Denny (hybrid hominin)

• 1. Introduction

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  Denny is represented by a single bone fragment, about 2 centimeters long. Russian archaeologists recovered it in 2012 inside Denisova Cave, a site in the Altai Mountains of Siberia. That fragment spent three years in a bag with thousands of other unidentified pieces before anyone recognized what it was. When scientists ran it through a protein fingerprinting method and extracted its DNA, the results had no precedent in science. Denny was the daughter of a Neanderthal mother and a Denisovan father: the only known first-generation offspring of two distinct ancient human species. She died approximately 90,000 years ago, at least thirteen years old. How did that fragment of bone survive to carry that story? And what does her existence reveal about how ancient humans actually lived when they met?

• 2. The Search Among Thousands

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  In 2015, Tom Higham and Katerina Douka made a decision that would change paleoanthropology. With the cooperation of site excavators Michael Shunkov and Anatoly Derevianko, they transported bags of unidentified bone fragments to the University of Oxford. Their aim was to test whether emerging scientific methods could locate human remains among thousands of indistinguishable pieces. Samantha Brown, an MSc student at Oxford, took on the screening as part of her dissertation. She examined more than 2,000 bone fragments using Zooarchaeology by Mass Spectrometry, a technique known as ZooMS. ZooMS works by comparing collagen protein fingerprints from unknown bones against a reference database of animals and humans. Working with Michael Buckley's laboratory at the University of Manchester, the team identified fragment DC1227 as belonging to an archaic human.

  Fiona Brock at Cranfield University then subjected DC1227 to a micro-computed tomography scan. The scan revealed acid etching and pitting on the bone's surface. That pattern of damage suggested the bone may have passed through the digestive system of an animal, likely a hyena. Direct radiocarbon dating placed the specimen at more than 50,000 years old. Scientists at the Max Planck Institute for Evolutionary Anthropology sequenced the bone's mitochondrial DNA and found a sequence consistent with Neanderthal ancestry. That finding prompted a much deeper investigation of the fragment's full genome.

• 3. Reading the Genome

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  Before any genetic material was extracted, DC1227 weighed 1.68 grams and measured 24.7 millimeters by 8.39 millimeters. Paleogeneticists Viviane Slon and Svante Pääbo led the analysis at the Max Planck Institute in Leipzig. They extracted six DNA samples from the specimen and produced ten libraries of complete genome sequences, achieving an average coverage of 2.6-fold. The analysis of mitochondrial DNA and nuclear DNA together revealed that the specimen contained nearly equal proportions of Neanderthal and Denisovan ancestry. A comparison of the X chromosomes and autosomes confirmed that DC1227 was female.

  The estimated genetic heterozygosity of the specimen was comparable to that of present-day Africans. That comparability pointed strongly to a first-generation hybrid. Slon, Pääbo, and their colleagues published their results in 2018, with the paper providing the first direct evidence of archaic human interbreeding. Pontus Skoglund, a population geneticist at the Francis Crick Institute in London, called the find 'absolutely extraordinary.' He described it as 'really great science coupled with a little bit of luck.' He predicted it would 'go into the textbooks right away.'

• 4. Her Parents' Origins

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  Denny's Denisovan father carried Neanderthal ancestry from 300 to 600 generations before his own lifetime, according to analysis of his daughter's nuclear genome. That makes Denny's genome the first direct evidence of at least two independent episodes of interbreeding between Neanderthals and Denisovans. She stands as the first physical confirmation that those two groups met, mated, and left offspring more than once.

  Denny's Neanderthal mother's genome yielded a separate surprise. Her mother's DNA was more closely related to Neanderthal genetic material from Vindija Cave in Croatia than to the Neanderthals associated with Denisova Cave itself. Croatia lies thousands of miles west of Siberia. That geographic mismatch suggests Neanderthal populations migrated from western Europe into Central Eurasia in multiple waves, encountering Denisovans along the way. Researchers noted that Denny was the first ancient individual confirmed to have parents from two discrete species of humans. Her genome offers a genetic comparison point available in no other known fossil.

• 5. Human Evolution Reimagined

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  Since Neanderthal remains were first described in the 19th century, many scientists had entertained the idea that ancient human species interbred. By the 1970s, discoveries of additional ancient human species cast serious doubt on the clean linear model of human evolution. Advances in molecular biology eventually allowed whole-genome sequencing of Neanderthal and human samples. In 2010, published evidence confirmed interbreeding between archaic and modern humans during the Middle Paleolithic and early Upper Paleolithic. Modern Eurasian genomes carry approximately 2% Neanderthal DNA. Modern Melanesian people carry an average of 4-6% Denisovan DNA.

  Denny gave those inherited percentages a tangible ancestor. Ackermann, Mackay, and Arnold confirmed: 'Recent genomic research has shown that hybridization between substantially diverged lineages is the rule, not the exception, in human evolution.' In January 2019, scientists published a chronology for the Pleistocene deposits at Denisova Cave. It concluded that Denisovans, Neanderthals, and related hybrids occupied the site from around 300,000 to 20,000 years ago. Stone tools, bracelets, and other ornaments found there suggest the Denisovans were capable of higher-order thought akin to modern humans. In February 2019, genetic studies using artificial intelligence pointed to the existence of an unknown human ancestor in modern human genomes. That ancestor was distinct from Neanderthals, Denisovans, and hybrids like Denny. That unknown ancestor has yet to be identified, and Denny's fully sequenced genome may serve as a baseline for any future attempt to find it.