Phylogenetic tree data for: Frequent hybridisation between parapatric lekking bird-of-paradise species

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 select..., 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; Astrapia and Paradigalla) including individuals from the genera Lycocorax, Manucodia and Phonygammus as an outgroup. 
All raw reads generated for this study have been deposited at the European Nucleotide Archive (ENA), accession number PRJEB73831., , # 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....,