Sequencing of Neanderthal Toe Bone Reveals Unknown Hominin Line

This week, in the journal Nature, scientists reported on the full sequencing of a Neanderthal toe bone found in the Denisova Cave in the Altai Mountains, the location where the Denisovan skeleton found in 2008 and sequenced earlier this year was also found.

The abstract of the paper, which is behind a paywall, says:

We present a high-quality genome sequence of a Neanderthal woman from Siberia. We show that her parents were related at the level of half-siblings and that mating among close relatives was common among her recent ancestors. We also sequenced the genome of a Neanderthal from the Caucasus to low coverage. An analysis of the relationships and population history of available archaic genomes and 25 present-day human genomes shows that several gene flow events occurred among Neanderthals, Denisovans and early modern humans, possibly including gene flow into Denisovans from an unknown archaic group. Thus, interbreeding, albeit of low magnitude, occurred among many hominin groups in the Late Pleistocene. In addition, the high-quality Neanderthal genome allows us to establish a definitive list of substitutions that became fixed in modern humans after their separation from the ancestors of Neanderthals and Denisovans.

The abstract also includes this graphic from the paper

Neanderthal 12-22-2013 cropped

This sequence is significant because of a number of unique findings.

  1. The skeleton showed physical traits of both Neanderthals and modern humans and is thought to be about 50,000 years old.
  2. Genetic sequencing revealed that this bone belonged to a Neanderthal woman, not a Denisovan, although other Denisovan remains, including one previously sequenced, have been found in this cave.
  3. The closest genetic relative is found in the Mezmaiskaya Cave in the Caucasus Mountains, some 2000+ miles distant.  Admittedly, we don’t have a lot of sequenced remains for comparison.
  4. Sequencing revealed a heretofore unknown genetic line of archaic humans.  This person obtained from between 2.7 to 5.8 percent of their genome from this unknown line. That percentage is equal to someplace between a great-great-great-grandparent and a great-great-great-great-great-grandparent, assuming only one ancestor was involved.  If this unknown human lineage was admixed into the population in multiple individuals, then the trace amounts could be passed around forever, just like the Neanderthal and Denisovan lineages are in Europeans today.
  5. This unknown line could be homo erectus.
  6. There is no evidence that this unknown human lineage interbred with either modern humans or Neanderthals.  I would presume this means that this unknown line then bred with the Denisovan group which did not manifest itself in contemporary humans.
  7. This individual was inbred with their parents being closely related, possibly half-siblings or an uncle and niece, or an aunt and nephew or a grandfather and granddaughter or grandmother and grandson.  Inbreeding was also common among the woman’s recent ancestors.  Another article headline this week pronounced that “Neanderthals Liked Incest” which I found to be offensive.  Incest is a highly negatively charged cultural word.  In the not so recent past, the practice of inbreeding was perfectly acceptable in European royalty.  Furthermore, we have no idea how these people felt about inbreeding, hence the word “liked” is misleading.  It could well be that they lived in a small nuclear family group and there were no other choices for partners.  There could also be other cultural and selection factors at play here of which we are unaware.  For example, perhaps males were more protective of mothers and children to whom they were related than ones where they had no family or group ties – increasing the likelihood of survival of offspring of women to whom the males were related.
  8. At least half of a percent of the Denisovan genome came from Neanderthals, but none of the Denisovan genome has yet been detected in Neanderthals.  If this holds, it would imply that our ancestors either bred with Neanderthals and Denisovans separately, or with Denisovans who carried Neanderthal DNA.  Given that most Europeans carry more Neanderthal DNA than Denisovan, the second scenario alone is unlikely.  It’s also possible that we simply haven’t found Neanderthal’s who did carry Denisovan DNA.
  9. More than 31,000 differences were found between modern humans and Neanderthals and Denisovans, many having to do with brain development.

Dienekes discussed this research in his blog as well.  Note his “family tree.”

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Neuroarchaeologists Uncover Iberian Origin of Unusual Alzheimer’s Gene Mutation

Alzheimers in IberiaNeuroarchaeologists, a term I haven’t heard before, but one we’ll likely hear into the future.  Genetics, neurology, genealogy, population genetics….they are all becoming intermixed today solving puzzles that are so complex that just a few years ago, there would have been no prayer of solving them at all.

Take early onset Alzheimers, for example.  Keep in mind that this type of Alzheimer’s is only one of several, and much about this disease remains unknown, but for this particular kind of Alzheimer’s disease, this breakthrough is monumental, as is the fact that they can trace it to the Iberian peninsula in the 16th century.

The history of our ancestors truly is in our genes.

This research was performed at the University of California at Santa Barbara and published this month in Alzheimer’s and Dementia, the Journal of the Alzheimer’s Association.  Unfortunately, the academic article is behind a paywall.

Researchers tested more than 100 family members who have the disease.  While many predictably showed onset signs of the disease as expected about age 45, some appeared to be protected by as much as a decade.  The question was what was protecting these people and does that protective mechanism have relevance for the rest of the people afflicted by Alzheimer’s disease.  The answer isn’t yet evident, and research continues, but the process they used to identify this mutation is fascinating.

The team worked with historians and genealogists and using records as old as 1540, managed to track this family, along with their mutation, to a single individual from the Iberian peninsula about the time that Spanish Conquistadors were colonizing Columbia in the early 1500s.

They may call this new field neuroarchaeology, but I think it’s more neurogenealogy, unless they’re excavating graves someplace.  But I bet they think neuroarchaeology just sounds more scientific.  So, want to get assistance with your genealogy….having a dread disease, or being a politician….either one will help immensely.

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400,000 Year Old DNA from Spain Sequenced

Atapuerca Cave Remains

Talk about record shattering.  400,000 year old DNA has now been sequenced, and that quite handily breaks the previous 100,000 year old record.  The only problem is that these ancient and archaic people weren’t staying where they were supposed to.  Well, that’s “supposed to” according to the story we thought we knew.  Obviously, we didn’t know, and ancient DNA is only beginning to tell the story, which isn’t at all like we thought it would be.

Before now, Neanderthals were thought to have settled in the west, meaning Europe primarily, and Denisovans in the East, in Siberia.  This is due to where bones have been found and the DNA sequenced from just a few.  However, this new find from a cave in Atapuerca, Spain changes all of that.  These people were not closely related to Neanderthal, who were later found in Germany, but instead are related to the Denisovans, their remains found some 4000 miles east, per mitochondrial DNA, meaning their direct matrilineal line.  However, even though they are related, they are distantly related.

Yesterday the mitochondrial sequence appeared on GenBank, after the release of the paper.  According to Ian Logan, this new sequence has just over 500 mutations, about half of which can be matched with Denisovan and the other half are unique.  So while the Denisovan and this new sequence do share a maternal ancestor, they are many, many generations distant.  Of course, that would be expected, because they are about 350,000 years apart too in terms of time, or a meager 14,000 generations.

What does this mean?  The scientists don’t know for sure.  Perhaps these Atapuerca Cave people were the ancestors of Denisovans and Neanderthals.  Perhaps the Denisovan mitochondrial DNA “washed out” over generations in the Neanderthal or maybe not enough Neanderthal remains have been located and sequenced.  Neither Neanderthal nor Denisovan mitochondrial DNA has been found in any living humans or relatively contemporary burials, meaning not outside of Neanderthals and Denisovans.  In short, we need more skeletons and more DNA to reveal more information about our ancient ancestors.  It opens the possibility that modern humans are but a small sprig on the larger and quite ancient Denisovan/Neanderthal Eurasian tree.  We don’t know where modern humans fit in all of this, but according to autosomal genetic results, everyone with either European or Asian heritage carries some of them in all of us, just not the mitochondrial line.  We are just beginning this journey of discovery.

For more, access the Science article, Dienekes Anthrolpology Blog and John Hawks blog.  The academic article in Nature, A mitochondrial genome sequence of a hominin from Sima de los Huesos, by Meyer et all is behind a paywall.

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Watson, Crick and Spotted Dick

dna 1953

In September, 2013, my husband, Jim, and I visited the British Isles.  This trip was planned around various aspects of genealogy and family history – all of which pertain to and were enabled by DNA.  I’m going to be sharing portions with you over the next several weeks.  These stories will all include DNA, but I’m also going to share other photos with you.  The culture, so different from ours, is critically important to understanding our ancestors and these areas are simply beautiful.  I’d like to share the entire experience, not just the DNA piece.  So I’m inviting you along on my day in London.  Come on….we’ll have fun!

I didn’t plan my trip to England with Watson and Crick’s DNA model in mind – that part just kind of evolved, a positive mutation, so to speak.

Jim and I traveled with a family group that indeed did make this trip as a result of DNA – but that is another story for another article, several, in fact.  In any case, we weren’t really in charge of where we were staying in London – the tour company took care of fanthat – supposedly.  That is a long and sorry saga which I’ll spare you.  Let’s just say we weren’t staying at the hotel where we were SUPPOSED to have reservations and the one where we were staying didn’t have air conditioning.  It was “broken.”  It should have been an aha moment when they handed me a fan when we checked in.  At least they did that much.  It was very hot.

Suffice it to say, we were close to Hyde Park and Kensington Gardens in London.  The idea was that we could take a walk in the park if we wanted to.  Flowers often grace every nook and cranny in Europe and the thought of walking and viewing was quite enticing to me.  Here is a rose garden in front of a private home near Hyde Park. Just lovely.

London rose garden

The London subway is a bit overwhelming, but it really a good transportation system once you get used to it.  You can get places far more quickly by subway than by car on the surface streets.

london subway

Still, you stand a high probability of getting lost, at least initially, and it’s pretty intimidating.  So we opted to walk when we could.  Plus, you get to see a lot more of the area that way.  After all, it’s not always the destination.  Sometimes, it’s about the journey.

Before we left for London, I searched for the location of the double helix model created by Watson and Crick in 1953 when they discovered DNA.  I found that it is in the British Science Museum.

After arrival in London, looking at the map, I discovered that the Science Museum was just on the other side of Hyde Park.  I asked and was told that it’s about a 10 minute walk.  Have I mentioned never to believe a British person about distances???  It must be genetic – they seem to have a distance judgment impairment gene!

Jim and I set out to walk to the Museum because it seemed like a much better option than three different subway transfers.  And after all, it was only 10 minutes away and only drizzling.

Me hyde park

We cut across the park and enjoyed the walk and found the museums, further away than we thought, of course.  We discovered we were walking on the Princess Diana Memorial walkway, and only after we got home and looked at the photo did I realize that Kensington Palace is behind me.

British parks and gardens are really quite remarkable.  There are a lot of them and they have beautiful statues and flowers. This statue is of Prince Albert.

prince albert

Half an hour or 45 minutes later, we arrived at the Science Museum.  It’s quite large, and we asked where the DNA exhibit was located, received directions, and off we went.  We were pleased to see that they had an entire exhibit area devoted not to DNA but to what makes people unique.  Of course DNA had a prominent position in that exhibit.

dna book

The “books of genes” shown above and below is actually the top back of a seat in the museum exhibit.

dna seat

But we were unable to find the Watson/Crick model.  We asked a second time and the guard told us that it was downstairs “by the autos.”  We had just come through that area and we didn’t quite believe it would be there, but since it wasn’t where we were, we went to look.  Sure enough, in with the 1950s cars and the earliest computers, in a display case but not near anything else similar, we found the double helix model with only a small display description.  In fact, we had walked right past it earlier and didn’t notice it because where it is located and how it is displayed is so nondescript.

dna sign

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The helix model itself is kind of difficult to see because it’s small and kind of thin and in the middle of a case with glass on all sides.  Jim is trying to get a good picture, but that is almost impossible between its position and the glass and lighting.

Crick Watson Jim

The model is constructed using clamps.

Crick Watson closeup

It’s actually difficult to see because the aluminum templates, shown below (wiki photo) are on a flat plane so they are being photographed sideways.

DNA model leaves

I was thrilled to see the model, but saddened that it has been relegated to the section of “vintage cars” when it was the discovery that fueled many of the life-changing medical discoveries of the past few years and nearly everything in the exhibit we had just seen about what makes people unique.  If not DNA, then what?

The Crick/Watson double helix model should be the crown jewel of these types of exhibits, not relegated to a place in the footnotes of the 1950s.

The model itself is elegant in that its simplicity belies the complexity of DNA.  Yet, that complexity is comprised of simplest of elements combined in the simplest of manners.  It’s hard to believe sometimes that we are looking at the recipe for reproduction, for all of life itself.

Here are Crick and Watson with the model.

crick watson with model

Of course, we walked back to our hotel, but we took a bit of a different route, past both sets of palace gates (below) and up some side streets.

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Glory be, we also found a Starbucks!!  We discovered a beautiful old church on Kensington High Street and slipped into the courtyard which is also the cemetery.

church high kensington

It’s hard to believe that just a few feet away on the other side of the fence the London traffic and hustle and bustle are in full force.

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This courtyard is a tiny haven of tranquility. Of course, I had to look at the stones to see if there were any familiar names.  After all, some of my ancestors were here – however, they weren’t wealthy enough to have stones in churchyards.

Some things have no equivalent here.

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Humps, in case you are wondering, are speed bumps.  The even more interesting sign was the one that had a picture of two humps, side by side, on the same sign.

We passed this lovely pub that is just so quintessentially English and so beautiful.  Surely looks inviting doesn’t it.  Want to have an ale???

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That evening, we met up with my cousins from New Zealand (more about that later) in The Swan Pub, a very quaint and very English old coaching pub across from Hyde Park, and had an English dinner of what else, fish and chips.

But that wasn’t the end of the adventures.  Nosiree….there was what we term as  “adventure eating” left to be done.  There was Spotted Dick on the dessert menu.  Yes, we did, we had to order that and try some.  Here’s Jim getting ready to try Spotted Dick.  Looks kind of apprehensive doesn’t he.  I must admit, it was very, very good.

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I hope you’ve enjoyed coming along with me on my day in London visiting Watson, Crick and Spotted Dick.

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Disclosure

I receive a small contribution when you click on some of the links to vendors in my articles. This does NOT increase the price you pay but helps me to keep the lights on and this informational blog free for everyone. Please click on the links in the articles or to the vendors below if you are purchasing products or DNA testing.

Thank you so much.

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Native American Gene Flow – Europe?, Asia and the Americas

Pre-release information from the paper, “Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans” which included results and analysis of DNA sequencing of 24,000 year old skeletal remains of a 4 year old Siberian boy caused quite a stir.  Unfortunately, it was also misconstrued and incorrectly extrapolated in some articles.  Some people misunderstood, either unintentionally or intentionally, and suggested that people with haplogroups U and R are Native American.  That is not what either the prerelease or the paper itself says.  Not only is that information and interpretation incorrect, the paper itself with the detailed information wasn’t published until November 20th, in Nature.

The paper is currently behind a paywall, so I’m going to discuss parts of it here, along with some additional information from other sources.  To help with geography, the following google map shows the following locations: A=the Altai Republic, in Russia, B=Mal’ta, the location of the 24,000 year old skeletal remains and C=Lake Baikal, the region from where the Native American population originated in Asia.

native flow map

Nature did publish an article preview.  That information is in bold, italics and I will be commenting in nonbold, nonitalics.

The origins of the First Americans remain contentious. Although Native Americans seem to be genetically most closely related to east Asians1, 2, 3, there is no consensus with regard to which specific Old World populations they are closest to4, 5, 6, 7, 8. Here we sequence the draft genome of an approximately 24,000-year-old individual (MA-1), from Mal’ta in south-central Siberia9, to an average depth of 1×. To our knowledge this is the oldest anatomically modern human genome reported to date.

Within the paper, the authors also compare the MA-1 sequence to that of another 40,000 year old individual from Tianyuan Cave, China whose genome has been partially sequenced.  This Chinese individual has been shown to be ancestral to both modern-day Asians and Native Americans.  This comparison was particularly useful, because it showed that MA-1 is not closely related to the Tianyuan Cave individual, and is more closely related to Native Americans.  This means that MA-1’s line and Tianyuan Cave’s line had not yet met and admixed into the population that would become the Native Americans.  That occurred sometime later than 24,000 years ago and probably before crossing Beringia into North America sometime between about 18,000 and 20,000 years ago.

The MA-1 mitochondrial genome belongs to haplogroup U, which has also been found at high frequency among Upper Palaeolithic and Mesolithic European hunter-gatherers10, 11, 12, and the Y chromosome of MA-1 is basal to modern-day western Eurasians and near the root of most Native American lineages5.

The paper goes on to say that MA-1 is a member of mitochondrial (maternal) haplogroup U, very near the base of that haplogroup, but without affiliation to any known subclade, implying either that the subclade is rare or extinct in modern populations.  In other words, this particular line of haplogroup U has NOT been found in any population, anyplace.  According to the landmark paper,  “A ‘‘Copernican’’ Reassessment of the Human Mitochondrial DNA Tree from its Root,” by Behar et al, 2012, haplogroup U itself was born about 46,500 years ago (plus or minus 3.200 years) and today has 9 major subclades (plus haplogroup K) and about 300 branching clades from those 9 subclades, excluding haplogroup K.

The map below, from the supplemental material included with the paper shows the distribution of haplogroup U, the black dots showing locations of haplogroup U comparison DNA.

Native flow Hap U map

In a recent paper, “Ancient DNA Reveals Key Stages in the Formation of Central European Mitochondrial Genetic Diversity” by Brandt et al (including the National Geographic Consortium) released in October 2013, the authors report that in the 198 ancient DNA samples collected from 25 German sites and compared to almost 68,000 current results, all of the ancient Hunter-Gatherer cultural results were haplogroup U, U4, U5 and U8.  No other haplogroups were represented.  In addition, those haplogroups disappeared from the region entirely with the advent of farming, shown on the chart below.

Native flow Brandt map

So, if someone who carries haplogroup U wants to say that they are distantly related to MA-1 who lived 24,000 years ago who was also related to their common ancestor who lived sometime prior to that, between 24,000 and 50,000 years ago, probably someplace between the Middle East where U was born, Mal’ta, Siberia and Western Europe, they would be correct.  They are also distantly related to every other person in the world who carries haplogroup U, and many much more closely that MA-1 whose mitochondrial DNA line is either rare as chicken’s teeth (i.e. never found) or has gone extinct.

Let me be very clear about this, there is no evidence, none, that mitochondrial haplogroup U is found in the Native American population today that is NOT a result of post-contact admixture.  In other words, in the burials that have been DNA tested, there is not one example in either North or South America of a burial carrying mitochondrial haplogroup U, or for that matter, male Y haplogroup R.  Native American haplogroups found in the Americas remain subsets of mitochondrial haplogroups A, B, C, D and X and Y DNA haplogroups C and Q.  Mitochondrial haplogroup M has potentially been found in one Canadian burial.  No other haplogroups have been found.  Until pre-contact remains are found with base haplogroups other than the ones listed above, no one can ethically claim that other haplogroups are of Native American origin.  Finding any haplogroup in a contemporary Native population does not mean that it was originally Native, or that it should be counted as such.  Admixture and adoption have been commonplace since Europeans first set foot on the soil of the Americas. 

Now let’s talk about the Y DNA of MA-1.

The authors state that MA-1’s results are found very near the base of haplogroup R.  They note that the sister lineage of haplogroup R, haplogroup Q, is the most common haplogroup in Native Americans and that the closest Eurasian Q results to Native Americans come from the Altai region.

The testing of the MA-1 Y chromosome was much more extensive than the typical STR genealogy tests taken by consumers today.  MA-1’s Y chromosome was sequenced at 5.8 million base pairs at a coverage of 1.5X.

The resulting haplotree is shown below, again from the supplementary material.

Native flow R tree

 native flow r tree text

The current haplogroup distribution range for haplogroup R is shown below, again with comparison points as black dots.

Native flow R map

The current distribution range for Eurasian haplogroup Q is shown on the map below.  Haplogroup Q is the most common haplogroup in Native Americans.

Native flow Q map

Similarly, we find autosomal evidence that MA-1 is basal to modern-day western Eurasians and genetically closely related to modern-day Native Americans, with no close affinity to east Asians. This suggests that populations related to contemporary western Eurasians had a more north-easterly distribution 24,000 years ago than commonly thought. Furthermore, we estimate that 14 to 38% of Native American ancestry may originate through gene flow from this ancient population. This is likely to have occurred after the divergence of Native American ancestors from east Asian ancestors, but before the diversification of Native American populations in the New World. Gene flow from the MA-1 lineage into Native American ancestors could explain why several crania from the First Americans have been reported as bearing morphological characteristics that do not resemble those of east Asians2, 13.

Kennewick Man is probably the most famous of the skeletal remains that don’t neatly fit into their preconceived box.  Kennewick man was discovered on the bank of the Columbia River in Kennewick, Washington in 1996 and is believed to be from 7300 to 7600 years old.  His anatomical features were quite different from today’s Native Americans and his relationship to ancient people is unknown.  An initial evaluation and a 2010 reevaluation of Kennewick Man let to the conclusion by Doug Owsley, a forensic anthropologist, that Kennewick Man most closely resembles the Ainu people of Japan who themselves are a bit of an enigma, appearing much more Caucasoid than Asian.  Unfortunately, DNA sequencing of Kennewick Man originally was ussuccessful and now, due to ongoing legal issues, more technologically advanced DNA testing has not been allowed.  Nova sponsored a facial reconstruction of Kennewick Man which you can see here.

Sequencing of another south-central Siberian, Afontova Gora-2 dating to approximately 17,000 years ago14, revealed similar autosomal genetic signatures as MA-1, suggesting that the region was continuously occupied by humans throughout the Last Glacial Maximum. Our findings reveal that western Eurasian genetic signatures in modern-day Native Americans derive not only from post-Columbian admixture, as commonly thought, but also from a mixed ancestry of the First Americans.

In addition to the sequencing they set forth above, the authors compared the phenotype information obtainable from MA-1 to the Tyrolean Iceman, typically called Otzi.  You can see Otzi’s facial reconstruction along with more information here.  This is particularly interesting in light of the pigmentation change from darker skin in Africa to lighter skin in Eurasia, and the question of when this appearance change occurred.  MA-1 shows a genetic affinity with the contemporary people of northern Europe, the population today with the highest frequency of light pigmentation phenotypes.  The authors compared the DNA of MA-1 with a set of 124 SNPs identified in 2001 by Cerquira as informative on skin, hair and eye pigmentation color, although they also caution that this method has limited prediction accuracy.  Given that, they say that MA-1 had dark hair, skin and eyes, but they were not able to sequence the full set of SNPs.  MA-1 also had the SNP value associated with a high risk of male pattern baldness, a trait seldom found in Native American people and was not lactose tolerant, a trait found in western Eurasians.  MA-1 also does not carry the mutation associated with hair thickness and shovel shaped incisors in Asians.

The chart below from the supplemental material shows the comparison with MA-1 and the Tyrolean Iceman.

Native flow Otzi table

The Tarim Mummies, found in the Tarim Basin in present-day Xinjiang, China are another example of remains that seem out of place.  The earliest Tarim mummies, found at Qäwrighul and dated to 1800 BCE, are of a Europoid physical type whose closest affiliation is to the Bronze Age populations of southern Siberia, Kazakhstan, Central Asia, and the Lower Volga.

The cemetery at Yanbulaq contained 29 mummies which date from 1100–500 BCE, 21 of which are Mongoloid—the earliest Mongoloid mummies found in the Tarim Basin—and eight of which are of the same Europoid physical type found at Qäwrighul.

Notable mummies are the tall, red-haired “Chärchän man” or the “Ur-David” (1000 BCE); his son (1000 BCE), a small 1-year-old baby with brown hair protruding from under a red and blue felt cap, with two stones positioned over its eyes; the “Hami Mummy” (c. 1400–800 BCE), a “red-headed beauty” found in Qizilchoqa; and the “Witches of Subeshi” (4th or 3rd century BCE), who wore 2-foot-long (0.61 m) black felt conical hats with a flat brim. Also found at Subeshi was a man with traces of a surgical operation on his neck; the incision is sewn up with sutures made of horsehair.

Their costumes, and especially textiles, may indicate a common origin with Indo-European neolithic clothing techniques or a common low-level textile technology. Chärchän man wore a red twill tunic and tartan leggings. Textile expert Elizabeth Wayland Barber, who examined the tartan-style cloth, discusses similarities between it and fragments recovered from salt mines associated with the Hallstatt culture.

DNA testing revealed that the maternal lineages were predominantly East Eurasian haplogroup C with smaller numbers of H and K, while the paternal lines were all R1a1a. The geographic location of where this admixing took place is unknown, although south Siberia is likely.  You can view some photographs of the mummies here.

In closing, the authors of the MA-1 paper state that the study has four important implications.

First, we find evidence that contemporary Native Americans and western Eurasians shareancestry through gene flow from a Siberian Upper  Palaeolithic population into First Americans.

Second, our findings may provide an explanation for the presence of mtDNA haplogroup X in Native Americans, which is related to western Eurasians but not found in east Asian populations.

Third, such an easterly presence in Asia of a population related to contemporary western Eurasians provides a possibility that non-east Asian cranial characteristics of the First Americans derived from the Old World via migration through Beringia, rather than by a trans-Atlantic voyage from Iberia as proposed by the Solutrean hypothesis.

Fourth, the presence of an ancient western Eurasian genomic signature in the Baikal area before and after the LGM suggests that parts of south-central Siberia were occupied by humans throughout the coldest stages of the last ice age.

The times, they are a changin’.

Dr. Michael Hammer’s presentation at the 9th Annual International Conference on Genetic Genealogy may shed some light on all of this seeming confusing and somewhat conflicting information.

The graphic below shows the Y haplogroup base tree as documented by van Oven.

Native flow basic Y

You can see, in the lower right corner, that Y haplogroup K (not to be confused with mtDNA haplogroup K discussed in conjunction with mtDNA haplogroup U) was the parent of haplogroup P which is the parent of both haplogroups Q and R.

It has always been believed that haplogroup R made its way into Europe before the arrival of Neolithic farmers about 10,000 years ago.  However, that conclusion has been called into question, also by the use of Ancient DNA results.  You can view additional information about Hammer’s presentation here, but in a nutshell, he said that there is no early evidence in burials, at all, for haplogroup R being in Europe at an early age.  In about 40 burials from several location, haplogroup R has never been found.  If it were present, especially in the numbers expected given that it represents more than half of the haplogroups of the men of Europe today, it should be represented in these burials, but it is not.  Hammer concludes that evidence supports a recent spread of haplogroup R into Europe about 5000 years ago.  Where was haplogroup R before spreading into Europe?  In Asia.

Native flow hammer dist

It appears that haplogroup K diversified in Southeast Asian, giving birth to haplogroups P, Q and R. Dr. Hammer said that this new information, combined with new cluster information and newly discovered SNP information over the past two years requires that haplogroup K be significantly revised.  Between the revision of haplogroup K, the parent of both haplogroup R, previously believed to be European, and haplogroup Q, known to be Asian, European and Native, we may be in for a paradigm shift in terms of what we know about ancient migrations and who is whom.  This path for haplogroup R into Europe really shouldn’t be surprising.  It’s the exact same distribution as haplogroup Q, except haplogroup Q is much less frequently found in Europe than haplogroup R.

What Can We Say About MA-1?

In essence, we can’t label MA-1 as paternally European because of Y haplogroup R which now looks to have had an Asian genesis and was not known to have been in Europe 24,000 years ago, only arriving about 5,000 years ago.  We can’t label haplogroup R as Native American, because it has never been found in a pre-Columbian New World burial.

We can say that mitochondrial haplogroup U is found in Europe in Hunter-Gatherer groups six thousand years ago (R  was not) but we really don’t know if haplogroup U was in Europe 24,000 years ago.  We cannot label haplogroup U as Native because it has never been found in a pre-Columbian New World burial.

We can determine that MA-1 did have ancestors who eventually became European due to autosomal analysis, but we don’t know that those people lived in what is now Europe 24,000 years ago.  So the migration might have been into Europe, not out of Europe.  MA-1, his ancestors and descendants, may have lived in Asia and subsequently settled in Europe or lived someplace inbetween.  We can determine that MA-1’s line of people eventually admixed with people from East Asia, probably in Siberia, and became today’s First People of North and South America.

We can say that MA-1 appears to have been about 30% what is today Western Eurasian and that he is closely related to modern day Native Americans, but not eastern Asians.  The authors estimate that between 14% and 38% of Native American ancestry comes from MA-1’s ancient population.

Whoever thought we could learn so much from a 4 year old?

For anyone seriously interested in Native American population genetics, “Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans” is a must read.

It’s been a great month for ancient DNA.  Additional recent articles which pertain to this topic include:

http://www.nytimes.com/2013/11/21/science/two-surprises-in-dna-of-boy-found-buried-in-siberia.html?src=me&ref=general&_r=0

http://www.sciencedaily.com/releases/2013/11/131120143631.htm

http://dienekes.blogspot.com/2013/11/ancient-dna-from-upper-paleolithic-lake.html

http://blogs.discovermagazine.com/gnxp/2013/11/long-first-age-mankind/#.Uo0eOcSkrIU

http://cruwys.blogspot.com/2013/11/day-1-at-royal-societys-2013-ancient.html

http://cruwys.blogspot.co.uk/2013/11/day-2-at-royal-societys-2013-ancient.html

http://www.sciencedaily.com/releases/2013/11/131118081251.htm

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Rosalind Franklin Gets a Google Doodle For Her 93rd Birthday

Rosalind_FranklinRosalind Franklin’s 93rd birthday is today.  Don’t know who she is?  Well, you’re not alone.  She is the unsung hero of DNA discovery.

Franklin is best known for her work on the X-ray diffraction images of DNA which led to the discovery of the DNA double helix. Her data, according to Francis Crick, were “the data we actually used” to formulate Crick and Watson’s 1953 hypothesis regarding the structure of DNA. Franklin’s images of X-ray diffraction confirming the helical structure of DNA were shown to Watson without her approval or knowledge. This image and her accurate interpretation of the data provided valuable insight into the DNA structure, but Franklin’s scientific contributions to the discovery of the double helix are often overlooked.

She may have been overlooked elsewhere, and particularly in terms of the Nobel prize awarded to Crick and Watson, but she has not been forgotten and was honored today by Google in a doodle!

rosalind franklin google doodle

http://en.wikipedia.org/wiki/Rosalind_Franklin

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James Watson on DNA

James Watson is most likely the most famous living scientist.  Everyone knows that he, along with Francis Crick discovered the DNA molecule back in 1953, 60 years ago.  In 1962, those two along with Maurice Wilkins were awarded the Nobel prize for their discovery.

As we remember scientists and their discoveries, I think we often miss the human element of the process.  How they feel and felt at the time, what they think and thought, the softer side of science.

Watson Crick 1953

This photos shows Francis Crick and James Watson together in 1953 at Cambridge, from the Collection of the Cold Springs Harbor Lab Archives.

CNN interviewed Watson recently, and you can read the article and see the video here.

I found some of his quotes to be very interesting.

“All you can say is that you were very lucky. You were born at the right time and your parents gave you books when you were young.”

I’m all for that.  I was and am an avid reader and I instilled that in both of my children as well.

Watson equates his passion for DNA and genetic research to his ancestor’s passion for the Gold Rush.  I can empathize with that – once the DNA bug bites you, it’s lifelong and unrelenting!  Passion fuels discovery of any type.  Watson discovered a very different kind of gold – the elixir of all humanity.

Of the day they discovered DNA, he says, “We went to lunch.  We had to tell people we’d done something important, but they didn’t know what we were saying.”  That’s certainly not the case today.  “Done something important” is an incredible understatement – perhaps the strongest understatement I’ve ever seen.

He said he felt queasy when they told everyone within hearing distance that they had found the secret of life.  Well, making the discovery of the millennium will do that to you!

I understand how he felt though.  I get the same look he must have received when I explain to my family how excited that I am that we’ve found a new haplogroup.  Thank heavens for our genetic genealogy community today.

Watson’s reaction to the Eureka moment of discovery, “All we could say when we got it: It’s so beautiful.”

watson crick dna model

DNA model built by Crick and Watson in 1953 is on display in the National Science Museum of London.  You can read the amazingly short paper published in Nature here or an annotated version here.

dna diagram from paperAt right is the diagram of DNA from the 1953 paper.  Its elegance, simplicity and symmetry is stunningly beautiful.

For those interested, Nature compiled what they consider to be the 5 classic DNA papers of which the Watson/Crick paper is one, of course.

Interestingly, Watson says he doesn’t want to die before he sees cancer cured and feels it could happen.  I certainly hope so.  Whenever this does happen, you know that genetics will certainly play a prominent role in the cure.  Discoveries in medicine as well as in other genetics fields like molecular biology, evolutionary genetics, population genetics and genetic genealogy continue to be made every day – all stemming from this monumental discovery in 1953.

Watson says of himself, “I wanted to understand the world about me better.  I wanted to do something important with my life.”  Do you think he succeeded?

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Disclosure

I receive a small contribution when you click on some of the links to vendors in my articles. This does NOT increase the price you pay but helps me to keep the lights on and this informational blog free for everyone. Please click on the links in the articles or to the vendors below if you are purchasing products or DNA testing.

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