Data from: Ultraconserved elements anchor thousands of genetic markers for target enrichment spanning multiple evolutionary timescales

Although massively parallel sequencing has facilitated large-scale DNA
sequencing, comparisons among distantly related species rely upon small
portions of the genome that are easily aligned. Methods are needed to
efficiently obtain comparable DNA fragments prior to massively parallel
sequencing, particularly for biologists working with non-model organisms.
We introduce a new class of molecular marker, anchored by ultraconserved
genomic elements (UCEs), that universally enable target enrichment and
sequencing of thousands of orthologous loci across species separated by
hundreds of millions of years of evolution. Our analyses here focus on use
of UCE markers in Amniota, because UCEs and phylogenetic relationships are
well known in some amniotes. We perform an in silico experiment to
demonstrate that sequence flanking 2,030 UCEs contains information
sufficient to enable unambiguous recovery of the established primate
phylogeny. We extend this experiment by performing an in vitro enrichment
of 2,386 UCE-anchored loci from nine, non-model avian species. We then use
alignments of 854 of these loci to unambiguously recover the established
evolutionary relationships within and among three ancient bird lineages.
Because many organismal lineages have UCEs, this type of genetic marker
and the analytical framework we outline can be applied across the tree of
life, potentially reshaping our understanding of phylogeny at many
taxonomic levels.