What Ancient Protein Tells Us About Evolution and Diet

The study of ancient proteins, known as paleoproteomics, offers a new window into the deep past. While ancient DNA has long been the focus for genetic information from extinct organisms, proteins are a valuable complementary tool. These durable molecules, left behind by organisms that died thousands or even millions of years ago, help scientists answer questions about evolution and how ancient life-forms interacted with their environment.

Finding and Analyzing Molecular Fossils

Ancient proteins are recovered from preserved organic materials, where they act as “molecular fossils.” The most productive sources are mineralized tissues like fossilized bones, eggshells, and teeth. Dental enamel is a rich source because its dense structure shields proteins from the external environment, allowing them to survive for long periods. Scientists also find ancient proteins in human-made artifacts, such as residues on ancient pottery that reveal what the vessels once held.

To identify these preserved proteins, researchers use a technique called mass spectrometry. The process begins with extracting protein remnants from a sample, which are then broken down into smaller fragments called peptides. These fragments are introduced into a mass spectrometer, which measures their mass-to-charge ratio with high precision.

By comparing the measured masses of the peptide fragments to databases of known protein sequences, scientists can identify the original protein. This probability-based matching has advanced the field, allowing for the analysis of previously inaccessible proteins. While a single ancient bone may contain fewer proteins than a modern one, the sensitivity of mass spectrometry is often sufficient to identify the key proteins that have survived.

Reconstructing Evolutionary History

The analysis of ancient proteins helps determine evolutionary relationships between species when skeletal remains are too fragmented for visual identification. The most abundant protein in bone is collagen, and its structure is unique to different animal groups. By sequencing the amino acids in ancient collagen fragments, scientists can identify the species from a small piece of bone, which is useful for sorting unidentifiable fragments from archaeological sites.

Comparing protein sequences between species allows scientists to construct evolutionary family trees, or phylogenies. Because the amino acid sequence of a protein is determined by an organism’s DNA, differences in these sequences reflect the genetic distance between species. The resulting evolutionary trees often align with those constructed using DNA from living species, confirming the method’s reliability and helping resolve puzzles that fossil morphology alone could not.

A key example is the study of Gigantopithecus blacki, a giant ape that became extinct around 300,000 years ago. Known only from teeth and jawbones, its evolutionary placement was debated. Researchers extracted proteins from the dental enamel of a 1.9-million-year-old Gigantopithecus tooth from a cave in Southern China.

The protein sequences revealed that the giant ape’s closest living relative is the modern orangutan, settling a major question in primate evolution. This discovery was significant because the fossil was found in a subtropical environment where DNA degrades rapidly, demonstrating how paleoproteomics extends beyond the limits of ancient DNA analysis.

Revealing Ancient Diets and Diseases

Beyond mapping the tree of life, ancient proteins offer a look into the daily lives of past populations, including what they ate and the illnesses they faced. One of the most revealing sources is dental calculus, the hardened plaque that builds up on teeth. As plaque mineralizes, it entombs and preserves biomolecules from food, the host, and the oral microbiome for thousands of years.

Analysis of proteins from ancient dental calculus provides direct evidence of specific foods. For instance, detecting milk proteins like β-lactoglobulin confirms dairy consumption. Researchers have also identified proteins from cereals and other plants, offering a more complete picture of ancient diets than can be inferred from seeds or bones alone. This method has even revealed dietary differences between the poor and affluent during the Irish Potato Famine.

Ancient proteins also serve as a record of past health. Analyzing dental calculus can reveal proteins from pathogenic bacteria, identifying microbes responsible for ancient infections like periodontal disease. The presence of human immune proteins in these samples can also show that an individual’s body was actively fighting an infection.

Why Proteins Survive Longer Than DNA

The rise of paleoproteomics is due to a chemical reality: proteins are more stable than DNA. While ancient DNA provides valuable insights, it is a fragile molecule that degrades quickly, especially in warm and humid environments. The oldest human DNA recovered is about 400,000 years old, placing a limit on genetic studies, but proteins can endure for millions of years.

The longevity of certain proteins is tied to their structure. Collagen, the primary protein in bone, is composed of long strands intertwined into a tough triple helix. This tightly wound, fibrous structure is resistant to degradation, particularly breakdown by water through hydrolysis. Research shows that atomic-level interactions within the collagen helix create a barrier that shields its chemical bonds from water.

This durability is why scientists can analyze proteins from fossils that are millions of years old, when recovering DNA of that age is impossible. The proteins found in dense materials like bone and tooth enamel are further protected from environmental decay, making them a valuable resource for exploring evolutionary history.