title: Ancient DNA and the tropics: a rodent's tale.
abstract: 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.
authors.affiliation: Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Ap. Postal 70-275, Ciudad Universitaria 04510, México taniagutierrezgarcia@gmail.com.
authors.forename: Tania A
authors.initials: TA
authors.lastname: Gutiérrez-García
authors.affiliation: Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Ap. Postal 70-275, Ciudad Universitaria 04510, México.
authors.forename: Ella
authors.initials: E
authors.lastname: Vázquez-Domínguez
authors.affiliation: Laboratorio de Arqueozoología, Instituto Nacional de Antropología e Historia, Moneda no. 16, Centro 06060, Distrito Federal, México.
authors.forename: Joaquín
authors.initials: J
authors.lastname: Arroyo-Cabrales
authors.affiliation: McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4L8.
authors.forename: Melanie
authors.initials: M
authors.lastname: Kuch
authors.affiliation: McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4L8.
authors.forename: Jacob
authors.initials: J
authors.lastname: Enk
authors.affiliation: McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4L8.
authors.forename: Christine
authors.initials: C
authors.lastname: King
authors.affiliation: McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4L8.
authors.forename: Hendrik N
authors.initials: HN
authors.lastname: Poinar
mesh_terms: D000818:Animals; D003411:Arvicolinae / Q000235:genetics*; D045303:Cytochromes b / Q000235:genetics; D004247:DNA / Q000235:genetics; D019143:Evolution, Molecular; D005580:Fossils; D008800:Mexico; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D013997:Time Factors; D014329:Tropical Climate
chemical_list: D004247:DNA; D045303:Cytochromes b
keywords: Cricetidae; Loltún cave; Mexico; Ototylomys phyllotis; Quaternary; Yucatan peninsula