Data from: Sequencing degraded DNA from non-destructively sampled museum specimens for RAD-tagging and low-coverage shotgun phylogenetics

Ancient and archival DNA samples are valuable resources for the study of
diverse historical processes. In particular, museum specimens provide
access to biotas distant in time and space, and can provide insights into
ecological and evolutionary changes over time. However, archival specimens
are difficult to handle; they are often fragile and irreplaceable, and
typically contain only short segments of denatured DNA. Here we present a
set of tools for processing such samples for state-of-the-art genetic
analysis. First, we report a protocol for minimally destructive DNA
extraction of insect museum specimens, which produced sequenceable DNA
from all of the samples assayed. The 11 specimens analyzed had fragmented
DNA, rarely exceeding 100 bp in length, and could not be amplified by
conventional PCR targeting the mitochondrial cytochrome oxidase I gene.
Our approach made these samples amenable to analysis with commonly used
next-generation sequencing-based molecular analytic tools, including
RAD-tagging and shotgun genome re-sequencing. First, we used museum ant
specimens from three species, each with its own reference genome, for
RAD-tag mapping. Were able to use the degraded DNA sequences, which were
sequenced in full, to identify duplicate reads and filter them prior to
base calling. Second, we re-sequenced six Hawaiian Drosophila species,
with millions of years of divergence, but with only a single available
reference genome. Despite a shallow coverage of 0.37±0.42 per base, we
could recover a sufficient number of overlapping SNPs to fully resolve the
species tree, which was consistent with earlier karyotypic studies, and
previous molecular studies, at least in the regions of the tree that these
studies could resolve. Although developed for use with degraded DNA, all
of these techniques are readily applicable to more recent tissue, and are
suitable for liquid handling automation.