Data from: An assessment of ancient DNA preservation in Holocene-Pleistocene fossil bone excavated from the world heritage Naracoorte Caves, South Australia

Although there is a long history of research into the fossil deposits of
the Naracoorte Caves (South Australia), ancient DNA (aDNA) has not been
integrated into any palaeontological study from this World Heritage site.
Here, we provide the first evidence of aDNA preservation in Holocene- and
Pleistocene-aged fossil bone from a deposit inside Robertson Cave. Using a
combination of metabarcoding and shotgun next-generation sequencing
approaches, we demonstrate that aDNA from diverse taxa can be retrieved
from bulk bone as old as 18 600 cal a BP. However, the DNA is highly
degraded and contains a lower relative proportion of endogenous sequences
in bone older than 8400 cal a BP. Furthermore, modelling of DNA
degradation suggests that the decay rate is rapid, and predicts a very low
probability of obtaining informative aDNA sequences from extinct
megafaunal bones from Naracoorte (ca. 50 000 cal a BP). We also provide
new information regarding the past faunal biodiversity of Robertson Cave,
including families that have not been formerly described in the fossil
record from here before. Collectively, these data demonstrate the
potential for future aDNA studies to be conducted on material from
Naracoorte, which will aid in the understanding of faunal turnover in
southern Australia.