Parallel evolution of bower-building behavior in two groups of bowerbirds suggested by phylogenomics

The bowerbirds in New Guinea and Australia include species that build the largest and perhaps most elaborately decorated constructions outside of humans. The males use these courtship bowers, along with their displays, to attract females. In these species, the mating system is polygynous and the females alone incubate and feed the nestlings. The bowerbirds also include 10 species of the socially monogamous catbirds in which the male participates in most aspects of raising the young. How the bower-building behavior evolved has remained poorly understood, as no comprehensive phylogeny exists for the family. It has been assumed that the monogamous catbird clade is sister to all polygynous species. We here test this hypothesis using a newly developed pipeline for obtaining homologous alignments of thousands of exonic and intronic regions from genomic data to build a phylogeny. Our well-supported species tree shows that the polygynous, bower-building species are not monophyletic. The result ..., This is supplementary material to the manuscript \"Parallel evolution of bower-building behavior and polygyny in two groups of bowerbirds suggested by phylogenomics\". We used the Birdscanner pipeline (available at github.com/Naturhistoriska/birdscanner.git) to obtain homologous alignments of 5653 exonic and 7020 intronic regions from whole-genome sequence data. The pipeline utilize probabilistic queries using hidden Markov models that were used to probe the mapped bowerbird genomes to find where they had their best fit. For each query and taxon we obtained genomic coordinates for the best hits that were then ranked according to their “sequence E-values”, i.e. the expected number of false positives (non-homologous sequences) that scored this well or better. For each query and taxon the sequences for the hits with the lowest values were parsed out using the genomic coordinates. These were then aligned in separate files for exonic and intronic loci. Poorly aligned sequences were identified,..., This Dryad submission consists of:
1. one file with a description of the content (readme.txt).
2. two tar-zipped files with individual alignments of exonic and intronic loci, respectively, obtained from whole-genome sequencing data of 37 bowerbird taxa and 3 outgroups. NOTE: the file with intronic alignments has been updated to include all 7020 loci.
3. two tar-zipped files with individual treefiles obtained by the program IQTREE for 5653 exonic and 7020 intronic loci, respectively.
4. three files with concatenations of the individual treefiles for a) 5653 exonic loci, b) 7020 intronic loci, and c) these exonic and intronic loci combined.
5. three tree files obtained by ASTRAL for a) 5653 exonic loci, b) 7020 intronic loci, and c) these exonic and intronic loci combined.
6. two files with alignments of concatenations of all intronic and exonic loci, respectively.
7. one file with the alignment of 11 mitochondrial coding genes (10,560 bp) for 34 bowerbird taxa and 3 outgroups.
8. one pdf...,