Hoyo Negro skeleton mtDNA

For those of you who haven't been keeping up on cave archaeology in Mesoamerica, a remarkably complete skeleton of late Pleistocene girl was discovered deep underwater in a cave near Tulum, Quintana Roo, a couple of years ago. Reports of skeletons and other artifacts in similar contexts have been floating around for years. Most of us presumed, I think, that these remains were quite early because the caves were flooded by post-Pleistocene sea-level rise. The cave near Tulum was named Hoyo Negro, and the remains of the young woman were nicknamed Naia. In 2014, her mtDNA sequence was reported along with dates suggesting the skeleton was 12,000 to 13,000 years old (1).

In today's issue of Science, Kay Prufer and Matthias Meyer of the Max Planck Institute for Evolutionary Anthropology argue in a comment (2) on the original article that mtDNA haplotype was incorrectly identified and was came from modern contamination because it did not show the level and type of damage they would have predicted.

The response (3) is robust. While conceding that the lack of damage to parts of the DNA sequence is perhaps unexpected, they argue that damage to ancient DNA is poorly understood and unpredictable. Therefore, it cannot be used by itself to prove or disprove that a particular sequence or segment of DNA is ancient. They also provide a reasonably compelling argument against contamination.

Both the comment and the response discussed whether and how DNA might be damaged  in different environments, including the tropical environment of Quintana Roo. What surprised me was the lack of any explicit consideration of the fact that the bones had been deep underwater for thousands of years. That seems like a noteworthy omission.

1. James C. Chatters, Douglas J. Kennett, Yemane Asmerom, Brian M. Kemp, Victor Polyak, Alberto Nava Blank, Patricia A. Beddows, Eduard Reinhardt, Joaquin Arroyo-Cabrales, Deborah A. Bolnick, Ripan S. Malhi, Brendan J. Culleton, Pilar Luna Erreguerena, Dominique Rissolo, Shanti Morell-Hart, and Thomas W. Stafford Jr. (2014). Late Pleistocene Human Skeleton and mtDNA Link Paleoamericans and Modern Native Americans. Science 344: 750-754.

2. Prufer, Kay and Matthias Meyer (2015). Comment on "Late Pleistocene Human Skeleton and mtDNA Link Paleoamericans and Modern Native Americans." Science 347:835-a.

3. Brian M. Kemp, John Lindo, Deborah A. Bolnick, Ripan S. Malhi, and James C. Chatters (2015). Response to Comment on "Late Pleistocene Human Skeleton and mtDNA Link Paleoamericans and Modern Native Americans." Science 347:835-b.