DENISOVA CAVE
COMPILATION AND COMMENTARY
BY LUCY WARNER
FEBRUARY 13, 2018


TODAY I LOOKED AT THE TERM DENISOVAN FOR MORE INFORMATION AFTER STUMBLING INTO A TARPIT OF IDIOCY WEBSITES LAST NIGHT. I FOUND A DOCUCOCKNBULL THAT MADE AMAZING AND UNBELIEVABLE CLAIMS FOR THE DENISOVANS, SO I WENT ALL OUT TO FIND OUT EVERYTHING I COULD ABOUT THEM. I WATCH ARCHAEOLOGICAL OR HISTORICAL DOCUMENTARIES AT NIGHT OFTEN TO GET TO SLEEP, ALL ON YOUTUBE. THE REALLY RIDICULOUS ONE THAT TOOK ME UP SHORT ON THE MIRACULOUS DENISOVANS, IS PUT OUT BY A GROUP OR ENTITY CALLED “ZEG* TV HIDDEN FROM THE PUBLIC.” “HIDDEN FROM THE PUBLIC” IS A DEAD GIVEAWAY THAT THIS PROBABLY CAME OUT OF THE FAR REACHES OF THE FORMER RUSSIAN EMPIRE WHERE THE RUSSIAN FAKE NEWS SITES ARE BASED, MACEDONIA, FOR INSTANCE. PAINFULLY, THIS IS THE KIND OF THING THAT A CERTAIN TYPE OF AMERICAN IS WATCHING REGULARLY TO AVOID THE DANGEROUS “FAKE NEWS” OF CBS, NBC, NPR, BBC, AND THE LIKE.

SO, THIS “ZEG TV” PRODUCTION WAS ON THE SUBJECT OF THE DENISOVANS, AND INCLUDED MATERIAL THAT SEEMED TO ME TO BE BEYOND THE SPECULATIVE AND INTO THE TRUE FRINGE ZONE. AS A RESULT, I AM NOW LOOKING UP GENUINE ARTICLES ON THE SCIENTIFIC WORK THAT ACTUALLY IS GOING ON AT THE DENISOVA CAVE IN SIBERIA. IT ISN’T JUST A SMALL FIND OF ONE OR TWO BONES THAT HAVE BEEN TESTED FROM THE CAVE THERE, BUT 100, 000 YEARS WORTH OF FOUND MATERIALS DEPOSITED IN THE CAVE. NOT SURPRISINGLY, THERE WAS ALSO A ZEG PRODUCTION ON THE SUBJECT OF A GROUP OF SPACE ALIEN SKULLS THAT WERE UNEARTHED. THE ADAGE “LET THE BUYER BEWARE” SHOULD BE STATED, BUT AFTER THAT, READ ON CAUTIOUSLY FOR YOUR PLEASURE AND IMPROVEMENT.

MOVING RIGHT ALONG, UNTIL FIVE OR SIX YEARS AGO I HAD NEVER ENCOUNTERED THE TERM “THE DENISOVANS,” BUT IT QUICKLY BECAME BIG NEWS, AS THEIR DNA ALONG WITH NEANDERTHAL DNA, WAS FOUND LINKED TOGETHER IN THE CELLS OF MODERN HUMANS FROM MULTIPLE PARTS OF THE GLOBE. I’M SURE THAT A LOT OF WHAT’S OUT THERE IS BUNCOMBE, BUT I WANT TO FIND WHAT CAN BE VERIFIED.

GENETICISTS SEEM TO FEEL SURE THESE DAYS THAT ALL THREE OF THOSE HOMO GROUPS DID INTERBREED. YOUR FIRST THOUGHT MIGHT BE THAT THEY SURELY WOULDN’T BE ATTRACTED TO EACH OTHER, THEY WOULD BE SO “DIFFERENT” AND ALL, BUT IT SEEMS CLEAR TO ME THAT THEY VERY LIKELY DIDN’T LOOK SO DIFFERENT AS TO BE FRIGHTENING, AND GIVEN THE OVERALL RANDINESS OF MORE OR LESS ALL OF THE PRIMATE SPECIES, THEY WEREN’T “DISGUSTING,” EITHER. IN ADDITION TO THOSE THINGS, THE FACT THAT THE GENETIC MIXING HAS BEEN DISCOVERED BY APPARENTLY HONEST SCIENTISTS OF GOOD REPUTE, THEY MUST NOT HAVE LOOKED, ACTED, OR SMELLED TOO UNATTRACTIVE TO ALLOW THAT UNEXPECTED CLOSENESS. I SUSPECT THAT SUCH VERY ECLECTIC BREEDING IS EXACTLY WHY WE HAVE IN OUR GENES A WIDE RANGE OF ADAPTABLE CHARACTERISTICS, FROM INTELLIGENCE TO STRENGTH, IMMUNITIES AND ENDURANCE.

SEVERAL OF MY INFO SOURCES IN THE LAST YEAR OR TWO OR THREE HAVE STATED THAT THE HUMAN “FAMILY TREE” IS MORE OF A “BUSH” – MANY CLOSELY RELATED, THOUGH ASSUMED TO BE DIFFERENT, GROUPS OF HOMININS FROM AUSTRALOPITHECINES ON UP ARE SHOWING UP IN EVER MORE VARIETIES, AND SHARING DNA. AS ONE ARCHAEOLOGIST SPEAKING ON ONE OF MY DOCUMENTARIES SAID (MORE OR LESS CORRECTLY QUOTED) “IF I WERE TO LOOK OUT ACROSS A FOOTBALL FIELD AND SEE AN AUSTRALOPITHECINE, LUCY FOR INSTANCE, I WOULD CALL THE ZOO AND SAY ‘COME AND GET THIS APE.’ IF, ON THE OTHER HAND I SAW A HOMO ERECTUS, I WOULD CALL THE POLICE DEPARTMENT AND SAY ‘COME AND GET THIS LUNATIC, AND BRING SOME CLOTHES FOR HIM.’” IF I COULD REMEMBER WHICH VIDEO I SAW THAT STATEMENT IN, I WOULD GIVE THE ARCHAEOLOGIST CREDIT FOR HIS WORDS.

IN THIS DENISOVA CAVE, TWO OR THREE DIFFERENT SAMPLES THAT WERE NOT EQUALLY CLOSE IN THEIR GENETIC CHARACTERISTICS TO EACH OTHER, NOR TO MODERN HUMAN SAMPLES, WERE FOUND IN THE SAME CAVE. OF COURSE, PERHAPS THEY INHABITED THE CAVE AT DIFFERENT TIMES OVER THE 100,000 YEARS INVOLVED. IT WOULD BE INTERESTING, THOUGH, EXCITING EVEN, IF THEY WERE ALL LIVING TOGETHER AT THE SAME TIME, GLORYING IN THEIR EGALITARIAN “BUSHINESS.”

GIVEN OUR PRESENT-DAY FINICKINESS OF ALL KINDS, THAT CERTAINLY WOULDN’T HAPPEN. SOME OF US CAN’T EVEN SIT ON A PUBLIC TOILET IN A BEAUTIFULLY CLEAN RESTAURANT FOR FEAR OF BEING TAINTED BY SOMEONE OF A BROWN SKIN COLOR. OUR MANY AND VARIOUS GENETIC PATTERNS ARE RESPONSIBLE FOR BIGGER AND BETTER BRAINS, BETTER ADAPTED BODIES TO ENVIRONMENTS RANGING FROM GLACIER OR TO DESERT, AND SO ON. LIKE IT OR NOT, UNIQUENESS IS ESSENTIAL TO NICHE SURVIVAL. THAT ISN’T EXACTLY WHAT CHARLES DARWIN SAID, BUT IT MEANS ABOUT THE SAME THING, I THINK.

AND TO THINK THAT ALL THIS BEGAN WITH A SIBERIAN HERMIT NAMED “DENIS.”


ZEG* --

“ZEG*” MEANS “SAY” OR “THE DAY AFTER TOMORROW.” SAY MAKES MORE SENSE TO ME, SO I AM ASSUMING THIS PROLIFIC VIDEO SITE IS DUTCH RATHER THAN “RUSSKY.” WHEREVER IT COMES FROM, DON’T BELIEVE A WORD OF IT. BETTER STILL, DON’T CLICK ON IT. MAYBE IT IS SPREADING MALWARE.:

https://www.duolingo.com/dictionary/Dutch/zeg/df5cc93b13520956448c77f47d836df6
zeg pronunciation
DUTCH

zeg

ENGLISH
say, tell

https://www.urbandictionary.com/define.php?term=zeg
TOP DEFINITION

zeg

The Georgian word for "the day after tomorrow". There's actually no equivalent word in English.

by Daedalus Suburbanus July 28, 2013



THIS ARTICLE CONTAINS INFORMATION ON THE CAVE ITSELF, AND ON THE ARCHAEOLOGY GOING ON THERE. “A BONE NEEDLE DATED TO 50,000 YEARS AGO WAS DISCOVERED AT THE ARCHAEOLOGICAL SITE IN 2016 AND IS DESCRIBED AS THE MOST ANCIENT NEEDLE KNOWN.” THIS IS A VERY GOOD ARTICLE, THOUGH I ONLY CLIPPED PART OF IT. THE FOLLOWING TWO ARE MORE SCIENTIFIC.

DENISOVA CAVE

https://en.wikipedia.org/wiki/Denisova_Cave
Denisova Cave
From Wikipedia, the free encyclopedia

Denisova Cave (Russian: Дени́сова Пеще́ра, Altay: Аю-Таш = Ayu Tash = Bear Rock) is a cave in the Bashelaksky Range of the Altai mountains, Siberia, Russia. The cave is of great paleoarchaeological and paleontological interest. Bone fragments of the Denisova hominin, sometimes called the "X woman" (referring to the maternal descent of mitochondrial DNA) originate from the cave, including artifacts dated to around 40,000 BP.

The cave is located in a region thought to have been inhabited concurrently in the past by Neanderthals and modern humans. A bone needle dated to 50,000 years ago was discovered at the archaeological site in 2016 and is described as the most ancient needle known.[1]

Description

Located in Altai Krai, at the border of the Altai Republic, the cave is near the village of Chorny Anui (Чёрный Ануй), and some 150 km south of Barnaul, the nearest major city.[2] The cave, which is approximately 28 m (92 ft) above the right bank of the Anuy River (a left tributary of the Ob), has formed in upper Silurian limestone and contains a floor area of about 270 m2 (2,900 sq ft). The cave is composed of three galleries. The central chamber, the Main Gallery, contains a floor of 9 m (30 ft) x 11 m (36 ft) with side galleries, the East Gallery and the South Gallery.[3][4] It has been described as both as a karst cave[2] and as a sandstone cave.[4]

Cave sediments are rich with remnants of animals, including extinct ones. Remains of 27 species of large and medium-sized mammals have been found, (such as cave hyena, cave lion, etc.) and 39 species of small mammals, as well as remnants of reptiles, 50 bird species and other vertebrates.[5][6] Pollen in the cave sediments are used for palaeoclimatological research.

History
In the 18th century, the cave was inhabited by a hermit, Dionisij (Denis), and was named after him, while the indigenous Altay people call it Ayu-Tash (Bear Rock).[2] In the 1970s, Soviet scientists discovered paleoarcheological remains in the cave that led to further explorations.[2] So far, 22 strata have been identified, with archeological artifacts that cover the time from Dionisij back to about 125,000–180,000 years ago.[4] The dating of the strata was accomplished by the use of thermoluminescence dating of sediments, or, in some cases, radiocarbon dating on charcoal.[4]

Among the archeological artifacts are Mousterian- and Levallois-style tools attributed to Neanderthals.[7] Beside tools, researchers found decorative objects of bone, mammoth tusk, animal teeth, ostrich egg shell, fragments of a stone bracelet made of drilled, worked, and polished dark green chloritolite, and pendants.[4] A 7 cm (2.8 in) sewing needle made from bird bone, estimated to be around 50,000 years-old, was found in Denisova Cave.[8] The cave also contains stone tools and bone artifacts made by modern humans, and Pääbo commented: "The one place where we are sure all three human forms have lived at one time or another is here in Denisova Cave."[9]

Archaeogenetics

The average annual temperature of the cave remains at 0 °C (32 °F), which has contributed to the preservation of archaic DNA among the remains discovered.[10]

Denisova hominin
Main article: Denisova hominin

Scientists from the Institute of Archaeology and Ethnology of Novosibirsk have investigated the cave. Among the artifacts which had been left about 30,000 to 48,000 years ago (strata 9-11), bones were identified. One of these bones was a piece of phalanx of a child found in layer 11.2 of the East Gallery. The fossil element was analyzed by Svante Pääbo and coworkers from the Max Planck Institute for Evolutionary Anthropology in Leipzig; its mitochondrial DNA revealed a structure that differs from known human patterns and has been ascribed to "Denisova hominin", apparently an extinct hominin species or subspecies.[7] Further analysis revealed the Denisovans were related to the Neanderthals and interbred with the ancestors of modern Melanesians.[11]

Neanderthal remains

In 2011, a toe bone was discovered in the cave, in layer 11.4 of the East Gallery, and therefore contemporary with the Denisovan finger bone. Preliminary characterization of the bone's mitochondrial DNA suggested it belonged to a Neanderthal, not a Denisovan.[9] Later analysis confirmed the toe bone as coming from a Neanderthal.[12] The first high-coverage genome of Neanderthals was taken from this toe bone.[12]

In 2015, researchers applied a new technique via species identification by collagen peptide mass fingerprinting, Zooarchaeology by Mass Spectrometry (ZooMS), to sort through 2,315 unidentified bone fragments retrieved from a 2014 excavation.[13][14] They found that one sample, DC1227, taken from layer 12 of the East Gallery, carried human traits. This was the first time that this technique was used to successfully identify the presence of an extinct human.[14] DC1227 was a bone fragment weighing 1.68 g (0.059 oz), measuring in with a maximum length of 24.7 mm (0.97 in) and maximum width of 8.39 mm (0.330 in).[13] mtDNA analysis revealed that the owner of the bone fragment was a Neanderthal, with closest affinity to other Neanderthals discovered in the Altai region.[13][14]

DNA from soil

In 2017, researchers successfully sequenced DNA from soil samples taken from Denisova Cave. They were able to identify Neanderthal and Denisovan mtDNA from several samples, as well as the DNA of several animals. The researchers identified Neanderthal mtDNA from soil samples taken from layer 15 from the Main Gallery, a layer associated with Paleolithic artifacts where no Neanderthal fossil has ever been found. The researchers also identified Neanderthal and Denisovan mtDNA taken from layers 14 and 15, respectively, from the East Gallery, at layers lower than any previous fossil finds, layers where no hominin fossil has ever been found.[3]

Ovodov horse

In 2017, researchers successfully recovered mtDNA from an equiid fossil, dating to around 32,000 years ago, taken from Denisova Cave. The equiid fossil is described by its authors as coming from Equus ovodovi (Ovodov horse), an extinct species first described in 2010 based on a 40,000 year old fossil taken from Proskuryakova Cave in Khakassia, Russia. The mtDNA of the Denisova sample shows close affinity for that taken from Proskuryakova Cave. DNA analysis places Equus ovodovi as a phylogenetically basal group for non-caballine horses, with closest genetic affinity for zebras.[15]

Fossils
So far, the fossils of six distinct individuals from Denisova Cave have been identified through their DNA. Four of the individuals, Denisova 2, Denisova 3, Denisova 4 and Denisova 8 are classified as Denisovans.[16] Denisova 2 and Denisova 3 are young girls, while Denisova 4 and Denisova 8 are adult males.[16][17] mtDNA analysis of the Denisovan individuals suggests that Denisova 2 is the oldest, followed by Denisova 8, while Denisova 3 and Denisova 4 are roughly contemporaneous.[16]

One of the individuals, the Altai Neanderthal, is a Neanderthal woman.[12] Before its DNA was sequenced, the Altai Neanderthal had been given the provisional name of Denisova 5.[17] In 2016, Denisova 11 was identified as a Neanderthal based on mtDNA evidence.[13]

During DNA sequencing, Denisova 2, Denisova 4 and Denisova 8 yielded low-coverage genomes, while Denisova 3 and the Altai Neanderthal yielded high-coverage genomes.[17][16]

[GO TO WIKIPEDIA WEBSITE FOR CHART OF FINDINGS BY THE TEAM LED BY MICHAEL SHUNKOV.]

ANATOMY

Little is known of the precise anatomical features of the Denisovans, since the only physical remains discovered thus far are the finger bone, two teeth from which genetic material has been gathered and a toe bone. The single finger bone is unusually broad and robust, well outside the variation seen in modern people. Surprisingly, it belonged to a female individual, indicating that the Denisovans were extremely robust, perhaps similar in build to the Neanderthals. The tooth that has been characterized shares no derived morphological features with Neanderthal or modern humans.[22] 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 that the morphology was inconclusive. This toe bone's DNA was analyzed by Pääbo.[28] After looking at the full genome, Pääbo and others confirmed that humans produced hybrids with Denisovans.[29]

Some older finds may or may not belong to the Denisovan line. These include the skulls from Dali and Maba, and a number of more fragmentary remains from Asia. Asia is not well mapped with regard to human evolution, and the above finds may represent a group of "Asian Neanderthals".

Mitochondrial DNA analysis

The mtDNA from the finger bone 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.[6] This suggested a divergence time around one million years ago. The mtDNA from a tooth bore a high similarity to that of the finger bone, indicating that they belonged to the same population.[22] From a second tooth, an mtDNA sequence was recovered that showed an unexpectedly large number of genetic differences compared to that found in the other tooth and the finger, suggesting a high degree of mtDNA diversity. These two individuals from the same cave showed more diversity than seen among sampled Neanderthals from all of Eurasia, and were as different as modern-day humans from different continents.[12]

Nuclear genome analysis

In the same second 2010 paper, the authors reported 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, in spite of the apparent divergence of their mitochondrial sequence, that the Denisova population shared a common branch with Neanderthals 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 the time 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 drift or else an introgression from an older hominin lineage.[22]

In 2013, an mtDNA sequence from the femur of a 430,000 year old Homo heidelbergensis from the Sima de los Huesos cave in Spain was found to be related to that of the Neanderthals and the Denisovans, but closer to the latter.[30][31] Later analysis of nuclear DNA sequences from two specimens showed they were more closely related to Neanderthals rather than to Denisovans, while one of these samples also had the Denisovan-related mtDNA.[32] The authors suggest that the mtDNA found in these specimens represent an archaic sequence indicative of Neanderthal's kinship with Denisovans that was subsequently lost in Neanderthals due to replacement by a more modern-human-related sequence.



2010 – NEW INFORMATION ON THREE GROUPS OF ANCIENT HUMANS WHO SIMULTANEOUSLY OCCUPIED ALTAI MOUNTAINS, CIRCA 40,000 BP.

http://www.sciencemag.org/news/2010/03/researchers-discover-new-lineage-ancient-human
Researchers Discover New Lineage of Ancient Human
By Michael Balter Mar. 24, 2010 , 2:28 PM

Photograph -- Hominin land. Ancient DNA suggests that THREE SPECIES of ancient humans occupied Russia's Altai Mountains at about the same time. Johannes Krause et al., Nature (Advanced Online Edition) ©2010 Mcmillian Publishing Limited

DNA from a 40,000-year-old human finger bone found in a Siberian cave points to a new lineage of ancient human, researchers report today. The find—the first made with genetic, not fossil evidence—suggests that Central Asia was occupied at that time not only by Neandertals and Homo sapiens but also by a third, previously unknown hominin lineage. "This is the most exciting discovery to come from the ancient DNA field so far," says Chris Tyler-Smith, a geneticist at the Wellcome Trust Sanger Institute in Hinxton, United Kingdom.

The work complicates the human story once again, much as the discovery of the controversial H. floresiensis—a.k.a. the hobbit—has upset earlier and simpler views of early human migrations around the globe. If four early humans including the hobbit were alive about 40,000 years ago, "the amount of [human] biodiversity ... was pretty remarkable," says geneticist Sarah Tishkoff of the University of Pennsylvania.

A team led by archaeologists Michael Shunkov and Anatoli Derevianko of the Russian Academy of Sciences in Novosibirsk found the finger bone in 2008 at Denisova Cave in Russia's Altai Mountains. The cave, which has many archaeological layers spanning 100,000 years, has yielded both Neandertal and modern human stone tools and a small collection of hominin bones too fragmentary to be identified. The finger bone came from a layer radiocarbon dated to between 48,000 and 30,000 years ago. Evolutionary geneticists Svante Pääbo, Johannes Krause, and colleagues at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, ground up a 30-milligram sample and extracted and sequenced all of the 16,569 base pairs of its mtDNA genome, using new techniques Pääbo's group has successfully employed to sequence both Neandertal and prehistoric modern human DNA. The researchers compared the new mtDNA sequence with that of 54 living people from around the world, a roughly 30,000-year-old modern human from another Russian site, and six Neandertals.

They got a big surprise: Although Neandertals differ from modern humans at an average of 202 nucleotide positions in the mitochondrial genome, the Denisova hominin differed at an average of 385 positions from modern humans and 376 from Neandertals, the team reports online today in Nature. When mtDNA from chimpanzees and bonobos was added to the mix, the researchers were able to estimate that the new hominin had shared a common ancestor with Neandertals and modern humans about 1 million years ago.

But who was this mystery hominin? The team says the date is too late for Asian H. erectus, which first migrated out of Africa about 1.8 million years ago. And it's too early for H. heidelbergensis, which arose in Africa and Europe about 650,000 years ago and is thought by many researchers to be the common ancestor of humans and Neandertals. There's "no evidence" that these or other known species "persisted that late" in mainland Asia, says paleoanthropologist Russell Ciochon of the University of Iowa in Iowa City. Chris Stringer, a paleoanthropologist at the Natural History Museum in London, says the new species could represent "a pre-heidelbergensis, post-erectus dispersal" out of Africa "that we haven't picked up yet."

For now, Pääbo's team is not giving the new lineage a species name, at least until they know more about it. Next, the researchers plan to try to sequence nuclear DNA from the finger bone. If they succeed, they might discover the secret identity of Hominin X.

For full coverage, see the 26 March issue of Science.

Photograph -- Michael Balter
Email Michael



“... THE DATA SUGGEST THAT IT CONTRIBUTED 4–6% OF ITS GENETIC MATERIAL TO THE GENOMES OF PRESENT-DAY MELANESIANS....” THE IMAGINATION OF ARCHAEOLOGISTS IS VIBRANT, BUT THE MORE CONSERVATIVE THINKERS HALT AT ASSUMING THINGS. IT IS CLEAR, HOWEVER, THAT A GENETIC LINK WITH MELANESIANS, IN ORDER FOR THAT TRIAD OF BLOODLINES TO HAVE EMERGED THOUSANDS OF MILES IN THE PACIFIC OCEAN AND SO FROM SIBERIA MUST HAVE OCCURRED IN ASIA AND EARLY. WHAT HAD TO OCCUR BEFORE THEY MADE THEIR WAY ACROSS THE PACIFIC OCEAN BY BOAT OR ON FOOT – UNLESS THERE WERE MANY OTHER PLACES AROUND THE GLOBE AS WELL -- WHERE THE DENISOVANS, THE NEANDERTHALERS AND HOMO SAPIENS OCCASIONALLY HAD SOME SEXUAL CONTACT. WHATEVER THE CASE, THEY WERE CLEARLY CLEVER, AND I BELIEVE ABSOLUTELY HAD LANGUAGE OF SOME SORT. WHEN I WAS IN COLLEGE ANTHROPOLOGISTS WERE STILL SAYING THAT IT WAS UNCLEAR WHETHER NEANDERTHAL PEOPLE COULD SPEAK. ANOTHER BIAS AMONG ANTHROPOLOGISTS IN THE 1970S WAS THAT THERE WAS THE ASSUMPTION OF A CLEAR INTELLECTUAL DEFICIT, AND THAT IS OF COURSE LINKED WITH DARK SKIN AND EYES. I THINK GRADUALLY WE ARE OUTGROWING ALL OF THAT, AT LEAST WITHIN THE SCIENCES.

SO, HOW EARLY DID PEOPLE FIGURE OUT HOW TO CUT TREES, BIND THEM TOGETHER IN A RAFT, AND SET OFF? OR BURN AND CORE OUT A HUMAN SIZED SPACE IN A LOG TO MAKE A DUGOUT CANOE. ALSO, THE GLACIATION OF THE TIME DID CONTRIBUTE TO A SHALLOWER OCEAN, AND THE PACIFIC IS FULL OF EVER GROWING AND EVER NEW VOLCANIC MOUNTAINS, SO IT IS POSSIBLE THAT THEY WALKED! ONE ARTICLE DID SUGGEST THAT.

THE FIRST TIME I LOOKED AT THIS SUBJECT WAS IN THE RANGE OF FIVE YEARS AGO, WHEN I FOUND AN ARTICLE CLAIMING A NATIVE AMERICAN SITE ON THE COAST OF SOUTH AMERICA, CHILE I THINK, WHERE CHARCOAL WAS RADIOCARBON DATED TO 30,000 BP – 20,000 OLDER THAN ANY OTHER NORTH AMERICAN SITE. FASCINATING AS THAT WAS, THE SITE WAS DISCREDITED AMONG MOST (BUT NOT ALL) ARCHAEOLOGISTS OF THE TIME BECAUSE THEY FOUND INSUFFICIENT PROOF THAT IT WAS ACTUALLY A HEARTH SITE. IN OTHER WORDS, THE CLAIM WAS MADE THAT IT COULD HAVE BEEN MERELY A FOREST FIRE. WELL, I GUESS THAT IMMEDIATELY AFTER THE FOREST FIRE, A MAJOR LANDSLIDE COVERED UP THOSE CHARCOAL PIECES SO THAT THEY WERE NOT REMOVED FROM THE SITE. WHAT I DISLIKE IS THAT CLASSICAL ARCHAEOLOGISTS ARE SO CAREFUL TO AVOID THE CHANCE OF A RUSH TO JUDGEMENT THAT THEY REFUSE TO ALLOW OPEN DISCUSSION OF THINGS THAT ARE RATIONAL AND IMPORTANT IN UNDERSTANDING THE OVERALL PICTURE. IT IS CLEAR TO ME THAT THE HUMAN CREATURE HAS BEEN A WANDERER, AN EXPLORER, A SCIENTIST, RELIGIOUS IN CERTAIN WAYS – ANIMISM, FOR INSTANCE – AND MORE.

OUR INTELLIGENCE DIDN’T START WITH WHITE SKIN, NOR DID IT START AS LATE AS 30,000 BP. "CAVEMEN" WERE NO LESS INTELLIGENT THAN WE ARE. WHAT FOOLS PEOPLE ABOUT EVOLUTION IS THAT IN TERMS OF HUMAN CULTURE, GROWTH IS A PROCESS OF ACCRETION AND NEW SOURCES OF INFORMATION RATHER THAN A SUDDEN LEAP OF GENIUS, AT LEAST 99% OF THE TIME. AGRICULTURE IS THE DISCOVERY OF A PERSON, ALMOST CERTAINLY A WOMAN, GRINDING WILD GRAIN ON HER GRINDSTONE WHEN, AFTER A RAIN, BEAUTIFUL LITTLE SEEDLINGS EMERGED OUT OF THE GROUND BESIDE AND AROUND THE GRINDSTONE. AFTER ALL, THE CONCEPT OF WHAT A “SEED” ACTUALLY IS HAD TO BE DEVELOPED RATIONALLY AND THEN ALSO CULTURALLY. I EXPECT THAT SHE PROBABLY EXPERIMENALLY SET ASIDE A SMALL FURROW TO PLANT THEM IN AS WELL, JUST TO BE SURE. REMEMBERING ABOUT THE RAINSTORM, SHE ADDED WATER TO COMPLETE THE EXPERIMENTL CONDITIONS. IT IS MY THEORY THAT THE FIRST FARMER WAS A WOMAN WHO PAID CLOSE ATTENTION TO THE WORLD AS SHE GROUND HER GRAIN AND GOSSIPPED TO HER FRIEND MEANWHILE. "LOOK AT THESE NEW PLANTS!" SADLY FOR US TODAY, THERE WAS NO MEANS OF WRITING THAT INFORMATION DOWN TO PRESERVE IT FOR POSTERITY, SO IT WAS LOST!


https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4306417/
Genetic history of an archaic hominin group from Denisova Cave in Siberia
Nature. Author manuscript; available in PMC 2015 Jan 26.
Published in final edited form as:
Nature. 2010 Dec 23; 468(7327): 1053–1060.
doi: 10.1038/nature09710

The publisher's final edited version of this article is available at Nature
See other articles in PMC that cite the published article.

Abstract

Using DNA extracted from a finger bone found in Denisova Cave in southern Siberia, we have sequenced the genome of an archaic hominin to about 1.9-fold coverage. This individual is from a group that shares a common origin with Neanderthals. This population was not involved in the putative gene flow from Neanderthals into Eurasians; however, the data suggest that it contributed 4–6% of its genetic material to the genomes of present-day Melanesians. We designate this hominin population ‘Denisovans’ and suggest that it may have been widespread in Asia during the Late Pleistocene epoch. A tooth found in Denisova Cave carries a mitochondrial genome highly similar to that of the finger bone. This tooth shares no derived morphological features with Neanderthals or modern humans, further indicating that Denisovans have an evolutionary history distinct from Neanderthals and modern humans.

Less than 200,000 years ago, anatomically modern humans (that is, humans with skeletons similar to those of present-day humans) appeared in Africa. At that time, as well as later when modern humans appeared in Eurasia, other ‘archaic’ hominins were already present in Eurasia. In Europe and western Asia, hominins defined as Neanderthals on the basis of their skeletal morphology lived from at least 230,000 years ago before disappearing from the fossil record about 30,000 years ago1. In eastern Asia, no consensus exists about which groups were present. For example, in China, some have emphasized morphological affinities between Neanderthals and the specimen of Maba2, or between Homo heidelbergensis and the Dali skull3. However, others classify these specimens as ‘early Homo sapiens’4. In addition, until at least 17,000 years ago, Homo floresiensis, a short-statured hominin that seems to represent an early divergence from the lineage leading to present-day humans5-7, was present on the island of Flores in Indonesia and possibly elsewhere.

DNA sequences retrieved from hominin remains offer an approach complementary to morphology for understanding hominin relationships. For Neanderthals, the nuclear genome was recently determined to about 1.3-fold coverage8. This revealed that Neanderthal DNA sequences and those of present-day humans share common ancestors on average about 800,000 years ago and that the population split of Neanderthal and modern human ancestors occurred 270,000–440,000 years ago. It also showed that Neanderthals shared more genetic variants with present-day humans in Eurasia than with present-day humans in sub-Saharan Africa, indicating that gene flow from Neanderthals into the ancestors of non-Africans occurred to an extent that 1–4% of the genomes of people outside Africa are derived from Neanderthals8. In addition, ten partial and six complete mitochondrial (mt)DNA sequences have been determined from Neanderthals9-17. This has shown that all Neanderthals studied so far share a common mtDNA ancestor on the order of 100,000 years ago10, and in turn, share a common ancestor with the mtDNAs of present-day humans about 500,000 years ago10,18,19 (as expected, this is older than the Neanderthal–modern human population split time of 270,000–440,000 years ago estimated from the nuclear genome8). One of these mtDNA sequences has also shown that hominins carrying mtDNAs typical of Neanderthals were present as far east as the Altai Mountains in southern Siberia13.

In 2008, the distal manual phalanx of a juvenile hominin was excavated at Denisova Cave. This site is located in the Altai Mountains in southern Siberia, and is a reference site for the Middle to Upper Palaeolithic of the region where systematic excavations over the past 25 years have uncovered cultural layers indicating that human occupation at the site started up to 280,000 years ago20. The phalanx was found in layer 11, which has been dated to 50,000 to 30,000 years ago. This layer contains microblades and body ornaments of polished stone typical of the ‘Upper Palaeolithic industry’ generally thought to be associated with modern humans, but also stone tools that are more characteristic of the earlier Middle Palaeolithic, such as side-scrapers and Levallois blanks21-23.

Recently, we used a DNA capture approach10 in combination with high-throughput sequencing to determine a complete mtDNA genome from the Denisova phalanx. Surprisingly, this mtDNA diverged from the common lineage leading to modern human and Neanderthal mtDNAs about one million years ago19, that is, about twice as far back in time as the divergence between Neanderthal and modern human mtDNAs. However, mtDNA is maternally inherited as a single unit without recombination, and therefore is subject to chance events such as genetic drift, as well as gene flow and positive selection. In contrast, the nuclear genome comprises tens of thousands of unlinked, mostly neutrally evolving loci. This allows for analyses of genetic relationships that are robust to the STOCHASTICITY* of genetic drift, and are much less affected by positive selection. To clarify the relationship of the Denisova individual to other hominin groups, we have therefore sequenced the Denisova nuclear genome and analysed its genomic relationships to Neanderthals and present-day humans. We have also attempted to clarify the chronology of hominin occupation of the cave and have identified a tooth from this group of hominins among material excavated in Denisova Cave.

[NOTE: https://en.wikipedia.org/wiki/Stochastic, The word STOCHASTIC is an adjective in English that describes something that was randomly determined.[1] The word first appeared in English to describe a mathematical object called a stochastic process, but now in mathematics the terms stochastic process and random process are considered interchangeable.[2][3][4][5][6] The word, with its current definition meaning random, came from German, but it originally came from Greek στόχος (stokhos), meaning 'aim, guess'.]

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DNA sequence determination

The entire internal portion of the phalanx sample was used for DNA extraction in our clean-room facility, where procedures to minimize contamination from present-day human DNA are rigorously implemented24,25 (Supplementary Information section 1). The DNA was treated with two enzymes: uracil-DNA-glycosylase, which removes uracil residues from DNA to leave abasic sites26, and endonuclease VIII, which cuts DNA at the 5′ and 3′ sides of abasic sites. Subsequent incubation with T4 polynucleotide kinase and T4 DNA polymerase was used to generate 5′-phosphorylated blunt ends that are amenable to adaptor ligation. Because the great majority of uracil residues occur close to the ends of ancient DNA molecules, this procedure leads to only a moderate reduction in average length of the molecules in the library, but a several-fold reduction in uracil-derived nucleotide misincorporation27.

Two independent sequencing libraries (SL3003 and SL3004) were created from the DNA, using a modified Illumina protocol28 where a polymerase chain reaction (PCR) is used to add a 7-nucleotide index (in this case 5′-GTCGACT-3′) to the library molecules. This index ensures that the libraries are not contaminated by other sequencing libraries when they are taken out of the clean room to be sequenced29. The libraries were sequenced on the Illumina Genome Analyser IIx platform for 101 cycles from each end of the molecules and an additional 7 cycles for determination of the index until almost every unique sequence in the libraries had been seen multiple times, that is, almost every clone present in the libraries has been sequenced (Supplementary Information section 1). Bases were called using the machine-learning algorithm Ibis30 and an overlap of at least 11 bases was required for paired-end reads to be fused to full-molecule-size DNA sequences that were further analysed. This results in a greatly reduced error rate27, although it removes the few molecules that are above 191 nucleotides in length from analysis (~0.1% in SL3003 and ~0.2% in SL3004). Sequences were mapped using the program BWA31 to the human (hg18/NCBI 36) and the chimpanzee (panTro2/CGSC 2.1) genomes as well as to the inferred ancestral genome of these species (from the six-way Enredo-Pecan-Ortheus alignment)32. PCR duplicates were identified and used to further increase sequence accuracy by calling consensus sequences.

A total of 82,227,320 sequences mapped uniquely (mapping quality $30) to the human genome, yielding about 5.2 gigabases of DNA sequences (1.9-fold genomic coverage), and 72,304,848 sequences mapped uniquely to the chimpanzee genome. When the substitutions inferred to have occurred on the Denisova and the present-day human lineages were compared, the relative numbers of different classes of nucleotide substitutions are remarkably similar, and the excess number of candidate substitutions on the Denisova lineage relative to the present-day human lineage is only 1.7-fold (Supplementary Fig. 2.2 and Supplementary Table 2.4). This reflects an improvement in error rate over the Neanderthal genome by over an order of magnitude8 and is mainly due to the enzymatic removal of uracil residues from the Denisova DNA27. We estimate that most errors in the Denisova DNA sequences are due to low genomic coverage rather than to any features typical of ancient DNA.

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Human DNA contamination estimates

Although rigorous measures to prevent contamination of the experiments by DNA from present-day humans were implemented at all laboratory steps, it is impossible to completely prevent contamination because bone samples as well as reagents may be contaminated before they enter the clean-room facility. To estimate the levels of contamination in the sequences produced we used three approaches (Supplementary Information section 3).

First, we estimated the level of mtDNA contamination using 276 sequence positions where the Denisova mtDNA differs from >99% of present-day human mtDNAs. For library SL3003, we observed 7,433 unique sequences that covered such positions and 7,421 were of the Denisova type. For library SL3004 the corresponding numbers were 5,042 and 5,036, indicating that the mtDNA contamination in the libraries is on the order of 0.2% (95% confidence interval (CI): 0.1–0.3%) and 0.1% (CI: 0.1–0.3%), respectively.

Second, we identified sequences that are unique to the Y chromosome8. If the individual from whom the phalanx derives is female, the number of such sequences represents the extent of male DNA contamination. We found zero and three such Y chromosomal sequences in the two libraries, respectively, whereas 1,449 and 696 are expected if the individual is male. Thus, the bone derives from a female and male DNA contamination in the two libraries is on the order of 0.00% (CI: 0.00–0.25%) and 0.43% (CI: 0.09–1.26%), respectively.

Third, to estimate the extent of nuclear DNA contamination we used one library to identify positions where the Denisova individual carries an ancestral, that is, chimpanzee-like, sequence variant that among present-day humans is derived and not known to vary. We then examined sequences that map at these positions in the other library and determined if they carry the ancestral sequence or the derived sequence. Observation of a derived sequence in the second library could be due to one of three possibilities: that the DNA fragment in question comes from present-day human contamination; that the Denisova individual is heterozygous at the position in question; or that there has been a sequencing error. We implemented a maximum likelihood method that uses the number of independent observations of ancestral and derived states across positions to co-estimate contamination along with heterozygosity and sequencing error as nuisance parameters (Supplementary Information section 3). From this analysis, both libraries are inferred to have contamination rates of less than 1%.

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Ancestral features and duplications

The Denisova draft genome sequence allows features that are ancestral in the Denisova genome and derived in present-day humans to be identified. We previously described a set of 10.5 million single nucleotide differences and about half a million insertion/deletions (indels) inferred to be due to changes that occurred on the human lineage since the split from the common ancestor with the chimpanzee8. Of these, 4,267,431 (40.5%) single nucleotide differences and 105,372 (22.0%) indels are covered by the Denisova sequences. We identified 129 inferred amino substitutions and 14 indels in the coding sequences of genes where the Denisova individual carries the ancestral alleles at positions where present-day humans carry derived alleles and are not known to vary (Supplementary Information section 4). We also identified 90 such sites in 5′ untranslated regions (UTRs), 392 in 39 UTRs, two in microRNA genes and 104 in human accelerated regions. When we compared the Denisova and Neanderthal genomes we found that they carry the same assigned state at single nucleotide differences in 87.9% of the ancestral positions and 97.7% of the derived positions. The results for indels are similar: 87.6% for ancestral states and 98.6% for the derived states (Supplementary Table 4.3).

We analysed the segmental duplication content of the Denisova genome by detecting regions with an excess read depth (Supplementary Information section 5). In a three-way comparison of Denisova, Neanderthal and present-day human genomes, we found an excess of private Denisova duplications (2.27 megabases (Mb)) compared with duplications that were private in Neanderthals (0.60 Mb) or present-day humans (1.32 Mb). These regions were identified based on signatures of both excess read depth and increased sequence divergence, making them unlikely to be artefacts. We also identified two regions where the duplication architecture of Denisova is more similar to that of chimpanzee than to that of either Neanderthals or present-day humans, including two chromosomal regions associated with neurological disease in humans: spinal muscular atrophy on 5q13 (including SMN2, one of the most recent gene duplications in the human lineage) and neuropsychiatric disease on 16p12.1.

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Relationship to Neanderthals and modern humans

A fundamental question is whether the Denisova individual is an outgroup to Neanderthals and modern humans, as the mtDNA suggests19, whether it is a sister group to Neanderthals or to modern humans, or whether it falls within the range of variation of either of these two groups. We addressed this by estimating the divergence between the Denisova and the human genome reference sequence as a fraction of the divergence between present-day humans and the common ancestor shared with the chimpanzee. To do this, we scored the frequency with which the Denisova genome carries the human versus the chimpanzee state at positions where the human and chimpanzee reference genomes differ; assuming constant evolutionary rates (Supplementary Information section 2). We restricted this analysis to the parts of the human reference genome that are of African ancestry33 as gene flow from Neanderthals to non-Africans8 could otherwise complicate these analyses. The Denisova genome diverged from the reference human genome 11.7% (CI: 11.4–12.0%) of the way back along the lineage to the human–chimpanzee ancestor. For the Vindija Neanderthal, the divergence is 12.2% (CI: 11.9–12.5%). Thus, whereas the divergence of the Denisova mtDNA to present-day human mtDNAs is about twice as deep as that of Neanderthal mtDNA19, the average divergence of the Denisova nuclear genome from present-day humans is similar to that of Neanderthals.

A possible explanation for the similar divergence of the Denisova individual and Neanderthals from present-day Africans is that they both descend from a common ancestral population that separated earlier from ancestors of present-day humans. Such a scenario would predict a closer relationship between the Denisova individual and Neanderthals than between either of them and present-day humans. To test this prediction, we estimated the divergence between pairs of seven ancient and modern genomes (Denisova, Neanderthals, French, Han, Papuan, Yoruba and San), using an approach where we correct for error rates in each genome based on the assumption that each has the same number of true differences from chimpanzee (Supplementary Information section 6). The average divergence between Denisova and Vindija Neanderthals is estimated to be 9.84% of the way to the chimpanzee–human ancestor; that is, less than the average 12.38% divergence of both from present-day Africans. Assuming 6.5 million years for human–chimpanzee divergence, this implies that DNA sequences of Neanderthals and the Denisova individual diverged on average 640,000 years ago, and from present-day Africans 804,000 years ago.

To analyse further the relationship of the Denisova individual and Neanderthals, we aligned Denisova, Neanderthal and Yoruba sequences to the chimpanzee genome, picked a single sequence at random to represent each group, and examined sites where two copies of a derived and one copy of an ancestral allele were observed. Sequencing errors are expected to make a negligible contribution at such sites. The number of sites where the Denisova individual and Neanderthal cluster to the exclusion of the Yoruba and chimpanzee is 46,362, compared with an average of 22,012 sites for the other two possible patterns (Yoruba and Denisova, or Yoruba and Neanderthal). This excess of sites where Denisova and Neanderthal cluster supports the view that the Denisova individual and Neanderthals share a common history since separating from the ancestors of modern humans (Supplementary Information section 6).

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A Neanderthal-specific bottleneck

The fact that the Denisova nuclear genome on average shares a more recent common ancestor with Neanderthal than with present-day humans raises the question of whether the overall DNA sequence divergence of the Denisova individual falls inside the group morphologically and geographically defined as Neanderthals, or if it represents a sister group to Neanderthals.

To investigate this question, we took advantage of the fact that in addition to the three individuals from Vindija Cave, Croatia, from which most of the Neanderthal genome sequences were produced, we have determined nuclear DNA sequences from three further Neanderthal individuals from Russia, Spain and Germany8. Of these, the 60,000–70,000-year-old skeleton of a Neanderthal child found in Mezmaiskaya Cave, Russia, is both oldest and geographically closest to the Denisova individual. Using the 56 Mb of autosomal DNA sequences determined from this specimen8, we estimate that the DNA sequence divergence between the Vindija and Mezmaiskaya Neanderthals corresponds to a date of 140,000 ± 33,000 years ago (Supplementary Information section 6) (Fig. 1). This remarkably low divergence—which is about one-third of the closest pair of present-day humans that we analysed—is in agreement with the observation that diversity among Neanderthal mtDNAs is low relative to present-day humans10 and indicates that the Vindija and Mezmaiskaya Neanderthals descend from a common ancestral population that experienced a drastic bottleneck since separating from the ancestors of the Denisova individual.

Figure 1
Figure 1
A neighbour-joining tree based on pairwise autosomal DNA sequence divergences for five ancient and five present-day hominins

To understand further the bottleneck in the history of Vindija and Mezmaiskaya Neanderthals, we examined four-way alignments of the Vindija Neanderthal genome sequence, the Mezmaiskaya Neanderthal, the Denisova individual and the chimpanzee genome. At transversion substitutions where two copies of the derived alleles are observed, we detect 924 substitutions that cluster the Vindija and Mezmaiskaya Neanderthals, 80 that cluster Vindija and Denisova, and 81 that cluster Mezmaiskaya and Denisova. This corresponds to at least a 65% probability that the DNA sequences in the Neanderthals share a common ancestor more recently than their split from the ancestor of the Denisova individual (Supplementary Information section 7). It is much higher than the 15–20% probability associated with the ‘Out of Africa’ bottleneck common to present-day non-Africans34. If we replace the Mezmaiskaya Neanderthal in this analysis with a Neanderthal from El Sidron, Spain, or from Feldhofer, Germany, results are qualitatively similar although numbers are smaller (Supplementary Information section 7). Thus, we conclude that late Neanderthals across a broad geographical range have a population history distinct from that of the Denisova individual in that they share a strong population bottleneck not experienced by the ancestors of the Denisova individual. We call the group to which this individual belonged Denisovans in analogy to Neanderthals, as Denisovans are described for the first time based on molecular data from Denisova Cave just as Neanderthals were first described based on skeletal remains retrieved in the Neander Valley in Germany.

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No Denisovan gene flow into all Eurasians

We have previously shown that Vindija Neanderthals share more derived alleles with non-Africans than with Africans, consistent with Neanderthals contributing 1–4% of the genomes of present-day humans across Eurasia8. To investigate the extent to which the Denisova individual shares this pattern, we examined alignments of sets of four genomes, each consisting of an African (Yoruba or San), a Eurasian (French or Han), an archaic hominin (Neanderthal or Denisovan) and the chimpanzee. We randomly sampled one allele from each of the three hominins, and counted all transversion differences between the African and the Eurasian where the archaic individual carries the derived allele (the ‘D statistics’ of ref. 8). Neanderthals match the French genome on average 4.6 ± 0.7% more often than they match the Yoruba genome (Table 1). Although the Denisova individual also matches the French more than the Yoruba genome, this skew is significantly less strong at 1.8 ± 0.5%. The estimates of D statistics were quantitatively consistent (within two standard deviations) for all other choices of Eurasian and African populations (Table 1). These findings indicate that the archaic component of the Eurasian gene pool is less closely related to the Denisova individual than to Neanderthals.

Table 1
Table 1
Sharing of derived alleles between present-day and archaic hominins

We also examined 13 genomic regions that we previously identified as candidates for a contribution of archaic genetic material into non-Africans, based on their deeper genetic divergences in non-Africans than in Africans8. Using ‘tag SNPs’ that are informative about whether a haplotype is from the lineage unique to non-Africans, we find that the Denisova individual matches the deeply diverged non-African haplotype in 6 cases, whereas Neanderthals do so in 11 cases (Supplementary Information section 7). Thus, both Neanderthals and Denisovans are more related than would be expected by chance to these genomic segments, but the signal in Denisovans is weaker.

These analyses indicate that Neanderthals are more closely related than Denisovans to the population that contributed to the gene pool of the ancestors of present-day Eurasians. The fact that Eurasians share some additional affinity with the Denisova individual relative to Africans is compatible with a scenario in which Denisovans shared some of their history with Neanderthals before the gene flow from Neanderthals into modern humans occurred.

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Denisovan gene flow into the ancestors of Melanesians

Although the Denisova individual derives from a population that was not directly involved in the gene flow from Neanderthals to Eurasians, it is possible that Denisovans admixed with the ancestors of present-day people in some parts of the Old World. To investigate this, we analysed the relationship of the Denisova genome to the genomes of 938 present-day humans from 53 populations that have been geno-typed at 642,690 single nucleotide polymorphisms (SNPs)35. We scored each of these present-day humans based on their relative proximity to Neanderthals and the Denisova individual at positions where we have high-quality data for both the Neanderthal and Denisova genomes (Supplementary Information section 8). Using the means of the 53 populations, the first two principal components separate the populations into three groups (Fig. 2): first, the 7 sub-Saharan African populations; second, a group of 44 non-African populations as well as one north African group; and third, Papuan and Bougainville populations from Melanesia. When individuals from selected populations are analysed separately, the Papuan and Bougainville islanders remain distinct from almost all individuals outside Africa (Supplementary Fig. 8.1b). Thus, with respect to their relationship to Neanderthals and Denisovans, the Melanesian populations stand out relative to other non-African populations.

Figure 2
Figure 2
Relationship of present-day populations to the Denisova individual and Neanderthals based on 255,077 SNPs

To explore this further, we analysed the relationship of the Denisova genome to the genomes of five present-day humans that we previously sequenced to about fivefold coverage8 (a Yoruba and a San genome from Africa, a French genome from Europe, a Han genome from China and a Papuan genome from Melanesia), as well as seven present-day humans that we sequenced to 1–2-fold coverage for this study (a Mbuti genome from Africa, a Sardinian genome from Europe, a Mongolian genome from Central Asia, a Cambodian genome from South-East Asia, an additional Papuan genome from Melanesia, a Bougainville islander genome from Melanesia, and a Karitiana genome from South America) (Supplementary Information section 9). We used the D statistic8 to test if various pairs of present-day humans share equal numbers of derived alleles with the Denisova individual. To do this, we restricted comparisons to pairs of present-day humans sequenced at the same time to minimize the chance that differences in sample processing could affect the results. We find that the fivefold coverage Papuan individual shares 4.0 ± 0.7% more alleles with the Denisova individual than does the French individual, and we observed a similar skew in all 10 comparisons of Melanesian and other non-African populations (Table 1). When we stratified the data by base substitution class and chromosome, the D statistics are qualitatively unchanged (Supplementary Information section 10). Similarly, the D statistics are consistent for all depths of read coverage, indicating that mapping errors, for example due to segmental duplications, are not likely to explain these results. Finally, differences in sequencing error rate across samples cannot explain the observed D statistics (Supplementary Information section 10).

Under the assumption that gene flow explains these observations, we determined the direction of this gene flow by asking whether Melanesians and other Eurasians share derived alleles with Africans equally often. If the gene flow was entirely into the ancestors of the Denisovan individual, we would not expect this to affect the relationship of Africans to Melanesians and other Eurasians and thus we would expect them to share derived alleles equally often with Africans. However, we find that derived alleles in Africans match Melanesians 3.4 ± 0.4% less often than other non-Africans (Z = 10.8). Because this skew is seen without using Denisovan data it cannot be explained by gene flow into Denisovans or, for example, by contamination of the Denisova sample by present-day Melanesian DNA. Thus, at least some of the putative gene flow must have been into Melanesians (Supplementary Information section 8).

When we compare the skew in the fraction of derived alleles shared with the two archaic hominins to what would be expected for individuals of 100% Neanderthal or Denisova ancestry, respectively (Supplementary Information section 8 and ref. 8), we estimate that 2.5 ± 0.6% of the genomes of non-African populations derive from Neanderthals, in agreement with our previous estimate of 1–4%8. In addition, we estimate that 4.8 ± 0.5% of the genomes of Melanesians derive from Denisovans. Altogether, as much as 7.4 ± 0.8% of the genomes of Melanesians may thus derive from recent admixture with archaic hominins.

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A model of population history

To understand the implications of the relationships observed among the Denisova individual, the Neanderthals and present-day humans, we fit the D statistics described in the previous sections to a parameterized model of population history. The D statistics for the Denisova individual differ in two important ways from those for the Neanderthal. First, the Denisova individual shares fewer derived alleles with either the French or Han Chinese populations than do the Neanderthals. Second, the Denisova individual shares more derived alleles with the Papuans than do the Neanderthals. We are able to fit the data with a model that assumes the Denisovans are a sister group of Neanderthals with a population divergence time of one-half to two-thirds of the time to the common ancestor of Neanderthals and humans. After the divergence of the Denisovans from Neanderthals, there was gene flow from Neanderthals into the ancestors of all present-day non-Africans. Later there was admixture between the Denisovans and the ancestors of Melanesians that did not affect other non-African populations. This model is illustrated in Fig. 3 and is described in detail in Supplementary Information section 11.

Figure 3
Figure 3
A model of population history compatible with the data

Other, more complex models could also explain the data. For example, a model that invokes only gene flow from Denisovans to Melanesian ancestors outside Africa and assumes four subpopulations in Africa that existed between the times of the origin of Denisovan and Neanderthal ancestors and the ancestors of present-day Eurasians could also fit the data (Supplementary Fig. 11.4). However, because barriers to gene flow between such subpopulations would have to persist for hundreds of thousands of years to create the observed patterns, such a model is less plausible on biological grounds than a model that invokes two instances of gene flow outside Africa.

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Discordance of mtDNA and nuclear histories

The population history indicated by the nuclear genome is different from that indicated by the mtDNA phylogeny. There are two possible explanations for this. One is that the mtDNA lineage was introduced into Denisovan ancestors by admixture from another hominin lineage for which we have no data. The other is that the discordance is the result of ‘incomplete lineage sorting’, that is, the random assortment of genetic lineages due to genetic drift which may have allowed a divergent mtDNA lineage to survive in Denisovans by chance while becoming lost in Neanderthals and modern humans. A large ancestral population size makes incomplete lineage sorting more likely to occur. In Supplementary Information section 11, we show that given reasonable assumptions about the size of the ancestral populations, the discordance of the mtDNA phylogeny with that indicated by the nuclear DNA can be explained either by a small amount of admixture from another archaic hominin or by incomplete lineage sorting. Thus, the data do not allow us to favour one hypothesis over the other.

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A tooth from Denisova Cave

In 2000, a hominin tooth was discovered in layer 11.1 of the south gallery of Denisova Cave (Fig. 4a, b). The tooth is from a young adult and therefore from another individual than the phalanx which stems from a juvenile (Supplementary Information section 12). To elucidate the relationship of the tooth to the individual from which the phalanx is derived, we extracted DNA from 50 mg of dentin from the root of the tooth and prepared a sequencing library (Supplementary Information section 13). About 0.17% of random DNA sequences determined from this library aligned to the human genome, whereas the rest is likely to represent microbial contamination common in ancient bones. We therefore used a novel DNA capture approach36 to isolate mtDNA sequences from the sequencing library. A total of 15,094 sequences were identified which allowed the complete mtDNA genome to be assembled at an average coverage of 58-fold. This sequence differs at two positions from the mtDNA of the phalanx whereas it differs at about 380 positions from both Neanderthal and present-day humans. The time since the most recent common ancestor of the two mtDNAs from Denisova Cave is estimated to be 7,500 years, with a 95% upper bound of 16,000 years (Supplementary Information section 13). We conclude that the tooth and the phalanx derive from two different individuals that are probably from the same hominin population.

Figure 4
Figure 4
Morphology of the Denisova molar
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Morphology of the Denisova molar

The tooth is an almost complete left, probably third, but possibly second, upper molar (Fig. 4b). The crown is trapezoidal and tapers strongly distally, with bulging lingual and buccal walls giving the tooth an inflated appearance (Supplementary Information section 12). The roots are short but robust and strongly flaring.

Overall, the tooth is very large (mesiodistal diameter, 13.1 mm; buccolingual, 14.7 mm). As a third molar, it is outside the range of normal size variation of all fossil taxa of the genus Homo, with the exception of H. habilis and H. rudolfensis, and comparable to Australopithecines (Fig. 4c). Compared to second molars, it is larger than Neanderthals or early modern humans, but similar to H. erectus and H. habilis (Supplementary Fig. 12.1).

Besides size, it is also distinguished from most Neanderthal third molars by the absence of hypocone reduction, and from both second and third Neanderthal molars by the presence of a large talon basin and the strong flare of the crown. Furthermore, it lacks the lingual hypocone projection seen in all Neanderthal first and many second molars, and has strongly diverging roots, unlike the closely spaced and frequently fused roots of Neanderthals.

It is of particular interest to compare the Denisova molar to Middle Pleistocene hominins from China, where H. erectus and other archaic forms, sometimes interpreted as H. heidelbergensis, may have survived until recently. Unfortunately, very few of these fossils preserve third upper molars. Of the few examples that are available, most differ from the Denisova molar by their strongly reduced size. Second molars are more frequent than third molars, and most have a trapezoidal shape like Denisova, but they do not have the lingually skewed position of the hypocone and metacone and the strong basal flare of the crown.

The Denisova molar supports the DNA evidence that the Denisovan population is distinct from late Neanderthals as well as from modern humans. In fact, the primitive traits of the Denisova tooth suggest that Denisovans may have been separated from the Neanderthal lineage before Neanderthal dental features are documented in Western Eurasia (>300,000 years BP) (Supplementary Information section 12), although we cannot exclude the possibility that the Denisovan dental morphology results from a reversion.

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Stratigraphy and dating

The small size of both the phalanx and the tooth precludes direct radiocarbon dating. We instead dated seven bone fragments found close to the hominin remains in layer 11 in the east and south galleries. To ensure that they were associated with human occupation of the cave we chose bones that have evidence of human modification, including a rib with regular incisions and a bone projectile point blank generally associated with Upper Palaeolithic cultural assemblages. In the south gallery, where modified bones were not available, we used herbivore bones (Supplementary Information section 12).

Four of the seven dates are infinite dates older than 50,000 years BP (uncalibrated), whereas three are finite dates between 16,000 and 30,000 years BP (Supplementary Table 12.1). The rib with incisions and the projectile point blank are about 30,000 and 23,000 years BP, respectively. Together with three previous dates23 this shows that layer 11 contains cultural remains from at least two different time periods, one period older than 50,000 years BP and one more recent period. However, the stratigraphy is complicated by the discovery of a wedge-shaped area close to the area where the phalanx was found that is likely to be disturbed (Supplementary Information section 12). Hominin remains large enough to allow direct radiocarbon dates may eventually be discovered in the cave, but a reasonable hypothesis is that the phalanx and molar belong to the older occupation.

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Discussion

The molecular preservation of the Denisova phalanx is exceptional in that the fraction of endogenous relative to microbial DNA is about 70%. By contrast, in all Neanderthal remains studied so far the relative abundance of endogenous DNA is below 5%, and typically below 1%. Furthermore, the average length of hominin DNA fragments in the Denisova phalanx is 58 base pairs (bp) (SL3003) and 74 bp (SL3004) in spite of the enzymatic treatment that removes uracil residues and decreases the average fragment size, whereas in most well-preserved Neanderthal samples it is 50 bp or smaller without this treatment. Thus, although many Neanderthals are preserved under conditions apparently similar to those in Denisova Cave, the Denisova phalanx is one of few bones found in temperate conditions that are as well preserved as many permafrost remains37,38. It is not clear why this is. It is not due to some condition that affects all hominin remains in Denisova Cave because the fraction of endogenous DNA in the tooth is 0.17%; that is, typical of other Late Pleistocene hominin remains. It is possible that a rapid desiccation of the tissue after death, which would limit degradation of the DNA by endogenous enzymes as well as microbial growth, has allowed this exceptional preservation.

The Denisova individual and the population to which it belonged carry some exceptionally archaic molecular (mtDNA) as well as morphological (dental) features. Nevertheless, the picture that emerges from analysis of the nuclear genome is one where the Denisova population is a sister group to Neanderthals. Three possibilities could account for how such archaic features have come to be present in Denisovans. One possibility is that these features were retained in Denisovans but became lost in modern humans and Neanderthals. A second, not mutually exclusive, possibility is that they entered the Denisova population through gene flow from some even more diverged hominin. Although such gene flow cannot be detected with the current mtDNA and nuclear DNA data, further sequencing of other hominin remains may in the future allow testing for it. A third possibility that could account for the apparently archaic dental morphology, but not the mtDNA, is a reversal to ancestral traits.

After they diverged from one another, Denisovans and Neanderthals had largely separate population histories as shown by a number of observations. First, patterns of allele sharing indicate that Denisovan ancestors did not contribute genes at a detectable level to present-day people all over Eurasia whereas Neanderthals did8. Thus, Neanderthals at some point interacted with ancestors of present-day Eurasians independently of Denisovans. Second, the genetic diversity of Neanderthals across their geographical range in the last thirty or forty thousand years of their history was extremely low, indicating that they experienced one or more strong genetic bottlenecks independently of the Denisovans. Third, our results indicate that Denisovans but not Neanderthals contributed genes to ancestors of present-day Melanesians. Fourth, the dental morphology shows no evidence of any derived features seen in Neanderthals. In fact, dental remains from the Sima de los Huesos of Atapuerca, for which ages between 350,000 and 600,000 years have been proposed39,40, already carry Neanderthal-like morphological features that are not seen in the Denisova molar.

An interesting question is how widespread Denisovans were. A possibility is that they lived in large parts of East Asia at the time when Neanderthals were present in Europe and western Asia. One observation compatible with this possibility is that Denisovan relatives seem to have contributed genes to present-day Melanesians but not to present-day populations which currently live much closer to the Altai region such as Han Chinese or Mongolians (Table 1). Thus, they have at least at some point been present in an area where they interacted with the ancestors of Melanesians and this was presumably not in southern Siberia. Further studies of both molecular and morphological features of hominin remains across Asia should clarify how widespread Denisovans were and how they were related to archaic hominins other than Neanderthals.

<b>The Denisova individual belongs to a hominin group that shares a common ancestor with Neanderthals but has a distinct population history. We define this group based on genomic evidence and call it Denisovans, but refrain from any formal Linnaean taxonomic designations that would indicate species or subspecies status for either Neanderthals or Denisovans. In our view, these results show that on the Eurasian mainland there existed at least two forms of archaic hominins in the Upper Pleistocene: a western Eurasian form with morphological features that are commonly used to define them as Neanderthals, and an eastern form to which the Denisova individuals belong. In the future, when more complete genomes from these and other archaic hominins will be sequenced from remains that allow more morphological features to assessed, their relationships will become even better understood. This will be an important endeavour as the emerging picture of Upper Pleistocene hominin evolution is one in which gene flow among different hominin groups was common.

Acknowledgements
We thank C. Bustamante, A. I. Krivoshapkin, M. Lachmann, R. Nielsen, K. Pruefer, A. Tsybankov, L. Vigilant and W. Zhai for comments; K. Finstermeier for graphics work; the MPI-EVA sequencing group, R. Schultz and S. Weihnachtsmann for technical support; and P. Fujita, A. Hinrichs and K. Learned for designing the UCSC genome browser portal to the Denisova data. The Presidential Innovation Fund of the Max Planck Society and the Krekeler Foundation provided financial support. M.S. was supported by a US National Institutes of Health grant (R01-GM40282). The National Science Foundation provided an International Postdoctoral Fellowship (OISE-0754461) to J.M.G., a Fellowship in Biological Informatics to P.L.F.J. and a HOMINID grant (1032255) to D.R.

Footnotes
Supplementary Information is linked to the online version of the paper at www.nature.com/nature.

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References
. . . .


DENISOVAN

https://en.wikipedia.org/wiki/Denisovan
Denisovan
From Wikipedia, the free encyclopedia

"Woman X" redirects here. For other uses, see X woman (disambiguation) and Madame X (disambiguation).
"Denisovans" redirects here. For the English darts player, see Denis Ovens.

The Denisovan or Denisova hominin ( /dɪˈniːsəvə/ di-NEE-sə-və) is an extinct species or subspecies of human in the genus Homo. Pending its status as either species or subspecies it currently carries the temporary names Homo sp. Altai,[1] or Homo sapiens ssp. Denisova.[2][3] In March 2010, scientists announced the discovery of a finger bone fragment of a juvenile female who lived about 41,000 years ago, found in the remote Denisova Cave in the Altai Mountains in Siberia, a cave that has also been inhabited by Neanderthals and modern humans.[4][5][6] The mitochondrial DNA (mtDNA) of the finger bone showed it to be genetically distinct from Neanderthals and modern humans.[7] The nuclear genome from this specimen suggested that Denisovans shared a common origin with Neanderthals, that they ranged from Siberia to Southeast Asia, and that they lived among and interbred with the ancestors of some modern humans,[8] with about 3% to 5% of the DNA of Melanesians and Aboriginal Australians deriving from Denisovans.[9][10][11]

A 2013 comparison with the genome of another Neanderthal from the Denisova cave revealed local interbreeding with local Neanderthal DNA representing 17% of the Denisovan genome, and evidence of interbreeding with an as yet unidentified ancient human lineage.[12] Analysis of DNA from two teeth found in layers different from the finger bone revealed an unexpected degree of mtDNA divergence among Denisovans.[12] Two teeth belonging to different members of the Denisova cave population have been reported in November 2015, a tooth fossil containing DNA was reported to have been found and studied.[13][14]

Discovery

The Denisova Cave is located in south-western Siberia, in the Altai Mountains near the border with China and Mongolia. It is named after Denis, a Russian hermit who lived there in the 18th century. The cave was originally explored in the 1970s by Russian paleontologist Nikolai Ovodov, who was looking for remains of canids.[15] In 2008, Michael Shunkov from the Russian Academy of Sciences and other Russian archaeologists from the Institute of Archaeology and Ethnology of Novosibirsk investigated the cave. They found the finger bone of a juvenile hominin, known as both the "X woman" (referring to the maternal descent of mitochondrial DNA),[16] and the Denisova hominin. Artifacts (including a bracelet) excavated in the cave at the same level were dated using radiocarbon and oxygen isotopes to around 40,000 BP.[17] Excavations have since revealed human artifacts showing an intermittent presence going back 125,000 years.[18]

A team of scientists led by Johannes Krause and Svante Pääbo from the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, sequenced mtDNA extracted from the fragment. The cool climate of the Denisova Cave preserved the DNA.[6] The average annual temperature of the cave is 0 °C, which has contributed to the preservation of archaic DNA among the remains discovered.[19] The analysis indicated that modern humans, Neanderthals, and the Denisova hominin last shared a common ancestor around 1 million years ago.[7]

The mtDNA analysis further suggested that this new hominin species was the result of an earlier migration out of Africa, distinct from the later out-of-Africa migrations associated with modern humans, but also distinct from the even earlier African exodus of Homo erectus.[7] Pääbo noted that the existence of this distant branch creates a much more complex picture of humankind during the Late Pleistocene.[16] This work shows that the Denisovans were actually a sister group to the Neanderthals,[20] branching off from the human lineage 600,000 years ago, and diverging from Neanderthals, probably in the Middle East, 200,000 years later.[21]

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 performed mitochondrial DNA analysis on the tooth and found it to have a sequence different from but similar to that of the finger bone, indicating a divergence time about 7,500 years before, and suggesting that it belonged to a different individual from the same population.[22]

Fossils
So far, the fossils of four distinct Denisovans from Denisova Cave have been identified through their DNA: Denisova 2, Denisova 3, Denisova 4, and Denisova 8. Denisova 2 and Denisova 3 are young girls, while Denisova 4 and Denisova 8 are adult males.[23] mtDNA analysis of the Denisovan individuals suggests that Denisova 2 is the oldest, followed by Denisova 8, while Denisova 3 and Denisova 4 are roughly contemporaneous.[23]

During DNA sequencing, Denisova 2, Denisova 4 and Denisova 8 yielded low-coverage genomes, while Denisova 3 yielded high-coverage genome.[14][23]


I’M PRESENTING THIS DAILY MAIL ARTICLE BECAUSE IT SEEMS TO ADD INTERESTING MATERIAL TO THIS WHOLE ANCESTRY ISSUE, BUT HAVING HEARD BAD THINGS ABOUT THEM ALSO, I AM REFERENCING THIS “QUORA” ARGUMENT ON THE VALIDITY OF THEIR WRITING. WHEN I LOOK AT THINGS LIKE THIS I TRY TO DIG INTO THE MATERIAL ENOUGH TO PULL OUT WHAT LOOKS TO BE BOTH LIKELY, AND LOGICAL. THEN I RESEARCH A LITTLE ON THAT. REMEMBER THAT EVEN THE MURDOCH PUBLICATIONS ALSO PRESENT SOME REAL NEWS FROM TIME TO TIME. LOOK AT THIS LAST IN THE LIGHT OF THOSE RELATED STORIES ABOVE.

http://www.dailymail.co.uk/sciencetech/article-3866832/Pacific-islanders-carry-DNA-unknown-human-species-Genetic-study-reveals-ancient-Melanesians-interbred-mysterious-hominid.html
Pacific islanders may carry the DNA of an unknown human species: Genetic study reveals ancient Melanesians interbred with a mysterious hominid
The island peoples of Melanesia have a distinct genetic ancestry

Analysis shows their ancestors bred with Neanderthals and Denisovans
But there is genetic evidence of a third unknown group of human species

This third group could add another twist in the tale of human evolution
By Ryan O'Hare for MailOnline

PUBLISHED: 07:45 EST, 24 October 2016 | UPDATED: 11:04 EST, 24 October 2016

Islanders in the Pacific Ocean may be may be carrying traces of a long lost human species locked up in their DNA.

Today, modern humans inherit a small chunk of our genes from Neanderthals, with evidence that some of us carry the genetic remnants of a lesser known sister group, called the Denisovans.

But genetic analysis of people living in modern Melanesia suggests they carry traces of a third, as yet unidentified prehistoric relative distinct from the others.

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The first pioneers to expand across Oceania may have originated from Melanesian societies, such as Papua New Guinea. Pictured are people from Papua New Guinea in traditional dress at a cultural Hagen show

Genetic analysis of people living in modern Melanesia suggests they carry traces of unknown prehistoric relative of humans. Pictured are people from Papua New Guinea at a cultural Hagen show

The island groups of Melanesia – which includes Papua New Guinea, Fiji and the Solomon Islands and others – are geographically cut off by the Pacific Ocean, with their DNA providing a unique window into how human ancestors spread across the region.

The latest research, presented at a meeting of the American Society for Human Genetics in Vancouver, bolsters previous findings that there may be another strand to the story of modern humans, with multiple groups of prehistoric human interbreeding.

Genetic analysis of Europeans, Asians and others with non-African descent hints that ancient humans interbred with Neanderthals.

Some groups inherited as much as four per cent of their DNA from these extinct human cousins.

A single finger bone and a few teeth found in a cave in Russia revealed another branch of the family tree, the Denisovans, also left their genetic calling card in modern humans, accounting for as much as four per cent of people’s DNA in Melanesia.

Native people from Papua New Guinea in Melanesia are believed to owe between two and four per cent of their DNA to Denisovans and carry less Neanderthal DNA than other Asians. But genetic data reveal their ancestors may have bred with a third species of ancient human

ANOTHER TWIST IN THE TALE OF HUMAN EVOLUTION?

The tantalising genetic evidence offers a hint of another branch of the human family tree

The island peoples in the Pacific Ocean have a distinct genetic ancestry.

Genetic analysis shows their ancestors bred with two groups of ancient humans, the Neanderthals and Denisovans.

This link is made by comparing samples of islanders with DNA sequences extracted from remains of these ancient human species.

But studying the rate of genetic mixing in Melanesia revealed a high proportion of other extinct ancestry which was unaccounted for.

Researchers believe this genetic evidence of a third unknown group of human species which predated the Denisovans by hundreds of thousands of years.

The tantalising genetic evidence offers a hint of another branch of the human family tree.

But unlike Neanderthals and Denisovans, there are no known physical remains to compare it with.

This unknown third group could add another twist in the tale of human evolution.

Now, the latest number crunching has revealed another genetic twist in the tale of modern humans.

Ryan Bohlender, a geneticist at the University of Texas, and colleagues looked at the rate of genetic mixing which would account for what’s seen in modern Melanisians and found that something didn’t add up.

As expected, their analysis found the genetic calling cards of Denisovans and Neanderthals, but it also revealed a high proportion of other extinct ancestry unaccounted for.

To explain this mystery DNA, the team believe that ancient Melanesians must have bred with a third group of hominids.

Presenting their findings in Vancouver, the team explained: ‘We suggest that a third archaic population related more closely to Neanderthal and Denisova than to modern humans introgressed into the San genomes studied here’.

Modern humans carry remnants of Neanderthals and Denisovans. The links have been made by comparing samples of modern human with DNA extracted from remains of these ancient human species, such as the tooth of a Denisovan found in Russia (pictured) +4
Modern humans carry remnants of Neanderthals and Denisovans. The links have been made by comparing samples of modern human with DNA extracted from remains of these ancient human species, such as the tooth of a Denisovan found in Russia (pictured)

Genetic analysis of Europeans, Asians and others with non-African descent hints that ancient humans interbred with Neanderthals, with some groups inheriting as much as 4 per cent of their DNA from these extinct human cousins. Pictured is a Neanderthal skull +4
Genetic analysis of Europeans, Asians and others with non-African descent hints that ancient humans interbred with Neanderthals, with some groups inheriting as much as 4 per cent of their DNA from these extinct human cousins. Pictured is a Neanderthal skull

By working out the amount of DNA shared by Neanderthals and Denisovans, they calculated that this third extinct human species likely branched off from their common ancestor 440,000 years ago.

'Overall, our findings confirm the human family tree is more complicated than we think it is,' said Dr Bohlender.

He exlained: 'Other archaic populations are likely to have existed, like the Denisovans, who we didn't know about except through genetics.'

Previous studies have shown that ancient Melanesians’ trysts with Denisovans may have helped them to adapt to new environments and spread across the Pacific and into Australia.

Among the Denisovan genes are those which boost resilience to viruses and provide metabolic benefits, including increasing blood glucose levels and breaking down fats.

Tracing the genetic lineage has revealed that modern humans interbred with Neanderthals a number of times and Denisovans at least once, before these two human cousins died out.

WHO WERE THE DENISOVANS?
A finger bone from the Denisova 3 find
A finger bone from the Denisova 3 find

The Denisovans are an extinct species of human that appear to have lived in Siberia and even down as far as southeast Asia.

Although remains of these mysterious early humans have only been discovered at one site - the Denisova Cave in the Altai Mountains in Siberia, DNA analysis has shown they were widespread.

DNA from these early humans has been found in the genomes of modern humans over a wide area of Asia, suggesting they once covered a vast range.

They are thought to have been a sister species of the Neanderthals, who lived in western Asia and Europe at around the same time.

The two species appear to have separated from a common ancestor around 200,000 years ago, while they split from the modern human Homo sapien lineage around 600,000 years ago.

Bone and ivory beads found in the Denisova Cave were discovered in the same sediment layers as the Denisovan fossils, leading to suggestions they had sophisticated tools and jewellery.

Professor Chris Stringer, an anthropologist at the Natural History Museum in London, said: 'Layer 11 in the cave contained a Denisovan girl's fingerbone near the bottom but worked bone and ivory artefacts higher up, suggesting that the Denisovans could have made the kind of tools normally associated with modern humans.

'However, direct dating work by the Oxford Radiocarbon Unit reported at the ESHE meeting suggests the Denisovan fossil is more than 50,000 years old, while the oldest 'advanced' artefacts are about 45,000 years old, a date which matches the appearance of modern humans elsewhere in Siberia.'


Read more:
DNA data offer evidence of unknown extinct human relative | Science News
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A FINAL PERENNIAL QUESTION IS WHERE DID WHITE SKIN ORIGINATE? I’VE REPEATEDLY HEARD THAT NEANDERTHALS BROUGHT IN THE LIGHT SKIN AND EYES GENES. AS RECENTLY AS SEVERAL YEARS AGO I’VE HEARD THAT STORY, BUT THIS INTERESTING ARTICLE FROM NEW SCIENTIST SAYS THAT NEANDERTHAL PEOPLE HAD DIFFERENT COLORING ACCORDING TO WHERE THEY WERE JUST AS MODERN HUMANS DO. THE DARKER COLORING GOES WITH NEARNESS TO THE EQUATOR.

IT WAS SAID IN ONE OF MY CLASSES IN COLLEGE THAT A HIGHER AMOUNT OF MELANIN BRINGS A PARTIAL PROTECTION AGAINST MALARIA. ON THE OTHER SIDE OF THE QUESTION, I HAVE READ TWICE NOW (ONCE IN ONE OF THESE ARTICLES) THAT PALE SKIN IS AN ADVANTAGE IN THE NORTH WHERE THERE IS INSUFFICIENT SUN FOR PROPER PRODUCTION OF VITAMIN D, AND MELANIN TENDS TO BLOCK IT. PARTICULARLY IN THE CASE OF PREGNANT WOMEN, WHOSE BODIES ARE BUSY MAKING BONE FOR THEIR BABIES, A CHARACTERISTIC THAT CAUSES WEAK BONES IN OFFSPRING WOULD BE A SEVERE PROBLEM TO BOTH MOTHER AND CHILD, AS A RESULT WEAKENING THE SPECIES.

https://www.newscientist.com/article/dn22308-europeans-did-not-inherit-pale-skins-from-neanderthals/
DAILY NEWS 26 September 2012
Europeans did not inherit pale skins from Neanderthals
By Karl Gruber

The people who built Stonehenge 5000 years ago probably had the same pallid complexion of many modern inhabitants of the UK. Now it seems that the humans occupying Britain and mainland Europe only lost the darker skins of their African ancestors perhaps just 6000 years earlier, long after Neanderthals had died out. The finding confirms that modern Europeans didn’t gain their pale skin from Neanderthals – adding to evidence suggesting that European Homo sapiens and Neanderthals generally kept their relationships strictly platonic.

There is a clear correlation between latitude and skin pigmentation: peoples that have spent an extended period of time at higher latitudes have adapted to those conditions by losing the skin pigmentation that is common at lower latitudes, says Sandra Beleza at the University of Porto in Portugal. Lighter skin can generate more vitamin D from sunlight than darker skin, making the adaptation an important one for humans who wandered away from equatorial regions.

Those wanderings took modern humans into Europe around 45,000 years ago – but exactly when the European skin adapted to local conditions had been unclear.

Three genes

Beleza and her colleagues studied three genes associated with lighter skin pigmentation. Although the genes are found in all human populations, they are far more common in Europe than in Africa, and explain a significant portion of the skin-colour differences between European and west African populations.

By analysing the genomes of 50 people with European ancestry and 70 people with sub-Saharan African ancestry, Beleza’s team could estimate when the three genes – and pale skin – first became widespread in European populations. The result suggested that the three genes associated with paler skin swept through the European population only 11,000 to 19,000 years ago.

“The selective sweeps for favoured European [versions of the three genes] started well after the first migrations of modern humans into Europe,” says Beleza.

The finding agrees with earlier studies suggesting that modern humans did not lose their dark skins immediately on reaching Europe, says Katerina Harvati at the University of Tübingen in Germany. “[The new study] is interesting because it suggests a very late differentiation of skin pigmentation among modern humans,” she says.

An earlier analysis of ancient DNA in 40,000 and 50,000-year-old Neanderthal bones, respectively from Spain and Italy, suggested that our extinct cousins had light-coloured skin and reddish hair in their European heartland. But the Neanderthals went extinct around 28,000 years ago – long before modern humans in Europe gained a pale skin. Evidently Neanderthals did not pass these useful local adaptations on to modern humans, despite genetic evidence that the two species interbred.

Middle Eastern contact

That might seem unusual given that the two species lived cheek-by-jowl in Europe for several thousand years. But it makes sense if the interbreeding evident in the genes occurred in the Middle East, where modern humans and Neanderthals first met, says Chris Stringer at the Natural History Museum, London.

In that region, Neanderthals may have had darker skins, explaining why our species did not gain a pale skin after interbreeding with them. Indeed, a study earlier this year of ancient DNA suggested that Neanderthals living in what is now Croatia had dark skin and brown hair.

“Neanderthal skin colour was probably variable, as might be expected for a large population spread out over a large territorial expanse,” says Harvati.

Journal reference: Molecular Biology and Evolution, doi.org/h9h


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The connection between Neanderthal, Denisovians and Sapiens!

This is a really amazing place. In this small cave all 3 hominid have watch the river down below over the past 120,000 years. The Denisovians themselves have only recently been identified and the study of their DNA and comparison with Neanderthal and Sapiens is very interesting. The cave itself is nice, not big (10-20 meters deep/wide) with high ceiling and a small sinkhole in the ceiling that must have been a great chimney for our ancestors (about 3000 generations before us !). THe wide opening of the cave face the river Anuy, and the valley has been a trade route from China to Russia for millennia. The river clearly has eroded a lot in 100,000 years !

The place is hard to reach has one has to fly to Novosibirsk or Barnoul (5 and 3 hours away by car), but this is the only know place on earth where all 3 hominids have been: quite an impressive location.