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-- DNA studies fail to locate root of the species - 9/20/12
-- Ancient DNA Unravels Europe's Genetic Diversity - 10/10/13
-- A lock of hair has helped scientists - 9/22/11
-- Early humans' route out of Africa 'confirmed'  - 2/11/11
-- Making of Europe unlocked by DNA - 4/23/13
-- Much Earlier Split for Neanderthals, Humans? - 10/21/13
 DNA studies fail to locate root of the species

September 20, 2012 By Erin Wayman Science News

The origin story for Homo sapiensis a messy tale. Rather than emerging from one small population, the human species likely evolved from a dispersed, complex network of groups that mixed and mated with each other, scientists report online September 20 in Science.

The new research is one of the largest genetic studies of southern Africa’s click-speaking hunter-gatherers known as the Khoisan. Sometimes called Bushmen, the Khoisan are the world’s most genetically diverse people and diverged from other populations very early in human history.

The new work dates the genetic split between the Khoisan and the rest of humankind to at least 100,000 years ago, which is in line with other estimates. That’s 55,000 years older than the next branch on the human family tree, when Central African pygmies split off. The researchers also found that the Khoisan divided into a northern and a southern group approximately 35,000 years ago.

But when the scientists looked for genetic clues pointing to where in sub-Saharan Africa humankind began, they couldn’t trace modern groups back to any one region. That suggests early humans came from a highly structured population with genetic exchange between subgroups.

“The complexity of the South African population is the big story,” says Adam Siepel, a computational biologist at Cornell University. “It undermines simpler stories trying to pinpoint a single geographic origin of modern humans.” Previous fossil evidence had suggested East Africa while smaller genetic analyses indicated South Africa.

In the new study, Carina Schlebusch of Sweden’s Uppsala University and colleagues looked at single nucleotide polymorphisms, or SNPs, which are locations in the genetic code where people commonly differ. The researchers surveyed 2.3 million SNPs in 220 individuals from 11 African populations, including seven Khoisan groups. After combining the new data with previously published data, the team assessed four measures of genetic variation to find where in Africa humans originated, but the results didn’t converge on one location.

A paper set to appear in an upcoming issue of Nature Communicationsreaches similar conclusions. Joseph Pickrell of Harvard Medical School and colleagues analyzed a different set of more than 565,000 SNPs in 187 individuals from 22 African populations. Like Schlebusch’s team, Pickrell’s group identified a split within the Khoisan that occurred roughly 30,000 years ago, breaking the population into a northwestern and a southeastern group. Their work also failed to find a single area where humans arose.

But you wouldn’t necessarily expect to find the cradle of humanity by looking at the evolutionary relationships of present-day Africans, says Sarah Tishkoff, a human geneticist at the University of Pennsylvania in Philadelphia. “When you look at modern populations, you see where they live today,” she says. “You don’t know where they were 50,000 or 60,000 years ago.”

Schlebusch’s team also searched for genetic changes that might reveal the evolutionary forces that shaped early Africans. The researchers found hints that selection acting on a few genes related to skeletal and neurological development may have played a role in the emergence of anatomically modern humans. That makes sense, says anthropologist John Hawks of the University of Wisconsin–Madison: “They confirm selection on a gene that differs between modern humans and the Neandertals, RUNX2, which may be involved in the unique physical form of our species relative to archaic humans.”

More extensive analyses that examine the complete genetic instruction book of people from different Khoisan groups are needed to confirm such findings, Tishkoff says. So far, scientists have only done this for one Khoisan man.

“We’re just at the beginning of understanding modern human history and origins in Africa,” Tishkoff says. “In the future, as we do more whole genome sequencing, it will become clearer.”


 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: http://www.sciencedaily.com/releases/2013/10/131010142650.htm

 A lock of hair has helped scientists to piece together the genome of Australian Aborigines and rewrite the history of human dispersal around the world.
22 September 2011 By Leila Battison
DNA from the hair demonstrates that indigenous Aboriginal Australians were the first to separate from other modern humans, around 70,000 years ago.

This challenges current theories of a single phase of dispersal from Africa.

An international team of researchers published their findings in the journal Science.

While the Aboriginal populations were trailblazing across Asia and into Australia, the remaining humans stayed around North Africa and the Middle East until 24,000 years ago.

Only then did they spread out and colonise Europe and Asia, but the indigenous Aborigines had been established in Australia for 25,000 years.

Australian Aborigines therefore have a longer claim to the land in which they now live than any other population known.

The research also highlights the exciting future possibilities of comparing the genomes of multiple individuals to track migration of small indigenous groups.

Tiny genetic differences

Archaeological remains are known from Australia from around 50,000 years ago, putting a maximum age of the Aborigines' settlement there.

But the history of their journey and their relationship with the indigenous people of Asia and Europe had not been solved.

Continue reading the main story “Start QuoteThey could walk almost the entire way because the sea level was much lower”
End Quote Dr Francois Balloux Imperial College London
It was previously thought that modern humans dispersed in one pulse out of Africa and the Middle East, and because of the distances involved, the modern Europeans would have separated from the Asians and Australians first.

Genetic information from a lock of Aboriginal hair has been used to show that the Australians set off a lot earlier.

By looking at the tiny (fraction of one percent) differences between the DNA of Aborigines and other ancient humans, the scientists show that the indigenous Australians were first isolated 70,000 years ago.

Dr Francois Balloux, of Imperial College London described how a "population expanded along the coastline because of the rich resources available there. They could walk almost the entire way because the sea level was much lower". Just one small sea crossing would be required to reach Australia.

Any potential archaeological remains of this journey, which lasted 25,000 years, would be lost to the deep sea under rising sea levels.

The remaining populations in the Middle East moved out to colonise Europe and Asia 24,000 years ago, and the aboriginal genome records some interbreeding between Asian populations and aboriginal ancestors at this time.

Discovering the history of human migration with DNA has been made possible by improvements in the techniques used to study the genome.

Traditionally, genetic divergence dates were arrived at by combining the number of unique mutations in the DNA with an assumed rate of acquiring those mutations.

Now, computationally powerful models can simulate lots of different scenarios for migration timings and directions, and researchers can compare and choose the situation that most closely matches what is seen in the genome.

By comparing the Aboriginal genome with the DNA of African, European and Han Chinese individuals it was possible to highlight the later interbreeding after initial colonisation.

Continue reading the main story Modern human migration The ancestors of Aboriginal Australians travelled through East Asia before reaching Australia some 50,000 years ago (red arrow).Others, including East Asians, spread out of Africa before splitting - one lineage crossing the Bering Strait to establish in North America (black arrow).
Comparison with Eurasian populations show that the Australian Aborigines have a similar percentage of Neanderthal genes within their DNA as their Eurasian counterparts, suggesting that any interbreeding occurred before the Aborigines embarked on their colonising journey.

The findings of these researchers are supported by an independent study, published this week in the American Journal of Human Genetics, which looks at the characteristic DNA from an extinct, archaic form of human, the Denisovans.

Denisovans lived over 30,000 years ago, and contributed genes mostly to present-day New Guineans.

This independent study identifies a pattern of Denisovan DNA in Asian individuals that can only be explained by two separate waves of human migration: the first of Aboriginals colonising Australia, and the second involving the occupation of Asia itself.

'Jurassic Park science'

The Aboriginal research was carried out on a single lock of hair, which was donated by a young Aboriginal man to the British anthropologist Dr A C Haddon in 1923.

"At this time, it was fashionable to take human samples," said Dr Balloux. The collection of hair was one of the more innocuous efforts of anthropologists at the time.

The researchers chose to examine the hair, as opposed to any other type of remains, for legal reasons. Hair is not classified as a human tissue.

"More important to us was that the research would be acceptable from a social and moral point of view" said Dr Balloux.To the surprise of the scientists, the people they consulted were very supportive of the study and its results. Dr Balloux explained that in the past, indigenous people have been "extremely sensitive of the motivations of western scientists".

The research has been published with "strong endorsement" from the Goldfields Land and Sea Council, the organisation that represents the Aboriginal traditional owners of parts of Western Australia, he said.

Genomics techniques like those used in this study have the potential to be used more extensively in the study of human migrations and the evolution of health and disease.

The international team next plans to look in more detail at the dispersal of modern humans out of Africa, as well as solving how and when the Americas were colonised.

Dr Balloux said he was excited about the unexpected potential of the techniques, describing it as "borderline Jurassic Park science".

First reported in http://www.bbc.co.uk/news/science-environment-15020799

 Early humans' route out of Africa 'confirmed'

2/11/2011     Published in the journal Molecular Biology and Evolution.

The study suggests early people crossed the Bab-el-Mandeb straits into Arabia

A six-year effort to map the genetic patterns of humankind appears to confirm that early people first left Africa by crossing into Arabia.  
Ancestors of modern people in Europe, Asia and Oceania migrated along a southern route, not a northern route through Egypt as some had supposed.

The results from the Genographic Project suggests an important role for South Asia in the peopling of the world.   The ancestors of present-day non-African people left their ancestral homeland some 70,000 years ago. 

The researchers found that Indian populations had more genetic diversity - which gives an indication of the age of a population - than either Europeans or East Asians.   This supports the idea that pioneering settlers followed a southern coastal route as they populated east Asia and continued into Oceania.

"This suggests that other fields of research such as archaeology and anthropology should look for additional evidence on the migration route of early humans," said co-author Ajay Royyuru, senior manager at IBM's Computational Biology Center, which was involved in analysing the study data.

A route out of Africa via the Arabian Peninsula, along the southern coast of Asia, explained the observed patterns in genetic diversity much better than a route through Egypt's Sinai desert.

This agrees with other evidence showing that sea levels might have been low enough around 60-70,000 years ago for humans to cross from the horn of Africa into Arabia via the Bab-el-Mandeb straits in the Red Sea.

The latest findings are based on a new analytical method which exploits patterns of recombination in human genomes. Recombination is the process by which molecules of DNA are broken up and recombine to form new pairs.

The scientists used these patterns of recombination to trace relationships between different present-day humans.

"Almost 99% of the genetic makeup of an individual are layers of genetic imprints of the individual's many lineages. Our challenge was whether it was even feasible to tease apart these lineages to understand the commonalities," said IBM researcher Laxmi Parida.

"Through a determined approach of analytics and mathematical modelling, we undertook the intricate task of reconstructing the genetic history of a population. In doing so, we now have the tools to explore much more of the human genome."

Dr Spencer Wells, director of the Genographic Project, said such methods could provide "greater insights into the migratory history of our species".

Nearly 500,000 individuals have participated in the project, making it one of the biggest surveys of human genetic variation ever conducted.

The DNA was contributed by indigenous peoples and by members of the general public.


 Making of Europe unlocked by DNA

23 April 2013    By Paul Rincon   Science editor, BBC News website

The Neolithic was a period of momentous cultural and demographic change:  DNA sequenced from nearly 40 ancient skeletons has shed light on the complex prehistoric events that shaped modern European populations.

A study of remains from Central Europe suggests the foundations of the modern gene pool were laid down between 4,000 and 2,000 BC - in Neolithic times.   These changes were likely brought about by the rapid growth and movement of some populations.

The work by an international team is published in Nature Communications.   Decades of study of the DNA patterns of modern Europeans suggests two major events in prehistory significantly affected the continent's genetic landscape: its initial peopling by hunter-gatherers in Palaeolithic times (35,000 years ago) and a wave of migration by Near Eastern farmers some 6,000 years ago. (in the early Neolithic)

Family tree

Analysis of DNA from ancient remains in Central and Northern Europe appears to show that the genetic legacy of the hunter-gatherers was all but erased by later migrations, including pioneer Neolithic farmers but possibly by later waves of people too.

The latest paper reveals that events some time after the initial migration of farmers into Europe did indeed have a major impact on the modern gene pool.

In the study, an international team of researchers focused on mitochondrial DNA (mtDNA), the information in the cell's "batteries". This type of DNA is passed down, almost unchanged, from a mother to her children.

By studying the mutations, or changes, in mtDNA sequences, researchers are able to probe the maternal histories of different human populations. It has enabled them to build a "family tree" of maternal ancestry, and group different mtDNA lineages together based on shared mutations.

For the latest paper, the authors chose to focus on one of these groupings known as haplogroup H.

Haplogroup H dominates mtDNA variation in Europe. Today, more than 40% of Europeans belong to this genetic "clan", with frequencies much higher in the west of the continent than in the east.

The DNA of "Beaker folk" resembled that of people from Spain and Portugal.   The team selected 37 human remains from the Mitelelbe Saale region of Germany and two from Italy, all of whom belonged to the "H" clan. This area has a very well preserved collection of human skeletons forming a continuous record of habitation across different archaeological cultures since Palaeolithic times.   The remains investigated here span 3,500 years of European prehistory, from the Early Neolithic to the Bronze Age.

Sequencing the mitochondrial genomes of these 39 remains revealed dynamic changes in DNA patterns over time. The team found that the genetic signatures of people from the Early Neolithic period were either rare or absent from modern populations.

And only about 19% of the Early Neolithic remains from Central Europe belonged to the H haplogroup.

But, from the Middle Neolithic onwards, DNA patterns more closely resembled those of people living in the area today, pointing to a major - and previously unrecognised - population upheaval around 4,000 BC.

Co-author Prof Alan Cooper, from the University of Adelaide in Australia, said: "What is intriguing is that the genetic markers of this first pan-European culture, which was clearly very successful, were then suddenly replaced around 4,500 years ago, and we don't know why.  "Something major happened, and the hunt is now on to find out what that was."   Population growth and migration from western Europe may have driven up the frequency of people carrying haplogroup H.

Migrant wave

A significant contribution appears to have been made in the Late Neolithic, by populations linked to the so-called Bell Beaker archaeological culture. Sub-types of haplogroup H that are common today first appear with the Beaker people and the overall percentage of individuals belonging to the H clan jumps sharply at this time.

The origins of the "Beaker folk" are the subject of much debate. Despite having been excavated from the Mittelelbe Saale region of Germany, the Beaker individuals in this study showed close genetic similarities with people from modern Spain and Portugal.

Other remains belonging to the Late Neolithic Unetice culture attest to links with populations further east.

"We have established that the genetic foundations for modern Europe were only established in the Mid-Neolithic, after this major genetic transition around 4000 years ago," said co-author Dr Wolfgang Haak.

"This genetic diversity was then modified further by a series of incoming and expanding cultures from Iberia and Eastern Europe through the Late Neolithic."

Dr Spencer Wells, director of the Genographic Project, which was behind the study, commented: "Studies such as this on ancient remains serve as a valuable adjunct to the work we are doing with modern populations in the Genographic Project.

"While the DNA of people alive today can reveal the end result of their ancestors' ancient movements, to really understand the dynamics of how modern genetic patterns were created we need to study ancient material as well."

First Published in http://www.bbc.co.uk/news/science-environment-22252099

 Much Earlier Split for Neanderthals, Humans?

Published October 21, 2013     National Geographic

Study challenges thinking on last common ancestor of Neanderthals, humans.

A skull of a Homo neanderthalensis (left) and a modern female Homo sapiens (right).

Photographs by David Liitschwager, National Geographic
.By Brian Switek

In the ranks of prehistoric humans, Neanderthals were our closest relatives.

We were so close, in fact, that our species interbred with theirs. Tracing back our lineages, there must have been a last common ancestor of Homo sapiens and Neanderthals sometime in prehistory. (Related: "Geno 2.0 Can Reveal How Neanderthal You Are.")

But who was this mystery human?

Picking out direct ancestors in the fossil record is tricky. To figure out when the last common ancestor of Homo sapiens and Neanderthals lived, paleoanthropologists have been sifting through both genetic and anatomical evidence.

In the last five years, anthropologists have used DNA to reconstruct the evolutionary history of humans. Researchers have suggested a range of dates for when the last common ancestor of our lineage and Neanderthals could have lived. (Related: "Last of the Neanderthals.")

The dates range from more than 800,000 years ago to less than 300,000, with many estimates in the neighborhood of 400,000 years ago. According to some studies, this time frame would seem to match that of the extinct species Homo heidelbergensis, which has been found in Africa, Europe, and possibly Asia.

But this may not be so. A new study theorizes that the last common ancestor of H. sapiens and Neanderthals lived longer ago than previously expected, with fossil evidence yet to be uncovered.

What's new?

In a study published on Monday in the Proceedings of the National Academy of Sciences, George Washington University anthropologist Aida Gómez-Robles and colleagues turned to teeth to test what had been gleaned from genetics.

Using a collection of 1,200 premolars and molars from a variety of prehistoric humans, the researchers pinpointed specific landmarks on the teeth. The landmarks were then used to reconstruct the tooth shapes of our common ancestors at critical points in evolutionary history.

The logic behind this method, Gómez-Robles says, is that "the most likely dental shape of an ancestral species is an intermediate shape between the one observed in both daughter species." In the case of H. sapiens and Neanderthals, the last common ancestor of both lineages would be expected to have teeth with a shape and anatomy in between those of the two species.

With that hypothetical shape in mind, Gómez-Robles and coauthors compared what was expected against fossils found so far.

"If a fossil species is very similar to the expected ancestral morphology, then that species is a plausible ancestor," Gómez-Robles says, though she stresses that such a match is a possibility rather than definite proof of ancestry.

Why is it important?

Estimates based on DNA show that the last common ancestor of H. sapiens and Neanderthals lived around 400,000 years ago. This made H. heidelbergensis, a widespread species alive at the time, seem like a good candidate for that ancestor.

The new study contradicts this idea. The tooth reconstruction of the last common ancestor of humans and Neanderthals created by Gómez-Robles and colleagues doesn't match the teeth of H. heidelbergensis.

In fact, the researchers found that none of the human species living during the time predicted by genetic data fit the tooth pattern generated by the new study. More than that, "European species that might be candidates show morphological affinities with Neanderthals," Gómez-Robles says, which hints that these humans were already on the Neanderthal side of the split.

This suggests that the last common ancestor of H. sapiens and Neanderthals lived sometime earlier, perhaps as far back as one million years ago.

What does it mean?

Paleoanthropologists have yet to find our last common ancestor with Neanderthals. Tracking this elusive human will require going back to museum collections and continuing searches in the field.

From the new study's results, Gómez-Robles says that "we think that candidates have to be looked for in Africa." At present, million-year-old fossils attributed to the prehistoric humans H. rhodesiensis and H. erectus look promising.

This critical window of human prehistory in Africa is still cloudy. "There are not so many African fossil remains dated to one million years ago," Gómez-Robles says, and those that have been found are often attributed to H. erectus.

But do they really belong to this species? There may be an as-yet-unknown human hiding in the mix, and this human may be key to solving the puzzle of when our ancestors split from Neanderthals.

Whether that species is waiting to be discovered in the field or is hiding within the broken and scattered remains of fossils already collected is a mystery waiting to be solved.


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