Posts Tagged ‘Denisova hominin’

Promiscuity in the pleistocene

January 2, 2014

Svante Pääbo of the Max Planck Institute for Evolutionary Anthropology and his colleagues from various institutions are making stunning advances in the analysis of ancient DNA. The complete genome of a Neanderthal has now been reconstructed with a remarkable level of detail.

The complete genome sequence of a Neanderthal from the Altai MountainsKay Prüfer et al, Nature 505, 43–49 (02 January 2014),  doi:10.1038/nature12886

Editors Summary: Recent excavations in the Denisova Cave in the Altai Mountains of southern Siberia have yielded a wealth of hominin fossils from a site that has been occupied for perhaps 250,000 years or more. Now a high-quality genome sequence has been determined from a circa 50,000-year-old toe bone — a proximal toe phalanx — excavated from the east gallery of Denisova Cave in 2010. The sequence is that of a Neanderthal woman whose parents were closely related — perhaps half-siblings or uncle and niece. Such inbreeding was also common among her recent ancestors. Comparisons with other archaic and present-day human genomes reveal several gene-flow events among Neanderthals, the closely related Denisovans and early modern humans, possibly including gene flow into Denisovans from an unknown archaic group. The high-quality Neanderthal genome also helps to establish a definitive list of substitutions that became fixed in modern humans after their separation from the ancestors of Neanderthals and Denisovans.

promiscuity in the pleistocene

But what is also becoming clear is that there were more “species” of homo erectus who existed in parallel than has generally been assumed and also that sexual encounters and interbreeding between these cousin-species has been a regular occurrence over some 250,000 years. And so there have been times when Anatomically Modern Humans (AMH), Neanderthals, Denisovans and the “unknown” hominim have co-existed.

The AMH-Neanderthals split is thought to have occurred about 400,000 years ago. The split with the unknown hominims then must have been around 500,000 years ago. The Denisovans split off from the Neanderthals perhaps about 300,000 years ago. The Out-of-Africa split among AMH was around 100,000 years ago.

A Neanderthal in our time. (copyright Nenderthal Museum / H Neumann)

A Neanderthal in our time. (copyright Nenderthal Museum / H Neumann)

These ancient splits were all probably in and around Africa even if the Out-of-Africa event for AMH is now more likely to have been  many such events and an expansion out of Africarabia. But it also means that a wave of “unknown hominims” split off from the mainline after a mainline group had left Africa and then spread out to unknown areas. Neanderthals probably split from their parent line of descent also outside of Africa but there must first have come a migration from Africa. The Neanderthal-Denisovan split must also have taken place outside of Africa. Clearly there have been many migrations Out of Africa over the last 400,000 years.

Carl Zimmer writes, “Evolution is a mixture of flow–the cascade of genes from parents to offspring, and the criss-cross movement between populations and species”.

But this generates a myriad of new questions. How large were the troops or tribes or clans of these ancient hunter-gatherers that they could sustain such large migrations? For how long and in what proximity did these different species of man co-exist. These troops – it is thought – probably did not number more than about 50. Some critical population would have been required for sufficient interactions to have taken place between the species. At any one time the total human population – of all species – may have approached 10 million (for if this was – say – just 1 million the opportunities to interbreed would not have been many). They all had fire, but did they all have some form of speech?

But most fascinating of all is how the interbreeding took place. Was it just a product of normal rape and pillage? Did violent clashes lead to the victors impregnating the vanquished, or were there other scenarios for individuals to mate? At some point there must have been children who were 50% Neanderthal and 50% AMH. And some who were 50% Neanderthal and 50% Denisovan. How did they survive? What kind of society existed in these ancient times that would permit such offspring not only to survive but also to mate and produce offspring in their turn? But however it happened, our ancestors in the pleistocene were a promiscuous lot.

Could it be that it was only among AMH  – after they had been vanquished and raped and pillaged by Neanderthal raids – that such mixed children were allowed not only to survive but also to thrive?

DNA sequenced from a 400,000 year old hominin from Spain

December 4, 2013

After developing techniques for extracting and analysing DNA from ancient (c. 40,000 years ago) Neanderthal and Denisovan specimens the Max Planck team have now taken a giant leap backwards in time in extracting and analysing an almost complete mitochondrial genome sequence of a 400,000-year-hominin. The specimen is from  Sima de los Huesos, a unique cave site in Northern Spain. The results show that it is related to the mitochondrial genome of Denisovans, extinct relatives of Neandertals in Asia. DNA this old has until recently been retrieved only from the permafrost.


The Sima de los Huesos hominins lived approximately 400,000 years ago during the Middle Pleistocene. © Kennis & Kennis, Madrid Scientific Films

The result itself is of great interest but it is the development of the techniques for extracting and analysing – without any contamination – and with sufficient confidence, the entire MtDNA sequence in such old specimens that is quite revolutionary. Archaeological evidence – and particularly of of such age – is subject to a great deal of subjective interpretation. But dating techniques and now DNA extraction techniques are removing much of this subjectivity and they are now providing the anchor points around which the evolutionary narrative must be built. And this narrative is now of a much more complex story of hominin expansions and admixture than has generally been thought. Ancient and presumed extinct hominin species are now showing themselves within us.

“Our results show that we can now study DNA from human ancestors that are hundreds of thousands of years old. This opens prospects to study the genes of the ancestors of Neandertals and Denisovans. It is tremendously exciting” says Svante Pääbo, director at the Max Planck Institute for Evolutionary Anthropology.

Matthias Meyer, Qiaomei Fu, Ayinuer Aximu-Petri, Isabelle Glocke, Birgit Nickel, Juan-Luis Arsuaga, Ignacio Martínez, Ana Gracia, José María Bermúdez de Castro, Eudald Carbonell, Svante PääboA mitochondrial genome sequence of a hominin from Sima de los HuesosNature, 2013; DOI: 10.1038/nature12788

Read the whole post in 6,000 Generations


New Denisovan genome indicates inter-breeding with another, unknown, archaic human

November 19, 2013

The period some 30,000 – 50,000 years ago is getting positively crowded with different branches of humans. The direct ancestors of modern humans lived and interbred not only with Neanderthals and Denisovans but also apparently with still another, as yet unknown, branch of humans.

NatureNew genome sequences from two extinct human relatives suggest that these ‘archaic’ groups bred with humans and with each other more extensively than was previously known.

The ancient genomes, one from a Neanderthal and one from a different archaic human group, the Denisovans, were presented on 18 November at a meeting at the Royal Society in London. They suggest that interbreeding went on between the members of several ancient human-like groups living in Europe and Asia more than 30,000 years ago, including an as-yet unknown human ancestor from Asia. ..

… All humans whose ancestry originates outside of Africa owe about 2% of their genome to Neanderthals; and certain populations living in Oceania, such as Papua New Guineans and Australian Aboriginals, got about 4% of their DNA from interbreeding between their ancestors and Denisovans, who are named after the cave in Siberia’s Altai Mountains where they were discovered. The cave contains remains deposited there between 30,000 and 50,000 years ago. 

Those conclusions however were based on low-quality genome sequences, riddled with errors and full of gaps, David Reich, an evolutionary geneticist at Harvard Medical School in Boston, Massachusetts said at the meeting. His team, in collaboration with Svante Pääbo at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, have now produced much more complete versions of the Denisovan and Neanderthal genomes — matching the quality of contemporary human genomes. The high-quality Denisovan genome data and new Neanderthal genome both come from bones recovered from Denisova Cave.

The new Denisovan genome indicates that this enigmatic population got around: Reich said at the meeting that they interbred with Neanderthals and with the ancestors of human populations that now live in China and other parts of East Asia, in addition to Oceanic populations, as his team previously reported. Most surprisingly, Reich said, the new genomes indicate that Denisovans interbred with another extinct population of archaic humans that lived in Asia more than 30,000 years ago, which is neither human nor Neanderthal.

It would seem that when the world was still in the grip of an ice age 30,000 – 50,000 years ago, the reality of human history was not so far away from Tolkien’s Middle Earth.  Ancient history but it was only 1,500 – 2,500 generations ago. Middle Earth was where men could breed with elves and hobbits were an off-shoot of men. The Druedain were also off-shoots of men and some – if not all – orcs were deliberately bred from elves while all trolls and dragons were artificially bred.

From the J.R.R. Tolkien Encyclopedia: Scholarship and Critical Assessment

from The biology of Middle eart - Tolkien Encyclopedia

from The biology of Middle Earth – JRR Tolkien Encyclopedia

180 million Neanderthals are among us

April 16, 2013

From John Hawks Weblog

Just got back proofs of a book chapter I have coming out soon with Zach Throckmorton. My favorite paragraph:

Nearly seven billion people inhabit our planet. At least six billion carry the genes of Neandertal ancestors. Inheritance from Neandertals makes up approximately 3% of the genomes of randomly chosen people outside sub-Saharan Africa today (Green et al., 2010; Reich et al., 2010). A back-of-the-envelope calculation shows if we took all of the Neandertal genes from today’s human population, we would have enough raw material to make up 180 million Neandertals.

I love that because it makes the Neandertals into the evolutionary success story they really were. They succeeded by becoming part of us.

The idea that all the various hominids who developed bipedalism have all disappeared except Anatomically Modern Humans does not appeal. I prefer to think that many of them – and not just the Neanderthals and Denisovans – live on; in us.

File:Homo-Stammbaum, Version Stringer.jpg

Possible archaic human admixture with modern Homo sapiens (Wikipedia)

Could Chemistry Nobel today go to evolutionary genetics?

October 10, 2012

UPDATE! Awarded to Robert J Lefkowitz and to Brian K Kobilka for studies of G-protein-coupled receptors“.


Thomson Reuters predicts conventional areas of research for the Chemistry Nobel

1. Louis E. Brus

For discovery of colloidal semiconductor nanocrystals (quantum dots)

2. Akira Fujishima

For the discovery of photocatalytic properties of titanium dioxide (the Honda-Fujishima Effect)


3. Masatake Haruta and Graham J. Hutchings

For independent foundational discoveries of catalysis by gold

But Swedish Radio is predicting / hoping that it might be awarded to a Swedish scientist Svante Pääbo who is himself the son of a Nobel laureate. He is Director, Department of Genetics at the Max Planck Institute for Evolutionary Anthropology. In February 2009 the Max Planck Institute completed the first draft version of the Neanderthal genome. In 2010 they discovered the Denisovan genome. The techniques developed by Pääbo and his team for the DNA analysis of ancient specimens is what might be acknowledged.

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