Lee, V. Y. K. | Search bioRxiv

bioRxiv2025

Improving archaeological metadata reporting in human paleogenomicstudies

Paleogenomic research has dramatically increased our understanding of past demographic and adaptive processes, but has also been criticized for a perceived disconnect between geneticists and other parties involved in the study of the past. For interdisciplinary research to be productive, contextual metadata associated with paleogenomic samples should be accessible in the same publication. Here, we conduct a pilot study examining the extent of archaeological metadata reporting in 30 peer-reviewed human paleogenomic studies, based on genetic sequences from 3911 ancient humans predominately from Western Eurasia, published between 2013 and 2024. We show inconsistent reporting of archaeological data across studies, and have sought to identify the driving factors. Overall, we found no strong explanatory variables, though some metadata fields - like Geolocation - have improved in completeness over time. These inconsistencies mean that metadata reporting is often insufficient to directly investigate the relationship between patterns of cultural and genetic change on the basis of published data alone. We propose a minimum information checklist as a best-practice guideline for collecting and reporting archaeological data in the future.

genomics↗

bioRxiv2024

Evidence for compensatory evolution within pleiotropic regulatory elements

Pleiotropy, measured as expression breadth across tissues, is one of the best predictors for protein sequence and expression conservation. In this study, we investigated its effect on the evolution of cis-regulatory elements (CREs). To this end, we carefully reanalyzed the Epigenomics Roadmap data for nine fetal tissues, assigning a measure of pleiotropic degree to nearly half a million CREs. To assess the functional conservation of CREs, we generated ATAC-seq and RNA-seq data from humans and macaques. We found that more pleiotropic CREs exhibit greater conservation in accessibility, and the mRNA expression levels of the associated genes are more conserved. This trend of higher conservation for higher degrees of pleiotropy persists when analyzing the transcription factor binding repertoire. In contrast, simple DNA sequence conservation of orthologous sites between species tends to be even lower for pleiotropic CREs than for species-specific CREs. Combining various lines of evidence, we suggest that the lack of sequence conservation for functionally conserved pleiotropic elements is due to compensatory evolution within these large pleiotropic CREs. Furthermore, for less pleiotropic CREs, we find an indication of compensation across CREs. This suggests that pleiotropy is also a good predictor for the functional conservation of CREs, but this is not reflected in the sequence conservation for pleiotropic CREs.

evolutionary biology↗