Most genetic studies of Holocene fauna have been performed with ancient samples from dry and cold regions, in which preservation of fossils is facilitated and molecular damage is reduced. Ancient DNA work from tropical regions has been precluded owing to factors that limit DNA preservation (e.g. temperature, hydrolytic damage). We analysed ancient DNA from rodent jawbones identified as
Ototylomys phyllotis
, found in Holocene and Late Pleistocene stratigraphic layers from Loltún, a humid tropical cave located in the Yucatan peninsula. We extracted DNA and amplified six short overlapping fragments of the cytochrome
b
gene, totalling 666 bp, which represents an unprecedented success considering tropical ancient DNA samples. We performed genetic, phylogenetic and divergence time analyses, combining sequences from ancient and modern
O. phyllotis
, in order to assess the ancestry of the Loltún samples. Results show that all ancient samples fall into a unique clade that diverged prior to the divergence of the modern
O. phyllotis
, supporting it as a distinct Pleistocene form of the
Ototylomys
genus. Hence, this rodent's tale suggests that the sister group to modern
O. phyllotis
arose during the Miocene–Pliocene, diversified during the Pleistocene and went extinct in the Holocene.
Ancient DNA preservation, genetic diversity and biogeography: A study of houseflies from Roman Qasr Ibrim, lower Nubia, Egypt