Data from: More than skin and bones: comparing extraction methods and alternative sources of DNA from avian museum specimens

Next-generation sequencing has greatly expanded the utility and value of
museum collections by revealing specimens as genomic resources. As the
field of museum genomics grows, so does the need for extraction methods
that maximize DNA yields. For avian museum specimens, the established
method of extracting DNA from toe pads works well for most specimens.
However, for some specimens, especially those of birds that are very small
or very large, toe pads can be a poor source of DNA. In this study, we
apply two DNA extraction methods (phenol-chloroform and silica column) to
three different sources of DNA (toe pad, skin punch, and bone) from ten
historical avian museum specimens. We show that a modified
phenol-chloroform protocol yielded significantly more DNA than a silica
column protocol (e.g., Qiagen DNeasy Blood & Tissue Kit) across
all tissue types. However, extractions using the silica column protocol
contained longer fragments on average than those using the
phenol-chloroform protocol, likely a result of loss of small fragments
through the silica column. While toe pads yielded more DNA than skin
punches and bone fragments, skin punches proved to be a reliable
alternative source of DNA and might be especially appealing when toe pad
extractions are impractical. Overall, we found that historical bird museum
specimens contain substantial amounts of DNA for genomic studies under
most extraction scenarios, but that a phenol-chloroform protocol
consistently provides the high quantities of DNA required for most current
genomic protocols.