Library preparation, and whole genome sequencing
We used a modified library preparation based on Illumina’s Nextera protocol to sequence entire genomes of 283 birds. To start, genomic DNA was standardized to 3ng/µl then underwent a tagmentation step using TDE1 enzyme and buffer (Illumina). Dual combination Nextera indexes (Illumina) were then added to tagged DNA fragments followed by a booster PCR using the Kapa HiFi Kit (Kapa Biosystems). Libraries were then bead cleaned and single size selected to remove fragments < 320bp using AMPure XP Beads (Beckman Coulter) and quantified using a Qubit Fluorometer (Thermo Fisher Scientific). All libraries were pooled equimolarly then visualized with a Bioanalyzer (Agilent). The pooled libraries were further size selected to 320-500bp fragments using Ampure XP Beads (Beckman Coulter). A subset of samples (N=40) was size selected using Blue Pippin (Sage Science; University of California Davis Genome Center). The final libraries were sequenced on an Illumina HiSeq 4000 as 150bp paired-end reads and the resulting sequences were demultiplexed by Novogene (Sacramento, CA, USA). The samples were sequenced across 7 lanes to target 2.5X coverage.