New method finds traces of two unknown hominin ancestors in modern human DNA

Researchers have developed a new computational method to detect past interbreeding between Homo sapiens and unknown hominin groups using only modern human genomes. The technique, described in a study published in Science, analyzes patterns of genetic variation in living populations to identify segments that likely originated from extinct relatives.

Unlike previous approaches that depend on recovered ancient DNA from fossils, this method works by comparing the genomes of modern humans from diverse populations and looking for distinctive signatures of archaic introgression. The researchers applied the technique to data from the 1000 Genomes Project, which includes genomes from 26 populations worldwide.

The analysis revealed evidence of genetic contributions from at least two previously unidentified hominin groups. One of these "ghost" lineages appears to have diverged from the modern human line approximately 1.8 million years ago, predating the emergence of Homo erectus. The other unknown group split more recently, though still hundreds of thousands of years in the past.

Both unknown groups interbred with ancestors of modern humans after the main out-of-Africa migration, leaving detectable traces in present-day genomes. The older lineage's genetic material was found primarily in African populations, while the younger lineage's contributions appear more widely distributed.

The study's authors note that the method cannot identify exactly which fossil species these ghost lineages correspond to, nor can it determine the timing or frequency of interbreeding events with precision. The findings are based on statistical inference rather than direct observation of ancient DNA.

Previous research had already established that modern humans interbred with Neanderthals and Denisovans, but this work suggests the web of archaic admixture is more complex than previously documented. The new method may allow researchers to uncover additional unknown hominin contributions as more diverse modern genomes are sequenced.

The research team emphasizes that their approach complements, rather than replaces, ancient DNA analysis. While ancient DNA provides direct evidence from specific fossils, the computational method can detect signals from groups that left no recoverable genetic material in the fossil record.

Future applications of this technique could help clarify the number and identity of hominin groups that contributed to the modern human gene pool, particularly in Africa where ancient DNA preservation is poor.