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 suggests either that bower-building behavior is an ancestral condition in the family that was secondarily lost in the catbirds, or that it has arisen in parallel in two lineages of bowerbirds. We favor the latter hypothesis based on an ancestral character reconstruction showing that polygyny but not bower-building is ancestral in bowerbirds, and on the observation that Scenopoeetes dentirostris, the sister species to one of the bower-building clades, does not build a proper bower but constructs a court for male display. This species is also sexually monomorphic in plumage despite having a polygynous mating system. We argue that the relatively stable tropical and subtropical forest environment in combination with low predator pressure and rich food access (mostly fruit) facilitated the evolution of these unique life-history traits. 

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, based on a calculated distance matrix using OD-Seq (github.com/PeterJehl/OD-Seq), and excluded from the further analyses. We also checked the alignments manually and removed those that included non-homologous sequences for some taxa (indicated by an extreme proportion of variable positions in the alignment) and those that contained no phylogenetically information. Individual trees were constructed using IQ-TREE that automatically selects the best substitution model for each loci alignment. We used ASTRAL-III to construct species trees from the gene trees both for the exonic and intronic loci separately and for all loci combined. ASTRAL estimates a species tree given a set of unrooted gene trees and branch support is calculated using local posterior probabilities. We assembled mitochondrial genomes from the resequenced data for each individual using MITObim , and used 12 of the 13 protein-coding genes to infer the phylogenetic tree. The aligned mitochondrial data set used in the analyses consists of 10,560 bp (3,520 codons). The phylogenetic analysis of the mitogenomic data set was performed with MEGA X . We estimated the maximum-likelihood tree for the mitochondrial data using 100 bootstrap replicates to assess the reliability of the branches. The data set was analyzed both with all codon positions present and with the third codon positions excluded.

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 file with more details about material and methods, figures and tables, as well as some text about the systematic relationships observed

9. one file with the time-tree (figure S5) in nexus format