New Genetic Research Information Released in India Stirs Controversy With Hindu Nationalists

There's "de Nile," and then there's denial, Denial and racist/bigot DENIAL that refuses to accept reality confirmed by independent evidence from elsewhere. 

From The Atlantic Magazine Online

A Burst of Clues to South Asians’ Genetic Ancestry
 A tiny ear bone from more than 4,000 years ago is shaping the story of migration and heritage in India. 

SARAH ZHANG
September 5, 2019

The climate of South Asia is not kind to ancient DNA. It is hot and it rains. In monsoon season, water seeps into ancient bones in the ground, degrading the old genetic material. So by the time archeologists and geneticists finally got DNA out of a tiny ear bone from a 4,000-plus-year-old skeleton, they had already tried dozens of samples—all from cemeteries of the mysterious Indus Valley civilization, all without any success.

Burial I6113 was the only one that yielded ancient DNA from the Indus Valley civilization.(VASANT SHINDE)

The Indus Valley civilization, also known as the Harappan civilization, flourished 4,000 years ago in what is now India and Pakistan. It surpassed its contemporaries, Mesopotamia and ancient Egypt, in size. Its trade routes stretched thousands of miles. It had agriculture and planned cities and sewage systems. And then, it disappeared. “The Indus Valley civilization has been an enigma for South Asians. We read about it in our textbooks,” says Priya Moorjani, a computational biologist at the University of California at Berkeley. “The end of the civilization was quite mysterious.” No one alive today is sure who the people of the Indus Valley civilization were or where they went.

A pair of newly published papers use ancient DNA to shed light on the Indus Valley civilization and the entire history of people in South and Central Asia. The first study is a sweeping collection of 523 genomes—300 to 12,000 years old—from a region spanned by Iran, Russia, and India. By comparing the results with modern South Asians’ genomes, the study showed that South Asians today descended from a mix of local hunter-gatherers, Iranian-related groups, and steppe pastoralists who came by way of Central Asia. It’s the largest number of ancient genomes reported in a single paper, all made possible by an ancient DNA “factory” the geneticist David Reich has built at Harvard. (Moorjani completed her doctorate in Reich’s lab and is a co-author on this paper.)

The second study focuses on just a single genome from the Indus Valley civilization: I6113, a woman who died more than 4,000 years ago. Her skeleton was the only one—out of more than 100 samples the researchers tested from 10 different Indus Valley–civilization sites—that yielded ancient DNA, but even then it was contaminated and of poor quality. “We had to squeeze, squeeze, squeeze the sample really hard, more than we’ve done in any other sample we’ve ever tried,” says Reich, who is also a senior author of the second paper. The team ultimately tried to sequence DNA from I6113’s ear bone more than 100 times, each time yielding a tiny dribble of genetic data. That I6113 gets her own paper is a testament to both the technical difficulty of sequencing her DNA and the importance of the Indus Valley civilization. Even before publication, rumors were swirling in India about what the ancient DNA would show, and how it would play into the politics of the Hindu-nationalist ruling party.

A Review of What We Know About Ancient Human "Species Interbreeding" (as the scientists call it, what bunk!)

Hola darlings!

A fundamental tenet of biology teaches us that like breeds with like.  As our technology continues to improve and we continue to dig more deeply into our human origins and people aren't afraid to toss off preconceived notions and never stop asking "but what about this? What about that?", I think all the crap some of learned in school (and some people still believe) about "ape men" and the classic Darwinian take on "evolution" is a bunch of baloney.  Now, on to the article at Phys Org - and do try to ignore the silly title:

How a one night stand in the Ice Age affects us all today

October 8, 2015 by Darren Curnoe, The Conversation

Over the past half decade, ancient DNA research has revealed some surprising aspects to our evolutionary history during the past 50,000 years.  Perhaps the most startling of these has been the extent to which the ancestors of living people across the planet interbred with other closely related species of human.

But where in the world did these cross-species matings occur? Which archaic species were involved? Just how much of the human genome comprises DNA from these archaic relatives?And what impact did interbreeding have on our evolution and general biology as a species?

These are questions are the core of current research into interbreeding as revealed by DNA sequences obtained from fossils in Europe and Asia, as well as from comparisons with the genomes of living people.

Genes Reveal History...

... or, more accurately, herstory.  By the way, I would not call rape "hanky panky."  Ahem.

Story at Nature.com
Check out the interactive map and related stories at the linked story. 

Modern genes yield atlas of ancient inter-ethnic sex

Encounters among populations left marks in the DNA of living people.

Daniel Cossins

13 February 2014

From invasions and migrations to slavery and trade, history is embroidered with events that led to interactions between previously separate populations — and, in many cases, hanky-panky. By mining genetic data from living people, researchers have now created a historical atlas of instances of such mixing.

Blue eyes, light hair and fair skin in Pakistan.  Wonder how much she'll be sold for. 
Photo credit: James L. Stanfield/National Geographic Creative

Caption:  The Kalash people who live in the Hindu Kush Mountains of modern Pakistan carry genes that probably originated in Europe and might have been carried East by the Macedonian Army of Alexander the Great.

The study, published today in Science¹, uses statistical methods to make inferences about which populations interbred, and when, over the past 4,000 years. The findings are also presented as an interactive map. The authors sequenced DNA from 1,490 people from 95 genetically distinct populations around the world, and tested almost 500,000 single-letter variations in DNA known as single nucleotide polymorphisms, or SNPs.

New "Archaic" Mystery Humans Uncovered in Latest DNA Genome Sequencing

Heh heh heh :)  I love this!

From Nature Magazine Online:

Mystery humans spiced up ancients’ rampant sex lives

Genome analysis suggests interbreeding between modern humans, Neanderthals, Denisovans and a mysterious archaic population.

• Ewen Callaway

19 November 2013

 

New genome sequences from two extinct human relatives suggest that these ‘archaic’ groups bred with humans and with each other more extensively than was previously known.

 

The ancient genomes, one from a Neanderthal and one from a different archaic human group, the Denisovans, were presented on 18 November at a meeting at the Royal Society in London. They suggest that interbreeding went on between the members of several ancient human-like groups living in Europe and Asia more than 30,000 years ago, including an as-yet unknown human ancestor from Asia.

“What it begins to suggest is that we’re looking at a ‘Lord of the Rings’-type world — that there were many hominid populations,” says Mark Thomas, an evolutionary geneticist at University College London who was at the meeting but was not involved in the work.

The first Neanderthal¹ and the Denisovan² genome sequences revolutionized the study of ancient human history, not least because they showed that these groups interbred with anatomically modern humans, contributing to the genetic diversity of many people alive today. [If their DNA is still extent in modern populations, can it truly be said that Neanderthan and Denisovan are extinct?]

All humans whose ancestry originates outside of Africa owe about 2% of their genome to Neanderthals; and certain populations living in Oceania, such as Papua New Guineans and Australian Aboriginals, got about 4% of their DNA from interbreeding between their ancestors and Denisovans, who are named after the cave in Siberia’s Altai Mountains where they were discovered. The cave contains remains deposited there between 30,000 and 50,000 years ago.

Those conclusions however were based on low-quality genome sequences, riddled with errors and full of gaps, David Reich, an evolutionary geneticist at Harvard Medical School in Boston, Massachusetts said at the meeting. His team, in collaboration with Svante Pääbo at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, have now produced much more complete versions of the Denisovan and Neanderthal genomes — matching the quality of contemporary human genomes. The high-quality Denisovan genome data and new Neanderthal genome both come from bones recovered from Denisova Cave.

The new Denisovan genome indicates that this enigmatic population got around: Reich said at the meeting that they interbred with Neanderthals and with the ancestors of human populations that now live in China and other parts of East Asia, in addition to Oceanic populations, as his team previously reported. Most surprisingly, Reich said, the new genomes indicate that Denisovans interbred with another extinct population of archaic humans that lived in Asia more than 30,000 years ago, which is neither human nor Neanderthal.

The meeting was abuzz with conjecture about the identity of this potentially new population of humans. “We don’t have the faintest idea,” says Chris Stringer, a paleoanthropologist at the London Natural History Museum, who was not involved in the work. He speculates that the population could be related to Homo heidelbergensis, a species that left Africa around half a million years ago and later gave rise to Neanderthals in Europe. “Perhaps it lived on in Asia as well,” Stringer says.

My question:  If their DNA still exists and can be measured in modern populations, can it truly be said that Neanderthal, Denisovan and the "unknown archaic humans" are extinct?

Old Genetic Link Between Mesopotamia and India

Visit Plosone.org for the much more technical (made my eyes cross) original research article:  mtDNA from the Early Bronze Age to the Roman Period Suggests a Genetic Link between the Indian Subcontinent and Mesopotamian Cradle of Civilization

From Past Horizons

Genetic link shown between Indian subcontinent and Mesopotamia

Article created on Thursday, September 26, 2013

The continuing debate regarding the origins of people inhabiting ancient Mesopotamia during the region’s long history led the authors of a new report published in the Open Access journal PLoS ONE to attempt an isolation and analysis of mtDNA sequences from the area.

Distribution of haplogroup L of Y-Chromosome – Possible time of origin 25,000-30,000 years BP. Image. Wikimedia
This image does not seem to have anything to do with the information discussed in this article -- mtDNA haplotypes corresponding to the M4b1, M49 and/or M61 haplogroups, unless the population that contained the "haplogroup L of Y-Chromosome" also contained the particular mtDNA haplotypes discussed in the article.  But for illustrative purposes
to demonstrate the range and relative degree of appearance of a particular haplogroup geographically, it sure is interesting.

Origins of populations

Ancient DNA methodology was applied to analyse sequences extracted from freshly unearthed remains (teeth) of 4 individuals deeply deposited in the slightly alkaline soil of Tell Ashara (ancient Terqa) and Tell Masaikh (ancient Kar-Assurnasirpal) – Syrian archaeological sites, both in the middle Euphrates valley.

Research was also carried out by another team (Sołtysiak et al 2013) examining fifty-nine dental non-metric traits on a sample of teeth from 350 human skeletons excavated at three sites in the lower middle Euphrates valley. This showed a stable population until after the Mongolian invasion which resulted in a large depopulation of northern Mesopotamia in the 13th century CE. The final major change occurred during the 17th century with Bedouin tribes arriving from the Arabian Peninsula.

Difficult procedure

Although it is not possible with DNA analysis to reconstruct the details of an individual’s life, it can provide insights into his/her ancestry. In ideal conditions, the fossil sequences are isolated from remains unearthed in permafrost or temperate regions and only in rare circumstances from skeletal material found in a subtropical arid climate, as it is suspected that the potential is highly limited in such cases.

Thus, only scarce datasets from the Mesopotamia region are available, but using ancient DNA methodology, the team were able to confirm the possibility of isolating amplifiable sequences from the skeletons under just such challenging conditions. In the case of one of the studied specimens the researchers analysed both mtDNA and nuDNA sequences.

Three others were analysed only to confirm their origin on the basis of HVR-I sequence. Studied remains were excavated at two archaeological sites in the middle Euphrates valley and dated between the Early Bronze Age and the Late Roman period (between 2500 BCE and 500 CE).

Origins in the Indian subcontinent

The studied individuals carried mtDNA haplotypes corresponding to the M4b1, M49 and/or M61 haplogroups, which are believed to have arisen in the area of the Indian subcontinent during the Upper Palaeolithic and are absent in people living today in Syria. However, these same haplogroups are present in people inhabiting today’s Tibet, Himalayas, India and Pakistan.

The suggestion is that these analysed remains from Mesopotamia belonged to people with a genetic affinity to the Indian subcontinent as the distribution of identified ancient haplotypes indicates a solid link with populations from the region of South Asia-Tibet (Trans-Himalaya).

This may represent either that the individuals are descendants of migrants from much earlier times (Palaeolithic), spreading the clades of the macrohaplogroup M throughout Eurasia and founding regional Mesopotamian groups like that of Terqa, or they are from merchants moving along trade routes passing near or through the region.

The obtained data has enriched the modest database of Mesopotamian ancient DNA and suggests a possible genetic link of the region with the Indian subcontinent in the past. There are no traces in the modern Syrian population, which is explainable as the dental study showed, by later depopulation and recolonisation, but opens up the possibilities of further work to examine the routes of both populations and civilisations.

PLoS ONE. Genetic link shown between Indian subcontinent and Mesopotamia. Past Horizons. September 26, 2013, from http://www.pasthorizonspr.com/index.php/archives/09/2013/genetic-link-shown-between-indian-subcontinent-and-mesopotamia

DNA Sequencing Possible for Ancient Egyptian Mummies

From Nature.com

Egyptian mummies yield genetic secrets

Next-generation sequencing finds DNA preserved in hot climates.

• Jo Marchant

12 April 2013

 

The ancient Egyptians could soon be getting their genomes sequenced as a matter of routine. That’s the view, at least, of the first researchers to use next-generation techniques to analyse DNA from Egyptian mummies.

 

In a preliminary study that the authors describe as “a first step”, they detected hints of one of the mummies’ ancestral origins, as well as pathogens and a range of plant materials presumably used in the embalming process. The researchers, led by Carsten Pusch, a geneticist at the University of Tübingen in Germany, published their findings last week in the Journal of Applied Genetics¹.

 

Previous studies of DNA from Egyptian mummies have used a technique called polymerase chain reaction (PCR) to amplify specific segments of DNA. But these studies have been controversial. The PCR method is susceptible to contamination with modern DNA, especially when amplifying genes from humans or bacteria that are likely to be present in the environment.

 

DNA degrades relatively quickly in warm conditions, leading to doubts that it would survive for long in the Egyptian desert. For example, a high-profile DNA analysis of 3,300-year-old royal mummies² published by Pusch and his colleagues in 2010 attracted scepticism. But the authors stood by their results, arguing that the embalming process must have preserved the DNA despite the heat.

 

Further support for their argument came in 2011, when researchers amplified DNA from 2,000-year-old mummified crocodile hatchlings³. So researchers on both sides of the debate have been looking forward to the application of next-generation sequencing techniques. Instead of amplifying specific sequences, these methods read millions of small fragments and give a broad picture of all the DNA present in a sample, making it easier to spot contamination.

 

Since 2010, next-generation sequencing has been used to decipher the genomes of a variety of ancient humans preserved in cold conditions, including a 4,000-year-old Palaeo-Eskimo dubbed Saqqaq Man⁴; ‘Denisova Man’, a novel hominin unearthed in Siberia[5]; and ‘Ötzi the Iceman’, a 5,300-year-old mummy found frozen in the Central Eastern Alps⁶.

 

Now, Pusch and his colleagues, including Rabab Khairat, have carried out next-generation sequencing on five Egyptian mummified heads held at the University of Tübingen. The heads date from relatively late in ancient Egyptian history — between 806 bc and 124 ad.

 

The data sets retrieved so far are small — a tiny fraction of what would be required for a whole genome sequence. But they show that human DNA survives in the mummies and that it is amenable to sequencing.

 

The researchers determined that one of the mummified individuals may belong to an ancestral group, or haplogroup, called I2, believed to have originated in Western Asia. They also retrieved genetic material from the pathogens that cause malaria and toxoplasmosis, and from a range of plants that includes fir and pine — both thought to be components of embalming resins — as well as castor, linseed, olive, almond and lotus.

 

According to Pusch, the proportion of human DNA in the identified sequences is comparable to that from frozen specimens, such as Saqqaq Man. In mummies, “DNA preservation appears to be independent of temperature,” he says.

 

But Tom Gilbert, who leads two research groups at the Center for GeoGenetics in Copenhagen and was part of the team that sequenced the Saqqaq genome, warns against making such a comparison, because many of the sequences obtained in the latest study were unidentifiable.

 

Now that Pusch and his colleagues have demonstrated next-generation sequencing in Egyptian mummies, however, moving on to entire genomes “isn’t rocket science”, Gilbert says. “What limits you is the size of a sample. For Denisova Man they had just a finger bone. Here they have the whole mummy.”

 

Indeed, Pusch and his colleagues say that they are now working on a more comprehensive analysis, and that “entire-genome sequencing of ancient Egyptian individuals is likely to become standard in the not-too-distant future”.

 

“It would be nice to know more about the origins of the ancient Egyptians,” says Pusch. “Where did they come from? Where did they go? Are there still traces of ancestral DNA in today’s Egypt?”

Journal name:

Nature

DOI:

doi:10.1038/nature.2013.12793

 

See article for references. 

Sweet Potato DNA Shows Early Polynesian-South America Contact

Oh, those ancient navigators!   Thor Heyderdahl may have had it backwards when he suggested it was travellers from Peru (South America) who settled some of Polynesia, but he showed in 1947 that the trans-Pacific voyage could be done using technology available at the time. 

From sciencemag.org

Clues to Prehistoric Human Exploration Found in Sweet Potato Genome

by Lizzie Wade on 21 January 2013, 3:00 PM

 

Europeans raced across oceans and continents during the Age of Exploration in search of territory and riches. But when they reached the South Pacific, they found they had been beaten there by a more humble traveler: the sweet potato. Now, a new study suggests that the plant's genetics may be the key to unraveling another great age of exploration, one that predated European expansion by several hundred years and remains an anthropological enigma.

 

Humans domesticated the sweet potato in the Peruvian highlands about 8000 years ago, and previous generations of scholars believed that Spanish and Portuguese explorers introduced the crop to Southeast Asia and the Pacific beginning in the 16th century. But in recent years, archaeologists and linguists have accumulated evidence supporting another hypothesis: Premodern Polynesian sailors navigated their sophisticated ships all the way to the west coast of South America and brought the sweet potato back home with them. The oldest carbonized sample of the crop found by archaeologists in the Pacific dates to about 1000 C.E.—nearly 500 years before Columbus's first voyage. What's more, the word for "sweet potato" in many Polynesian languages closely resembles the Quechua word for the plant [linguistic "borrowing"].

 

Studying the genetic lineage of the sweet potato directly has proved difficult, however. European traders exported varieties of sweet potato from Mexico and the Caribbean to the Pacific, and those breeds mixed with the older Polynesian varieties, obscuring their genetic history. Therefore, it's difficult to apply information culled from modern samples to older varieties without a prehistoric control.

 

Now a team of researchers working with France's Centre of Evolutionary and Functional Ecology and CIRAD, a French agricultural research and development center, has identified one such temporal control: sweet potato samples preserved in herbariums assembled by the first European explorers to visit many Polynesian islands. The study, which is published online today in the Proceedings of the National Academy of Sciences, provides strong evidence for prehistoric contact between Polynesia and South America.

 

By analyzing genetic markers specific to sweet potatoes in both modern samples of the plant and older herbarium specimens, the researchers discovered significant differences between varieties found in the western Pacific versus the eastern Pacific. This finding supports the so-called tripartite hypothesis, which argues that the sweet potato was introduced to the region three times: first through premodern contact between Polynesia and South America, then by Spanish traders sailing west from Mexico, and Portuguese traders coming east from the Caribbean. The Spanish and Portuguese varieties ended up in the western Pacific, while the older South American variety dominated in the east, which would explain the genetic differences the French team saw.

 

The decision to analyze herbarium specimens is "innovative" and provides another piece of strong evidence for the tripartite hypothesis, says archaeologist Patrick Kirch, of the University of California, Berkeley, who was not involved in the study. Lead author Caroline Roullier emphasizes that although her genetic analysis alone doesn't prove that premodern Polynesians made contact with South America, it strongly supports the existing archaeological and linguistic evidence pointing to that conclusion. "It's the combination of all different kinds of proof" that's really convincing, she says. Anthropologist Richard Scaglion of the University of Pittsburgh in Pennsylvania agrees, "All the lines of evidence coming together … really strengthens the case" for Polynesian contact with South America.

DNA Proves Romany Originated in NW India or Pakistan

So, the "Gypsies" aren't from ancient Egypt after all.  That blows up a lot of hypotheses favored by some.

European Romani Exodus Began 1,500 Years Ago, DNA Evidence Shows

Dec. 6, 2012 — Despite their modern-day diversity of language, lifestyle, and religion, Europe's widespread Romani population shares a common, if complex, past. It all began in northwestern India about 1,500 years ago, according to a study reported on December 6th in Current Biology, a Cell Press publication, that offers the first genome-wide perspective on Romani origins and demographic history.

The Romani represent the largest minority group in Europe, consisting of approximately 11 million people. That means the size of the Romani population rivals that of several European countries, including Greece, Portugal, and Belgium.

"We were interested in exploring the population history of European Romani because they constitute an important fraction of the European population, but their marginalized situation in many countries also seems to have affected their visibility in scientific studies," said David Comas of the Institut de Biologia Evolutiva at Universitat Pompeu Fabra in Spain.

The Romani people lack written historical records on their origins and dispersal. To fill in the gaps in the new study, Comas and Manfred Kayser from Erasmus University Rotterdam in the Netherlands, together with their international European colleagues, gathered genome-wide data from 13 Romani groups collected across Europe to confirm an Indian origin for European Romani, consistent with earlier linguistic studies.

The genome-wide evidence specified the geographic origin toward the north or northwestern parts of India and provided a date of origin of about 1,500 years ago. While the Middle East and Caucasus regions are known to have had an important influence on Romani language, the researchers saw limited evidence for shared genetic ancestry between the European Romani and those who live in those regions of the world today. Once in Europe, Romani people began settling in various locations, likely spreading across Europe via the Balkan region about 900 years ago.

"From a genome-wide perspective, Romani people share a common and unique history that consists of two elements: the roots in northwestern India and the admixture with non-Romani Europeans accumulating with different magnitudes during the out-of-India migration across Europe," Kayser said. "Our study clearly illustrates that understanding the Romani's genetic legacy is necessary to complete the genetic characterization of Europeans as a whole, with implications for various fields, from human evolution to the health sciences."

Genetic Link Between Native Americans and Europeans

Well of course there is, duh.  We all come from the same stock ultimately.

From Science Daily

Native Americans and Northern Europeans More Closely Related Than Previously Thought

ScienceDaily (Nov. 30, 2012) — Using genetic analyses, scientists have discovered that Northern European populations -- including British, Scandinavians, French, and some Eastern Europeans -- descend from a mixture of two very different ancestral populations, and one of these populations is related to Native Americans. This discovery helps fill gaps in scientific understanding of both Native American and Northern European ancestry, while providing an explanation for some genetic similarities among what would otherwise seem to be very divergent groups.

This research was published in the November 2012 issue of the Genetics Society of America's journal Genetics.

According to Nick Patterson, first author of the report, "There is a genetic link between the paleolithic population of Europe and modern Native Americans. The evidence is that the population that crossed the Bering Strait from Siberia into the Americas more than 15,000 years ago was likely related to the ancient population of Europe."

To make this discovery, Patterson worked with Harvard Medical School Professor of Genetics David Reich and other colleagues to study DNA diversity, and found that one of these ancestral populations was the first farming population of Europe, whose DNA lives on today in relatively unmixed form in Sardinians and the people of the Basque Country, and in at least the Druze population in the Middle East. The other ancestral population is likely to have been the initial hunter-gathering population of Europe. These two populations were very different when they met. Today the hunter-gathering ancestral population of Europe appears to have its closest affinity to people in far Northeastern Siberia and Native Americans.

The statistical tools for analyzing population mixture were developed by Patterson and presented in a systematic way in the report. These tools are the same ones used in previous discoveries showing that Indian populations are admixed between two highly diverged ancestral populations and showing that Neanderthals contributed one to four percent of the ancestry of present-day Europeans. In addition, the paper releases a major new dataset that characterizes genetic diversity in 934 samples from 53 diverse worldwide populations.

"The human genome holds numerous secrets. Not only does it unlock important clues to cure human disease, it also reveal clues to our prehistoric past," said Mark Johnston, Editor-in-Chief of the journal GENETICS. "This relationship between humans separated by the Atlantic Ocean reveals surprising features of the migration patterns of our ancestors, and reinforces the truth that all humans are closely related."

DNA Study Raises More Questins Than It Answers

Link to article:

Extensive DNA Study Sheds Light on Modern Human Origins
September 20, 2012

"The deepest divergence of all living people occurred some 100,000 years ago, well before modern humans migrated out of Africa and about twice as old as the divergences of central African Pygmies and East African hunter-gatherers and from other African groups," says lead author Dr Carina Schlebusch, a Wits University PhD-graduate now conducting post-doctoral research at Uppsala University in Sweden.

Questions:  Does this mean that African Pygmies and the "East African hunter-gatherers and 'other African groups' are not human as we understand the term today?  If they are not human, what are they?

Question:  Does this mean that once this "divergence" of the Khoe and San tribes took place in Africa, no further "evolution" happened?  Are we not all still homo sapiens sapiens, despite thousands of years passing since this "divergence" -- well, except for problem groups like the Pygmies (and let us not forget so-called 'Neanderthal' man, and the mysterious Denisovians)?   Are not Pygmies still Pygmies after even more thousands of years of their assumed "divergence" from whomever they are supposed to have "diverged" from?

Question: What is the difference between genetic drift and "evolution?"

The researchers also looked for signals across the genome of ancient adaptations that happened before the historical separation of the Khoe-San lineage from other humans. "Although all humans today carry similar variants in these genes, the early divergence between Khoe-San and other human groups allowed us to zoom-in on genes that have been fast-evolving in the ancestors of all of us living on the planet today," said Pontus Skoglund from Uppsala University.

Among the strongest candidates were genes involved in skeletal development that may have been crucial in determining the characteristics of anatomically modern humans.

Question:  If in the past certain genes were capable of "fast-evolving" - is this still happening today?  If not, why not?  And, if so, where is the evidence of human beings "evolving" into something - other? 

More on the Deciphering of DNA of Denisovan - Girl!

From BBC News - always so well written!

31 August 2012 Last updated at 02:17 ET

DNA of girl from Denisova cave gives up genetic secrets

By Helen Briggs BBC News

The DNA of a cave girl who lived about 80,000 years ago has been analysed in remarkable detail.

The picture of her genome is as accurate as that of modern day human genomes, and shows she had brown eyes, hair and skin.

The research in Science also sheds new light on the genetic differences between modern humans and their closest extinct relatives.

The cave dweller, a Denisovan, was a cousin of the Neanderthals.

Both groups of ancient humans died out about 30,000 years ago, but have left their mark in the gene pool of modern people.
Shadowy past
The Denisovans have mysterious origins. They appear to have left little behind for palaeontologists save a tiny finger bone and a wisdom tooth found in Siberia's Denisova cave in 2010.

Though some researchers have proposed a possible link between the Denisovans and human fossils from China that have previously been difficult to classify.

A Russian scientist sent a fragment of the bone from Siberia to a team led by Svante Paabo at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany.

He thought it might belong to an early modern human, but the results came as a surprise.

DNA analysis revealed a human who was neither a Neanderthal nor a modern human but the first of a new group of ancient humans.

Gene catalogue

Dr Paabo's team has now sequenced the genome of the Denisovan in much greater depth, using a new technique for studying ancient DNA.

The quality of the genome sequence is similar to that seen in genome studies of modern day humans.

"This is an extinct genome sequence of unprecedented accuracy," said Dr Matthias Meyer, the chief researcher on the study.

"For most of the genome we can even determine the differences between the two sets of chromosomes that the Denisovan girl inherited from her mother and father."

The scientists compared the girl's genome with that of Neanderthals and 11 modern humans from around the world.

This allowed them to catalogue the gene changes that make modern humans different from the two groups of extinct humans that were their closest relatives.

They include changes to only a single DNA letter in several genes involved in the wiring of the brain and nervous system, as well as those that affect the eye and the skin. [Emphasis added].

Dr Paabo said further investigation of changes in genes involved in connecting up the brain will be exciting to pursue.

He told BBC News: "To me the most exciting thing is having a good genome from our very closest extinct relatives which we can now compare ourselves to.

"It's a catalogue of what makes everyone on the planet unique compared with our closest extinct relatives."

The most detailed genetic analysis yet of the Denisovans also confirms that they bred with the ancestors of some people alive today, the researchers said.

It shows that about 3% of the genes of people living today in Papua New Guinea come from Denisovans, with a trace of their DNA lingering in the Han and Dai people from mainland China. [Emphasis added].

The genetic variation of Denisovans was very low, suggesting that although they were found in large parts of Asia their population remained small.


No matter what they say, like breeds with like to produce not only viable but also fertile offspring!  I probably will not live to see it, but someday scientists will inevitably acknowledge that so-called Neanderthal, Denisovan and Modern humans were all grapes from the same vine, making not only reproduction possible, but also producing offspring capable of producing offspring of their own.  That is the key - capable of producing offspring of their own.  Fertility.  I'm thinking that in the final analysis, a lot more DNA resemblance among the three "species" science continues to insist exist in humans will also be found as we get more sophisticated at recognizing an decoding "sequences."  I probably won't live to see that, either.  But there's hope.  There is always hope.

Denisovan Genome Deciphered!

Article at Popular Archaeology:

Archaic Human DNA Reveals its Secrets

Thu, Aug 30, 2012

 

Recently completed research has revealed the complete sequence of the Denisovan genome, the DNA "blueprint" or strands that describe the makeup of a new species of archaic human, fossils of which were first recovered in March, 2010 in a cave in southern Siberia*.

Although the available evidence for testing was slim -- the Denisovan finds have consisted only of a finger bone fragment and two teeth (the test sample itself was derived from the finger bone fragment) -- the researchers were able to develop a means to "unzip" the DNA such that its two strands could be used to generate new molecules for sequencing, permitting the team to determine a very complete genome sequence much like what can be obtained for a modern human genome. [So, basically, they made it up?] They then compared the genome with genomes of modern humans from around the world.

Among the study results, the researchers found that the Denisovans share more genes with individuals from Papua New Guinea than any other population, and that more Denisovan alleles were common with those of Asian and South American populations than European populations. The study authors suggest that the latter reflects interbreeding between modern humans and the Neandertals, who are also related to Neanderthals, rather than direct gene flow from the Denisovans. [What?] In addition, the study reports several other findings: One, that the Denisovan genome contained alleles that correspond to alleles in present-day humans that are associated with dark skin, brown hair and brown eyes; two, that there were a number of genetic changes in modern humans that occurred after the split from the Denisovans; and three, that Denisovan genetic diversity was extremely low, due, they suggest, to a small initial population that grew quickly, without time for genetic diversity to increase to any substantial degree. Along this vain, the authors suggest that if further research shows that the Neanderthal population size changed over time in a similar way, it could mean that a single population expanding out of Africa gave rise to both the Denisovans and Neandertals.

In conclusion, the study team remarks on the general implications of the research results for future endeavors. Reports M. Meyer, et. al.:

By providing a comprehensive catalog of features that became fixed in modern humans after their separation from their closest archaic relatives, this work will eventually lead to a better understanding of the biological differences that existed between the groups. This should ultimately aid in determining how it was that modern humans came to expand dramatically in population size as well as cultural complexity while archaic humans eventually dwindled in numbers and became physically extinct. [1]
 

* In March 2010, scientists announced the discovery of a finger bone fragment of a juvenile female that lived about 41,000 years ago, found in the remote Denisova Cave in the Altai mountains in Siberia, a region also inhabited at about the same time by Neanderthals and perhaps modern humans. Two other bone specimens belonging to different members of the same population have since been found.

[1] "A High-Coverage Genome Sequence from an Archaic Denisovan Individual," by M. Meyer; M. Kircher; M.-T. Gansauge; F. Racimo; K. Prüfer; C. de Filippo; Q. Fu; M. Siebauer; U. Stenzel; J. Dabney; A.M. Andrés; J. Kelso; S. Pääbo at Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. For a complete list of authors, please see the manuscript.

******************************

VAIN?  Are you kidding me?  Are there no longer people who know the difference between VEIN and VAIN?  Holy Goddess! 

Another Mystery Human Shows Up in Fossil Record

Interesting, very interesting...  Of course, scientists persist in their stereotyping use of the term "archaic" when speaking of certain humans.  Really?  This is like the white supremicist discovering he has black Africans in his ancestry.  Oops.  Yeah, there is a River Called De-Nile...

I may have already reported on this and if so, sorry for the duplication.
Genetic Data and Fossil Evidence Tell Differing Tales of Human Origins
By NICHOLAS WADE

Published: July 26, 2012

After decades of digging, paleoanthropologists looking for fossilized human bones have established a reasonably clear picture: Modern humans arose in Africa some 200,000 years ago and all archaic species of humans then disappeared, surviving only outside Africa, as did the Neanderthals in Europe. Geneticists studying DNA now say that, to the contrary, a previously unknown archaic species of human, a cousin of the Neanderthals, may have lingered in Africa until perhaps 25,000 years ago, coexisting with the modern humans and on occasion interbreeding with them.

The geneticists reached this conclusion, reported on Thursday in the journal Cell, after decoding the entire genome of three isolated hunter-gatherer peoples in Africa, hoping to cast light on the origins of modern human evolution. But the finding is regarded skeptically by some paleoanthropologists because of the absence in the fossil record of anything that would support the geneticists’ statistical calculations.
      

Two of the hunter-gatherers in the study, the Hadza and Sandawe of Tanzania, speak click languages and carry ancient DNA lineages that trace to the earliest branchings of the human family tree. The third group is that of the forest-dwelling pygmies of Cameroon, who also have ancient lineages and unusual blood types.

      

The geneticists, led by Joseph Lachance and Sarah A. Tishkoff of the University of Pennsylvania, decoded the entire genomes of five men from each of these groups. The costs of whole-genome sequencing have fallen so much that the technique can now be applied to populations for the first time, said Dr. Tishkoff, who paid the company Complete Genomics around $10,000 for each of the 15 genomes.

      

Among the DNA sequences special to pygmies, Dr. Tishkoff and colleagues found a variant of the usual gene that controls development of the pituitary gland, the source of the hormones that control reproduction and growth. This could be the cause of the pygmies’ short stature and early age of reproduction, the researchers say.

      

The genomes of the pygmies and the Hadza and Sandawe click-speakers contained many short stretches of DNA with highly unusual sequences. Through mutation, the genomes of species that once had a common ancestor grow increasingly unlike one another. Dr. Tishkoff’s team interprets these divergent DNA sequences as genetic remnants of an interbreeding with an archaic species of human. Genetic calculations suggest the interbreeding took place between 20,000 and 80,000 years ago.

      

From calculations of the amount of divergence in the DNA, the geneticists estimate that the archaic species split from the ancestors of modern humans about 1.2 million years ago, about the same time as did the ancestors of the Neanderthals, who dominated Europe during the end of the last ice age.

But the archaic species has a different DNA sequence from that of Neanderthals, whose genome has been reconstructed from DNA surviving in ancient bones, and so may be a sister species, the geneticists say.

      

Inquiries into human origins are on strong ground when genetic data and fossil evidence point in the same direction, but at present geneticists and paleoanthropologists have somewhat different stories to tell. All human fossil remains in Africa for the last 100,000 years, and probably the last 200,000 years, are of modern humans, providing no support for a coexistent archaic species. Another team of geneticists reported in 2010 the finding that Neanderthals had interbred 100,000 years ago with Europeans and Asians, but not Africans. This, too, conflicted with the fossil evidence in implying that modern humans left Africa 100,000 years ago, some 55,000 years before the earliest known fossil evidence of this exodus.

      

In a report still under review, a third group of geneticists says there are signs of Neanderthals having interbred with Asians and East Africans. But Neanderthals were a cold-adapted species that never reached East Africa.

These three claims of interbreeding have opened up a serious discordance between geneticists and paleoanthropologists. For digesting the geneticists’ claims, “sup with a long spoon,” advised Bernard Wood, a paleoanthropologist at George Washington University.

Richard Klein, a paleoanthropologist at Stanford University, said the new claim of archaic and modern human interbreeding “is a further example of the tendency for geneticists to ignore fossil and archaeological evidence, perhaps because they think it can always be molded to fit the genetics after the fact.”

      

Dr. Klein said the claims of interbreeding could be “a methodological artifact” in the statistical assumptions on which the geneticists’ calculations are based. The flaw may come to light when enough inconsistent claims are published. “Meanwhile, I think it’s important to regard such claims skeptically when they are so clearly at odds with the fossil and archaeological records,” he said.

Dr. Tishkoff said that she agreed on the need for caution in making statistical inferences, and that there are other events besides interbreeding, like a piece of DNA getting flipped around the wrong way, that can make a single DNA sequence look ancient. “But when you see it at a genomewide level, it’s harder to explain away,” she said.

      

A co-author, Joshua M. Akey of the University of Washington in Seattle, said he was “reasonably confident that what we are seeing in Africa does represent archaic introgression.” The archaic sequences make up only 2.5 percent of the genomes of the living hunter-gatherers, and there is no evidence that they are being favored by natural selection. They may, therefore, have no effect on a person’s physical form, which could explain why the fossils show little sign of them, Dr. Akey said.

Although all known African fossils are of modern humans, a 13,000-year-old skull from the Iwo Eleru site in Nigeria has certain primitive features. “This might have indicated interbreeding with archaics,” said Chris Stringer, a paleoanthropologist at the Natural History Museum in London. “For half of Africa we really have no fossil record to speak of, so I think it’s quite likely there were surviving archaic forms living alongside modern humans.”

      

Paleoanthropologists like Dr. Klein consider it “irresponsible” of the geneticists to publish genetic findings about human origins without even trying to show how they may fit in with the existing fossil and archaeological evidence. [Why assume they "fit" in?  What if the existing assumptions about what the fossil record allegedly shows is WRONG?] Dr. Akey said he agreed that genetics can provide only part of the story. “But hopefully this is just a period when new discoveries are being made and there hasn’t been enough incubation time to synthesize all the disparities,” he said.

Who Has What at Stake in Keeping Neanderthal an "Ape Man?"

Is this a case of follow the money?  Or follow the academic reputation(s) at stake?  Will the 19th century line of reasoning about where we came from and how we got here take over the top once again?  Or will the 21st century view propelled by new technologies and new views ultimately prevail?

13 August 2012 Last updated at 15:43 ET

Neanderthal breeding idea doubted

By Jonathan Ball BBC News

Similarities between the DNA of modern people and Neanderthals are more likely to have arisen from shared ancestry than interbreeding, a study reports.

That is according to research carried out at the University of Cambridge and published this week in PNAS journal.
Previously, it had been suggested that shared parts of the genomes of these two populations were the result of interbreeding.
However, the newly published research proposes a different explanation.
The origin of modern humans is a hotly debated topic; four main theories have arisen to describe the evolution of Homo sapiens.
All argue for an African origin, but an important distinction in these competing theories is whether or not interbreeding - or "hybridisation" - occurred between Homo sapiens and other members of the genus Homo.
In the current study, Cambridge evolutionary biologists Dr Anders Eriksson and Dr Andrea Manica used computer simulations to reassess the strength of evidence supporting hybridisation events.
They argue that the amount of DNA shared between modern Eurasian humans and Neanderthals - estimated at between 1-4% - can be explained if both arose from a geographically isolated population, most likely in North Africa, which shared a common ancestor around 300-350 thousand years ago.
When modern humans expanded out of Africa, around 60-70,000 years ago, they took that genetic similarity with them.
By contrast, previous ancient DNA studies of Neanderthal remains have shown that their genomes harbour genetic signatures - polymorphisms - that are also seen in the genomes of modern Europeans, East Asians and Oceanians (from Papua New Guinea) but not in modern African populations.
The findings challenged previously held views - based on several lines of evidence - that modern humans had replaced the Neanderthals with little or no gene flow occurring between the two groups.

The observations from the Neanderthal genome led some evolutionary biologists to argue that this genetic similarity had arisen through hybridisation between Neanderthals - already resident in Europe and western Asia - and the ancestors of present-day non-Africans.
Prof David Reich, from Harvard University in Cambridge, US - an exponent of the hybridisation theory - is not convinced that the data represents a powerful argument against interbreeding.
By using methods that are able to differentiate between genetic similarity caused by gene flow via hybridisation vs shared ancestry, he argues that "the patterns observed [in our analyses] are exactly what one would expect from recent gene flow" - a view shared by his collaborator Professor Svante Paabo from the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany.
Prof Reich went on to say that their data shows that Neanderthals and non-Africans last exchanged genetic material 47-65,000 years ago.

DNA v. Fossilized Bones

From The New York Times:

Genetic Data and Fossil Evidence Tell Differing Tales of Human Origins

By NICHOLAS WADE

Published: July 26, 2012

After decades of digging, paleoanthropologists looking for fossilized human bones have established a reasonably clear picture: Modern humans arose in Africa some 200,000 years ago and all archaic species of humans then disappeared, surviving only outside Africa, as did the Neanderthals in Europe. Geneticists studying DNA now say that, to the contrary, a previously unknown archaic species of human, a cousin of the Neanderthals, may have lingered in Africa until perhaps 25,000 years ago, coexisting with the modern humans and on occasion interbreeding with them.

The geneticists reached this conclusion, reported on Thursday in the journal Cell, after decoding the entire genome of three isolated hunter-gatherer peoples in Africa, hoping to cast light on the origins of modern human evolution. But the finding is regarded skeptically by some paleoanthropologists because of the absence in the fossil record of anything that would support the geneticists’ statistical calculations.

Two of the hunter-gatherers in the study, the Hadza and Sandawe of Tanzania, speak click languages and carry ancient DNA lineages that trace to the earliest branchings of the human family tree. The third group is that of the forest-dwelling pygmies of Cameroon, who also have ancient lineages and unusual blood types.

The geneticists, led by Joseph Lachance and Sarah A. Tishkoff of the University of Pennsylvania, decoded the entire genomes of five men from each of these groups. The costs of whole-genome sequencing have fallen so much that the technique can now be applied to populations for the first time, said Dr. Tishkoff, who paid the company Complete Genomics around $10,000 for each of the 15 genomes.

Among the DNA sequences special to pygmies, Dr. Tishkoff and colleagues found a variant of the usual gene that controls development of the pituitary gland, the source of the hormones that control reproduction and growth. This could be the cause of the pygmies’ short stature and early age of reproduction, the researchers say.

The genomes of the pygmies and the Hadza and Sandawe click-speakers contained many short stretches of DNA with highly unusual sequences. Through mutation, the genomes of species that once had a common ancestor grow increasingly unlike one another. Dr. Tishkoff’s team interprets these divergent DNA sequences as genetic remnants of an interbreeding with an archaic species of human. Genetic calculations suggest the interbreeding took place between 20,000 and 80,000 years ago.

From calculations of the amount of divergence in the DNA, the geneticists estimate that the archaic species split from the ancestors of modern humans about 1.2 million years ago, about the same time as did the ancestors of the Neanderthals, who dominated Europe during the end of the last ice age.

But the archaic species has a different DNA sequence from that of Neanderthals, whose genome has been reconstructed from DNA surviving in ancient bones, and so may be a sister species, the geneticists say.

Inquiries into human origins are on strong ground when genetic data and fossil evidence point in the same direction, but at present geneticists and paleoanthropologists have somewhat different stories to tell. All human fossil remains in Africa for the last 100,000 years, and probably the last 200,000 years, are of modern humans, providing no support for a coexistent archaic species. Another team of geneticists reported in 2010 the finding that Neanderthals had interbred 100,000 years ago with Europeans and Asians, but not Africans. This, too, conflicted with the fossil evidence in implying that modern humans left Africa 100,000 years ago, some 55,000 years before the earliest known fossil evidence of this exodus.

In a report still under review, a third group of geneticists says there are signs of Neanderthals having interbred with Asians and East Africans. But Neanderthals were a cold-adapted species that never reached East Africa.

These three claims of interbreeding have opened up a serious discordance between geneticists and paleoanthropologists. For digesting the geneticists’ claims, “sup with a long spoon,” advised Bernard Wood, a paleoanthropologist at George Washington University.

Richard Klein, a paleoanthropologist at Stanford University, said the new claim of archaic and modern human interbreeding “is a further example of the tendency for geneticists to ignore fossil and archaeological evidence, perhaps because they think it can always be molded to fit the genetics after the fact.”

Dr. Klein said the claims of interbreeding could be “a methodological artifact” in the statistical assumptions on which the geneticists’ calculations are based. The flaw may come to light when enough inconsistent claims are published. “Meanwhile, I think it’s important to regard such claims skeptically when they are so clearly at odds with the fossil and archaeological records,” he said.

Dr. Tishkoff said that she agreed on the need for caution in making statistical inferences, and that there are other events besides interbreeding, like a piece of DNA getting flipped around the wrong way, that can make a single DNA sequence look ancient. “But when you see it at a genomewide level, it’s harder to explain away,” she said.

A co-author, Joshua M. Akey of the University of Washington in Seattle, said he was “reasonably confident that what we are seeing in Africa does represent archaic introgression.” The archaic sequences make up only 2.5 percent of the genomes of the living hunter-gatherers, and there is no evidence that they are being favored by natural selection. They may, therefore, have no effect on a person’s physical form, which could explain why the fossils show little sign of them, Dr. Akey said.

Although all known African fossils are of modern humans, a 13,000-year-old skull from the Iwo Eleru site in Nigeria has certain primitive features. “This might have indicated interbreeding with archaics,” said Chris Stringer, a paleoanthropologist at the Natural History Museum in London. “For half of Africa we really have no fossil record to speak of, so I think it’s quite likely there were surviving archaic forms living alongside modern humans.”

Paleoanthropologists like Dr. Klein consider it “irresponsible” of the geneticists to publish genetic findings about human origins without even trying to show how they may fit in with the existing fossil and archaeological evidence. Dr. Akey said he agreed that genetics can provide only part of the story. “But hopefully this is just a period when new discoveries are being made and there hasn’t been enough incubation time to synthesize all the disparities,” he said.

Thirty Founding Mothers of Madagascar!

It's absolutely fascinating what we are learning these days through DNA analysis! 

I had NO idea that Madagascar was settled only about 1200 years ago!  If asked, I would have suggested that since it was so close to the east coast of Africa, and since we know that early man sailed all over the place 50,000 years ago (maybe even further back but 50,000 is the number that is lodged in my memory), that Madagascar had been settled by so-called "modern" humans about the same time they allegedly started trekking "out of Africa" (anywhere from 100,000 to 60,000 years ago).

I find this very interesting. What I would have expected given what is generally accepted as truth regarding evolution and the "out of Africa" thing, is that the "out of Africa" exodus people would have settled Madagascar early on.  It is closer to the eastern coast of Africa than Athens is to Crete, for instance.  So, what were all of those early ancestors of ours doing instead of casting eyes upon a large piece of land so close by (only about 225 miles away from the nearest point off the coast of Africa to Madascar)?  I don't get it. 

We know people were travelling from the Anatolian peninsula (Turkey), the Greek islands, and Egypt to Crete, thousands of years ago -- much earlier than circa 900 CE when the hypothesized shipwreck occurred!  Check out some of these distances between population hot spots back in the "olden days:"

• Approximate distance as the crow flies in miles from Cairo Egypt to Nikolaos Crete Greece is 509 miles or 818.98 Kilometers
• Distance between Athens (Greece) and Crete is 319.78 km.
  This distance is equal to 198.7 miles, and 172.55 nautical miles (island-hopping would make the relative distance longer but would make each individual journey from Athens to island, from island to island, etc., shorter than the shortest distance between two points: Athens to near Heraklion, Crete)
• Approximate distance as the crow flies in miles from Nikolaos Crete Greece to Izmir Turkey is 230 miles or 370.07 Kilometers

So, I can't help but wonder what the full story is.  Is there a reason why humans never settled Madagascar until about 800 CE, evidently only because of a fricking shipwreck of a boatload of women with a few men from Indonesia?  Are you kidding me?  OHMYGODDESS!

Story from Discovery News

Madagascar Founded By Women
The discovery negates a prior theory about how the island was first found.
By Jennifer Viegas
Tue Mar 20, 2012 07:01 PM ET
Madagascar was first settled and founded by approximately 30 women, mostly of Indonesian descent, who may have sailed off course in a wayward vessel 1200 years ago.

The discovery negates a prior theory that a large, planned settlement process took place on the island of Madagascar, located off the east coast of Africa. Traditionally it was thought to have been settled by Indonesian traders moving along the coasts of the Indian Ocean.

Most native Madagascar people today, called Malagasy, can trace their ancestry back to the founding 30 mothers, according to an extensive new DNA study published in the latest Proceedings of the Royal Society B,. Researchers focused on mitochondrial DNA, passed down from mothers to their offspring. Scientists assume some men were with the women.

“I’m afraid this wasn’t a settlement by Amazon seafarers!” lead author Murray Cox told Discovery News. “We propose settlement by a very small group of Indonesian women, around 30, but we also presume from the genetics that there were at least some Indonesian men with them. At this stage, we don’t know how many.”

Cox, a senior lecturer at Massey University’s Institute of Molecular BioSciences, and his colleagues analyzed genetic samples from 2745 individuals hailing from 12 Indonesian archipelago island groups. They then compared the results with genetic information from 266 individuals from three Malagasy ethnic groups: Mikea hunter-gatherers, semi-nomadic Vezo fishermen and the dominant Andriana Merina ethnic group.

Many Malagasy carry a gene tied to Indonesia. The DNA detective work indicates just 30 Indonesian women founded the Malagasy population, with a much smaller biological contribution from Africa. The women may have mated with their male Indonesian travel companions, or with men from Africa. [Well, duh!  Where else would the African DNA have come from?]

“The small number of Indonesian women is consistent with a single boatload of voyagers,” Cox said, adding that “typical Indonesian trading ships in the mid first millennium A.D. could hold around 500 people. “ [Compare the early Indonesian ships to the "high technology" of the day when Columbus set sail with his puny little ships the Nina, Pinta and Santa Maria, nearly 700 years later!]

The distance between Indonesia and Madagascar is close to 5000 miles, so the women and their travel mates must have had quite a journey, especially if it was unintended. 

“The small founder population of Indonesian women makes this scenario fairly unlikely,” Cox said. “Instead, our new evidence favors a small movement of people, and perhaps even an unplanned crossing of the Indian Ocean.” [Or, there is a whopping good story to be told that, unfortunately, we will never know. Perhaps they were a boatload of prostitutes shipped off from some city or other because they were considered "unclean."  The possibilities for dramatic story-telling is endless....]

Scant archaeological evidence, consisting of a few bones marked by stone tools and an increased rate of forest fires, suggests people may have first visited, but not settled, Madagascar around 2000 years ago. Even that is very recent in terms of overall human history.

Madagascar was one of the last places on earth to have been settled, with remote islands like New Zealand, Hawaii and Easter Island being in the short group of places that were settled later -- about 900 years ago.

“Our best argument is that these islands were just extremely difficult to get to,” Cox said.
Matthew Hurles, a senior group leader at the Wellcome Trust Sanger Institute, has also studied the genetic heritage of Madagascar’s native people. He and his team also noted the Indonesian connection.

"Malagasy peoples are a roughly 50:50 mix of two ancestral groups: Indonesians and East Africans,” Hurles said. “It is important to realize that these lineages have intermingled over intervening centuries since settlement, so modern Malagasy have ancestry in both Indonesia and Africa."
Cox concluded, “It is worth emphasizing that Madagascar wasn’t a ‘sealed box’ after its initial settlement. There are notable later contributions by Africans, Arabs and Europeans. All of these contributions show up in the DNA of Malagasy today.”

*****************************************************************

Come on!  The article comes right out and says that the admixtures of different DNA (Africans, Arabs and Europeans) can pretty much be pin-pointed generationally, so why even bring it up?  People of African, Arabic and European descent were showing up at Madagascar at some point AFTER these Indonesian women showed up - or they were there when the Indonesian women arrived.  So, at some point, travel to Madagascar was not impossible!

How difficult could it have been to get to Madagascar from the east coast of Africa, some 225 miles away?  I don't get it!  Is it a tidal thing?  A prevailing wind thing?  Horrible sea monsters devouring all floating vessels that set out toward Madagascar from the east coast of Africa for the past 50,000 years?  WHAT? 

In any event, Hail to the Founding Mothers of Madagascar!  I think someone should start a petition (maybe me) to change the national flag of Madagascar to two breasts and a "delta." 

Another Shot Across the Bow in the DNA Wars!

23 August 2011 Last updated at 19:15 ET
Study deals blow to theory of European origins
By Paul Rincon
Science editor, BBC News website
[Note: The title is wrong. The gist of the article is that this latest research study shows the opposite!]
A new study deals a blow to the idea that most European men are descended from farmers who migrated from the Near East 5,000-10,000 years ago.

The findings challenge previous research showing that the genetic signature of the farmers displaced that of Europe's indigenous hunters. The latest research leans towards the idea that most of Europe's males trace a line of descent to stone-age hunters. But the authors say more work is needed to answer this question.

The study, by an international team, is published in the journal Proceedings of the Royal Society B.
Archaeological finds show that modern humans first settled in Europe from about 40,000 years ago - during a time known as the Palaeolithic. [For convenience, I call these "the first settlers who became Europeans"].

These people survived an Ice Age some 20,000 years ago by retreating to relatively warm refuges in the south of the continent, before expanding into northern Europe again when the ice melted. But just a few thousand years after Europe had been resettled by these hunter-gatherers ['Europeans'], the continent underwent momentous cultural change. Farmers spread westwards from the area that is now Turkey, bringing with them a new economy and way of life. [See my comment below].

The extent to which modern Europeans are descended from these early farmers versus the indigenous hunter-gatherers who settled the continent thousands of years previously is a matter of heated debate. The results vary depending on the genetic markers studied and are subject to differing interpretations. [In other words, our technology is not up to the task of answering the question at present.  A refreshing change from most "scientific" articles that present the latest as the truth, the whole truth, and nothing but the truth!]

Family tree

The latest study focused on the Y chromosome - a package of DNA which is passed down more or less unchanged from father to son.  The Y chromosomes carried by people today can be classified into different types, or lineages, which - to some extent - reflect their geographical origins.

More than 100 million European men carry a type called R-M269, so identifying when this genetic group spread out is vital to understanding the peopling of Europe. R-M269 is most common in western Europe, reaching frequencies of 90% or more in Spain, Ireland and Wales.

But while this type reaches its highest distribution on the Atlantic fringe, Patricia Balaresque and colleagues at the University of Leicester published a paper in 2010 showing that the genetic diversity of R-M269 increases as one moves east - reaching a peak in Anatolia (modern Turkey). [Hmm...]

Genetic diversity is used as a measure of age; lineages that have been around for a long time accumulate more diversity. So this principle can be used to estimate the age of a population. [A clear and concise statement that diametrically opposes at least one other statement in an article discussing a DNA study that said diversity decreases in a given population over time.  That was so counter-intuitive to general principles of logic that I wrote to Mr. Don about it and asked him to read the article and see what he thought - and if I was just reading it wrong.  He read the article and agreed with me.  But tonight, I'm tired and I'm not going to go digging around in old archived emails to find the specific email and article!]

When the Leicester team estimated how old R-M269 was in different populations across Europe, they found the age ranges were more compatible with an expansion in Neolithic times (between 5,000 and 10,000 years ago). [In other words, some people from the Middle East followed their idea of 'farming' into the West some several thousands of years after that idea had already been spread - by whatever means - into Europe, beginning with "Old Europe" and eventually spreading westward all the way to the edges of 'Europe.']

The team's conclusions received support from papers published in August 2010 and in June this year. But one study which appeared last year backed the idea of a more ancient, Palaeolithic origin for R-M269.

Age estimates

Now, a team including Cristian Capelli and George Busby at Oxford University have explored the question.

Their results, based on a sample of more than 4,500 men from Europe and western Asia, showed no geographical trends in the diversity of R-M269. Such trends would be expected if the lineage had expanded from Anatolia with Neolithic farmers.

Furthermore, they suggest that some of the markers on the Y chromosome are less reliable than others for estimating the ages of genetic lineages. On these grounds, they argue that current analytical tools are unsuitable for dating the expansion of R-M269. [Damn right. If I'm reading this correctly, 50% of the most current research says "they came from the Middle East" and 50% of the research says "nope, they were "always" here. LOL!]

Indeed, Dr Capelli and his team say the problem extends to other studies of Y-chromosome lineages: dates based on the analysis of conventional DNA markers may have been "systematically underestimated", they write in Proceedings B.

But Dr Capelli stressed that his study could not answer the question of when the ubiquitous R-M269 expanded in Europe, although his lab is carrying out more work on the subject.

"At the moment it's not possible to claim anything about the age of this lineage," he told BBC News, "I would say that we are putting the ball back in the middle of the field."

Co-author Dr Jim Wilson from the University of Edinburgh explained: "Estimating a date at which an ancestral lineage originated is an interesting application of genetics, but unfortunately it is beset with difficulties."

The increasing frequency of R-M269 towards western Europe had long been seen by some researchers as an indication that Palaeolithic European genes survived in this region - alongside other clues.

A more recent origin for R-M269 than the Neolithic is also possible. But researchers point out that after the advent of agriculture, populations in Europe exploded, meaning that it would have been more difficult for incoming migrants to displace local people.

Study of Horse Domestication Focuses on Y Chromosome

Interesting press release - but please, give it to me in "layman's English" next time, heh?

Public release date: 23-Aug-2011
Contact: David Garner
University of York

Ancient wild horses help unlock past

An international team of researchers has used ancient DNA to produce compelling evidence that the lack of genetic diversity in modern stallions is the result of the domestication process.

The team, which was led by Professor Michi Hofreiter from the University of York, UK, has carried out the first study on Y chromosomal DNA sequences from extinct ancient wild horses and found an abundance of diversity.

The results, which are published in Nature Communications, suggest the almost complete absence of genetic diversity in modern male horses is not based on properties intrinsic to wild horses, but on the domestication process itself.

Professor Hofreiter said: "Unlike modern female domestic horses where there is plenty of diversity, genetic diversity in male horses is practically zero.

"One hypothesis to explain this suggests modern horses have little Y chromosome diversity because the wild horses from which they were domesticated were also not diverse, due in part to the harem mating system in horses, implying skewed reproductive success of males. Our results reject this hypothesis as the Y chromosome diversity in ancient wild horses is high. Instead our results suggest that the lack of genetic diversity in modern horses is a direct consequence of the domestication process itself."

The Y chromosome is a valuable tool in population genetics, providing a means of directly assessing evolutionary processes that only affect the paternal lineage. So far mitochondrial DNA studies have failed to discover the origin of domestic horses. However, these new Y chromosomal markers now open the possibility of solving this issue in detail.

As part of the study, researchers sequenced Y chromosomal DNA from eight ancient wild horses dating back from around 15,000 to more than 47,000 years and a 2,800-year-old domesticated horse. The results were compared to DNA sequences from Przewalski horses - the only surviving wild horse population – and 52 domestic horses, representing 15 modern breeds, which had been sequenced previously.

Domestication of horses dates back approximately 5,500 years. DNA from the skeletal remains of a 2,800-year-old domesticated stallion from Siberia showed that in contrast to modern horses, Y chromosomal diversity still existed several thousand years after the initial domestication event for horses.

Professor Hofreiter said: "This suggests some level of Y chromosomal diversity still existed in domestic horses several thousand years after domestication, although the lineage identified was closely related to the modern domestic lineage."

The study was carried out in Germany by Sebastian Lippold, from the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. The results were then independently replicated at the Centre for GeoGenetics at Copenhagen University, Denmark.

Sebastian Lippold said: "Working on ancient Y chromosomal DNA was especially challenging but the only opportunity to investigate Y chromosomal diversity in wild horses. For now we have a first idea of ancestral diversity and therefore a better impression of how much diversity has been lost. Basically this was an important first step and points to the potential the Y chromosomal marker could have in order to further investigate domestication history in horses."

Beth Shapiro, an Assistant Professor in the Department of Biology at the Pennsylvania State University, USA, carried out the analysis and interpretation.

She said: "Most ancient DNA research until now has focused on a different part of the genome – the mitochondrion – which is much more abundant in cells and therefore much easier to work with when the DNA is degraded. This has been a serious limitation in ancient DNA research, because we generally only have a good idea what happened along the maternal line. Here, we've been able to look at what happened along the paternal lineage, and, probably unsurprisingly, we see something different going on in males than in females.

"This is exciting stuff, and means we can start getting a much better picture of how events like domestication and climate change have shaped the diversity of organisms alive today."

Researchers had found that Przewalski's horse displays DNA haplotypes not present in modern domestic horses, suggesting they are not ancestral to modern domestic horses. However, while the Y chromosome data supported historic isolation, it also suggests a close evolutionary relationship between the domestic horse and the Przewalski's horse, since the Przewalski Y chromosomal haplotype is more similar to the two domestic ones than any of the ancient wild horse haplotypes.

So, does the last sentence indicate that there is or are one or more at present unknown ancestors between the domestic horse and Przewalski's horse? And if that is indeed the case, why didn't they just say so? Perhaps this all make sense to people schooled in the field, but to the average person interested in ancient and not-so-ancient history and other related subjects, it's like trying to read the Cyrillic alphebet (in other words, nearly impossible without a road map and much labor translating from "techno-speak" into plain understandable English words.)