Insights into hominin phenotypic and dietary evolution from ancient DNA sequence data

Area of Science:

• Paleogenomics
• Human Evolutionary Biology
• Paleoecology

Background:

• Nuclear genome sequences from Neandertals, Denisovans, and archaic humans offer insights into hominin evolution.
• Analyzing these genomes aids in understanding archaic hominin phenotypes, introgressed alleles in modern humans, and evolutionary timing of genetic changes.

Purpose of the Study:

• To review and reanalyze Neandertal and Denisovan genome data to infer the evolutionary timing of specific gene presence/absence changes.
• To investigate potential links between these genetic changes and hominin-specific dietary adaptations.

Main Methods:

• Reanalysis of published Neandertal and Denisovan genome sequence data.
• Inference of the evolutionary timing of five human gene presence/absence variations.
• Discussion of findings within the context of hominin evolutionary ecology.

Main Results:

• Gene loss mutations in TAS2R62, TAS2R64 (bitter taste receptors), and MYH16 (masticatory myosin) occurred after hominin-chimpanzee divergence but before human/Neandertal/Denisovan divergence.
• Absence of functional MYH16 in archaic hominins may correlate with reduced jaw muscles and the adoption of cooking.
• Salivary amylase gene (AMY1) duplications were absent in Neandertal and Denisovan genomes, indicating a recent origin in modern humans.
• A heterozygous mutation in TAS2R38 (bitter taste receptor) was found in a Neandertal individual, suggesting functional variation.

Conclusions:

• Specific gene losses, including MYH16, likely influenced hominin physical traits and behaviors like cooking.
• Recent AMY1 duplications in modern humans suggest limited starch digestion capabilities in earlier hominins consuming underground storage organs.
• The TAS2R38 finding highlights conserved bitter taste variation across hominins.