf-phylo output for 5000bp autosomal summary coalescent phylogenetic tree. #### File: 5000_bp_autosomal_windows_ASTRAL.tree **Description:** nf-phylo output for 5000bp autosomal summary coalescent phylogenetic tree. #### File: 1000_bp_autosomal_windows_ASTRAL_wCF_sCF.cf.tree.nex **Description:** nf-phylo output for 1000bp autosomal summary coalescent phylogenetic tree. #### File: 1000_bp_autosomal_windows_ASTRAL_wCF_sCF.cf.tree **Description:** nf-phylo output for 1000bp autosomal summary coalescent phylogenetic tree. #### File: 1000_bp_autosomal_windows_ASTRAL_wCF_sCF.cf.stat **Description:** nf-phylo output for 1000bp autosomal summary coalescent phylogenetic tree. #### File: 1000_bp_autosomal_windows_ASTRAL_wCF_sCF.cf.branch **Description:** nf-phylo output for 1000bp autosomal summary coalescent phylogenetic tree. #### File: 1000_bp_autosomal_windows_ASTRAL.tree **Description:** nf-phylo output for 1000bp autosomal summary coalescent phylogenetic tree. #### File: AstPar_mtDNA_mafft_Ginsi_GTR_G.raxml.support **Description:** RAxML-NG output for Mitocondrial phylogenetic tree. #### File: AstPar_mtDNA_mafft_Ginsi_GTR_G.raxml.mlTrees **Description:** RAxML-NG output for Mitocondrial phylogenetic tree. #### File: AstPar_mtDNA_mafft_Ginsi_GTR_G.raxml.bestTree **Description:** RAxML-NG output for Mitocondrial phylogenetic tree. #### File: AstPar_mtDNA_mafft_Ginsi_GTR_G.raxml.bestModel **Description:** RAxML-NG output for Mitocondrial phylogenetic tree. #### File: AstPar_mtDNA_mafft_Ginsi_GTR_G.raxml.startTree **Description:** RAxML-NG output for Mitocondrial phylogenetic tree. #### File: AstPar_mtDNA_mafft_Ginsi_GTR_G.raxml.bootstraps **Description:** RAxML-NG output for Mitocondrial phylogenetic tree. #### File: AstPar_mtDNA_mafft_Ginsi_GTR_G.raxml.reduced.phy **Description:** RAxML-NG output for Mitocondrial phylogenetic tree. #### File: AstPar_mtDNA_mafft_Ginsi.fa **Description:** Mitochondrial alignment. #### File: 5000bp_autosomal_windows_concat_wCF_sCF.cf.tree.nex **Description:** nf-phylo output for 5000bp concatenated phylogenetic tree. #### File: 5000bp_autosomal_windows_concat_wCF_sCF.cf.tree **Description:** nf-phylo output for 5000bp concatenated phylogenetic tree.  #### File: 5000bp_autosomal_windows_concat_wCF_sCF.cf.stat **Description:** nf-phylo output for 5000bp concatenated phylogenetic tree.  #### File: 5000bp_autosomal_windows_concat_wCF_sCF.cf.branch **Description:** nf-phylo output for 5000bp concatenated phylogenetic tree.  #### File: 5000bp_autosomal_windows_concat.treefile **Description:** nf-phylo output for 5000bp concatenated phylogenetic tree.  #### File: 20000bp_autosomal_windows_concat_wCF_sCF.cf.tree.nex **Description:** nf-phylo output for 20000bp concatenated phylogenetic tree. #### File: 20000bp_autosomal_windows_concat_wCF_sCF.cf.stat **Description:** nf-phylo output for 20000bp concatenated phylogenetic tree. #### File: 20000bp_autosomal_windows_concat_wCF_sCF.cf.tree **Description:** nf-phylo output for 20000bp concatenated phylogenetic tree. #### File: 20000bp_autosomal_windows_concat_wCF_sCF.cf.branch **Description:** nf-phylo output for 20000bp concatenated phylogenetic tree. #### File: 20000bp_autosomal_windows_concat.treefile **Description:** nf-phylo output for 20000bp concatenated phylogenetic tree. #### File: 1000bp_autosomal_windows_concat_wCF_sCF.cf.tree.nex **Description:** nf-phylo output for 1000bp concatenated phylogenetic tree. #### File: 1000bp_autosomal_windows_concat_wCF_sCF.cf.tree **Description:** nf-phylo output for 1000bp concatenated phylogenetic tree. #### File: 1000bp_autosomal_windows_concat_wCF_sCF.cf.branch **Description:** nf-phylo output for 1000bp concatenated phylogenetic tree. #### File: 1000bp_autosomal_windows_concat.treefile **Description:** nf-phylo output for 1000bp concatenated phylogenetic tree. #### File: 1000bp_autosomal_windows_concat_wCF_sCF.cf.stat **Description:** nf-phylo output for 1000bp concatenated phylogenetic tree.