SignificanceAncient DNA has revolutionized the field of archaeology, but in the Caribbean and other tropical regions of the world, the work has been hampered by poor DNA preservation. We present an ancient human genome from the Caribbean and use it to shed light on the early peopling of the islands. We demonstrate that the ancestors of the so-called “Taino” who inhabited large parts of the Caribbean in pre-Columbian times originated in northern South America, and we find evidence that they had a comparatively large effective population size. We also show that the native components in some modern Caribbean genomes are closely related to the ancient Taino, suggesting that indigenous ancestry in the region has survived through the present day.

El Mirón is an important archaeological cave site in Cantabria (Spain) with a stratigraphy covering the late Middle Paleolithic to the Modern Period. The Magdalenian levels are especially rich in artifacts, faunal remains, and features, and included the burial of an adult female (“the Red Lady”), as well as other scattered human remains, while the Neolithic levels contained the oldest combined evidence of ceramics, domesticated grain and livestock in the region. However, in the absence of diagnostic artifacts in many levels that would always provide a traditional cultural chronology, radiocarbon dating has been essential in understanding the temporal framework for human activity at the site. Over the duration of more than two decades, the El Mirón Project has therefore obtained 93 radiocarbon dates, which cover the entire stratigraphic record as found in several different excavation areas. In light of the considerable methodological advances that radiocarbon dating has seen since 1996 we aim to evaluate the reliability of the published 14C record for El Mirón Cave, and to improve the accuracy of the radiocarbon based chronostratigraphy through Bayesian modeling. The results shed light on which dates may be used for future research and where dating discrepancies reflect taphonomic processes, thereby advancing intra-site and regional archaeological comparisons.

The influence of hydrochloric acid pretreatment on F14C and radiocarbon dates from dental enamel was investigated. Samples from modern equine incisors, a Roman cattle molar, and a Paleolithic woolly rhino molar were sampled and subsequently divided into five fractions. Each fraction was pretreated with a different acid solution, analyzed with Fourier transform infrared spectroscopy (FTIR), and accelerator mass spectrometry (AMS) 14C dated at the Oxford Radiocarbon Accelerator Unit (ORAU). When compared to a control date (e.g. dentine collagen), better results were observed when increased concentrations of hydrochloric acid solution were used in the chemical pretreatment. This pilot study suggests that decontamination of younger samples may be possible. However, for more fossilized samples with a high level of contamination (e.g. from the European Paleolithic), acid pretreatment under the conditions used in this study does not remove all contamination.

Isotope analyses are some of the most common analytical methods applied to ancient bone, aiding the interpretation of past diets and chronology. For this, the evaluation of “collagen yield” (as defined in radiocarbon dating and stable isotope research) is a routine step that allows for the selection of specimens that are deemed adequate for subsequent analyses, with samples containing less than ∼1% “collagen yield” normally being used for isotopic analysis but discounted for radiocarbon dating. The aims of this study were to use proteomic methods of MALDI–TOF (matrix assisted laser desorption ionization time-of-fligh mass spectrometry) and LC−ESI−MS/MS (liquid chromatography electrospray ionization tandem mass spectrometry) to investigate the endogeneity of the dominant proteinaceous biomolecules within samples that are typically considered to contain poorly preserved protein. Taking 29 archaeological samples, we evaluated the proteome variability between different acid-soluble fractions removed prior to protein gelatinization and considered waste as part of the radiocarbon dating process. We then correlated these proteomes against the commonly used “collagen yield” proxy for preservation. We found that these waste fractions contained a significant amount of both collagenous and noncollagenous proteins (NCPs) but that the abundance of these was not correlated with the acquired “collagen yield”. Rather than a depleted protein load as would be expected from a low “collagen yield”, the variety of the extracted NCPs was comparable with that commonly obtained from ancient samples and included informative proteins useful for species identification, phylogenetic studies, and potentially even for isotopic analyses, given further method developments. Additionally, we did not observe any correlation between “collagen yield” and peptide mass fingerprint success or between the different fractions taken from the same sample but at different radiocarbon pretreatment stages. Overall, these findings highlight the value in retaining and analyzing sample fractions that are otherwise discarded as waste during the radiocarbon dating process but more importantly, that low “collagen yield” specimens that are often misinterpreted by archaeologists as being devoid of protein can still yield useful molecular sequence-based information.