Scientists Found DNA from Not One, but Two ‘Ghost Species’ Hiding in Our Genetic Code

3 min readHere’s what you’ll learn when you read this story:UC Berkeley researchers created a framework designed to identify regions of our genome with super-archaic DNA. Experts believe we somehow inherited that DNA either directly or indirectly through interbreeding between species.Whether early Homo sapiens interbred with ghost species or inherited ghost DNA through Neanderthals and Densiovans who interbred with them, their identity still eludes us.Our ancestors were not an insular species. Early Homo sapiens interbred with hominins who lived alongside them until those species were either absorbed into our gene pool or went extinct for other reasons. It often explains the small percentage of unknown genes on DNA tests, which may be Neanderthal (predominantly for European populations) or Denisovan (predominantly for Asian populations). But going further back in time, before what are now known as modern humans began to trek out of Africa, there were even more hominin lineages that intermingled with Homo sapiens enough that they still haunt our genome as “ghost DNA” to this day.Researchers from UC Berkeley were determined to find ancient areas of the genome where there is neither Neanderthal or Denisovan DNA, but there is something else. Postdoctoral researcher Arjun Biddanda and graduate student Yulin Zhang led an investigation into Homo sapiens lineages that account for 1% of our genome (about as much as the Neanderthal average), but are still a mystery. While modern humans appeared later on, the lineage from which we evolved from is thought to have begun as far back as 550,000 to 750,000 years ago. This ghost species responsible for that mystery 1% of DNA probably lived around a million years ago.Previously, it was unknown whether this ghost species was present only in African populations, or all Homo sapiens. Now, scientists are getting a better idea.“We find evidence for at least one ghost introgression predating the [out of Africa] expansion that contributed ancestry to all present-day populations,” Biddanda and Zhang said in a study recently published in Science. “This finding […] extends that model by showing that the event affected all modern human populations rather than being localized to West Africans.”To identify regions of super-archaic DNA in modern humans, the researchers used a new framework they developed called TRACE (TRacking Archaic Contributions via ARG Estimation). In doing so, they found that one ghost lineage diverged around the time that modern humans split from Neanderthals, making it more recent than other super-archaic lineages that may have influenced our genes. This lineage likely integrated into our own genes around 300,000 years ago through the process of introgression (the transfer of genes between different species). The hybrid offspring that result from this process keep the lineage alive through backcrossing, which results from hybrids interbreeding with each other.But that lineage certainly wasn’t alone—evidence for multiple introgression events was found with TRACE. Next to predictable Neanderthal and Denisovan ancestry, the framework revealed signs of archaic ancestry from ghost groups that still remain unidentified. Even older lineages were found within the Denisovan ancestry of Oceanian populations, which strengthens the evidence for Homo sapiens being related to a super-archaic hominin species. Evidently, these unidentified lineages either entered our genome through interbreeding with early Homo sapiens or our direct ancestors (Neanderthals and Denisovans), and when their descendants interbred with modern humans, they introduced incredibly ancient genes into our species.Despite the breakthrough, there are still uncertainties. While we now know that DNA from archaic hominins makes up about 2% of the Homo sapiens genome, which ghost species these are continues to elude us—Zhang and Biddanda think they might be Homo erectus or Homo heidelbergensis. Additionally, there might be hominin species present that remain unidentified, whether they are missing from the fossil record or simply undetectable in our genes.When and where the introgression events that introduced ghost DNA happened also cannot yet be inferred. However, the researchers predict that new reference genomes may eventually elucidate this, and could also tell us something about how the ghost genes contributed to human evolution.“[Ghost genes’] roles in immunity and metabolism have yet to be fully characterized,” they said. “Future studies that integrate additional ancient genomes at deep timescales, particularly from Africa and Asia, will be critical for refining the timing, sources, and evolutionary consequences of these introgression events.”Elizabeth Rayne is a creature who writes. Her work has appeared in Popular Mechanics, Ars Technica, SYFY WIRE, Space.com, Live Science, Den of Geek, Forbidden Futures and Collective Tales. She lurks right outside New York City with her parrot, Lestat. When not writing, she can be found drawing, playing the piano or shapeshifting.