Wednesday, 30 December 2015

Nuclear and mitochondrial DNA sequences from two Denisovan individual

Nuclear and mitochondrial DNA sequences from two Denisovan individuals

Significance

Denisovans are a sister group of Neandertals that were identified on the basis of a nuclear genome sequence from a bone from Denisova Cave (Siberia). The only other Denisovan specimen described to date is a molar from the same site. We present here nuclear DNA sequences from this molar and a morphological description, as well as mitochondrial and nuclear DNA sequences from another molar from Denisova Cave, thus extending the number of Denisovan individuals known to three. The nuclear DNA sequence diversity among the Denisovans is higher than among Neandertals, but lower than among present-day humans. The mtDNA of one molar has accumulated fewer substitutions than the mtDNAs of the other two specimens, suggesting Denisovans were present in the region over several millennia.

Abstract

Denisovans, a sister group of Neandertals, have been described on the basis of a nuclear genome sequence from a finger phalanx (Denisova 3) found in Denisova Cave in the Altai Mountains. The only other Denisovan specimen described to date is a molar (Denisova 4) found at the same site. This tooth carries a mtDNA sequence similar to that of Denisova 3. Here we present nuclear DNA sequences from Denisova 4 and a morphological description, as well as mitochondrial and nuclear DNA sequence data, from another molar (Denisova 8) found in Denisova Cave in 2010. This new molar is similar to Denisova 4 in being very large and lacking traits typical of Neandertals and modern humans. Nuclear DNA sequences from the two molars form a clade with Denisova 3. The mtDNA of Denisova 8 is more diverged and has accumulated fewer substitutions than the mtDNAs of the other two specimens, suggesting Denisovans were present in the region over an extended period. The nuclear DNA sequence diversity among the three Denisovans is comparable to that among six Neandertals, but lower than that among present-day humans.

Freely available online through the PNAS open access option.

http://www.pnas.org/preview_site/misc/userlicense.xhtml

Neolithic and Bronze Age migration to Ireland and establishment of the insular Atlantic genome

Significance

Modern Europe has been shaped by two episodes in prehistory, the advent of agriculture and later metallurgy. These innovations brought not only massive cultural change but also, in certain parts of the continent, a change in genetic structure. The manner in which these transitions affected the islands of Ireland and Britain on the northwestern edge of the continent remains the subject of debate. The first ancient whole genomes from Ireland, including two at high coverage, demonstrate that large-scale genetic shifts accompanied both transitions. We also observe a strong signal of continuity between modern day Irish populations and the Bronze Age individuals, one of whom is a carrier for the C282Y hemochromatosis mutation, which has its highest frequencies in Ireland today.

Abstract

The Neolithic and Bronze Age transitions were profound cultural shifts catalyzed in parts of Europe by migrations, first of early farmers from the Near East and then Bronze Age herders from the Pontic Steppe. However, a decades-long, unresolved controversy is whether population change or cultural adoption occurred at the Atlantic edge, within the British Isles. We address this issue by using the first whole genome data from prehistoric Irish individuals. A Neolithic woman (3343–3020 cal BC) from a megalithic burial (10.3× coverage) possessed a genome of predominantly Near Eastern origin. She had some hunter–gatherer ancestry but belonged to a population of large effective size, suggesting a substantial influx of early farmers to the island. Three Bronze Age individuals from Rathlin Island (2026–1534 cal BC), including one high coverage (10.5×) genome, showed substantial Steppe genetic heritage indicating that the European population upheavals of the third millennium manifested all of the way from southern Siberia to the western ocean. This turnover invites the possibility of accompanying introduction of Indo-European, perhaps early Celtic, language. Irish Bronze Age haplotypic similarity is strongest within modern Irish, Scottish, and Welsh populations, and several important genetic variants that today show maximal or very high frequencies in Ireland appear at this horizon. These include those coding for lactase persistence, blue eye color, Y chromosome R1b haplotypes, and the hemochromatosis C282Y allele; to our knowledge, the first detection of a known Mendelian disease variant in prehistory. These findings together suggest the establishment of central attributes of the Irish genome 4,000 y ago.

Freely available online through the PNAS open access option.

http://www.pnas.org/preview_site/misc/userlicense.xhtml

Saturday, 7 November 2015

Greenpeace says its charitable registration to operate in India has been revoked.

Greenpeace office in Bangalore — Image captionThe organisation plans to challenge the decision in court

Greenpeace says its charitable registration to operate in India has been revoked.

The environmental campaign group says that the decision effectively shuts it down in India.

The government of Narendra Modi has previously accused Greenpeace of flouting tax laws and having an anti-development agenda.

The pressure group has been working in India for 14 years and employs more than 300 people.

The BBC's correspondent in Delhi, Justin Rowlatt, says Mr Modi's government has been accused of a major crackdown on NGOs and charitable groups ever since he came to power in 2014.

Greenpeace says it plans to challenge this latest decision. It follows a ruling that the organisation could not raise money abroad - which was itself successfully challenged.

Interim Executive Director Vinuta Gopal said in a statement:

"We are confident that we are on strong legal ground. We have faith in the legal process and are confident of overcoming this order."

Thursday, 5 November 2015

Did a Comet Hit Earth 12,000 Years Ago?

Nanodiamonds found across North America suggest that major climate change could have been cosmically instigated

By David Biello | January 2, 2009

younger-dryas-boundary — *Courtesy of Doug Kennett*

Roughly 12,900 years ago, massive global cooling kicked in abruptly, along with the end of the line for some 35 different mammal species, including the mammoth, as well as the so-called Clovis culture of prehistoric North Americans. Various theories have been proposed for the die-off, ranging from abrupt climate change tooverhunting once humans were let loose on the wilds of North America. But now nanodiamonds found in the sediments from this time period point to an alternative: a massive explosion or explosions by a fragmentary comet, similar to but even larger than the Tunguska event of 1908 in Siberia.

Sediments from six sites across North America—Murray Springs, Ariz.; Bull Creek, Okla.; Gainey, Mich.; Topper, S.C.; Lake Hind, Manitoba; and Chobot, Alberta—yielded such teensy diamonds, which only occur in sediment exposed to extreme temperatures and pressures, such as those from an explosion or impact, according to new research published today in Science.

The discovery lends support to a theory first advanced last year in that some type of cosmic impact or impacts—a fragmented comet bursting in the atmosphere or raining down on the oceans—set off the more than 1,300-year cooling period in the Northern Hemisphere known as the Younger Dryas for the abundance of an alpine flower's pollen found during the interval.

The cooling period interrupted an extended warming out of an ice age predicted by slight changes in Earth's orbit (known as Milankovitch cycles) that continues today. And it remains an unexplained anomaly in the climate record.

But a series of cometary fragments exploding over North America might explain a layer of soil immediately prior to the cooling containing unusually high levels of iridium—an element more common in cosmic wanderers like meteoroids than in Earth's crust. Paired with the fact that this layer occurs directly before the extinction of at least 35 genera of large mammals, including mammoths, it is strong circumstantial evidence for a cosmic event.

"Very strong impact indicators are found in the sediments directly above, and often shrouding in the case of Murray Springs, the remains of these animals and the people who were hunting them," says archaeologist and study co-author Doug Kennett of the University of Oregon in Eugene, the son in the father–son team helping to advance the new impact theory. "Is it a comet? Is it a carbonaceous chondrite? Was it fragmented? Was it focused? Based on the distribution of the diamonds, it was certainly large scale."

Preliminary searches further afield—Europe, Asia and South America—have turned up similar minerals and elements in sediments of the same age, Kennett says, and his own work on California's Channel Islands tells a tale of a massive burn-off, followed by erosion and a total change in the flora of the region.

"It's consistent with a fragmentary body breaking up with air shocks and possible surface impacts in various parts of North America. It could be above the ice sheet or offshore in the ocean," he says, explaining why no impact crater(s) has been found to date. "Immediate effects on the ground include high temperatures and pressures triggering major transformations of the vegetation, knocking trees over but also burning."

And that would make the climate shift of the Younger Dryas a closer cousin to the massive asteroid impact that wiped out the dinosaurs 65 million years ago. "This is an event that happened on one day," Kennett notes. "We're going to need high-resolution climate records, archaeological records, paleontological records to try to explore the effects."

Tuesday, 6 October 2015

'oldest cave art'

Bristol researchers removing samples for dating from Tito Bustillo Cave

The El Castillo Cave has numerous red discs on its walls. One was dated to 40,800 years ago

Red dot becomes 'oldest cave art'

A look inside the Altamira Cave in northern Spain

Red dots, hand stencils and animal figures represent the oldest examples yet found of cave art in Europe.

The symbols on the walls at 11 Spanish locations, including the World Heritage sites of Altamira, El Castillo and Tito Bustillo have long been recognised for their antiquity.
But researchers have now used refined dating techniques to get a more accurate determination of their ages.
One motif - a faint red dot - is said to be more than 40,000 years old.
"In Cantabria, [in] El Castillo, we find hand stencils that are formed by blowing paint against the hands pressed against the wall of a cave," explained Dr Alistair Pike from Bristol University, UK, and the lead author on a scholarly paper published in the journal Science.
"We find one of these to date older than 37,300 years on 'The Panel of Hands', and very nearby there is a red disc made by a very similar technique that dates to older than 40,800 years.
"This now currently is Europe's oldest dated art by at least 4,000 years," he told reporters. It is arguably also the oldest reliably dated cave art anywhere in the world.
The team arrived at the ages by examining the calcium carbonate (calcite) crusts that had formed on top of the paintings.
This material builds up in the exact same way that stalagmites and stalactites form in a cave.
In the process, the calcite incorporates small numbers of naturally occurring radioactive uranium atoms. These atoms decay into thorium at a very precise rate through the ages, and the ratio of the two different elements in any sample can therefore be used as a kind of clock to time the moment when the calcite crust first formed.
Uranium-thorium dating has been around for decades, but the technique has now been so refined that only a tiny sample is required to get a good result.
This enabled the team to take very thin films of deposits from just above the paint pigments; and because the films were on top, the dates they gave were minimum ages - that is, the paintings had to be at least as old as the calcite deposits, and very probably quite a bit older.
The oldest dates coincide with the first known immigration into Europe of modern humans (Homo sapiens). Before about 41,000 years ago, it is their evolutionary cousins, the Neanderthals (Homo neanderthalensis), who dominate the continent.
Dr Pike's and colleagues' work therefore raises some intriguing questions about who might have authored the markings.
If anatomically modern humans were responsible then it means they engaged in the activity almost immediately on their arrival in Europe.
If Neanderthals were the artisans, it adds another layer to our understanding of their capabilities and sophistication.

The Panel of Hands: Produced by blowing paint over a hand pressed against the wall

The great antiquity of the paintings leads co-author Joao Zilhao, a research professor at ICREA, University of Barcelona, to think the Neanderthals produced the motifs. Finding even older paintings than the red dot at El Castillo might confirm that "gut feeling", he said.
"There is a strong chance that these results imply Neanderthal authorship," Prof Zilhao explained.
"But I will not say we have proven it because we haven't, and it cannot be proven at this time.
"What we have to do now is go back, sample more and find out whether we can indeed get dates older than 42, 43, 44,000.
"There is already a sampling programme going on. We have samples from more sites in Spain, from sites in Portugal and from other caves in Western Europe and so eventually we will be able to sort it out."
Tracing the origins of abstract throught and behaviours, and the rate at which they developed, are critical to understanding the human story.
The use of symbolism - the ability to let one thing represent another in the mind - is one of those traits that set our animal species apart from all others.
It is what underpins artistic endeavour and also the use of language.

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Wednesday, 30 December 2015