DNA News - Page 15
 



--
-- Mixed genes
-- Blue eyes and dark skin, that’s how the European hunter-gatherer looked
-- Putting ‘Adam’ in his rightful place in evolutionary history - Posted 2/11/14
-- 400K DNA Found - posted 12/9/13
-- Ancient DNA Unravels Europe's Genetic Diversity - 10/10/13
-- Basque Roots Revealed Through Dna Analysis - 3/06/12
-- A Paper on Lebanon and the crusades (I and R1b haplogroups in abundance)

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 Mixed genes: Interactive world map of human genetic history reveals likely genetic impacts of historical events
Date:February 13, 2014
Source:Max-Planck-Gesellschaft

This is a schematic of the admixture process.
Credit: The chromosome painting collective (http://www.paintmychromosomes.com)[Click to enlarge image]When individuals from different groups interbreed, their offspring's DNA becomes a mixture of the DNA from each admixing group. Pieces of this DNA are then passed along through subsequent generations, carrying on all the way to the present day. Researchers from the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, Oxford University and University College London (UCL) have now produced a global map detailing the genetic histories of 95 different populations across the world, spanning the last four millennia.

The interactive world map that is accessible via the internet, details the histories of genetic mixing between each of the 95 populations across Europe, Africa, Asia and South America. It shows likely genetic impacts of historical events including European colonialism, the Mongol Empire, the Arab slave trade and European traders near the Silk Road mixing with people in China.

The study, published this week in Science, is the first to simultaneously identify, date and characterise genetic mixing between populations. To do this, the researchers developed sophisticated statistical methods to analyse the DNA of 1490 individuals in 95 populations around the world. "DNA really has the power to tell stories and uncover details of humanity's past," said Simon Myers of Oxford University's Department of Statistics and Wellcome Trust Centre for Human Genetics, co-senior author of the study. "Because our approach uses only genetic data, it provides information independent from other sources. Many of our genetic observations match historical events, and we also see evidence of previously unrecorded genetic mixing. For example, the DNA of the Tu people in modern China suggests that in around 1200CE, Europeans similar to modern Greeks mixed with an otherwise Chinese-like population. Plausibly, the source of this European-like DNA might be merchants travelling the nearby Silk Road."

The powerful technique, christened 'Globetrotter', provides insight into past events such as the genetic legacy of the Mongol Empire. Historical records suggest that the Hazara people of Pakistan are partially descended from Mongol warriors, and this study found clear evidence of Mongol DNA entering the population during the period of the Mongol Empire. Six other populations, from as far west as Turkey, showed similar evidence of genetic mixing with Mongols around the same time.

"What amazes me most is simply how well our technique works," said Garrett Hellenthal of the UCL Genetics Institute, lead author of the study. "Although individual mutations carry only weak signals about where a person is from, by adding information across the whole genome we can reconstruct these mixing events. Sometimes individuals sampled from nearby regions can have surprisingly different sources of mixing. For example, we identify distinct events happening at different times among groups other than the Hazara sampled within Pakistan, with some inheriting DNA from sub-Saharan Africa, perhaps related to the Arab Slave Trade, another from East Asia, and yet another from ancient Europe. Nearly all our populations show mixing events, so they are very common throughout recent history and often involve people migrating over large distances."

The team used genome data for all 1490 individuals to identify 'chunks' of DNA that were shared between individuals from different populations. Populations sharing more ancestry share more chunks, and individual chunks give clues about the underlying ancestry along chromosomes.

"Each population has a particular genetic 'palette'," said Daniel Falush of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, co-senior author of the study. "If you were to paint the genomes of people in modern-day Maya, for example, you would use a mixed palette with colours from Spanish-like, West African and Native American DNA. This mix dates back to around 1670AD, consistent with historical accounts describing Spanish and West African people entering the Americas around that time. Though we can't directly sample DNA from the groups that mixed in the past, we can capture much of the DNA of these original groups as persisting, within a mixed palette of modern-day groups."

As well as providing fresh insights into historical events, the new research might have implications for how DNA impacts health and disease in different populations.

Story Source:

The above story is based on materials provided by Max-Planck-Gesellschaft. Note: Materials may be edited for content and length.

Journal Reference:

1.Garrett Hellenthal, George B.J. Busby, Gavin Band, James F. Wilson, Cristian Capelli, Daniel Falush, Simon Myers. A Genetic Atlas of Human Admixture History. Science, 14 February 2014 DOI: 10.1126/science.1243518
 

 Blue eyes and dark skin, that’s how the European hunter-gatherer looked

Jan 27, 2014

La Braña 1, name used to baptize a 7,000 years old individual from the Mesolithic Period, whose remains were recovered at La Braña-Arintero site in Valdelugueros (León, Spain) had blue eyes and dark skin.   La Braña 1 represents the first recovered genome of an European hunter-gatherer.  These details are the result of a study conducted by Carles Lalueza-Fox, researcher from the Spanish National Research Council (CSIC), in collaboration with the Centre for GeoGenetics (Denmark).  The research is published in Nature.   Credit: PELOPANTON / CSIC:


The Mesolithic, a period that lasted from 10,000 to 5,000 years ago (between the Paleolithic and the Neolithic), ends with the advent of agriculture and livestock farming, coming from the Middle-East. The arrival of the Neolithic, with a carbohydrate-based diet and new pathogens transmitted by domesticated animals, entailed metabolic and immunological challenges that were reflected in genetic adaptations of post-Mesolithic populations. Among these is the ability to digest lactose, which La Braña individual could not do.

Lalueza-Fox states: “However, the biggest surprise was to discover that this individual possessed African versions in the genes that determine the light pigmentation of the current Europeans, which indicates that he had dark skin, although we can not know the exact shade”.

CSIC researcher, who works at the Institute of Evolutionary Biology (a joint centre of CSIC and the University Pompeu Fabra (UPF), located in Barcelona, adds: “Even more surprising was to find that he possessed the genetic variations that produce blue eyes in current Europeans, resulting in a unique phenotype in a genome that is otherwise clearly northern European”.

The study of the genome suggests that current populations nearest to La Braña 1 are in northern Europe, such as Sweden and Finland. In addition, the work points out that La Braña 1 has a common ancestor with the settlers of the Upper Paleolithic site of Mal’ta, located in Lake Baikal (Siberia), whose genome was recovered a few months ago. Lalueza-Fox concludes: “These data indicate that there is genetic continuity in the populations of central and western Eurasia. In fact, these data are consistent with the archeological remains, as in other excavations in Europe and Russia, including the site of Mal’ta, anthropomorphic figures –called Paleolithic Venus– have been recovered and they are very similar to each other”.

DNA with an “exceptional” preservation

 La Braña-Arintero site was discovered by chance in 2006 and excavated by Julio Manuel Vidal Encinas, archeologist of the Council of Castilla y León. The cave, located in a cold mountainous area with a steady temperature and 1,500 meters below the sea level, contributed to the “exceptional” preservation of the DNA from two individuals found inside, and they were called La Braña 1 and La Braña 2.

According to Iñigo Olalde, lead author of the study, “the intention of the team is to try to recover the genome of the individual called La Braña 2, which is worse preserved, in order to keep obtaining information about the genetic characteristics of these early Europeans”.

Contributing Source : Spanish National Research Council (CSIC)

© Copyright 2014 HeritageDaily - Heritage & Archaeology News
 

 Putting ‘Adam’ in his rightful place in evolutionary history

Jan 23, 2014:  Our most common male ancestor walked the earth 209,000 years ago – earlier than scientists commonly thought – according to new research from the University of Sheffield.

The pioneering study, conducted by Dr Eran Elhaik from the University of Sheffield and Dr Dan Graur from the University of Houston, also debunked the discovery of the Y chromosome that supposedly predated humanity.

In the new research, published in the European Journal of Human Genetics, Dr Elhaik and Dr Graur used conventional biological models to date our most common male ancestor ‘Adam’ in his rightful place in evolutionary history.

The ground breaking results showed that this is 9,000 years earlier than scientists originally believed.

Their findings put ‘Adam’ within the time frame of his other half ‘Eve’, the genetic maternal ancestor of mankind. This contradicts a recent study1 which had claimed the human Y chromosome originated in a different species through interbreeding which dates ‘Adam’ to be twice as old.

Debunking unscientific theories is not new to Dr Elhaik. Earlier this year he debunked Hammer’s previous work on the unity of the Jewish genome and together with Dr Graur they refuted the proclamations made by the ENCODE project on junk DNA.

“We can say with some certainty that modern humans emerged in Africa a little over 200,000 years ago,” said Dr Elhaik.

“It is obvious that modern humans did not interbreed with hominins living over 500,000 years ago. It is also clear that there was no single ‘Adam’ and ‘Eve’ but rather groups of ‘Adams and ‘Eves’ living side by side and wandering together in our world.”

Dr Elhaik added: “We have shown that the University of Arizona study lacks any scientific merit.
“In fact, their hypothesis creates a sort of ‘space-time paradox ‘whereby the most ancient individual belonging to Homo sapiens species has not yet been born. If we take the numerical results from previous studies seriously we can conclude that the past may be altered by the mother of ‘Adam’ deciding not to conceive him in the future, thus, bringing a retroactive end to our species.

“Think of the movie Back to the Future, when Marty was worried that his parents would not meet and as a result he wouldn’t be born – it’s the same idea.

“The question to what extend did our humans forbearers interbreed with their closest relatives is one of the hottest questions in anthropology that remains open.”

Header Image : Human Genome : Credit : Richard Ricciardi

Contributing Source : University of Sheffield
 
Editor Notes: This is an interesting article, is has a comment that debunks the test that showed human ancestors at 400,000 years, which may refer to the next article 400,000-year-old human DNA adds new tangle to our origin story  . But I notice that here they refer to Homo-Sapiens while the "Older article" refers only to Humans and Hominins, but not Homo-Sapiens.  So maybe the author of this article misunderstood what was said.
 

 400,000-year-old human DNA adds new tangle to our origin story   

 Basque Roots Revealed Through Dna Analysis

3/06/12    Glynnis Breen & Colby Bishop

WASHINGTON (March 6, 2012)—The Genographic Project announced today the most comprehensive analysis to date of Basque genetic patterns, showing that Basque genetic uniqueness predates the arrival of agriculture in the Iberian Peninsula some 7,000 years ago.   Through detailed DNA analysis of samples from the French and Spanish Basque regions, the Genographic team found that Basques share unique genetic patterns that distinguish them from the surrounding non-Basque populations.

Published in the American Journal of Human Genetics, the study was led by Lluis Quintana-Murci, principal investigator of Genographic's Western European regional center. “Our study mirrors European history and could certainly extend to other European peoples. We found that Basques share common genetic features with other European populations, but at the same time present some autochthonous (local) lineages that make them unique,” said Quintana-Murci. “This is reflected in their language, Euskara, a non-Indo-European language, which altogether contributes to the cultural richness of this European population.”
The genetic finding parallels previous studies of the Basque language, which has been found to be a linguistic isolate, unrelated to any other language in the world. It is the ancestral language of the Basque people who inhabit a region spanning northeastern Spain and southwestern France and has long been thought to trace back to the languages spoken in Europe prior to the arrival of the Indo-European languages more than 4,000 years ago. (English, Spanish, French and most other European languages are Indo-European).


BASQUE STUDY - PAGE 2
Genographic Project researchers studied mitochondrial DNA (mtDNA), which has been widely applied to the study of human history and is perhaps best known as the tool used to reveal ‘Mitchondrial Eve,’ the female common ancestor of all modern humans who lived in Africa approximately 200,000 years ago. It has also been used to study regional variation both within and outside Africa, providing detailed insights into more recent migration patterns.

“This Genographic study tells a realistic story of gene and language continuity in a defined region that nevertheless was also subject to repeated gene flow. It is a perfect example of why insisting and persisting on accuracy and the deepest possible phylogenetic analysis is a standard to be followed.   We simply could not detect the signal in a lower level of resolution — it may have even led us to a completely opposite conclusion,” said Dr. Doron Behar, a population geneticist and coauthor of the paper, based in the Rambam Medical Center, Haifa, Israel.

The Genographic Project, launched in 2005, enters its eighth year this spring. Nearly 75,000 participants from over 1,000 indigenous populations around the world have joined the initiative, along with more than 440,000 members of the general public who have purchased a testing kit online, swabbed their cheeks and sent their samples to the Genographic lab for processing. This unprecedented collection of samples and data is a scientific resource that the project plans to leverage moving forward.

Genographic Project Director and National Geographic Explorer-in-Residence Dr. Spencer Wells noted, “The Basque research is a wonderful example of how we are studying the extensive Genographic sample collection using the most advanced genetic methods. In some cases, the most appropriate tool may be mtDNA, while in others the Y-chromosome or autosomal markers may be more informative. Ultimately, the goal of the project is to use the latest genetic technology to understand how our ancestors populated the planet.”

NOTES: To view this publication (http://www.ncbi.nlm.nih.gov/pubmed/22365151) contact American Journal of Human Genetics. The Genographic Project will publish additional publications on the population history of Basques based on mtDNA and Y-chromosome variation in the coming months.


BASQUE STUDY - PAGE 3

Background: The Genographic Project seeks to chart new knowledge about the migratory history of the human species and answer age-old questions surrounding the genetic diversity of humanity. The project is a nonprofit, multi-year, global research partnership of National Geographic and IBM with field support by the Waitt Family Foundation. At the core of the project is a global consortium of 11 regional scientific teams following an ethical and scientific framework and who are responsible for sample collection and analysis in their respective regions. Members of the public can participate in the Genographic Project by purchasing a public participation kit from the Genographic Web site (www.genographic.com), where they can also choose to donate their genetic results to the expanding database. Sales of the kits help fund research and support a Legacy Fund for indigenous and traditional peoples‟ community-led language revitalization and cultural projects.

First published in
https://genographic.nationalgeographic.com/wp-content/uploads/2012/07/Basque-Paradigm-Release-3-6-12-3.pdf
 

 Crusader Y Chromosomes in Lebanon

WASHINGTON (Mar. 27, 2008)—The most comprehensive genetic study yet on the world’s ancient crossroads – Lebanon – reveals the legacies left by travelers to and invaders of Lebanon - showing that the Crusaders left chromosomes as well as castles. The results were obtained by a global team of Genographic scientists, led by Dr. Pierre Zalloua of Lebanese American University, Beirut and Dr. Chris Tyler-Smith of the Wellcome Trust Sanger Institute, Hinxton, near Cambridge, UK.

While all religious communities living in Lebanon carry very similar genetic markers, the new analysis of 926 men from the Christian, Muslim and Druze communities of Lebanon reveals that recent historical migrations had detectable consequences. Lebanese Christian men are more likely to carry genetic signatures found in Europe – and thought to have been carried there by the Crusades; Lebanese Muslim men are more likely to carry genetic signatures deriving from the Muslim expansions of the 7th and 8th centuries. This is one of the few times that scientists have been able to relate distinct genetic patterns to well-documented population movements within a geographic region.

Genographic Associate Researcher Chris Tyler-Smith said: “We are fortunate that the history of Lebanon is so well documented. History gives us a perfect starting point and historians have known about these migrations for centuries. Now we geneticists can detect them as well. It shows how powerful genetics has become and is great news for future studies of places where we don’t know so much about the history.”

The analysis of the Y chromosome, a “genetic surname” specific to men, reveals that Lebanese populations are very closely related, and the novel findings result from a detailed analysis of many more markers and many more people than has been attempted before. However, over the past 1400 years geographically distinct populations from Europe and the Arabian Peninsula have entered Lebanon.

The data revealed several interesting findings. A genetic signature called WES1 that is found only in European populations was found also in Lebanese Christian men. Also, Lebanese Muslim men have very high frequencies of J1, typical of the populations of the Arabian Peninsula that were involved in the Muslim expansion. The study found no impact of the Ottoman expansion from Turkey in the 16th century.

Pierre Zalloua,Genographic Principal Investigator, Middle East/North Africa said: “This is the most careful and comprehensive study of these populations ever undertaken, and it's revealed new insights into the complex history of my country. The subtle effects we have detected are really exciting but should not obscure the extensive underlying similarity among all of the populations of present-day Lebanon, a country that for too long has been divided along religious lines.” The study made use of comparative data from Genographic public participants living in Europe. Over 8,000 people from France, Italy and the UK have now participated – anonymously - in the project, and a subset of their data was used for comparative purposes to track the expansion of these lineages during the time of the Crusades.

Dr Spencer Wells, Genographic Project Director, said: “The massive database that we have assembled from Middle Eastern and European populations, including Genographic public participants, has allowed us to detect the subtle genetic impact of these historical events. This study illustrates the power of large amounts of data, and demonstrates how public participants from around the world can help to decipher historical migratory events.”

Background: The Genographic Project was launched in 2005, by National Geographic and IBM, with field research supported by the Waitt Family Foundation, using genetics as a tool to address anthropological questions on a global scale. At the core of the project is a global consortium of ten regional scientific teams following an ethical and scientific framework and who are responsible for sample collection and analysis in their respective regions. The Project is open to members of the public to participate through purchasing a public participation kit from the Genographic website, where they can also choose to donate their genetic results to the expanding database. Sales of the kits are returned to the research and a Legacy Fund for indigenous peoples’ community-led language revitalization and cultural projects.

Credits:
https://genographic.nationalgeographic.com/wp-content/uploads/2012/12/Crusader-Y-Chromosomes-Lebanon.pdf
 

 Ancient DNA Unravels Europe's Genetic Diversity

Oct. 10, 2013 — Science Daily

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.

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

 


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