DNA News Page 4  -  last update 7/26/2006

-- Genetic diversity exploded in recent millennia - 11/28/12
-- Maghrebi origin of early south Iberian Neolithic
-- European Roots: Human ancestors go back in time in Spanish cave
-- Oldest European Human Fossil Found in Spain
-- Scientists Say They’ve Found a Code Beyond Genetics in DNA
-- Family Tree DNA Announces

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 Genetic diversity exploded in recent millennia

Vast number of human DNA variants arose only in the past 5,000 years

By Tina Hesman Saey

Web edition: November 28, 2012
Print edition: December 29, 2012; Vol.182 #13(p. 13)

A new look at living people’s DNA reveals that the human genome just isn’t what it was in Neolithic times.

Most of the genetic quirks people carry today popped up within the last 5,000 years or so, researchers report online November 28 in Nature.Human populations exploded from no more than a few million to 7 billion, thanks largely to the rise of agriculture.

Researchers examined more than 15,000 genes in each of 6,515 people of European-American or African-American ancestry, looking for genetic variants. Previously, the team reported finding a plethora of rare genetic variants in a smaller sample. Now, the researchers have been able to date when most of the variants arose.

Of the 709,816 genetic variants found in European-Americans in the study, more than 81 percent arose in the past 5,000 years, the researchers determined. African-Americans in the study collectively carried 643,128 genetic variants, more than 58 percent of which are less than 5,000 years old. That may seem like a long time, but it’s only about 5 percent of the time humans have existed in modern form, says study coauthor Joshua Akey, a geneticist at the University of Washington in Seattle.

Although the human population explosion has been obvious from a demographer’s point of view, that growth has been all but invisible to geneticists studying common genetic variants. It takes time for a genetic variant, if it’s not discarded, to rise to prominence. Common variants — those found in 5 percent or more of the population — tend to be old tweaks that have stuck around, usually because they usually don’t have a big effect on health.

The new study will give scientists a clear picture of the stamp the recent population explosion has left on human genes, says Sarah Tishkoff, a geneticist at the University of Pennsylvania in Philadelphia. The work may help track down variants that affect people’s risk of developing common diseases, she says. Currently, by linking common variants to illness, scientists can explain only a small fraction of the genetic role in disease risk.

When humans migrated out of Africa about 70,000 years ago, they carried with them mutated versions of genes that natural selection might have weeded out had they stayed in Africa, the researchers found. By chance, many of these potentially harmful mutations endured in the migrants, and then were passed along to myriad descendants as the emigrants began to expand their populations in Europe. But many other potentially harmful mutations — if carried by only a small fraction of ancient migrants — were lost as small groups of humans trickled out of the African continent to populate the rest of the world.

In European-Americans, variants predicted to have harmful effects tend to be younger than those in African-Americans — 3,000 years old on average in European-Americans versus 6,200 years old in African-Americans. (African populations have grown in recent millennia, but not as much as populations outside Africa, which went from zero to billions in less than 100,000 years.) Evolution has not had time to purge the newest harmful changes in either group, and many of them pack a wallop in terms of disease risk.

Even though most of the genetic variants the researchers uncovered are predicted to change the workings of proteins in harmful ways, some of the genetic tweaks might someday give humans an evolutionary advantage, says Akey. Exactly which variants turn out to be good and which will cause trouble is unpredictable. “It’s hard to speculate on the genetic health of our species when the environment is changing,” he says. “We’ll have to check back in a few thousand years.” But, he adds, one thing is for certain: “If we stop changing, we’re evolutionarily dead.”

 Maghrebi origin of early south Iberian Neolithic

Quaternary Research    Volume 77, Issue 2, March 2012, Pages 221–234

The Mesolithic–Neolithic transition in southern Iberia       Miguel Cortés Sánchez et al.

New data and a review of historiographic information from Neolithic sites of the Malaga and Algarve coasts (southern Iberian Peninsula) and from the Maghreb (North Africa) reveal the existence of a Neolithic settlement at least from 7.5 cal ka BP.

The agricultural and pastoralist food producing economy of that population rapidly replaced the coastal economies of the Mesolithic populations. The timing of this population and economic turnover coincided with major changes in the continental and marine ecosystems, including upwelling intensity, sea-level changes and increased aridity in the Sahara and along the Iberian coast.

These changes likely impacted the subsistence strategies of the Mesolithic populations along the Iberian seascapes and resulted in abandonments manifested as sedimentary hiatuses in some areas during the Mesolithic–Neolithic transition.   The rapid expansion and area of dispersal of the early Neolithic traits suggest the use of marine technology.   Different evidences for a Maghrebian origin for the first colonists have been summarized. The recognition of an early North-African Neolithic influence in Southern Iberia and the Maghreb is vital for understanding the appearance and development of the Neolithic in Western Europe. Our review suggests links between climate change, resource allocation, and population turnover.

  European Roots: Human ancestors go back in time in Spanish cave

Bruce Bower

Fossil finds in Spain have yielded the earliest known skeletal evidence of human ancestors in Europe, according to a new report. A fossil jaw and tooth from the same individual, found during excavations of a cave called Sima del Elefante in northern Spain's Atapuerca Mountains, date to between 1.2 million and 1.1 million years old, say anthropologist Eudald Carbonell of Universitat Rovira i Virgili in Tarragona, Spain, and his colleagues. 
CAVE SAVE. Researchers who retrieved this fossil jaw from a Spanish cave conclude that human ancestors reached Western Europe more than 1 million years ago.
EIA/Jordi Mestre

The investigators assign the new discoveries to the species Homo antecessor. A decade ago, they identified 800,000-year-old fossils from another Atapuerca site as H. antecessor. In the Spanish scientists' view, H. antecessor was an evolutionary precursor of European Neandertals and modern humans.

Many scientists remain skeptical of that proposal and classify the Spanish fossils as the oldest examples of Homo heidelbergensis, a roughly 600,000-year-old species first found in Germany a century ago.

However this debate plays out, the Sima del Elefante fossils "provide the oldest direct evidence, to our knowledge, for a human presence in Europe," Carbonell says.

Anthropologist Bernard Wood of George Washington University in Washington, D.C., agrees that the find provides the first solid evidence that human ancestors reached Europe more than 1 million years ago. "Before this report, the evidence for an early occupation of Europe had substantial and important caveats," he says.

The newly unearthed specimens were found in sediment that also contained stone tools, stone flakes produced during toolmaking, and numerous animal bones bearing butchery marks.

Carbonell's team describes its work at Sima del Elefante in the March 27 Nature.

Several lines of evidence provided an age estimate for the Spanish fossils. Reversals in Earth's magnetic field recorded in fossil-bearing sediments bracketed the fossils' age at between 1.78 million and 780,000 years old. The decay rate of certain radioactive isotopes in rock buried near the fossils—along with analyses of the types of now-extinct animals strewn among the finds—narrowed the age estimate down to 1.2 million to 1.1 million years old.

The new finds strengthen earlier, contested evidence from other European sites—mainly consisting of stone implements, not fossils—that suggests human ancestors occupied the region at least 1 million years ago, Carbonell says. A broad anthropological consensus holds that large groups of human ancestors lived in Western Europe by 500,000 years ago.

The Atapuerca investigators suggest that Western Europe was settled between 2 million and 1 million years ago by a Homo species that trekked out of Africa, perhaps into central Asia, and then moved westward. That species then evolved into H. antecessor, in their view.

One possible ancestor of the ancient Atapuerca population has been found at the Dmanisi site in the central Asian nation of Georgia. Excavations there have yielded 1.77-million-year-old remains that may come from an early, highly mobile form of Homo erectus (SN: 9/22/07, p. 179).

The Sima del Elefante fossils show no obvious anatomical links to the Dmanisi remains, Wood says. Still, an evolutionary connection between Dmanisi and Atapuerca is plausible, he says.

It's unknown whether enough human ancestors entered Western Europe before 1 million years ago to establish a permanent presence in the region so that they could evolve into later European Homo species, Wood notes.

 Oldest European Human Fossil Found in Spain

Thursday , March 27, 2008

MADRID, Spain — 

A small piece of jawbone unearthed in a cave in Spain is the oldest known fossil of a human ancestor in Europe and suggests that people lived on the continent much earlier than previously believed, scientists say.

The researchers said the fossil found last year at Atapuerca in northern Spain, along with stone tools and animal bones, is up to 1.3 million years old.

That would be 500,000 years older than remains from a 1997 find that prompted the naming of a new species: Homo antecessor, or Pioneer Man, possibly a common ancestor to Neanderthals and modern humans.

The new find appears to be from the same species, researchers said.

A team co-led by Eudald Carbonell, director of the Catalan Institute of Human Paleo-Ecology and Social Evolution, reported their find in Thursday's issue of the scientific journal Nature.

The timing of the earliest occupation of Europe by humans that emerged from Africa has been controversial for many years.

Some archeologists believe the process was a stop-and-go one in which species of hominins — a group that includes the extinct relatives of modern humans — emerged and died out quickly only to be replaced by others, making for a very slow spread across the continent, Carbonell said in an interview.

Until now the oldest hominin fossils found in Europe were the Homo antecessor ones, also found at Atapuerca, but at a separate digging site, and a skull from Ceprano in Italy.

Carbonell's team has tentatively classified the new fossil as representing an earlier example of Homo antecessor. And, critically, the team says the new one also bears similarities to much-older fossils dug up since 1983 in the Caucasus at a place called Dmanisi, in the former Soviet republic of Georgia.

These were dated as being up to 1.8 million years old.

"This leads us to a very important, very interesting conclusion," Carbonell said.

It is this: that hominins which emerged from Africa and settled in the Caucasus eventually evolved into Homo antecessor, and that the latter populated Europe not 800,000 years ago, but at least 1.3 million years ago.

"This discovery of a 1.3 million-year-old fossil shows the process was accelerated and continuous; that the occupation of Europe happened very early and much faster than we had thought," Carbonell said.

Chris Stringer, a leading researcher in human origins at the Natural History Museum in London and not involved in the project, said Carbonell's team had done solid dating work to estimate the antiquity of the new Atapuerca fossil by employing three separate techniques — some researchers only use one or two — including a relatively new one that measures radioactive decay of sediments.

"This is a well-dated site, as much as any site that age can be," Stringer said.

But he also expressed some caution about Carbonell's conclusions.

First of all, the newly found jawbone fragment, which measures about two inches long and has teeth attached to it, preserves a section not seen in the equivalent pieces found at Atapuerca in 1997. So assigning both to the same species must be provisional, Stringer said.

And on the broader issue of tracing the new fossil back to the species unearthed at Dmanisi — Carbonell's big leap arguing continuity — Stringer said this too must be tentative because it is based on just a piece of a front of a jawbone and the time lapse is half a million years.

"That is a long period of time to talk about continuity," Stringer said.

Still, there are similarities between the two and this along with other archaeological evidence, suggests southern Europe did in fact begin to be colonized from western Asia not long after humans emerged from Africa — "something which many of us would have doubted even five years ago," Stringer said.

Carbonell says that with the finding of human fossils 1.3 million years old in Europe, researchers can now expect to find older ones, even up to 1.8 million years old, in other parts of the continent.

"This has to be the next discovery," he said. "This is the scientific hypothesis."

 Scientists Say They’ve Found a Code Beyond Genetics in DNA

By NICHOLAS WADE   July 25, 2006
Loren Williams/Chemistry and Biochemistry, Georgia Institute of Technology

Researchers believe they have found a second code in DNA in addition to the genetic code.

In a living cell, the DNA double helix wraps around a nucleosome, above center, and binds to some of its proteins, known as histones.  The genetic code specifies all the proteins that a cell makes. The second code, superimposed on the first, sets the placement of the nucleosomes, miniature protein spools around which the DNA is looped. The spools both protect and control access to the DNA itself.

The discovery, if confirmed, could open new insights into the higher order control of the genes, like the critical but still mysterious process by which each type of human cell is allowed to activate the genes it needs but cannot access the genes used by other types of cell.

The new code is described in the current issue of Nature by Eran Segal of the Weizmann Institute in Israel and Jonathan Widom of Northwestern University in Illinois and their colleagues.

There are about 30 million nucleosomes in each human cell. So many are needed because the DNA strand wraps around each one only 1.65 times, in a twist containing 147 of its units, and the DNA molecule in a single chromosome can be up to 225 million units in length.

Biologists have suspected for years that some positions on the DNA, notably those where it bends most easily, might be more favorable for nucleosomes than others, but no overall pattern was apparent. Drs. Segal and Widom analyzed the sequence at some 200 sites in the yeast genome where nucleosomes are known to bind, and discovered that there is indeed a hidden pattern.

Knowing the pattern, they were able to predict the placement of about 50 percent of the nucleosomes in other organisms.

The pattern is a combination of sequences that makes it easier for the DNA to bend itself and wrap tightly around a nucleosome. But the pattern requires only some of the sequences to be present in each nucleosome binding site, so it is not obvious. The looseness of its requirements is presumably the reason it does not conflict with the genetic code, which also has a little bit of redundancy or wiggle room built into it.

Having the sequence of units in DNA determine the placement of nucleosomes would explain a puzzling feature of transcription factors, the proteins that activate genes. The transcription factors recognize short sequences of DNA, about six to eight units in length, which lie just in front of the gene to be transcribed.

But these short sequences occur so often in the DNA that the transcription factors, it seemed, must often bind to the wrong ones. Dr. Segal, a computational biologist, believes that the wrong sites are in fact inaccessible because they lie in the part of the DNA wrapped around a nucleosome. The transcription factors can only see sites in the naked DNA that lies between two nucleosomes.

The nucleosomes frequently move around, letting the DNA float free when a gene has to be transcribed. Given this constant flux, Dr. Segal said he was surprised they could predict as many as half of the preferred nucleosome positions. But having broken the code, “We think that for the first time we have a real quantitative handle” on exploring how the nucleosomes and other proteins interact to control the DNA, he said.

The other 50 percent of the positions may be determined by competition between the nucleosomes and other proteins, Dr. Segal suggested.

Several experts said the new result was plausible because it generalized the longstanding idea that DNA is more bendable at certain sequences, which should therefore favor nucleosome positioning.

“I think it’s really interesting,” said Bradley Bernstein, a biologist at Massachusetts General Hospital.

Jerry Workman of the Stowers Institute in Kansas City said the detection of the nucleosome code was “a profound insight if true,” because it would explain many aspects of how the DNA is controlled.

The nucleosome is made up of proteins known as histones, which are among the most highly conserved in evolution, meaning that they change very little from one species to another. A histone of peas and cows differs in just 2 of its 102 amino acid units. The conservation is usually attributed to the precise fit required between the histones and the DNA wound around them. But another reason, Dr. Segal suggested, could be that any change would interfere with the nucleosomes’ ability to find their assigned positions on the DNA.

In the genetic code, sets of three DNA units specify various kinds of amino acid, the units of proteins. A curious feature of the code is that it is redundant, meaning that a given amino acid can be defined by any of several different triplets. Biologists have long speculated that the redundancy may have been designed so as to coexist with some other kind of code, and this, Dr. Segal said, could be the nucleosome code.

 Family Tree DNA Announces Agreement to Acquire DNA-FingerPrint of Germany

Family Tree DNA is pleased to announce the signing of a Letter of Agreement with DNA-FingerPrint of Germany, to acquire and merge DNA-FingerPrint with Family Tree DNA.

This agreement will result in the establishment of a state of the art lab in Houston, adjacent to Family Tree DNA headquarters, as well as collaborative efforts to develop new tests to benefit the genetic genealogy community.

Thomas Krahn, the principal of DNA-Fingerprint will be at Family Tree DNA's Houston's headquarters in early August 2006. There he will assist in organizing the state-of-the-art laboratory, with the aim of pursuing research and development of new tests, as well as processing the tests that DNA-Fingerprint currently offers. All DNA-Fingerprint tests will be available to Family Tree DNA customers once the lab is fully operational, which is scheduled for September 15, 2006.

"Following our pioneering of the use of DNA for genealogy six years ago, this will be looked upon as a new milestone for the entire genealogical community, and we are very happy to have Thomas Krahn join the Family Tree DNA team" said Bennett Greenspan, Family Tree DNA's President and Founder. "In addition to that, DNAFingerprint's knowledge of the German market will open new opportunities for surname project administrators to access participants in the German speaking countries in Europe."

Thomas Krahn, the scientific head of DNA-Fingerprint added: "We see a big future for new developments in DNA analysis to answer genealogical questions. Our new technologies will make it possible to resolve previously inconclusive genealogies even outside of the direct male or female lines. All the new technologies, like linked X-STR testing or sequencing of larger chromosomal regions will only make sense if they are accessible to a huge international customer base, which Family Tree DNA already has."

The new laboratory in Houston will allow multi-parallel processing with modern equipment including, among others, new ABI 3730 sequencer, a state of the art robot platform and customer DNA library to preserve samples in an automated storage freezer system.


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