The Denisova hominin is the name given to the remains of a member of the genus Homo which may be a previously unknown species based on an analysis of its mitochondrial DNA (mtDNA). In March 2010, discovery was announced of bone fragments of a juvenile that lived about 41,000 years ago found in Denisova Cave (Altai Krai, Russia) - a region also inhabited at about the same time by Neanderthals and modern humans.

The mtDNA of the Denisova hominin is distinct from the mtDNAs of Neanderthals and modern humans. In December 2010, an international team of scientists determined sequence from the nuclear genome of this group (known as the Denisovans) from this finger bone. Based on their analysis, this group was related to the Neanderthals and interbred with the ancestors of modern Melanesians.

Little is known of the anatomical features of the individual in question since the only physical remains discovered thus far are the finger bone from which only mitochondrial genetic material was gathered. The Siberian bone's mtDNA differs from that of modern humans by 385 bases (nucleotides) in the mtDNA strand out of approximately 16,500, whereas the difference between modern humans and Neanderthals is around 202 bases.

In contrast, the difference between chimpanzees and modern humans is approximately 1,462 mtDNA base pairs. Analysis of the specimen's nuclear DNA shows it to be a branch of the Neanderthal lineage. Even though the Denisova hominin's mtDNA lineage predates the divergence of modern humans and Neanderthals, coalescent theory does not preclude a more recent divergence date for her nuclear DNA.

In 2008, Russian archeologists working at the site of Denisova Cave in the Altai Mountains of Siberia uncovered a small bone fragment from the fifth finger of a juvenile hominin, dubbed the "X-woman" (referring to the maternal descent of mitochondrial DNA), or the Denisova hominin. Artifacts, including a bracelet, excavated in the cave at the same level were carbon dated to around 40,000 BC.

A team of scientists led by Johannes Krause and Swedish biologist Svante PŠŠbo from the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany sequenced mtDNA extracted from the fragment. Because of the cool climate in the location of the Denisova Cave, the discovery benefited from DNA's ability to survive for longer periods at lower temperatures.

The analysis indicated that modern humans, Neanderthals, and the Denisova hominin last shared a common ancestor around 1 million years ago. Modern humans are known to have overlapped with Neanderthals in Europe for more than 10,000 years, and the discovery raises the possibility that Neanderthals, modern humans and the Denisovan hominin may have co-existed.

The DNA analysis further indicated that this new hominin species was the result of an early migration out of Africa, distinct from the later out-of-Africa migrations associated with Neanderthals and modern humans, but also distinct from the earlier African exodus of Homo erectus.

Professor Chris Stringer, human origins researcher at London's Natural History Museum and one of the leading proponents of the recent single-origin hypothesis, remarked: "This new DNA work provides an entirely new way of looking at the still poorly understood evolution of humans in central and eastern Asia." Paabo noted that the existence of this distant branch creates a much more complex picture of humankind during the Late Pleistocene.

In 2010, a second paper from the Svante Paabo group reported the prior discovery, in 2000, of a 3rd upper molar from a young adult, dating from about the same time (the finger was from level 11 in the cave sequence, the tooth from level 11.1).

The tooth differed in several aspects from those of Neanderthal, while having archaic characteristics similar to the teeth of Homo erectus. They again performed mitochondrial DNA analysis on the tooth and found it to have a different but similar sequence to that from the bone, indicating a divergence time about 7500 years before, and suggesting it belonged to a different individual from the same population.

  Ancient humans, dubbed 'Denisovans', interbred with us   BBC - December 23, 2010

In the same 2010 paper, the authors report the isolation and sequencing of nuclear DNA from the Denisova finger bone. This specimen showed an unusual degree of DNA preservation and low level of contamination. They were able to achieve near-complete genomic sequencing, allowing a detailed comparison with Neanderthal and modern humans.

From this analysis, they concluded that in spite of the apparent divergence of their mitochondrial sequence, the Denisova population along with Neanderthal shared a common branch from the lineage leading to modern African humans. They suggest that the divergence of the Denisova mtDNA results either from the persistence of a lineage purged from the other branches of humanity through genetic drift or else an introgression from an older hominin lineage.

In addition to genetic studies linking approximately 4% of non-African modern human DNA to Neanderthals, these tests comparing the Denisova hominin genome with those of modern humans from Africa, Europe, East Asia and Melanesia showed that between 4% and 6% of the genome of Melanesians derives from a Denisovan population, introduced after the lineage leading to Melanesians diverged from that leading to other Eurasians.

Denisova Hominin  Wikipedia

Asians, Too, Mated With Archaic Humans, DNA Hints   National Geographic - November 1, 2011
First it was the earliest Europeans and Neanderthals. Now it appears that modern humans in Southeast Asia also became intimate with their prehistoric relatives. About one percent of the genetic makeup of people from southern China and the surrounding region comes from an extinct group of humans dubbed the Denisovans, a new study says. Considered by some to be a sort of sister species to the Neanderthals, the Denisovans - who may have represented an entirely separate human species - are largely a mystery, though they're thought to have had big teeth. The latest find suggests that the two human types mated and bore offspring, and their descendants are still alive today in mainland Asia.