Multi-Omics Analysis of Tissue Taphonomy for Forensics and Bioarchaeological Applications

Abstract

Taphonomy is the study of how an organism decays upon death, and within a biological context account for structural changes on histological to molecular level. Understanding and accurately estimating the taphonomic processes has been a long-standing problem within both bioarchaeology and forensic science, and current research investigations has been limited to bone diagenesis or single-omics biomolecular studies. Although loss of omics data is irreversible, identifying these mechanisms with innovative multi-omics technologies is key to enhancing current understanding. To address this, we implemented a multi-omics approach for the first time to analyse soft tissue taphonomy across different artificial degradation models. This was first utilised in the successful recovery post-mortem proteomes, lipidomes, metabolomes and genomes from desiccated pig brains using a novel integrated extraction protocol, before optimising the mass spectrometric acquisition of protein, lipid and metabolite content from decomposing porcine leg skeletal muscle and skin. Muscle and skin taphonomy over a post-mortem timeseries were subsequently investigated by developing downstream bioinformatic pipelines to enrich for univariate and integrative analyses in metabolomic, proteomic and lipidomic taphonomy. Multi-omics data was successfully recovered across brain, skin and muscle taphonomy respectively, whilst the acquisition of positive and negative lipid ions and acquisition of data dependent and data independent protein spectra were successfully compared. The development of a combined Lipidomic-Metabolomic pipeline facilitated the identification of temporal taphonomy patterns across skin and muscle respectively, not limited to common lipid degradation mechanisms and differential post-mortem metabolite biomarkers, which were supplemented with the enrichment of tissue-specific protein diagenesis. This characterisation provided the first comprehensive overview of multi-omics in soft tissues post-mortem, and lays the foundations for further integrative network analyses, taphonomy repositories and integrated methodologies to recover, acquire and analyse degraded biomolecules for forensic and bioarchaeological taphonomy applications.

Date of Award	15 Apr 2025
Original language	English
Awarding Institution	The University of Manchester
Supervisor	Konstantina Drosou, BSc, MSc, PhD (Supervisor), Michael Buckley (Supervisor), Anthony Freemont (Supervisor) & Adam Stevens (Supervisor)