Denisova hominin
Encyclopedia
Denisova hominins or Denisovans, are Paleolithic
-Era members of the genus Homo
that may belong to a previously unknown species. In , scientists announced the discovery of a finger bone fragment of a juvenile female that lived about 41,000 years ago, found in Denisova Cave
in Altai Krai
, Russia, a region also inhabited at about the same time by Neanderthal
s and perhaps modern humans
. A tooth and toe bone belonging to different members of the same population have since been found.
Analysis of the mitochondrial DNA
(mtDNA) of the finger bone showed it to be distinct from the mtDNAs of Neanderthals and modern humans. Subsequent studies on the nuclear genome
from this specimen, as well as mtDNA from the tooth, determined that this group shares a common origin with Neanderthals and interbred with the ancestors of some present-day Melanesians
and Australian Aborigines. Similar analysis of a toe bone discovered in 2011 is underway.
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 BP
.
A team of scientists led by Johannes Krause and Swedish biologist Svante Pääbo
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 years ago. Some studies suggest that modern humans coexisted with Neanderthals in Europe, 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." Pääbo noted that the existence of this distant branch creates a much more complex picture of humankind during the Late Pleistocene
.
Later in 2010, a second paper from the Svante Pääbo group reported the prior discovery, in 2000, of a third 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 Neanderthals 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 of the finger bone, indicating a divergence time about 7,500 years before, and suggesting it belonged to a different individual from the same population. In 2011, a toe bone was discovered in the same layer of the Denisova cave and hence contemporary with the finger bone.
and tooth from which genetic material has been gathered, and a toe bone
. The tooth shares no derived morphological features with Neanderthal or modern humans. An initial morphological characterization of the toe bone led to the suggestion that it may have belonged to a Neanderthal-Denisovan hybrid individual, although a critic suggested the morphology was inconclusive. It is currently undergoing DNA analysis by Pääbo.
s) 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 chimpanzee
s and modern humans is approximately 1,462 mtDNA base pairs. This suggested a divergence time around one million years ago. mtDNA from the tooth bore a high similarity to that of the finger bone, indicating that they belonged to the same population.
or else an introgression
from an older hominin lineage.
study confirms that approximately 4% of non-African modern human DNA
relates to Neanderthal
s. Tests comparing the Denisova hominin genome
with those of six modern humans: a ǃKung from South Africa, a Nigerian, a Frenchman
, a Papua New Guinean, a Bougainville Island
er and a Han Chinese
showed that between 4% and 6% of the genome
of Melanesians
(represented by the Papua New Guinean and Bougainville Islander) derives from a Denisovan population. The genes were possibly introduced during the early migration
of the ancestors of Melanesians into Southeast Asia. This history of interaction suggests that Denisovans once ranged widely over eastern Asia.
Later research suggests that modern-day descendants of Denisovans range wider afield than Melanesia. Mark Stoneking, molecular anthropologist at the Max Planck Institute for Evolutionary Anthropology, led the research team which found genetic evidence that, in addition to Melanesians, Australian Aborigines
, and some small, scattered groups of people in Southeast Asia, such as the Negrito
Mamanwa in the Philippines
, share varying levels of Denisovan ancestry. However, not all Negritos were found to possess Denisovan genes; Andaman Islanders and Malaysian Jehai
, for example, were found to have no Denisovan inheritance. With their results, they challenged the belief that the Denisovans interbred in mainland Asia before spreading to the island from southeast Asia, Melanesia, and Australia. They said that their data "can be
most parsimoniously explained if the Denisova gene flow occurred in Southeast Asia itself."
In August 2011, Denisovan and Neanderthal archaic HLA types were found to represent more than half the HLA alleles of modern Eurasians. The apparent over-representation of these alleles suggests a positive selective pressure for their retention in the human population.
Paleolithic
The Paleolithic Age, Era or Period, is a prehistoric period of human history distinguished by the development of the most primitive stone tools discovered , and covers roughly 99% of human technological prehistory...
-Era members of the genus Homo
Homo
Homo may refer to:*the Greek prefix ὅμο-, meaning "the same"*the Latin for man, human being*Homo, the taxonomical genus including modern humans...
that may belong to a previously unknown species. In , scientists announced the discovery of a finger bone fragment of a juvenile female that lived about 41,000 years ago, found in Denisova Cave
Denisova Cave
Denisova Cave is a cave in the Bashelaksky Range of the Altai mountains, Siberia, Russia. The cave is of paleoarchaeological and paleontological interest. Bone fragments of the Denisova hominin, sometime called the "X-woman" originate from the cave, including artifacts dated to ~40,000 Before...
in Altai Krai
Altai Krai
Altai Krai is a federal subject of Russia . It borders with, clockwise from the south, Kazakhstan, Novosibirsk and Kemerovo Oblasts, and the Altai Republic. The krai's administrative center is the city of Barnaul...
, Russia, a region also inhabited at about the same time by Neanderthal
Neanderthal
The Neanderthal is an extinct member of the Homo genus known from Pleistocene specimens found in Europe and parts of western and central Asia...
s and perhaps modern humans
Anatomically modern humans
The term anatomically modern humans in paleoanthropology refers to early individuals of Homo sapiens with an appearance consistent with the range of phenotypes in modern humans....
. A tooth and toe bone belonging to different members of the same population have since been found.
Analysis of the mitochondrial DNA
Mitochondrial DNA
Mitochondrial DNA is the DNA located in organelles called mitochondria, structures within eukaryotic cells that convert the chemical energy from food into a form that cells can use, adenosine triphosphate...
(mtDNA) of the finger bone showed it to be distinct from the mtDNAs of Neanderthals and modern humans. Subsequent studies on the nuclear genome
Nuclear gene
A Nuclear gene is a gene located in the cell nucleus of a eukaryote. The term is used to distinguish nuclear genes from the genes in the mitochondrion, and in case of plants, also the chloroplast, which host their own genetic system and can produce proteins from scratch...
from this specimen, as well as mtDNA from the tooth, determined that this group shares a common origin with Neanderthals and interbred with the ancestors of some present-day Melanesians
Melanesians
Melanesians are an ethnic group in Melanesia. The original inhabitants of the group of islands now named Melanesia were likely the ancestors of the present-day Papuan-speaking people...
and Australian Aborigines. Similar analysis of a toe bone discovered in 2011 is underway.
Discovery
In 2008, Russian archeologists from the Institute of Archaeology and Ethnology of NovosibirskNovosibirsk
Novosibirsk is the third-largest city in Russia, after Moscow and Saint Petersburg, and the largest city of Siberia, with a population of 1,473,737 . It is the administrative center of Novosibirsk Oblast as well as of the Siberian Federal District...
working at the site of Denisova Cave
Denisova Cave
Denisova Cave is a cave in the Bashelaksky Range of the Altai mountains, Siberia, Russia. The cave is of paleoarchaeological and paleontological interest. Bone fragments of the Denisova hominin, sometime called the "X-woman" originate from the cave, including artifacts dated to ~40,000 Before...
in the Altai Mountains of Siberia
Siberia
Siberia is an extensive region constituting almost all of Northern Asia. Comprising the central and eastern portion of the Russian Federation, it was part of the Soviet Union from its beginning, as its predecessor states, the Tsardom of Russia and the Russian Empire, conquered it during the 16th...
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
Radiocarbon dating
Radiocarbon dating is a radiometric dating method that uses the naturally occurring radioisotope carbon-14 to estimate the age of carbon-bearing materials up to about 58,000 to 62,000 years. Raw, i.e. uncalibrated, radiocarbon ages are usually reported in radiocarbon years "Before Present" ,...
to around 40,000 BP
Before Present
Before Present years is a time scale used in archaeology, geology, and other scientific disciplines to specify when events in the past occurred. Because the "present" time changes, standard practice is to use AD 1950 as the origin of the age scale, reflecting the fact that radiocarbon...
.
A team of scientists led by Johannes Krause and Swedish biologist Svante Pääbo
Svante Pääbo
Svante Pääbo is a Swedish biologist specializing in evolutionary genetics. He was born in 1955 in Stockholm to Sune Bergström, who shared the Nobel Prize in Physiology or Medicine with Bengt I. Samuelsson and John R. Vane in 1982, and his mother, Estonian Karin Pääbo.He earned his PhD from Uppsala...
from the Max Planck Institute for Evolutionary Anthropology
Max Planck Institute for Evolutionary Anthropology
The Max Planck Institute for Evolutionary Anthropology is a research institute based in Leipzig, Germany, founded in 1997. It is part of the Max Planck Society network....
in Leipzig
Leipzig
Leipzig Leipzig has always been a trade city, situated during the time of the Holy Roman Empire at the intersection of the Via Regia and Via Imperii, two important trade routes. At one time, Leipzig was one of the major European centres of learning and culture in fields such as music and publishing...
, Germany, sequenced
DNA sequencing
DNA sequencing includes several methods and technologies that are used for determining the order of the nucleotide bases—adenine, guanine, cytosine, and thymine—in a molecule of DNA....
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 years ago. Some studies suggest that modern humans coexisted with Neanderthals in Europe, 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
Recent African origin of modern humans
In paleoanthropology, the recent African origin of modern humans is the most widely accepted model describing the origin and early dispersal of anatomically modern humans...
, 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
Homo erectus
Homo erectus is an extinct species of hominid that lived from the end of the Pliocene epoch to the later Pleistocene, about . The species originated in Africa and spread as far as India, China and Java. There is still disagreement on the subject of the classification, ancestry, and progeny of H...
. Professor Chris Stringer
Chris Stringer
Christopher Brian Stringer FRS, better known as Chris Stringer, is a British anthropologist.He is one of the leading proponents of the recent single-origin hypothesis or "Out of Africa" theory, which hypothesizes that modern humans originated in Africa over 100,000 years ago and replaced the...
, human origins researcher at London
London
London is the capital city of :England and the :United Kingdom, the largest metropolitan area in the United Kingdom, and the largest urban zone in the European Union by most measures. Located on the River Thames, London has been a major settlement for two millennia, its history going back to its...
's Natural History Museum
Natural History Museum
The Natural History Museum is one of three large museums on Exhibition Road, South Kensington, London, England . Its main frontage is on Cromwell Road...
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." Pääbo noted that the existence of this distant branch creates a much more complex picture of humankind during the Late Pleistocene
Late Pleistocene
The Late Pleistocene is a stage of the Pleistocene Epoch. The beginning of the stage is defined by the base of the Eemian interglacial phase before the final glacial episode of the Pleistocene 126,000 ± 5,000 years ago. The end of the stage is defined exactly at 10,000 Carbon-14 years BP...
.
Later in 2010, a second paper from the Svante Pääbo group reported the prior discovery, in 2000, of a third 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 Neanderthals 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 of the finger bone, indicating a divergence time about 7,500 years before, and suggesting it belonged to a different individual from the same population. In 2011, a toe bone was discovered in the same layer of the Denisova cave and hence contemporary with the finger bone.
Anatomy
Little is known of the precise anatomical features of the Denisovans since the only physical remains discovered thus far are the finger bonePhalanges of the hand
The phalanges of the hand are commonly known as the finger bones. They are fourteen in number, three for each finger, and two for the thumb.Each consists of a body and two extremities....
and tooth from which genetic material has been gathered, and a toe bone
Phalanges of the foot
The Olphalanges of the foot are the bones in the toes. They correspond, in number and general arrangement, with those of the hand; there are two in the big toe, and three in each of the other toes...
. The tooth shares no derived morphological features with Neanderthal or modern humans. An initial morphological characterization of the toe bone led to the suggestion that it may have belonged to a Neanderthal-Denisovan hybrid individual, although a critic suggested the morphology was inconclusive. It is currently undergoing DNA analysis by Pääbo.
Mitochondrial DNA analysis
The mtDNA from the finger bone differs from that of modern humans by 385 bases (nucleotideNucleotide
Nucleotides are molecules that, when joined together, make up the structural units of RNA and DNA. In addition, nucleotides participate in cellular signaling , and are incorporated into important cofactors of enzymatic reactions...
s) 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 chimpanzee
Chimpanzee
Chimpanzee, sometimes colloquially chimp, is the common name for the two extant species of ape in the genus Pan. The Congo River forms the boundary between the native habitat of the two species:...
s and modern humans is approximately 1,462 mtDNA base pairs. This suggested a divergence time around one million years ago. mtDNA from the tooth bore a high similarity to that of the finger bone, indicating that they belonged to the same population.
Nuclear genome analysis
In the same second 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. The estimated average time of divergence between Denisovan and Neanderthal sequences is 640,000 years ago, and that between both of these and the sequences of modern Africans is 804,000 years ago. 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 driftGenetic drift
Genetic drift or allelic drift is the change in the frequency of a gene variant in a population due to random sampling.The alleles in the offspring are a sample of those in the parents, and chance has a role in determining whether a given individual survives and reproduces...
or else an introgression
Introgression
Introgression, also known as introgressive hybridization, in genetics is the movement of a gene from one species into the gene pool of another by the repeated backcrossing of an interspecific hybrid with one of its parent species...
from an older hominin lineage.
Interbreeding with modern humans
GeneticGenetics
Genetics , a discipline of biology, is the science of genes, heredity, and variation in living organisms....
study confirms that approximately 4% of non-African modern human DNA
DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...
relates to Neanderthal
Neanderthal
The Neanderthal is an extinct member of the Homo genus known from Pleistocene specimens found in Europe and parts of western and central Asia...
s. Tests comparing the Denisova hominin genome
Genome
In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA....
with those of six modern humans: a ǃKung from South Africa, a Nigerian, a Frenchman
French people
The French are a nation that share a common French culture and speak the French language as a mother tongue. Historically, the French population are descended from peoples of Celtic, Latin and Germanic origin, and are today a mixture of several ethnic groups...
, a Papua New Guinean, a Bougainville Island
Bougainville Island
Bougainville Island is the main island of the Autonomous Region of Bougainville of Papua New Guinea. This region is also known as Bougainville Province or the North Solomons. The population of the province is 175,160 , which includes the adjacent island of Buka and assorted outlying islands...
er and a Han Chinese
Han Chinese
Han Chinese are an ethnic group native to China and are the largest single ethnic group in the world.Han Chinese constitute about 92% of the population of the People's Republic of China , 98% of the population of the Republic of China , 78% of the population of Singapore, and about 20% of the...
showed that between 4% and 6% of the genome
Genome
In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA....
of Melanesians
Melanesians
Melanesians are an ethnic group in Melanesia. The original inhabitants of the group of islands now named Melanesia were likely the ancestors of the present-day Papuan-speaking people...
(represented by the Papua New Guinean and Bougainville Islander) derives from a Denisovan population. The genes were possibly introduced during the early migration
Human migration
Human migration is physical movement by humans from one area to another, sometimes over long distances or in large groups. Historically this movement was nomadic, often causing significant conflict with the indigenous population and their displacement or cultural assimilation. Only a few nomadic...
of the ancestors of Melanesians into Southeast Asia. This history of interaction suggests that Denisovans once ranged widely over eastern Asia.
Later research suggests that modern-day descendants of Denisovans range wider afield than Melanesia. Mark Stoneking, molecular anthropologist at the Max Planck Institute for Evolutionary Anthropology, led the research team which found genetic evidence that, in addition to Melanesians, Australian Aborigines
Australian Aborigines
Australian Aborigines , also called Aboriginal Australians, from the latin ab originem , are people who are indigenous to most of the Australian continentthat is, to mainland Australia and the island of Tasmania...
, and some small, scattered groups of people in Southeast Asia, such as the Negrito
Negrito
The Negrito are a class of several ethnic groups who inhabit isolated parts of Southeast Asia.Their current populations include 12 Andamanese peoples of the Andaman Islands, six Semang peoples of Malaysia, the Mani of Thailand, and the Aeta, Agta, Ati, and 30 other peoples of the Philippines....
Mamanwa in the Philippines
Philippines
The Philippines , officially known as the Republic of the Philippines , is a country in Southeast Asia in the western Pacific Ocean. To its north across the Luzon Strait lies Taiwan. West across the South China Sea sits Vietnam...
, share varying levels of Denisovan ancestry. However, not all Negritos were found to possess Denisovan genes; Andaman Islanders and Malaysian Jehai
Jehai language
Jahai is an aboriginal Mon–Khmer language spoken in Malaya. The small number of speakers is increasing.-Further reading:*Burenhult, N. . A grammar of Jahai. Pacific linguistics, 566. Canberra: Pacific Linguistics. ISBN 0858835541...
, for example, were found to have no Denisovan inheritance. With their results, they challenged the belief that the Denisovans interbred in mainland Asia before spreading to the island from southeast Asia, Melanesia, and Australia. They said that their data "can be
most parsimoniously explained if the Denisova gene flow occurred in Southeast Asia itself."
In August 2011, Denisovan and Neanderthal archaic HLA types were found to represent more than half the HLA alleles of modern Eurasians. The apparent over-representation of these alleles suggests a positive selective pressure for their retention in the human population.