DOI: 10.5061/dryad.6hdr7sqwp
title: Data from: Parallel evolution of bower-building behavior in two groups of bowerbirds suggested by phylogenomics

description: 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. 
description: 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.
description: 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