Next-generation sequencing reveals phylogeographic structure and a species tree for recent bird divergences

► We demonstrate a way to generate multilocus DNA data using next-generation sequencing. ► The method produces thousands of loci and hundreds of SNPs. ► The loci appear to be randomly distributed in the genome. ► We found evidence for phylogeographic structure in four recently-diverged bird systems. ► The data are amenable to both SNP- and coalescent-based analysis.