Recent remarkable progress in biology and medicine, are continuously reshaping how we conceive research in multi-expertise or cross-transversal disciplines. Biological anthropology embraces methods and significance of how to determine and explain variations among individuals or between populations through time and geography, especially with ancient DNA (aDNA), is benefiting from several fields such bioinformatics, epigenomics, and proteomics.
Ancient DNA (aDNA) research achieved significant advances through the incorporation of high-throughput sequencing (HTS) technologies. However, environmental factors affect DNA conservation within ancient remains, narrowing the possibility to obtain expressive DNA fragments that extraction and sampling methods try to overcome. The biological profiling of ancient individuals or populations, exceeding essential data (mtDNA and Y haplotypes, sex, ancestrality, or autosomal analysis) has lately strengthened the basis of the genotype-phenotype association analysis, which permitted to initiate a new field based on epigenetics. Paleoepigneomics by mapping ancient epigenetic marks, mostly by DNA methylation and histone post-translational modifications (PTMs), as they play important roles in chromatin structure and function leads to new insights by characterizing this additional layer of information, which represents an interface between the genome and the environment and is not coded within modifications of the DNA sequence itself. These ancient epigenetic maps would provide, at the individual level, unique molecular phenotypes (age of death, diet and other stress conditions even sociocultural changes), while, at the population level, they can complement classical inference based on genetic information to reveal the regulatory changes underlying divergence, migration, or extinction.
Additionally, paleoproteomics research has surfaced and explained some situations and provided interesting alternative views for ancient remains to reveal more on their history. The combined lecturing from ancient proteins and DNA would bring supplementary comprehension to gene expression regulation, disease and environmental factors such as nutrition, stress, and other external factors that could have long-term effects on epigenomes. Finally, it could lead to the emergence of paleoproteogenomics.
Lately, there is a growing concern in the contribution of the environment encountered during early developmental stages and considerable interest in inter-generational effects. Developmental programming is the concept that early-life factors affect long-term health and disease through a permanent response of the developing organism to environmental stimuli such as maternal nutritional status, infant feeding, maternal stress, and infection. Furthermore, nutrition and dietary practices are one of the influential environmental factors that stabilize the genome through ”epi-nutrients” and exert a deep effect on immune system development and function, through inflammatory factors.
Our goal is to build an experimental proof of concept and further more a workflow of combined protocols to explore the human nutrition within a biological framework that incorporates genetics, physical plasticity and epigenetic change as interactive adaptations to dietary changes through diachronic periods in general and at crucial events such the agriculture transition. In addition to using paleogenomics and paleoproteomics methods, we have to build DNA methylomes maps, follow PTM-omes and correlate them with inflammatory factors mapping that would interconnect the underlying processes from nutrition adaptations to pathologies such as tuberculosis, osteosarcoma and celiac disease within the mechanism of development reprogramming through genotype-phenotype association assessment. Our research objectives are thoroughly interdisciplinary, as our proposed research scope will earn interest from technical specialists as well as from non-specialists who wish to include biomolecules methods and data to answer hypotheses from ancient populations.