DNA News Page 9  -  last update 3/7/2012

-- Modern Europe's Genetic History Starts in Stone Age - 4/23/13
-- Genes and Race: The Distant Footfalls of Evidence - 5/13/14
-- Ancient DNA Unravels Europe's Genetic Diversity - 10/10/13
-- Hunter-Gatherers and Immigrant Farmers - 10/10/13
-- Genetic 'Adam' and 'Eve' uncovered - 8/02/13
-- mitochondrial sequencing in Mexican Americans suggests a reappraisal - 3/07/12
-- Wikipedia site For Scandinavian Y-DNA type I1 (on WEB)
-- 700,000-Year-Old Horse Becomes Oldest Creature With Sequenced Genome - 6/26/13

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 Modern Europe's Genetic History Starts in Stone Age

Scientists create the first detailed genetic history of modern Europe

PUBLISHED APRIL 23, 2013 Ker Than for National Geographic News

Europeans as a people are younger than we thought, a new study suggests.

DNA recovered from ancient skeletons reveals that the genetic makeup of modern Europe was established around 4,500 B.C. in the mid-Neolithic—or 6,500 years ago—and not by the first farmers who arrived in the area around 7,500 years ago or by earlier hunter-gatherer groups. (Read about Europe's oldest known town.)

"The genetics show that something around that point caused the genetic signatures of previous populations to disappear," said Alan Cooper, director of the Australian Centre for Ancient DNA at the University of Adelaide, where the research was performed.

"However, we don't know what happened or why, and [the mid-Neolithic] has not been previously identified as [a time] of major change," he said.

Furthermore, the origins of the mid-Neolithic populations that did form the basis of modern Europe are also unknown.

"This population moves in around 4,000 to 5,000 [B.C.], but where it came from remains a mystery, as we can't see anything like it in the areas surrounding Europe," Cooper said.

The surprising findings are part of a new study, published in this week's issue of the journal Nature Communications, that provides the first detailed genetic history of modern Europe.

The study shows that "relatively recent migrations seem to have had a significant genetic impact on the population of Central Europe," said study co-author Spencer Wells, who leads National Geographic's Genographic Project. (Read about Europe's "Wild Men" in National Geographic magazine.)

Genetic Signature

In the study, Cooper and his colleagues extracted mitochondrial DNA—which children inherit only from their mothers—from the teeth and bones of 39 skeletons found in central Germany. The skeletons ranged in age from about 7,500 to 2,500 years old.

The team focused on a group of closely related mitochondrial lineages—mutations in mitochondrial DNA that are similar to one another—known as haplogroup H, which is carried by up to 45 percent of modern Europeans.

Cooper and his colleagues focused on haplogroup H because previous studies have indicated the mutations might have been present in Europeans' genetic makeup for several thousand years.

It's unclear how this haplogroup became dominant in Europe. Some scientists have proposed that it spread across the continent following a population boom after the end of the last ice age about 12,000 years ago.

But the new data paint a different picture of the genetic foundation of modern Europe: Rather than a single or a few migration events, Europe was occupied several times, in waves, by different groups, from different directions and at different times.

The first modern humans to reach Europe arrived from Africa 35,000 to 40,000 years ago. By about 30,000 years ago, they were widespread throughout the area while their close cousins, the Neanderthals, disappeared. Hardly any of these early hunter-gatherers carried the H haplogroup in their DNA.

About 7,500 years ago during the early Neolithic period, another wave of humans expanded into Europe, this time from the Middle East. They carried in their genes a variant of the H haplogroup, and in their minds knowledge of how to grow and raise crops. (Related: "Egypt's Earliest Farming Village Found.")

Archeologists call these first Central European farmers the linear pottery culture (LBK)—so named because their pottery often had linear decorations.

The genetic evidence shows that the appearance of the LBK farmers and their unique H haplogroups coincided with a dramatic reduction of the U haplogroup—the dominant haplogroup among the hunter-gatherers living in Europe at that time.

Farmers Move In

The findings settle a longstanding debate among archaeologists, said Wells, who is also a National Geographic explorer-in-residence.

Archaeology alone can't determine whether cultural movements—such as a new style of pottery or, in this case, farming—were accompanied by the movements of people, Wells said in an email.

"In this study we show that changes in the European archaeological record are accompanied by genetic changes, suggesting that cultural shifts were accompanied by the migration of people and their DNA."

The LBK group and its descendants were very successful and spread quickly across Europe. "They became the first pan-European culture, if you like," Cooper said.

Given their success, it would be natural to assume that members of the LBK culture were significant genetic ancestors of many modern Europeans.

But the team's genetic analysis revealed a surprise: About 6,500 years ago in the mid-Neolithic, the LBK culture was itself displaced. Their haplogroup H types suddenly became very rare, and they were subsequently replaced by populations bearing a different set of haplogroup H variations.

Mysterious Turnover

The details of this "genetic turnover" event are murky. Scientists don't know what prompted it, or even where the new colonizers came from.

"The extent or nature of this genetic turnover are not clear, and we don't know how widespread it is," Cooper said.

If this turnover were widespread, it could have been prompted by climate change or disease, he said.

"All we know is that the descendants of the LBK farmers disappeared from Central Europe about 4,500 [B.C.], clearing the way for the rise of populations from elsewhere, with their own unique H signatures."

Peter Bogucki, an archeologist at Princeton University who has studied early farming societies in Europe, called the finding "really interesting" and noted the timing of the genetic turnover is curious.

"At the end of the fifth millennium—[about] 4,000 B.C.—there are a lot of changes in the archeological record," said Bogucki, who was not involved in the study.

For example, the long houses that LBK farmers and their descendants favored became less common. Also, the settlement patterns of people living in Central Europe began changing, as did their stone tools.

"There are major transformations during this time that haven't really been all that well explained in interior Central Europe," Bogucki said.

"It looks like the whole system of agricultural settlement that got established with the LBK ran its course through the fifth millennium and something caused people to change."

Of Unknown Origins

Bogucki agrees that climate change might have been a trigger for the change in Europe's genetic makeup, but he thinks it was only a factor and not the sole cause.

One thing that is clear from the genetic data is that nearly half of modern Europeans can trace their origins back to this mysterious group.

"About [4,500 B.C.], you start seeing a diversity and composition of genetic signatures that are beginning to look like modern [Central] Europe," Cooper said. "This composition is then modified by subsequent cultures moving in, but it's the first point at which you see something like the modern European genetic makeup in place."

Whatever prompted the replacement of genetic signatures from the first pan-European culture, Cooper is clearly intrigued. "Something major happened," he said in a statement, "and the hunt is now on to find out what that was."

Correction: The original version of this article stated that the genetic makeup of modern Europeans emerged 4,500 years ago. The text has been updated to reflect the correct timing as 4,500 B.C., or 6,500 years ago.


 Genes and Race: The Distant Footfalls of Evidence

By Ashutosh Jogalekar | May 13, 2014

 A review of Nicholas Wade’s book, “A Troublesome Inheritance: Genes, Race and Human History“.

In this book NYT science writer Nicholas Wade advances two simple premises: firstly, that we should stop looking only toward culture as a determinant of differences between populations and individuals, and secondly, that those who claim that race is only a social construct are ignoring increasingly important findings from modern genetics and science. The guiding thread throughout the book is that “human evolution is recent, copious and regional” and that this has led to the genesis of distinct differences and classifications between human groups. What we do with this evidence should always be up for social debate, but the evidence itself cannot be ignored.

That is basically the gist of the book. It’s worth noting at the outset that at no point does Wade downplay the effects of culture and environment in dictating social, cognitive or behavioral differences – in fact he mentions culture as an important factor at least ten times by my count – but all he is saying is that, based on a variety of scientific studies enabled by the explosive recent growth of genomics and sequencing, we need to now recognize a strong genetic component to these differences.

The book can be roughly divided into three parts. The first part details the many horrific and unseemly uses that the concept of race has been put to by loathsome racists and elitists ranging from Social Darwinists to National Socialists. Wade reminds us that while these perpetrators had a fundamentally misguided, crackpot definition of race, that does not mean race does not exist in a modern incarnation. This part also clearly serves to delineate the difference between a scientific fact and what we as human beings decide to do with it, and it tells us that an idea should not be taboo just because murderous tyrants might have warped its definition and used it to enslave and decimate their fellow humans.

The second part of the book is really the meat of the story and Wade is on relatively firm ground here. He details a variety of studies based on tools like tandem DNA repeats and single nucleotide polymorphisms (SNPs) that point to very distinctive genetic differences between populations dictating both physical and mental traits. Many of the genes responsible for these differences have been subject to selection in the last five thousand years or so, refuting the belief that humans have somehow “stopped evolving” since they settled down into agricultural communities. For me the most striking evidence that something called race is real comes from the fact that when you ask computer algorithms to cluster genes based on differences and similarities in an unbiased manner, these statistical programs consistently settle on the five continental races as genetically distinct groups – Caucasian, East Asian, African, Native American and Australian Aboriginal. Very few people would deny that there are clear genetic underpinnings behind traits like skin color or height among people on different continents, but Wade’s achievement here is to clearly explain how it’s not just one or two genes underlying such traits but a combination of genes – the effects of many of which are not obvious – that distinguish between races. The other point that he drives home is that even minor differences between gene frequencies can lead to significant phenotypic dissimilarities because of additive effects, so boiling down these differences to percentages and then interpreting these numbers can be quite misleading.

Wade also demolishes the beliefs of many leading thinkers who would rather have differences defined almost entirely by culture – these include Stephen Jay Gould who thought that humans evolved very little in the last ten thousand years (as Wade points out, about 14% of the genome has been under active selection since modern humans appeared on the scene), and Richard Lewontin who perpetuated a well-known belief that the dominance of intra as opposed to inter individual differences makes any discussion of race meaningless. As Wade demonstrates through citations of solid research, this belief is simply erroneous since even small differences between populations can translate to large differences in physical, mental and social features depending on what alleles are involved; Lewontin and his followers’ frequent plea that inter-group differences are “only 15%” thus ends up essentially translating to obfuscation through numbers. Jared Diamond’s writings are also carefully scrutinized and criticized; Diamond’s contention that the presence of the very recently evolved gene for malaria resistance can somehow be advanced as a dubious argument for race is at best simplistic and at worst a straw man. The main point is that just because there can be more than one method to define race, or because definitions of race seem to fray at their edges, does not mean that race is non-existent and there is no good way to parse it.
The last part of the book is likely to be regarded as more controversial because it deals mainly with effects of genetics on cognitive, social and personality traits and is much more speculative. However Wade fully realizes this and also believes that “there is nothing wrong with speculation, of course, as long as its premises are made clear”, and this statement could be part of a scientist’s credo. The crux of the matter is to logically ask why genes would also not account for mental and social differences between races if they do account for physical differences. The problem there is that although the hypothesis is valid, the evidence is slim for now. Some of the topics that Wade deals with in this third part are thus admittedly hazy in terms of corroboration. For instance there is ample contemplation about whether a set of behavioral and genetic factors might have made the West progress faster than the East and inculcated its citizens with traits conducive to material success. However Wade also makes it clear that “progressive” does not mean “superior”; what he is rather doing is sifting through the evidence and asking if some of it might account for these more complex differences in social systems. Similarly, while there are pronounced racial differences in IQ, one must recognize the limitations of IQ, but more importantly should recognize that IQ says nothing about whether one human is “better” or “worse” than another; in fact the question is meaningless.

Wade brings a similar approach to exploring genetic influences on cognitive abilities and personality traits; evidently, as he recognizes, the evidence on this topic is just emerging and therefore not definitive. He looks at the effects of genes on attributes as diverse as language, reciprocity and propensity to dole out punishment. This discussion makes it clear that we are just getting started and there are many horizons that will be uncovered in the near future; for instance, tantalizing hints of links between genes for certain enzymes and aggressive or amiable behavior are just emerging. Some of the other paradigms Wade writes about, such as the high intelligence of Ashkenazi Jews, the gene-driven contrast between chimp and human societies and the rise of the West are interesting but have been covered by authors like Steven Pinker, Greg Cochran and Gregory Clark. If I have a criticism of the book it is that in his efforts to cover extensive ground, Wade sometimes gives short shrift to research on interesting topics like oxytocin and hormonal influences. But what he does make clear is that the research opportunities in the field are definitely exciting, and scientists should not have to tiptoe around these topics for political reasons.

Overall I found this book extremely well-researched, thoughtfully written and objectively argued. Wade draws on several sources, including the peer reviewed literature and work by other thinkers and scientists. The many researchers whose work Wade cites makes the writing authoritative; on the other hand, where speculation is warranted or noted he usually explicitly points it out as such. Some of these speculations such as the effects of genetics on the behavior of entire societies are quite far flung but I don’t see any reason why, based on what we do know about the spread of genes among groups, they should be dismissed out of hand. At the very least they serve as reasonable hypotheses to be pondered, thrashed out and tested. Science is about ideas, not answers.

But the real lesson of the book should not be lost on us: A scientific topic cannot be declared off limits or whitewashed because its findings can be socially or politically controversial; as Wade notes, “Whether or not a thesis might be politically incendiary should have no bearing on the estimate of its scientific validity.” He gives nuclear physics as a good analogy; knowledge of the atom can lead to both destruction and advancement, but without this knowledge there will still be destruction. More importantly, one cannot hide the fruits of science; how they are used as instruments of social or political policy is a matter of principle and should be decoupled from the science itself. In fact, knowing the facts provides us with a clear basis for making progressive decisions and gives us a powerful weapon for defeating the nefarious goals of demagogues who would use pseudoscience to support their dubious claims. In that sense, I agree with Wade that even if genetic differences between races become enshrined into scientific fact, it does not mean at all that we will immediately descend into 19th-century racism; our moral compass has already decided the direction of that particular current.

Ultimately Wade’s argument is about the transparency of knowledge. He admonishes some of the critics – especially some liberal academics and the American Anthropological Association – for espousing a “culture only” philosophy that is increasingly at odds with scientific facts and designed mainly for political correctness and a straitjacketed worldview. I don’t think liberal academics are the only ones guilty of this attitude but some of them certainly embrace it. Liberal academics, however, have also always prided themselves on being objective examiners of the scientific truth. Wade rightly says that they should join hands with all of us in bringing that same critical and honest attitude to examining the recent evidence about race and genetics. Whatever it reveals, we can be sure that as human beings we will try our best not to let it harm the cause of our fellow beings. After all we are, all of us, human beings first and scientists second.

A modified version of this review was first published on Amazon.com.

About the Author: Ashutosh (Ash) Jogalekar is a chemist interested in the history and philosophy of science. He considers science to be a seamless and all-encompassing part of the human experience. Follow on Twitter @curiouswavefn.
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The views expressed are those of the author and are not necessarily those of Scientific American.

Scientific American is a trademark of Scientific American, Inc., used with permission

© 2013 Scientific American, a Division of Nature America, Inc.

 Ancient DNA Unravels Europe's Genetic Diversity

Oct. 10, 2013 — Ancient DNA recovered from a time series of skeletons in Germany spanning 4,000 years of prehistory has been used to reconstruct the first detailed genetic history of modern-day Europeans.

The study, published today in Science, reveals dramatic population changes with waves of prehistoric migration, not only from the accepted path via the Near East, but also from Western and Eastern Europe.

The research was a collaboration between the Australian Centre for Ancient DNA (ACAD), at the University of Adelaide, researchers from the University of Mainz, the State Heritage Museum in Halle (Germany), and National Geographic Society's Genographic Project. The teams used mitochondrial DNA (maternally inherited DNA) extracted from bone and teeth samples from 364 prehistoric human skeletons ‒ ten times more than previous ancient DNA studies.

"This is the largest and most detailed genetic time series of Europe yet created, allowing us to establish a complete genetic chronology," says joint-lead author Dr Wolfgang Haak of ACAD. "Focussing on this small but highly important geographic region meant we could generate a gapless record, and directly observe genetic changes in 'real-time' from 7,500 to 3,500 years ago, from the earliest farmers to the early Bronze Age."

"Our study shows that a simple mix of indigenous hunter-gatherers and the incoming Near Eastern farmers cannot explain the modern-day diversity alone," says joint-lead author Guido Brandt, PhD candidate at the University of Mainz. "The genetic results are much more complex than that. Instead, we found that two particular cultures at the brink of the Bronze Age 4,200 years ago had a marked role in the formation of Central Europe's genetic makeup."

Professor Kurt Alt (University of Mainz) says: "What is intriguing is that the genetic signals can be directly compared with the changes in material culture seen in the archaeological record. It is fascinating to see genetic changes when certain cultures expanded vastly, clearly revealing interactions across very large distances." These included migrations from both Western and Eastern Europe towards the end of the Stone Age, through expanding cultures such as the Bell Beaker and the Corded Ware (named after their pots).

"This transect through time has produced a wealth of information about the genetic history of modern Europeans," says ACAD Director Professor Alan Cooper. "There was a period of stasis after farming became established and suitable areas were settled, and then sudden turnovers during less stable times or when economic factors changed, such as the increasing importance of metal ores and secondary farming products. While the genetic signal of the first farming populations becomes increasingly diluted over time, we see the original hunter-gatherers make a surprising comeback."

Dr Haak says: "None of the dynamic changes we observed could have been inferred from modern-day genetic data alone, highlighting the potential power of combining ancient DNA studies with archaeology to reconstruct human evolutionary history." The international team has been working closely on the genetic prehistory of Europeans for the past 7-8 years and is currently applying powerful new technologies to generate genomic data from the specimens.

Credit: Science Daily

 Hunter-Gatherers and Immigrant Farmers Lived Together for 2,000 Years in Central Europe

Oct. 10, 2013 — Indigenous hunter-gatherers and immigrant farmers lived side-by-side for more than 2,000 years in Central Europe, before the hunter-gatherer communities died out or adopted the agricultural lifestyle. The results come from a study undertaken by the Institute of Anthropology at Johannes Gutenberg University Mainz (JGU) that has just been published in the journal Science.

A team led by Mainz anthropologist Professor Joachim Burger studied bones from the 'Blätterhöhle' cave near Hagen in Germany, where both hunter-gatherers and farmers were buried. "It is commonly assumed that the Central European hunter-gatherers disappeared soon after the arrival of farmers," said Dr. Ruth Bollongino, lead author of the study. "But our study shows that the descendants of Mesolithic Europeans maintained their hunter-gatherer way of life and lived in parallel with the immigrant farmers, for at least 2,000 years. The hunter-gathering lifestyle thus only died out in Central Europe around 5,000 years ago, much later than previously thought."

Until around 7,500 years ago all central Europeans were hunter-gatherers. They were the descendants of the first anatomically modern humans to arrive in Europe, around 45,000 years ago, who survived the last Ice Age and the warming that started around 10,000 years ago. But previous genetic studies by Professor Burger's group indicated that agriculture and a sedentary lifestyle were brought to Central Europe around 7,500 years ago by immigrant farmers. From that time on, little trace of hunter-gathering can be seen in the archaeological record, and it was widely assumed that the hunter-gatherers died out or were absorbed into the farming populations.

The relationship between these immigrant agriculturalists and local hunter-gatherers has been poorly researched to date. The Mainz anthropologists have now determined that the foragers stayed in close proximity to farmers, had contact with them for thousands of years, and buried their dead in the same cave. This contact was not without consequences, because hunter-gatherer women sometimes married into the farming communities, while no genetic lines of farmer women have been found in hunter-gatherers. "This pattern of marriage is known from many studies of human populations in the modern world. Farmer women regarded marrying into hunter-gatherer groups as social anathema, maybe because of the higher birthrate among the farmers," explains Burger.

For the study published in Science, the team examined the DNA from the bones from the 'Blätterhöhle' cave in Westphalia, which is being excavated by the Berlin archaeologist Jörg Orschiedt. It is one of the rare pieces of evidence of the continuing presence of foragers over a period of about 5,000 years.

For a long time the Mainz researchers were unable to make sense of the findings. "It was only through the analysis of isotopes in the human remains, performed by our Canadian colleagues, that the pieces of the puzzle began to fit," states Bollongino. "This showed that the hunter-gatherers sustained themselves in Central and Northern Europe on a very specialized diet that included fish, among other things, until 5,000 years ago.

The team also pursued the question of what impact both groups had on the gene pool of modern Europeans. Dr. Adam Powell, population geneticist at the JGU Institute of Anthropology, explains: "Neither hunter-gatherers nor farmers can be regarded as the sole ancestors of modern-day Central Europeans. European ancestry will reflect a mixture of both populations, and the ongoing question is how and to what extent this admixture happened."

It seems that the hunter-gatherers' lifestyle only died out in Central Europe 5,000 years ago. Agriculture and animal husbandry became the way of life from then on. However, some of the prehistoric farmers had foragers as ancestors, and the, hunter-gatherer genes are found in Central Europeans today.

Credit: Science Daily

 Genetic 'Adam' and 'Eve' uncovered
By Tia Ghose /
Published August 02, 2013 / LiveScience

Almost every man alive can trace his origins to one man who lived about 135,000 years ago, new research suggests. And that ancient man likely shared the planet with the mother of all women.

The findings, detailed Thursday, Aug. 1, in the journal Science, come from the most complete analysis of the male sex chromosome, or the Y chromosome, to date. The results overturn earlier research, which suggested that men's most recent common ancestor lived just 50,000 to 60,000 years ago.

Despite their overlap in time, ancient "Adam" and ancient "Eve" probably didn't even live near each other, let alone mate. [The 10 Biggest Mysteries of the First Humans]

"Those two people didn't know each other," said Melissa Wilson Sayres, a geneticist at the University of California, Berkeley, who was not involved in the study.

Tracing history
Researchers believe that modern humans left Africa between 60,000 and 200,000 years ago, and that the mother of all women likely emerged from East Africa. But beyond that, the details get fuzzy.

The Y chromosome is passed down identically from father to son, so mutations, or point changes, in the male sex chromosome can trace the male line back to the father of all humans. By contrast, DNA from the mitochondria, the energy powerhouse of the cell, is carried inside the egg, so only women pass it on to their children. The DNA hidden inside mitochondria, therefore, can reveal the maternal lineage to an ancient Eve.

But over time, the male chromosome gets bloated with duplicated, jumbled-up stretches of DNA, said study co-author Carlos Bustamante, a geneticist at Stanford University in California. As a result, piecing together fragments of DNA from gene sequencing was like trying to assemble a puzzle without the image on the box top, making thorough analysis difficult.

Y chromosome
Bustamante and his colleagues assembled a much bigger piece of the puzzle by sequencing the entire genome of the Y chromosome for 69 men from seven global populations, from African San Bushmen to the Yakut of Siberia.

By assuming a mutation rate anchored to archaeological events (such as the migration of people across the Bering Strait), the team concluded that all males in their global sample shared a single male ancestor in Africa roughly 125,000 to 156,000 years ago.

In addition, mitochondrial DNA from the men, as well as similar samples from 24 women, revealed that all women on the planet trace back to a mitochondrial Eve, who lived in Africa between 99,000 and 148,000 years ago almost the same time period during which the Y-chromosome Adam lived.

More ancient Adam
But the results, though fascinating, are just part of the story, said Michael Hammer, an evolutionary geneticist at the University of Arizona who was not involved in the study.

A separate study in the same issue of the journal Science found that men shared a common ancestor between 180,000 and 200,000 years ago.

And in a study detailed in March in the American Journal of Human Genetics, Hammer's group showed that several men in Africa have unique, divergent Y chromosomes that trace back to an even more ancient man who lived between 237,000 and 581,000 years ago. [Unraveling the Human Genome: 6 Molecular Milestones]

"It doesn't even fit on the family tree that the Bustamante lab has constructed. It's older," Hammer told LiveScience.

Gene studies always rely on a sample of DNA and, therefore, provide an incomplete picture of human history. For instance, Hammer's group sampled a different group of men than Bustamante's lab did, leading to different estimates of how old common ancestors really are.

Adam and Eve?
These primeval people aren't parallel to the biblical Adam and Eve. They weren't the first modern humans on the planet, but instead just the two out of thousands of people alive at the time with unbroken male or female lineages that continue on today.

The rest of the human genome contains tiny snippets of DNA from many other ancestors they just don't show up in mitochondrial or Y-chromosome DNA, Hammer said. (For instance, if an ancient woman had only sons, then her mitochondrial DNA would disappear, even though the son would pass on a quarter of her DNA via the rest of his genome.)

As a follow-up, Bustamante's lab is sequencing Y chromosomes from nearly 2,000 other men. Those data could help pinpoint precisely where in Africa these ancient humans lived.

"It's very exciting," Wilson Sayres told LiveScience. "As we get more populations across the world, we can start to understand exactly where we came from physically."

Copyright 2013 LiveScience, a TechMediaNetwork company. All rights reserved. This material may not be published, broadcast, rewritten or redistributed.

 Large scale mitochondrial sequencing in Mexican Americans suggests a reappraisal of Native American origins

Conclusions from a paper found in PubMed Central: posted 3/7/12
 by Satish Kumar,1 Claire Bellis,1 Mark Zlojutro,1 Phillip E Melton,1 John Blangero,1 and Joanne E Curran1

Analysis of a data set of 568 mitochondrial genomes from North, Central and South America, as well as Beringia and Siberia-Asia suggest that American founders diverged from their Siberian-Asian progenitors sometime during LGM and expanded into America soon after the LGM peak (~20-16 kya). Further, time between the Native American divergence from Siberian-Asians to the expansion into America was shorter than the previous estimates. The phylogeography of haplogroup C1 suggest that this American founder haplogroup differentiated in Siberia-Asia. Although it is not clear for the haplogroup B2, haplogroups A2 and D1 might have differentiated soon after the Native American founder's divergence. A moderate population bottle neck in American founder populations just before the expansion  most plausibly resulted in few founder types in America. The similar estimates of the diversity indices and Bayesian skyline analysis in North America, Central America and South America suggest almost simultaneous (over a period of approximately 2.0 ky from South to North America) colonization of these geographical regions with rapid population expansion differentiating into more or less regional branches across the pan American haplogroups A2, B2, D1 and the C1b, C1c, C1d subhaplogroups of C1. However, some sub branches (B2b, C1b, C1c, C1d and D1f) already existed in American founder haplogroups before expansion into the Americas."

Found at http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3217880/ 3/7/2012

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 700,000-Year-Old Horse Becomes Oldest Creature With Sequenced Genome

by Gisela Telis on 26 June 2013

Wild horses. A genome sequence derived from a 700,000-year-old horse fossil sheds new light on equine evolution and confirms that Przewalski's horse is indeed genetically distinct from domesticated breeds.

Scientists have sequenced the oldest genome to date—and shaken up the horse family tree in the process. Ancient DNA derived from a horse fossil that's between 560,000 and 780,000 years old suggests that all living equids—members of the family that includes horses, donkeys, and zebras—shared a common ancestor that lived at least 4 million years ago, approximately 2 million years earlier than most previous estimates. The discovery offers new insights into equine evolution and raises the prospect of recovering and exploring older DNA than previously thought possible.

"There's no question this is a landmark study," says David Lambert, an evolutionary biologist at Griffith University in Australia who was not involved in the work. "It's well beyond the time period where I thought we had any prospect of getting a genome."

The study began with a walk in the permafrost. Evolutionary biologist Eske Willerslev of the University of Copenhagen joined a team of geologists on a 2003 expedition in Canada's Yukon Territory. The group was exploring a site that holds ice and volcanic ash that date back more than 700,000 years. There, Willerslev spotted a piece of bone jutting from the frozen ground and decided he would study it.

The fossil, a fragment of horse leg bone, was too old for radiocarbon dating, but Willerslev estimated, based on its location in the permafrost, that it was between 560,000 and 780,000 years old. He and an international team of colleagues then set about scouring the fragment for any trace of collagen or other material that could harbor the ancient horse's DNA.

The odds were against the team. No DNA had been salvaged and sequenced from a fossil more than 130,000 years old (that was a polar bear jawbone), and theoretical estimates put the upper limit of DNA survival at about 1 million years. Yet, a preliminary analysis of the sample hinted that it might contain a few remaining pockets of collagen and blood.  Using the detailed, time-consuming process with which Willerslev sequenced an ancient human's DNA in 2010, the researchers were able to reconstruct the equid's genetic code. For comparison, they also sequenced the genomes of a Late Pleistocene horse that lived about 43,000 years ago, a contemporary donkey, five different domestic horse breeds, and a Przewalski's horse, which is considered the world's only remaining wild horse and a source of controversy.  Genetically speaking, other so-called wild horses—for example, the mustangs of the American West—are simply domesticated horses gone feral. Przewalski's horse is thought to be genetically distinct, but some experts have expressed doubt over whether this cousin of the domesticated horse carries some domesticated horse genes.

By comparing mutations across all the samples, the team determined that the fossil came from a male horse that lived about 700,000 years ago and most likely shared a common ancestor with the rest of the Equus lineage—all donkeys, horses, zebras—about 4 million to 4.5 million years ago. That finding alone may help settle a long-standing debate over Equus origins.  Experts disagree over the timeline of equine evolution and have posited that the last common Equus ancestor lived anywhere between 2 million and 6 million years ago. But the data, published online today in Nature, also solve another mystery.  They suggest that the Przewalski's horse hasn't mingled genetically with domestic horse breeds, confirming that this endangered native of the Mongolian steppes really is distinct from its domesticated cousins.

As for what the ancient horse looked like, Willerslev says that he was large but not as tightly muscled as a modern horse. "This was a tall guy, on the order of Arabian horses," he says. "But I don't think he's something Napoleon would ride into town on."

The sequenced genome offers a glimpse at the ancient horse and how equine genes have evolved. Genes that are involved in immunity, the sense of smell, and muscle development have all changed significantly since this ancient horse roamed the Yukon, Willerslev says.

Beyond its implications for equine evolution, the study pushes the envelope for ancient DNA research, Willerslev says. "It was not that long ago that people in the field of ancient DNA would have said you can't retrieve data from something this old, but here we have a whole genome."

Lambert agrees that the team's work creates new possibilities for DNA research, including applying the technique to ancient human fossils to gain a clearer picture of human evolution. "This study will encourage people to say, 'Maybe we should give this a go,' " he says. "It makes you wonder if a million-year-old genome would be possible."

Credits: Science Magazine  -  Found at http://news.sciencemag.org/sciencenow/2013/06/700000-year-old-horse-becomes-ol.html
Credit: Claudia Feh/Association pour le cheval de Przewalski, France

Eske Willerslev:  is an internationally recognised researcher in the fields of ancient DNA, DNA degradation, and evolutionary biology. He has 18 publications in Science and Nature, and 128 publications in other high profile peer review journals

His research interests include: palaeoecology, palaeontology, archaeology, domestication, climatology, ancient microbial biology, DNA degradation and repair, exobiology, phylogenetics, molecular evolution, barcoding, and genomics.