Biology subjects

Becerra-Valdivia, L.

Publications and source records attributed to Becerra-Valdivia, L..

3 recordsLinked to original sources

bioRxiv2026

AncientMetagenomeDir dating metadataset highlights need for standardised radiocarbon reporting in ancient DNA

Ancient DNA is a valuable data source for the understanding of our past. However, to effectively interpret this data, it is essential to know the age of the samples from which the DNA is obtained. Although the field of palaeogenomics has been recognised for its robust open data sharing practices, dating information associated with analysed samples is not reported consistently across palaeogenomic studies, nor is it included as metadata in most genetic data repositories. Here, we describe the addition of standardised precise dating information for ancient microbial genomes into the AncientMetagenomeDir metadata repository of published ancient metagenomic samples. This extension currently includes dating information for over 700 ancient microbial genomic datasets, of which 333 are dated using historical, contextual, or stratigraphic methods, and 405 are radiocarbon dated. We quantitatively assess the quality of radiocarbon date reporting and find that, despite established reporting conventions, radiocarbon dating information is often reported inconsistently across ancient metagenomic studies. This new resource provides ancient microbial researchers with standardised dating information that facilitates more accurate and consistent analysis of metagenomic sequencing data. The dataset also highlights the need for greater standardisation of radiocarbon date reporting in original publications in order to allow effective reuse of this and future ancient microbial data.

bioinformatics↗

bioRxiv2026

Diverse megamammals exploited by humans, chronology and palaeoecology at Taima-Taima, Late Pleistocene, South America

The arrival of humans to the Americas at the end of the Pleistocene has been one of the foundations of the hypothesis that hunter-gatherer groups had a direct role in the extinction of megafauna. However, empirical evidence of the exploitation of megafauna by humans and associated chronological context are still scarce, especially in South America. Using evidence of modifications on osteological remains, we provide a reassessment of the megafauna that was exploited at the classic Taima-Taima site (Venezuela), with an updated chronology and paleoenvironmental inferences. Our results show that, at least, five species of extinct megaherbivores were probably exploited at the site, expanding the previous records, restricted to the proboscidean Notiomastodon platensis and the giant armadillo Glyptotherium cf. G. cylindricum. The new data of the other exploited taxa include the terrestrial sloth Glossotherium, the macrauchenid cf. Xenorhinotherium bahiense and a toxodontid; both killing and slaughtering activities were likely practised at the site. Seven new enamel radiocarbon dates show an age of 15.3-17.8 cal kyr BP for the fossiliferous strata, although this is likely to be a minimum age given the materials propensity for modern carbon uptake. The study of phytoliths and starch grains from the dental calculus of N. platensis identified five plant taxa from the phytoliths: arboreal dicotyledons, Poaceae, Marantaceae, Asteraceae and Arecaceae. Ecometrics studies of dental diversity reveal how no other single site on the continent preserves such a diversity of grazing and browsing megaherbivores exploited by humans.

paleontology↗

bioRxiv2025

{micro}CT Scanning Effects on DNA and a Multi-Step Workflow for Archaeological Petrous Bones

The petrous portion of the temporal bone is a key element in human evolutionary studies due to its exceptional preservation of biomolecules and morphological information. However, intensive and often redundant sampling has raised concerns about sustainability and long-term conservation. Here we present the first systematic evaluation of whether micro-Computed Tomography ({micro}CT)--a widely used tool for digital preservation--affects ancient DNA (aDNA) integrity in human petrous bones. We analyzed 93 archaeological samples from Argentina, of which 50 had been scanned using {micro}CT and 43 had not. We compared six molecular parameters, including endogenous content, read length, cytosine deamination patterns and contamination estimates. No statistically significant differences were observed between scanned and unscanned samples across any parameter (Mann-Whitney/Wilcoxon tests, p <0.05). Although mitochondrial contamination was marginally higher in scanned samples (p = 0.051), this was not driven by contamination estimates above the widely accepted 5% threshold for genomic analysis, Moreover, this pattern was not observed when considering nuclear contamination. These results indicate that, under appropriate scanning conditions, {micro}CT imaging does not compromise DNA preservation. Building on this evidence, we propose a sustainable, multi-step workflow that integrates biological profiling, osteobiography, imaging, and compositional pre-screening prior to molecular sampling. This interdisciplinary approach maximizes the scientific information obtained from skeletal collections while minimizing destructive practices, thereby promoting ethical and sustainable research on irreplaceable anthropological remains, and fosters collaboration across research fields.

paleontology↗