Stop and Smell the Flowers

Posted on June 17, 2014 by Roberta Estes

Some days DNA is just such fun. My cousin, Marja, Facebooked me and suggested that I check and see if I carried the Neanderthal SNP for heightened smell. Now, being a DNA junkie, of course, I had to do just that.

It turns out that our DNA location Rs6591536, if coded with G, increases our odor sensitivity – a characteristic shared by our Neanderthal cousins.

I would certainly think that heightened smell would enhance chances of survival. Although, in contemporary society, I’m not sure heightened smell is that much of a blessing. Floral is fine, some others odors aren’t and heightened sensitivity to smell knows no boundaries. To me, some smells are simply overwhelming – like a candle or potpourri shop, or someone who took a bath in perfume, for example. On the other hand, there is just nothing that compares to lavender.

To find out, I checked my raw data files. In fact, I checked both mine and my mother’s raw data files. Let’s take a look.

This shows that Mom carried nucleotides AA and I carry AG. G provides me with the enhanced odor sensitivity. Clearly, Mom didn’t have a G to give me, so this tells me that I received this trait from my father, not my mother. So something I share with my Dad.

Hmmm, now that I think of it, the flowers on my desk have passed their prime….I can tell by the way they smell!

Marja is preparing a presentation related to Neanderthal DNA. I love this type of exploratory science. I hope that she will present her findings in November at the Genetic Genealogy Conference in Houston. It’s fun getting to know yourself, your parents, and your Neanderthal cousins.

Curious about how much and which specific DNA locations you might carry from our Neanderthal ancestors? You’re in luck, courtesy of Marja and SNPedia….here’s a list.

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Finding Native American Ethnic Results in Germanic People

Posted on May 21, 2014 by Roberta Estes

I’m often asked about the significance of small percentages of autosomal DNA in results. Specifically, the small percentages are often of Native American or results that would suggest Native admixture. One of the first questions I always ask is whether or not the individual has Germanic or eastern European admixture.

Why?

Take a look at this map of the Invasion of the Roman Empire. See the Huns and their path?

It’s no wonder we’re so admixed.

Here’s a map of the Hunnic empire at its peak under Attila between the years 420-469.

But that wasn’t the end of the Asian invasions. The Magyars, who settled in Hungary arrived from Asia as well, in the 800s and 900s, as shown on this map from LaSalle University.

Since both the Hungarians and some Germanic people descend from Asian populations, as do Native Americans, albeit thousands of years apart, it’s not unrealistic to expect that, as populations, they share a genetic connection.

Therefore, when people who carry heritage from this region of the world show small amounts of Native or Asian origin, I’m not surprised. However, for Americans, trying to sort out their Native ethnic heritage, this is most unhelpful.

Let’s take a look at the perfect example candidate. This man is exactly half Hungarian and half German. Let’s see what his DNA results say, relative to any Asian or Native heritage, utilizing the testing companies and the free admixture tools at www.gedmatch.com.

He has not tested at Ancestry, but at Family Tree DNA, his myOrigins report 96% European, 4% Middle Eastern. At 23andMe in speculative view, he shows 99.7 European and .2 sub-saharan African.

Moving to the admixture tools at GedMatch, MDLP is not recommended for Asian or Native ancestry, so I have excluded that tool.

Eurogenes K13 is the most recently updated admixture tool, so let’s take a look at that one first.

Eurogenes K13

Eurogenes K13 showed 7% West Asian, which makes perfect sense considering his heritage, but it might be counted as “Native” in other circumstances, although I would certainly be very skeptical about counting it as such.

However, East Asian, Siberian and Amerindian would all be amalgamated into the Native American category, for a combined percentage of 1.31.

However, selecting the “admixture proportions by chromosome” view shows something a bit different. The cumulative percentages, by chromosome equate to 10.10%. Some researchers mistakenly add this amount and use that as their percentage of Native ancestry. This is not the case, because those are the portions of 100% of each individual chromosome, and the total would need to be divided by 22 to obtain the average value across all chromosomes. The total is irrelevant, and the average may not reflect how the developer determines the amount of admixture because chromosomes are not the same size nor carry the same number of SNPs. Questions relative to the functional underpinnings of each tool should be addressed to the developers.

Dodecad

I understand that there is a newer version of Dodecad, but that it has not been submitted to GedMatch for inclusion, per a discussion with GedMatch. I can’t tell which of the Dodecad versions on GedMatch is the most current, so I ran the results utilizing both v3 and 12b.

I hope v3 is not the most current, because it does not include any Native American category or pseudocategory – although there is a smattering of Northeast Asian at .27% and Southwest Asian at 1%.

Dodecad 12b below

The 12b version does show .52% Siberian and 2.6% Southwest Asian, although I’m not at all sure the Southwest Asian should be included.

HarappaWorld

Harappaworld shows .09 Siberian, .27% American (Native American), .23% Beringian and 1.8% Southwest Asian, although I would not include Southwest Asian in the Native calculation.

In Summary

Neither Family Tree DNA nor 23andMe find Native ancestry in our German/Hungarian tester, but all 3 of the admixture tools at Gedmatch find either small amounts of Native or Asian ancestry that could certainly be interpreted as Native, such as Siberian or Beringian.

Does this mean this German/Hungarian man has Native American ancestry? Of course not, but it does probably mean that the Native population and his ancestral populations did share some genes from the same gene pool thousands of years ago.

While you might think this is improbable, or impossible, consider for a minute that every person outside of Africa today carries some percentage of Neanderthal DNA, and all Europeans also carry Denisovan DNA. Our DNA does indeed have staying power over the millennia, especially once an entire population or group of people is involved. We’ve recently seen this same type of scenarios in the full genome sequencing of a 24,000 year old Siberian male skeleton.

Our German/Hungarian man carries 2.4% Neanderthal DNA according to 23andMe and 2.7% according to the Genographic Project, which also reports that he carries 3.9% Denisovan. The European average is about 2% for Neanderthal.

The net-net of this is that minority admixture is not always what it seems to be, especially when utilizing autosomal DNA to detect small amounts of Native American admixture. The big picture needs to be taken into consideration. Caution is advised.

When searching for Native admixture, when possible, both Y DNA and mitochondrial DNA give specific answers for specific pedigree lines relative to ancestry. Of course, to utilize Y or mtDNA, the tester must descend from the Native ancestor either directly paternally to test the male Y chromosome, or directly matrilineally to test the mitochondrial line. You can read about this type of testing, and how it works, in my article, Proving Native American Ancestry Using DNA. You can also read about other ways to prove Native ancestry using autosomal DNA, including how to unravel which pedigree line the Native ancestry descends from, utilizing admixture tools, in the article, “The Autosomal Me.”

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Clovis People Are Native Americans, and from Asia, not Europe

Posted on February 13, 2014 by Roberta Estes

In a paper published in Nature today, titled “The genome of a Late Pleistocene human from a Clovis burial site in western Montana,” by Rasmussen et al, the authors conclude that the DNA of a Clovis child is ancestral to Native Americans. Said another way, this Clovis child was a descendant, along with Native people today, of the original migrants from Asia who crossed the Bering Strait.

This paper, over 50 pages including supplemental material, is behind a paywall but it is very worthwhile for anyone who is specifically interested in either Native American or ancient burials. This paper is full of graphics and extremely interesting for a number of reasons.

First, it marks what I hope is perhaps a spirit of cooperation between genetic research and several Native tribes.

Second, it utilized new techniques to provide details about the individual and who in world populations today they most resemble.

Third, it utilized full genome sequencing and the analysis is extremely thorough.

Let’s talk about these findings in more detail, concentrating on information provided within the paper.

The Clovis are defined as the oldest widespread complex in North America dating from about 13,000 to 12,600 calendar years before present. The Clovis culture is often characterized by the distinctive Clovis style projectile point. Until this paper, the origins and genetic legacy of the Clovis people have been debated.

These remains were recovered from the only known Clovis site that is both archaeological and funerary, the Anzick site, on private land in western Montana. Therefore, the NAGPRA Act does not apply to these remains, but the authors of the paper were very careful to work with a number of Native American tribes in the region in the process of the scientific research. Sarah L. Anzick, a geneticist and one of the authors of the paper, is a member of the Anzick family whose land the remains were found upon. The tribes did not object to the research but have requested to rebury the bones.

The bones found were those of a male infant child and were located directly below the Clovis materials and covered in red ochre. They have been dated to about 12,707-12,556 years of age and are the oldest North or South American remains to be genetically sequenced.

All 4 types of DNA were recovered from bone fragment shavings: mitochondrial, Y chromosome, autosomal and X chromosome.

Mitochondrial DNA

The mitochondrial haplogroup of the child was D4h3a, a rather rare Native American haplogroup. Today, subgroups exist, but this D4h3a sample has none of those mutations so has been placed at the base of the D4h3a tree branch, as shown below in a grapic from the paper. Therefore, D4h3a itself must be older than this skeleton, and they estimate the age of D4h3a to be 13,000 plus or minus 2,600 years, or older.

Today D4h3a is found along the Pacific coast in both North and South America (Chile, Peru, Ecuador, Bolivia, Brazil) and has been found in ancient populations. The highest percentage of D4h3a is found at 22% of the Cayapa population in Equador. An ancient sample has been found in British Columbia, along with current members of the Metlakatla First Nation Community near Prince Rupert, BC.

Much younger remains have been found in Tierra del Fuego in South America, dating from 100-400 years ago and from the Klunk Mound cemetery site in West-Central Illinois dating from 1800 years ago.

It’s sister branch, D4h3b consists of only one D4h3 lineage found in Eastern China.

Y Chromosomal DNA

The Y chromosome was determined to be haplogroup Q-L54. Haplogroup Q and subgroup Q-L54 originated in Asia and two Q-L54 descendants predominate in the Americas: Q-M3 which has been observed exclusively in Native-Americans and Northeastern Siberians and Q-L54.

The tree researchers constructed is shown below.

They estimate the divergence between haplogroups Q-L54 and Q-M3, the two major haplogroup Q Native lines, to be about 16,900 years ago, or from between 13,000 – 19,700.

The researchers shared with us the methodology they used to determine when their most common recent ancestor (MCRA) lived.

“The modern samples have accumulated an average of 48.7 transversions [basic mutations] since their MCRA lived and we observed 12 in Anzick. We infer an average of approximately 36.7 (48.7-12) transversions to have accumulated in the past 12.6 thousands years and therefore estimate the divergence time of Q-M3 and Q-L54 to be approximately 16.8 thousands years (12.6ky x 48.7/36.7).”

Autosomal

They termed their autosomal analysis “genome-wide genetic affinity.” They compared the Anzick individual with 52 Native populations for which known European and African genetic segments have been “masked,” or excluded. This analysis showed that the Anzick individual showed a closer affinity to all 52 Native American populations than to any extant or ancient Eurasian population using several different, and some innovative and new, analysis techniques.

Surprisingly, the Anzick infant showed less shared genetic history with 7 northern Native American tribes from Canada and the Artic including 3 Northern Amerind-speaking groups. Those 7 most distant groups are: Aleutians, East Greenlanders, West Greenlanders, Chipewyan, Algonquin, Cree and Ojibwa.

They were closer to 44 Native populations from Central and South America, shown on the map below by the red dots. In fact, South American populations all share a closer genetic affinity with the Anzick individual than they do with modern day North American Native American individuals.

The researchers proposed three migration models that might be plausible to support these findings, and utilized different types of analysis to eliminate two of the three. The resulting analysis suggests that the split between the North and South American lines happened either before or at the time the Anzick individual lived, and the Anzick individual falls into the South American group, not the North American group. In other words, the structural split pre-dates the Anzick child. They conclude on this matter that “the North American and South American groups became isolated with little or no gene flow between the two groups following the death of the Anzick individual.” This model also implies an early divergence between these two groups.

In Eurasia, genetic affinity with the Anzick individual decreases with distance from the Bering Strait.

The researchers then utilized the genetic sequence of the 24,000 year old MA-1 individual from Mal’ta, Siberia, a 40,000 year old individual “Tianyuan” from China and the 4000 year old Saqqaq Palaeo-Eskimo from Greenland.

Again, the Anzick child showed a closer genetic affinity to all Native groups than to either MA-1 or the Saqqaq individual. The Saqqaq individual is closest to the Greenland Inuit populations and the Siberian populations close to the Bering Strait. Compared to MA-1, Anzick is closer to both East Asian and Native American populations, while MA-1 is closer to European populations. This is consistent with earlier conclusions stating that “the Native American lineage absorbed gene flow from an East Asian lineage as well as a lineage related to the MA-1 individual.” They also found that Anzick is closer to the Native population and the East Asian population than to the Tianyuan individual who seems equally related to a geographically wide range of Eurasian populations. For additional information, you can see their charts in figure 5 in their supplementary data file.

I have constructed the table below to summarize who matches who, generally speaking.

In addition, a French population was compared and only showed an affiliation with the Mal’ta individual and generically, Tianyuan who matches all Eurasians at some level.

Conclusions

The researchers concluded that the Clovis infant belonged to a meta-population from which many contemporary Native Americans are descended and is closely related to all indigenous American populations. In essence, contemporary Native Americans are “effectively direct descendants of the people who made and used Clovis tools and buried this child,” covering it with red ochre.

Furthermore, the data refutes the possibility that Clovis originated via a European, Solutrean, migration to the Americas.

I would certainly be interested to see this same type of analysis performed on remains from the eastern Canadian or eastern seaboard United States on the earliest burials. Pre-contact European admixture has been a hotly contested question, especially in the Hudson Bay region, for a very long time, but we have yet to see any pre-Columbus era contact burials that produce any genetic evidence of such.

Additionally, the Ohio burial suggests that perhaps the mitochondrial DNA haplogroup is or was more widespread geographically in North American than is known today. A wider comparison to Native American DNA would be beneficial, were it possible. A quick look at various Native DNA and haplogroup projects at Family Tree DNA doesn’t show this haplogroup in locations outside of the ones discussed here. Haplogroup Q, of course, is ubiquitous in the Native population.

National Geographic article about this revelation including photos of where the remains were found. They can make a tuft of grass look great!

Another article can be found at Voice of America News.

Science has a bit more.

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Neanderthal Genome Further Defined in Contemporary Eurasians

Posted on January 30, 2014 by Roberta Estes

A new study released by Howard Hughes Medical Institute at Harvard Medical School on January 29^th titled “When Populations Collide” provides some interesting insights about Neanderthal DNA in modern humans. This study compared the full Neanderthal genome to that of 1004 living individuals.

In general, people in East Asia carry more Neanderthal than Europeans who carry 1-3%, and Africans carry none or very little. It appears, according to David Reich, that Neanderthal DNA is not proportionately represented in contemporary humans, meaning that some areas of Neanderthal DNA are commonly found and others not at all. Some Neanderthal genes are carried by more than 60% of Europeans or Asians, most often associated with skin and hair color, or keratin. Reich’s thought is that people exiting Africa assimilated with Neanderthals and selected for these genes that gave them an adaptive and survival advantage in the cooler non-African climate.

One particularly big Neanderthal genetic desert is the X chromosome, a phenomenon called hybrid sterility. Reich suggests that this means that when Neanderthals and humans exiting from Africa interbred, they were on the cusp of being unable to reproduce successfully. Reich explains that “when two populations are distantly related, genes related to fertility inherited on the X chromosome can interact poorly with genes elsewhere in the genome and that interference can render males, who carry only one X, sterile.”

Given the recent discussions about the X chromosome and the possibility that it may be inherited in an all-or-nothing manner more often than the other chromosomes, I had to wonder how they determined that this was hybrid sterility and not an case of absence of recombination.

Reich’s team apparently had the same question, so they evaluated the genes related to the function of the testes, confirming they too had a particularly low inheritance frequency of Neanderthal DNA. These, combined, would eventually cause the X to be present in very small quantities in the genome of descendants since the Neanderthal X could only be inherited from women and then would cause the resulting males to be sterile. So in essence, only females could pass the X on and only their daughters would pass it further. Males carrying that X not only wouldn’t pass the X, they wouldn’t pass anything at all due to sterility.

If, in addition to this, the X has unusual recombination features, that could exacerbate the situation. Conversely, if the X is inherited intact more often than not at all, it could increase the likelihood of the X being brought forward in the population.

Reich says his team is now focused on looking at Neanderthal DNA and human disease genes. He says that his new study revealed that lupus, diabetes and Crohn’s Disease likely originate from Neanderthals.

Another study, published the same day in Science titled “Resurrecting Surviving Neandertal Lineages from Modern Human Genomes,” reaches the same conclusions about the Neanderthal inherited traits related to skin color. This study compared the full genomes of 379 East Asians and 286 Europeans to Neanderthal genomes and discovered that they could map about 20% of the Neanderthal DNA in those individuals today. This, conversely, means that 80% of the Neanderthal genome is missing, so either truly missing or simply missing in the people whose DNA they sequenced. It will be interesting to see what is found as more contemporary genetic sequences are compared against Neanderthal, and as more Neanderthal DNA is found and sequenced.

Fortunately, recent advances in dealing with contaminated ancient DNA hold a great deal of promise in terms of increasing our ability to sequence DNA that was previously thought to be useless. This report is described in the article “Separating endogenous ancient DNA from modern day contamination in a Siberian Neanderthal” and was used in the sequencing and analysis of the Neanderthal toe bone found in Siberia.

To better understand the legacy of Neanderthals, Dr. Reich and his colleagues are collaborating with the UK Biobank, which collects genetic information from hundreds of thousands of volunteers. The scientists will search for Neanderthal genetic markers, and investigate whether Neanderthal genes cause any noticeable differences in anything from weight to blood pressure to scores on memory tests.

“This experiment of nature has been done,” says Dr. Reich, “and we can study it.”

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2013’s Dynamic Dozen – Top Genetic Genealogy Happenings

Posted on December 28, 2013 by Roberta Estes

Last year I wrote a column at the end of the year titled “2012 Top 10 Genetic Genealogy Happenings.” It’s amazing the changes in this industry in just one year. It certainly makes me wonder what the landscape a year from now will look like.

I’ve done the same thing this year, except we have a dozen. I couldn’t whittle it down to 10, partly because there has been so much more going on and so much change – or in the case of Ancestry, who is noteworthy because they had so little positive movement.

If I were to characterize this year of genetic genealogy, I would call it The Year of the SNP, because that applies to both Y DNA and autosomal. Maybe I’d call it The Legal SNP, because it is also the year of law, court decisions, lawsuits and FDA intervention. To say it has been interesting is like calling the Eiffel Tower an oversized coat hanger.

I’ll say one thing…it has kept those of us who work and play in this industry hopping busy! I guarantee you, the words “I’m bored” have come out of the mouth of no one in this industry this past year.

I’ve put these events in what I consider to be relatively accurate order. We could debate all day about whether the SNP Tsunami or the 23andMe mess is more important or relevant – and there would be lots of arguing points and counterpoints…see…I told you lawyers were involved….but in reality, we don’t know yet, and in the end….it doesn’t matter what order they are in on the list:)

Y Chromosome SNP Tsunami Begins

The SNP tsumani began as a ripple a few years ago with the introduction at Family Tree DNA of the Walk the Y program in 2007. This was an intensively manual process of SNP discovery, but it was effective.

By the time that the Geno 2.0 chip was introduced in 2012, 12,000+ SNPs would be included on that chip, including many that were always presumed to be equivalent and not regularly tested. However, the Nat Geo chip tested them and indeed, the Y tree became massively shuffled. The resolution to this tree shuffling hasn’t yet come out in the wash. Family Tree DNA can’t really update their Y tree until a publication comes out with the new tree defined. That publication has been discussed and anticipated for some time now, but it has yet to materialize. In the mean time, the volunteers who maintain the ISOGG tree are swamped, to say the least.

Another similar test is the Chromo2 introduced this year by Britain’s DNA which scans 15,000 SNPs, many of them S SNPs not on the tree nor academically published, adding to the difficulty of figuring out where they fit on the Y tree. While there are some very happy campers with their Chromo2 results, there is also a great deal of sloppy science, reporting and interpretation of “facts” through this company. Kind of like Jekyll and Hyde. See the Sloppy Science section.

But Walk the Y, Chromo2 and Geno 2.0, are only the tip of the iceburg. The new “full Y” sequencing tests brought into the marketspace quietly in early 2013 by Full Genomes and then with a bang by Family Tree DNA with the their Big Y in November promise to revolutionize what we know about the Y chromosome by discovering thousands of previously unknown SNPs. This will in effect swamp the Y tree whose branches we thought were already pretty robust, with thousands and thousands of leaves.

In essence, the promise of the “fully” sequenced Y is that what we might term personal or family SNPs will make SNP testing as useful as STR testing and give us yet another genealogy tool with which to separate various lines of one genetic family and to ratchet down on the time that the most common recent ancestor lived.

http://dna-explained.com/2013/03/31/new-y-dna-haplogroup-naming-convention/

http://dna-explained.com/2013/11/10/family-tree-dna-announces-the-big-y/

http://dna-explained.com/2013/11/16/what-about-the-big-y/

http://www.yourgeneticgenealogist.com/2013/11/first-look-at-full-genomes-y-sequencing.html

http://cruwys.blogspot.com/2013/12/a-first-look-at-britainsdna-chromo-2-y.html

http://cruwys.blogspot.com/2013/11/yseqnet-new-company-offering-single-snp.html

http://cruwys.blogspot.com/2013/11/the-y-chromosome-sequence.html

http://cruwys.blogspot.com/2013/11/a-confusion-of-snps.html

http://cruwys.blogspot.com/2013/11/a-simplified-y-tree-and-common-standard.html

23andMe Comes Unraveled

The story of 23andMe began as the consummate American dotcom fairy tale, but sadly, has deteriorated into a saga with all of the components of a soap opera. A wealthy wife starts what could be viewed as an upscale hobby business, followed by a messy divorce and a mystery run-in with the powerful overlording evil-step-mother FDA. One of the founders of 23andMe is/was married to the founder of Google, so funding, at least initially wasn’t an issue, giving 23andMe the opportunity to make an unprecedented contribution in the genetic, health care and genetic genealogy world.

Another way of looking at this is that 23andMe is the epitome of the American Dream business, a startup, with altruism and good health, both thrown in for good measure, well intentioned, but poorly managed. And as customers, be it for health or genealogy or both, we all bought into the altruistic “feel good” culture of helping find cures for dread diseases, like Parkinson’s, Alzheimer’s and cancer by contributing our DNA and responding to surveys.

The genetic genealogy community’s love affair with 23andMe began in 2009 when 23andMe started focusing on genealogy reporting for their tests, meaning cousin matches. We, as a community, suddenly woke up and started ordering these tests in droves. A few months later, Family Tree DNA also began offering this type of testing as well. The defining difference being that 23andMe’s primary focus has always been on health and medical information with Family Tree DNA focused on genetic genealogy. To 23andMe, the genetic genealogy community was an afterthought and genetic genealogy was just another marketing avenue to obtain more people for their health research data base. For us, that wasn’t necessarily a bad thing.

For awhile, this love affair went along swimmingly, but then, in 2012, 23andMe obtained a patent for Parkinson’s Disease. That act caused a lot of people to begin to question the corporate focus of 23andMe in the larger quagmire of the ethics of patenting genes as a whole. Judy Russell, the Legal Genealogist, discussed this here. It’s difficult to defend 23andMe’s Parkinson’s patent while flaying alive Myriad for their BRCA patent. Was 23andMe really as altruistic as they would have us believe?

Personally, this event made me very nervous, but I withheld judgment. But clearly, that was not the purpose for which I thought my DNA, and others, was being used.

But then came the Designer Baby patent in 2013. This made me decidedly uncomfortable. Yes, I know, some people said this really can’t be done, today, while others said that it’s being done anyway in some aspects…but the fact that this has been the corporate focus of 23andMe with their research, using our data, bothered me a great deal. I have absolutely no issue with using this information to assure or select for healthy offspring – but I have a personal issue with technology to enable parents who would select a “beauty child,” one with blonde hair and blue eyes and who has the correct muscles to be a star athlete, or cheerleader, or whatever their vision of their as-yet-unconceived “perfect” child would be. And clearly, based on 23andMe’s own patent submission, that is the focus of their patent.

Upon the issuance of the patent, 23andMe then said they have no intention of using it. They did not say they won’t sell it. This also makes absolutely no business sense, to focus valuable corporate resources on something you have no intention of using? So either they weren’t being truthful, they lack effective management or they’ve changed their mind, but didn’t state such.

What came next, in late 2013 certainly points towards a lack of responsible management.

23andMe had been working with the FDA for approval the health and medical aspect of their product (which they were already providing to consumers prior to the November 22^nd cease and desist order) for several years. The FDA wants assurances that what 23andMe is telling consumers is accurate. Based on the letter issued to 23andMe on November 22^nd, and subsequent commentary, it appears that both entities were jointly working towards that common goal…until earlier this year when 23andMe mysteriously “somehow forgot” about the FDA, the information they owed them, their submissions, etc. They also forgot their phone number and their e-mail addresses apparently as well, because the FDA said they had heard nothing from them in 6 months, which backdates to May of 2013.

It may be relevant that 23andMe added the executive position of President and filled it in June of 2013, and there was a lot of corporate housecleaning that went on at that time. However, regardless of who got housecleaned, the responsibility for working with the FDA falls squarely on the shoulders of the founders, owners and executives of the company. Period. No excuses. Something that critically important should be on the agenda of every executive management meeting. Why? In terms of corporate risk, this was obviously a very high risk item, perhaps the highest risk item, because the FDA can literally shut their doors and destroy them. There is little they can do to control or affect the FDA situation, except to work with the FDA, meet deadlines and engender goodwill and a spirit of cooperation. The risk of not doing that is exactly what happened.

It’s unknown at this time if 23andMe is really that corporately arrogant to think they could simply ignore the FDA, or blatantly corporately negligent or maybe simply corporately stupid, but they surely betrayed the trust and confidence of their customers by failing to meet their commitments with and to the FDA, or even communicate with them. I mean, really, what were they thinking?

There has been an outpouring of sympathy for 23andme and negative backlash towards the FDA for their letter forcing 23andMe to stop selling their offending medical product, meaning the health portion of their testing. However, in reality, the FDA was only meting out the consequences that 23andMe asked for. My teenage kids knew this would happen. If you do what you’re not supposed to….X, Y and Z will, or won’t, happen. It’s called accountability. Just ask my son about his prom….he remembers vividly. Now why my kids, or 23andMe, would push an authority figure to that point, knowing full well the consequences, utterly mystifies me. It did when my son was a teenager and it does with 23andMe as well.

Some people think that the FDA is trying to stand between consumers and their health information. I don’t think so, at least not in this case. Why I think that is because the FDA left the raw data files alone and they left the genetic genealogy aspect alone. The FDA knows full well you can download your raw data and for $5 process it at a third party site, obtaining health related genetic information. The difference is that Promethease is not interpreting any data for you, only providing information.

There is some good news in this and that is that from a genetic genealogy perspective, we seem to be safe, at least for now, from government interference with the testing that has been so productive for genetic genealogy. The FDA had the perfect opportunity to squish us like a bug (thanks to the opening provided by 23andMe,) and they didn’t.

The really frustrating aspect of this is that 23andMe was a company who, with their deep pockets in Silicon Valley and other investors, could actually afford to wage a fight with the FDA, if need be. The other companies who received the original 2010 FDA letter all went elsewhere and focused on something else. But 23andMe didn’t, they decided to fight the fight, and we all supported their decision. But they let us all down. The fight they are fighting now is not the battle we anticipated, but one brought upon themselves by their own negligence. This battle didn’t have to happen, and it may impair them financially to such a degree that if they need to fight the big fight, they won’t be able to.

Right now, 23andMe is selling their kits, but only as an ancestry product as they work through whatever process they are working through with the FDA. Unfortunately, 23andMe is currently having some difficulties where the majority of matches are disappearing from some testers records. In other cases, segments that previously matched are disappearing. One would think, with their only revenue stream for now being the genetic genealogy marketspace that they would be wearing kid gloves and being extremely careful, but apparently not. They might even consider making some of the changes and enhancements we’ve requested for so long that have fallen on deaf ears.

One thing is for sure, it will be extremely interesting to see where 23andMe is this time next year. The soap opera continues.

I hope for the sake of all of the health consumers, both current and (potentially) future, that this dotcom fairy tale has a happy ending.

Also, see the Autosomal DNA Comes of Age section.

http://dna-explained.com/2013/10/05/23andme-patents-technology-for-designer-babies/

http://www.thegeneticgenealogist.com/2013/10/07/a-new-patent-for-23andme-creates-controversy/

http://dna-explained.com/2013/11/13/genomics-law-review-discusses-designing-children/

http://www.thegeneticgenealogist.com/2013/06/11/andy-page-fills-new-president-position-at-23andme/

http://dna-explained.com/2013/11/25/fda-orders-23andme-to-discontinue-testing/

http://dna-explained.com/2013/11/26/now-what-23andme-and-the-fda/

http://dna-explained.com/2013/12/06/23andme-suspends-health-related-genetic-tests/

http://www.legalgenealogist.com/blog/2013/11/26/fooling-with-fda/

Supreme Court Decision – Genes Can’t Be Patented – Followed by Lawsuits

In a landmark decision, the Supreme Court determined that genes cannot be patented. Myriad Genetics held patents on two BRCA genes that predisposed people to cancer. The cost for the tests through Myriad was about $3000. Six hours after the Supreme Court decision, Gene By Gene announced that same test for $995. Other firms followed suit, and all were subsequently sued by Myriad for patent infringement. I was shocked by this, but as one of my lawyer friends clearly pointed out, you can sue anyone for anything. Making it stick is yet another matter. Many firms settle to avoid long and very expensive legal battles. Clearly, this issue is not yet resolved, although one would think a Supreme Court decision would be pretty definitive. It potentially won’t be settled for a long time.

http://dna-explained.com/2013/06/13/supreme-court-decision-genes-cant-be-patented/

http://www.legalgenealogist.com/blog/2013/06/14/our-dna-cant-be-patented/

http://dna-explained.com/2013/09/07/message-from-bennett-greenspan-free-my-genes/

http://www.thegeneticgenealogist.com/2013/06/13/new-press-release-from-dnatraits-regarding-the-supreme-courts-holding-in-myriad/

http://www.legalgenealogist.com/blog/2013/08/18/testing-firms-land-counterpunch/

http://www.legalgenealogist.com/blog/2013/07/11/myriad-sues-genetic-testing-firms/

Gene By Gene Steps Up, Ramps Up and Produces

As 23andMe comes unraveled and Ancestry languishes in its mediocrity, Gene by Gene, the parent company of Family Tree DNA has stepped up to the plate, committed to do “whatever it takes,” ramped up the staff both through hiring and acquisitions, and is producing results. This is, indeed, a breath of fresh air for genetic genealogists, as well as a welcome relief.

http://dna-explained.com/2013/08/07/gene-by-gene-acquires-arpeggi/

http://dna-explained.com/2013/12/05/family-tree-dna-listens-and-acts/

http://dna-explained.com/2013/12/10/family-tree-dnas-family-finder-match-matrix-released/

http://www.haplogroup.org/ftdna-family-finder-matches-get-new-look/

http://www.haplogroup.org/ftdna-family-finder-new-look-2/

http://www.haplogroup.org/ftdna-family-finder-matches-new-look-3/

Autosomal DNA Comes of Age

Autosomal DNA testing and analysis has simply exploded this past year. More and more people are testing, in part, because Ancestry.com has a captive audience in their subscription data base and more than a quarter million of those subscribers have purchased autosomal DNA tests. That’s a good thing, in general, but there are some negative aspects relative to Ancestry, which are in the Ancestry section.

Another boon to autosomal testing was the 23andMe push to obtain a million records. Of course, the operative word here is “was” but that may revive when the FDA issue is resolved. One of the down sides to the 23andMe data base, aside from the fact that it’s not genealogist friendly, is that so many people, about 90%, don’t communicate. They aren’t interested in genealogy.

A third factor is that Family Tree DNA has provided transfer ability for files from both 23andMe and Ancestry into their data base.

Fourth is the site, GedMatch, at www.gedmatch.com which provides additional matching and admixture tools and the ability to match below thresholds set by the testing companies. This is sometimes critically important, especially when comparing to known cousins who just don’t happen to match at the higher thresholds, for example. Unfortunately, not enough people know about GedMatch, or are willing to download their files. Also unfortunate is that GedMatch has struggled for the past few months to keep up with the demand placed on their site and resources.

A great deal of time this year has been spent by those of us in the education aspect of genetic genealogy, in whatever our capacity, teaching about how to utilize autosomal results. It’s not necessarily straightforward. For example, I wrote a 9 part series titled “The Autosomal Me” which detailed how to utilize chromosome mapping for finding minority ethnic admixture, which was, in my case, both Native and African American.

As the year ends, we have Family Tree DNA, 23andMe and Ancestry who offer the autosomal test which includes the relative-matching aspect. Fortunately, we also have third party tools like www.GedMatch.com and www.DNAGedcom.com, without which we would be significantly hamstrung. In the case of DNAGedcom, we would be unable to perform chromosome segment matching and triangulation with 23andMe data without Rob Warthen’s invaluable tool.

http://dna-explained.com/2013/06/21/triangulation-for-autosomal-dna/

http://dna-explained.com/2013/07/13/combining-tools-autosomal-plus-y-dna-mtdna-and-the-x-chromosome/

http://dna-explained.com/2013/07/26/family-tree-dna-levels-the-playing-field-sort-of/

http://dna-explained.com/2013/08/03/kitty-coopers-chromsome-mapping-tool-released/

http://dna-explained.com/2013/09/29/why-dont-i-match-my-cousin/

http://dna-explained.com/2013/10/03/family-tree-dna-updates-family-finder-and-adds-triangulation/

http://dna-explained.com/2013/10/21/why-are-my-predicted-cousin-relationships-wrong/

http://dna-explained.com/2013/12/05/family-tree-dna-listens-and-acts/

http://dna-explained.com/2013/12/09/chromosome-mapping-aka-ancestor-mapping/

http://dna-explained.com/2013/12/10/family-tree-dnas-family-finder-match-matrix-released/

http://dna-explained.com/2013/12/15/one-chromosome-two-sides-no-zipper-icw-and-the-matrix/

http://dna-explained.com/2013/06/02/the-autosomal-me-summary-and-pdf-file/

DNAGedcom – Indispensable Third Party Tool

While this tool, www.dnagedcom.com, falls into the Autosomal grouping, I have separated it out for individual mention because without this tool, the progress made this year in autosomal DNA ancestor and chromosomal mapping would have been impossible. Family Tree DNA has always provided segment matching boundaries through their chromosome browser tool, but until recently, you could only download 5 matches at a time. This is no longer the case, but for most of the year, Rob’s tool saved us massive amounts of time.

23andMe does not provide those chromosome boundaries, but utilizing Rob’s tool, you can obtain each of your matches in one download, and then you can obtain the list of who your matches match that is also on your match list by requesting each of those files separately. Multiple steps? Yes, but it’s the only way to obtain this information, and chromosome mapping without the segment data is impossible

A special hats off to Rob. Please remember that Rob’s site is free, meaning it’s donation based. So, please donate if you use the tool.

http://www.yourgeneticgenealogist.com/2013/01/brought-to-you-by-adoptiondna.html

I covered www.Gedmatch.com in the “Best of 2012” list, but they have struggled this year, beginning when Ancestry announced that raw data file downloads were available. GedMatch consists of two individuals, volunteers, who are still struggling to keep up with the required processing and the tools. They too are donation based, so don’t forget about them if you utilize their tools.

Ancestry – How Great Thou Aren’t

Ancestry is only on this list because of what they haven’t done. When they initially introduced their autosomal product, they didn’t have any search capability, they didn’t have a chromosome browser and they didn’t have raw data file download capability, all of which their competitors had upon first release. All they did have was a list of your matches, with their trees listed, with shakey leaves if you shared a common ancestor on your tree. The implication, was, and is, of course, that if you have a DNA match and a shakey leaf, that IS your link, your genetic link, to each other. Unfortunately, that is NOT the case, as CeCe Moore documented in her blog from Rootstech (starting just below the pictures) as an illustration of WHY we so desperately need a chromosome browser tool.

In a nutshell, Ancestry showed the wrong shakey leaf as the DNA connection – as proven by the fact that both of CeCe’s parents have tested at Ancestry and the shakey leaf person doesn’t match the requisite parent. And there wasn’t just one, not two, but three instances of this. What this means is, of course, that the DNA match and the shakey leaf match are entirely independent of each other. In fact, you could have several common ancestors, but the DNA at any particular location comes only from one on either Mom or Dad’s side – any maybe not even the shakey leaf person.

So what Ancestry customers are receiving is a list of people they match and possible links, but most of them have no idea that this is the case, and blissfully believe they have found their genetic connection. They have found a genealogical cousin, and it MIGHT be the genetic connection. But then again, they could have found that cousin simply by searching for the same ancestor in Ancestry’s data base. No DNA needed.

Ancestry has added a search feature, allowed raw data file downloads (thank you) and they have updated their ethnicity predictions. The ethnicity predictions are certainly different, dramatically different, but equally as unrealistic. See the Ethnicity Makeovers section for more on this. The search function helps, but what we really need is the chromosome browser, which they have steadfastly avoided promising. Instead, they have said that they will give us “something better,” but nothing has materialized.

I want to take this opportunity, to say, as loudly as possible, that TRUST ME IS NOT ACCEPTABLE in any way, shape or form when it comes to genetic matching. I’m not sure what Ancestry has in mind by the way of “better,” but it if it’s anything like the mediocrity with which their existing DNA products have been rolled out, neither I nor any other serious genetic genealogist will be interested, satisfied or placated.

Regardless, it’s been nearly 2 years now. Ancestry has the funds to do development. They are not a small company. This is obviously not a priority because they don’t need to develop this feature. Why is this? Because they can continue to sell tests and to give shakey leaves to customers, most of whom don’t understand the subtle “untruth” inherent in that leaf match – so are quite blissfully happy.

In years past, I worked in the computer industry when IBM was the Big Dog against whom everyone else competed. I’m reminded of an old joke. The IBM sales rep got married, and on his wedding night, he sat on the edge of the bed all night long regaling his bride in glorious detail with stories about just how good it was going to be….

You can sign a petition asking Ancestry to provide a chromosome browser here, and you can submit your request directly to Ancestry as well, although to date, this has not been effective.

The most frustrating aspect of this situation is that Ancestry, with their plethora of trees, savvy marketing and captive audience testers really was positioned to “do it right,” and hasn’t, at least not yet. They seem to be more interested in selling kits and providing shakey leaves that are misleading in terms of what they mean than providing true tools. One wonders if they are afraid that their customers will be “less happy” when they discover the truth and not developing a chromosome browser is a way to keep their customers blissfully in the dark.

http://dna-explained.com/2013/03/21/downloading-ancestrys-autosomal-dna-raw-data-file/

http://dna-explained.com/2013/03/24/ancestry-needs-another-push-chromosome-browser/

http://dna-explained.com/2013/10/17/ancestrys-updated-v2-ethnicity-summary/

http://www.thegeneticgenealogist.com/2013/06/21/new-search-features-at-ancestrydna-and-a-sneak-peek-at-new-ethnicity-estimates/

http://www.yourgeneticgenealogist.com/2013/03/ancestrydna-raw-data-and-rootstech.html

http://www.legalgenealogist.com/blog/2013/09/15/dna-disappointment/

http://www.legalgenealogist.com/blog/2013/09/13/ancestrydna-begins-rollout-of-update/

Ancient DNA

This has been a huge year for advances in sequencing ancient DNA, something once thought unachievable. We have learned a great deal, and there are many more skeletal remains just begging to be sequenced. One absolutely fascinating find is that all people not African (and some who are African through backmigration) carry Neanderthal and Denisovan DNA. Just this week, evidence of yet another archaic hominid line has been found in Neanderthal DNA and on Christmas Day, yet another article stating that type 2 Diabetes found in Native Americans has roots in their Neanderthal ancestors. Wow!

Closer to home, by several thousand years is the suggestion that haplogroup R did not exist in Europe after the ice age, and only later, replaced most of the population which, for males, appears to have been primarily haplogroup G. It will be very interesting as the data bases of fully sequenced skeletons are built and compared. The history of our ancestors is held in those precious bones.

http://dna-explained.com/2013/01/10/decoding-and-rethinking-neanderthals/

http://dna-explained.com/2013/07/04/ancient-dna-analysis-from-canada/

http://dna-explained.com/2013/07/10/5500-year-old-grandmother-found-using-dna/

http://dna-explained.com/2013/10/25/ancestor-of-native-americans-in-asia-was-30-western-eurasian/

http://dna-explained.com/2013/11/12/2013-family-tree-dna-conference-day-2/

http://dna-explained.com/2013/11/22/native-american-gene-flow-europe-asia-and-the-americas/

http://dna-explained.com/2013/12/05/400000-year-old-dna-from-spain-sequenced/

http://www.thegeneticgenealogist.com/2013/10/16/identifying-otzi-the-icemans-relatives/

http://cruwys.blogspot.com/2013/12/recordings-of-royal-societys-ancient.html

http://cruwys.blogspot.com/2013/02/richard-iii-king-is-found.html

http://dna-explained.com/2013/12/22/sequencing-of-neanderthal-toe-bone-reveals-unknown-hominin-line/

http://dna-explained.com/2013/12/26/native-americans-neanderthal-and-denisova-admixture/

http://dienekes.blogspot.com/2013/12/ancient-dna-what-2013-has-brought.html

Sloppy Science and Sensationalist Reporting

Unfortunately, as DNA becomes more mainstream, it becomes a target for both sloppy science or intentional misinterpretation, and possibly both. Unfortunately, without academic publication, we can’t see results or have the sense of security that comes from the peer review process, so we don’t know if the science and conclusions stand up to muster.

The race to the buck in some instances is the catalyst for this. In other cases, and not in the links below, some people intentionally skew interpretations and results in order to either fulfill their own belief agenda or to sell “products and services” that invariably report specific findings.

It’s equally as unfortunate that much of these misconstrued and sensationalized results are coming from a testing company that goes by the names of BritainsDNA, ScotlandsDNA, IrelandsDNA and YorkshiresDNA. It certainly does nothing for their credibility in the eyes of people who are familiar with the topics at hand, but it does garner a lot of press and probably sells a lot of kits to the unwary.

I hope they publish their findings so we can remove the “sloppy science” aspect of this. Sensationalist reporting, while irritating, can be dealt with if the science is sound. However, until the results are published in a peer-reviewed academic journal, we have no way of knowing.

Thankfully, Debbie Kennett has been keeping her thumb on this situation, occurring primarily in the British Isles.

http://dna-explained.com/2013/08/24/you-might-be-a-pict-if/

http://cruwys.blogspot.com/2013/12/the-british-genetic-muddle-by-alistair.html

http://cruwys.blogspot.com/2013/12/setting-record-straight-about-sara.html

http://cruwys.blogspot.com/2013/09/private-eye-on-britainsdna.html

http://cruwys.blogspot.com/2013/07/private-eye-on-prince-williams-indian.html

http://cruwys.blogspot.com/2013/06/britainsdna-times-and-prince-william.html

http://cruwys.blogspot.com/2013/03/sense-about-genealogical-dna-testing.html

http://cruwys.blogspot.com/2013/03/sense-about-genetic-ancestry-testing.html

Citizen Science is Coming of Age

Citizen science has been slowing coming of age over the past few years. By this, I mean when citizen scientists work as part of a team on a significant discovery or paper. Bill Hurst comes to mind with his work with Dr. Doron Behar on his paper, A Copernican Reassessment of the Human Mitochondrial DNA from its Root or what know as the RSRS model. As the years have progressed, more and more discoveries have been made or assisted by citizen scientists, sometimes through our projects and other times through individual research. JOGG, the Journal of Genetic Genealogy, which is currently on hiatus waiting for Dr. Turi King, the new editor, to become available, was a great avenue for peer reviewed publication. Recently, research projects have been set up by citizen scientists, sometimes crowd-funded, for specific areas of research. This is a very new aspect to scientific research, and one not before utilized.

The first paper below includes the Family Tree DNA Lab, Thomas and Astrid Krahn, then with Family Tree DNA and Bonnie Schrack, genetic genealogist and citizen scientist, along with Dr. Michael Hammer from the University of Arizona and others.

http://dna-explained.com/2013/03/26/family-tree-dna-research-center-facilitates-discovery-of-ancient-root-to-y-tree/

http://dna-explained.com/2013/04/10/diy-dna-analysis-genomeweb-and-citizen-scientist-2-0/

http://dna-explained.com/2013/06/27/big-news-probable-native-american-haplogroup-breakthrough/

http://dna-explained.com/2013/07/22/citizen-science-strikes-again-this-time-in-cameroon/

http://dna-explained.com/2013/11/30/native-american-haplogroups-q-c-and-the-big-y-test/

http://www.yourgeneticgenealogist.com/2013/03/citizen-science-helps-to-rewrite-y.html

Ethnicity Makeovers – Still Not Soup

Unfortunately, ethnicity percentages, as provided by the major testing companies still disappoint more than thrill, at least for those who have either tested at more than one lab or who pretty well know their ethnicity via an extensive pedigree chart.

Ancestry.com is by far the worse example, swinging like a pendulum from one extreme to the other. But I have to hand it to them, their marketing is amazing. When I signed in, about to discover that my results had literally almost reversed, I was greeted with the banner “a new you.” Yea, a new me, based on Ancestry’s erroneous interpretation. And by reversed, I’m serious. I went from 80% British Isles to 6% and then from 0% Western Europe to 79%. So now, I have an old wrong one and a new wrong one – and indeed they are very different. Of course, neither one is correct…..but those are just pesky details…

23andMe updated their ethnicity product this year as well, and fine tuned it yet another time. My results at 23andMe are relatively accurate. I saw very little change, but others saw more. Some were pleased, some not.

The bottom line is that ethnicity tools are not well understood by consumers in terms of the timeframe that is being revealed, and it’s not consistent between vendors, nor are the results. In some cases, they are flat out wrong, as with Ancestry, and can be proven. This does not engender a great deal of confidence. I only view these results as “interesting” or utilize them in very specific situations and then only using the individual admixture tools at www.Gedmatch.com on individual chromosome segments.

As Judy Russell says, “it’s not soup yet.” That doesn’t mean it’s not interesting though, so long as you understand the difference between interesting and gospel.

http://dna-explained.com/2013/08/05/autosomal-dna-ancient-ancestors-ethnicity-and-the-dandelion/

http://dna-explained.com/2013/10/04/ethnicity-results-true-or-not/

http://www.legalgenealogist.com/blog/2013/09/15/dna-disappointment/

http://cruwys.blogspot.com/2013/09/my-updated-ethnicity-results-from.html?utm_source=feedburner&utm_medium=email&utm_campaign=Feed%3A+Cruwysnews+%28Cruwys+news%29

http://dna-explained.com/2013/10/17/ancestrys-updated-v2-ethnicity-summary/

http://dna-explained.com/2013/10/19/determining-ethnicity-percentages/

http://www.thegeneticgenealogist.com/2013/09/12/ancestrydna-launches-new-ethnicity-estimate/

http://cruwys.blogspot.com/2013/12/a-first-look-at-chromo-2-all-my.html

Genetic Genealogy Education Goes Mainstream

With the explosion of genetic genealogy testing, as one might expect, the demand for education, and in particular, basic education has exploded as well.

I’ve written a 101 series, Kelly Wheaton wrote a series of lessons and CeCe Moore did as well. Recently Family Tree DNA has also sponsored a series of free Webinars. I know that at least one book is in process and very near publication, hopefully right after the first of the year. We saw several conferences this year that provided a focus on Genetic Genealogy and I know several are planned for 2014. Genetic genealogy is going mainstream!!! Let’s hope that 2014 is equally as successful and that all these folks asking for training and education become avid genetic genealogists.

http://dna-explained.com/2013/08/10/ngs-series-on-dna-basics-all-4-parts/

https://sites.google.com/site/wheatonsurname/home

http://www.yourgeneticgenealogist.com/2012/08/getting-started-in-dna-testing-for.html

http://dna-explained.com/2013/12/17/free-webinars-from-family-tree-dna/

http://www.thegeneticgenealogist.com/2013/06/09/the-first-dna-day-at-the-southern-california-genealogy-society-jamboree/

http://www.yourgeneticgenealogist.com/2013/06/the-first-ever-independent-genetic.html

http://cruwys.blogspot.com/2013/10/genetic-genealogy-comes-to-ireland.html

http://cruwys.blogspot.com/2013/03/wdytya-live-day-3-part-2-new-ancient.html

http://cruwys.blogspot.com/2013/03/who-do-you-think-you-are-live-day-3.html

http://cruwys.blogspot.com/2013/03/who-do-you-think-you-are-live-2013-days.html

http://genealem-geneticgenealogy.blogspot.com/2013/03/the-surnames-handbook-guide-to-family.html

http://www.isogg.org/wiki/Beginners%27_guides_to_genetic_genealogy

A Thank You in Closing

I want to close by taking a minute to thank the thousands of volunteers who make such a difference. All of the project administrators at Family Tree DNA are volunteers, and according to their website, there are 7829 projects, all of which have at least one administrator, and many have multiple administrators. In addition, everyone who answers questions on a list or board or on Facebook is a volunteer. Many donate their time to coordinate events, groups, or moderate online facilities. Many speak at events or for groups. Many more write articles for publications from blogs to family newsletters. Additionally, there are countless websites today that include DNA results…all created and run by volunteers, not the least of which is the ISOGG site with the invaluable ISOGG wiki. Without our volunteer army, there would be no genetic genealogy community. Thank you, one and all.

2013 has been a banner year, and 2014 holds a great deal of promise, even without any surprises. And if there is one thing this industry is well known for….it’s surprises. I can’t wait to see what 2014 has in store for us!!! All I can say is hold on tight….

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Native Americans, Neanderthal and Denisova Admixture

Posted on December 26, 2013 by Roberta Estes

Recently, a Neanderthal toe bone yielded enough DNA to sequence the full genome of the woman whose remains were found in the Denisova Cave in the Altai Mountains, shown above. This information was published in the Journal Nature in an article titled “The complete genome sequence of a Neanderthal from the Altai Mountains” by Prufer et al. I wrote about what was found here, but it wasn’t until I really read the 200+ pages of supplemental information that I found additional buried information.

The article itself talks about some of the findings relative to Native Americans, but the supplemental information provides additional detail and the supporting charts.

In the paper, the Mixe and the Karitiana people of Mexico and Brazil, respectively were most often used to represent Native Americans. There are about 90,000 Mixe language speakers alive today, so their population is not small. However, the Karitiana are just the opposite, with only about 320 people in a very remote region of Brazil. The Karitiana shun contact with outsiders. In some parts of this study, additional population groups were used for additional Native samples.

Here’s what the article itself has to say about Neanderthals, Denisovans and Native Americans.

Denisovan gene flow in mainland Asia

We used the two high-coverage archaic genomes and a hidden Markov model (HMM) to identify regions of specifically Neanderthal and specifically Denisovan ancestry in 13 experimentally phased present-day human genomes (Supplementary Information sections 4 and 13). In the Sardinian and French genomes from Europe we find genomic regions of Neanderthal origin and few or no regions of Denisovan origin. In contrast, in the Han Chinese, the Dai in southern China, and the Karitiana and Mixe in the Americas, we find, in addition to regions of Neanderthal origin, regions that are consistent with being of Denisovan origin (Zscore54.3 excess relative to the Europeans) (Supplementary Information section 13), in agreement with previous analysis based on low-coverage archaic genomes. These regions are also more closely related to the Denisova genome than the few regions identified in Europeans (Supplementary Information section 13). We estimate that the Denisovan contribution to mainland Asian and Native American populations is ,0.2% and thus about 25 times smaller than the Denisovan contribution to populations in Papua New Guinea and Australia. The failure to detect any larger Denisovan contribution in the genome of a 40,000-year-old modern human from the Beijing area suggests that any Denisovan contribution to modern humans in mainland Asia was always quantitatively small. In fact, we cannot, at the moment, exclude that the Denisovan contribution to people across mainland Asia is owing to gene flow from ancestors of present-day people in Oceania after they mixed with Denisovans. We also note that in addition to this Denisovan contribution, the genomes of the populations in Asia and America appear to contain more regions of Neanderthal origin than populations in Europe (Supplementary Information sections 13 and 14).

The fascinating part of this, aside from the fact that Native people also carry both Denisovan and Neanderthal DNA, and that they carry more than Europeans, is that the Denisovan and Neanderthal DNA that they carry is different than that carried by Europeans. In fact, it appears that not all Europeans carry Denisovan DNA and this paper lowers the estimated percentage of Neanderthal for all Europeans.

This difference in the Neanderthal and Denisovan DNA might be able to help solve a long-standing mystery, and that’s whether or not part of the Native population of the Eastern seaboard, and in particular, the far Northeast part of that region, was populated by or admixed with Europeans long before the time of Columbus and other European pre-colonial explorers. This information, of course would have to come from pre-contact burials, but they do exist and with this new information in hand, they might just yield answers never before available.

Dr. Ricki Lewis, in her DNA Science Blog, mentioned something else quite interesting culled from a Christmas Day issue of Nature titled “Sequence variants in SLC16A11 are a common risk factor for type 2 diabetes in Mexico.” In a nutshell, from article introduction, we find this commentary:

“The risk haplotype carries four amino acid substitutions, all in SLC16A11; it is present at ~50% frequency in Native American samples and ~10% in east Asian, but is rare in European and African samples. Analysis of an archaic genome sequence indicated that the risk haplotype introgressed into modern humans via admixture with Neanderthals.”

Ricki extrapolated on this further:

“Researchers determine the degree to which a mutant gene differs from the most common sequence (wild type), then impose a time scale in the form of known mutation rates. The SLC16A11 five-site haplotype is so divergent that it goes back to nearly 800,000 years ago — before our ancestors expanded out of Africa.

The most plausible explanation, unexpected I suspect, seemed to be that the haplotype came from an archaic human – a Neanderthal or Denisovan or their as-yet unnamed contemporaries. And the haplotype indeed shows up in the skeleton of a Neanderthal found in the Denisovan cave in Siberia.”

And so, it seems that the Native American people today indeed inherited their propensity for type 2 diabetes from their ancient Neanderthal ancestors who lived in the Altai Mountains. It also appears that this genetic predisposition did not carry forward to Europe, if indeed this group of Neanderthals was ancestral to Europeans at all.

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Sequencing of Neanderthal Toe Bone Reveals Unknown Hominin Line

Posted on December 22, 2013 by Roberta Estes

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

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

The skeleton showed physical traits of both Neanderthals and modern humans and is thought to be about 50,000 years old.
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.
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.
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.
This unknown line could be homo erectus.
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.
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.
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.
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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400,000 Year Old DNA from Spain Sequenced

Posted on December 5, 2013 by Roberta Estes

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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The Autosomal Me – Testing Company Results

Posted on February 24, 2013 by Roberta Estes

This is Part 4 of a multi-part series, The Autosomal Me.

Part 1 was “The Autosomal Me – Unraveling Minority Admixture” and Part 2 was “The Autosomal Me – The Ancestors Speak.” Part 1 discussed the technique we are going to use to unravel minority ancestry, and why it works. Part 2 gave an example of the power of fragmented chromosomal mapping and the raw beauty of the results. Part 3, “The Autosomal Me – Who Am I?,” discussed how to use our pedigree charts to gauge expected results and how autosomal results are grouped into population buckets. We also named this technique, Minority Admixture Mapping, or MAP for short.

In this segment, Part 4, let’s take a look at what the testing company autosomal results look like. The results are presented in timeline order, with the oldest results first and the latest, and presumably most accurate results, last.

23andMe Version 1

23andMe was the first company to offer this type of testing affordably. They initially only offered 3 population groups, and one inferred that Asian was actually Native American. Of course, that wasn’t a valid assumption for everyone, but it was the best that could be done under the circumstances. This was my ethnicity results display at 23andMe until December 2012 went their updated version was released.

DeCode Genetics

DeCode Genetics initially offered autosomal tests for ancestry. Unfortunately, under the pressure of financial issues, they stepped away from the genetic genealogy marketspace and have since been sold.

Their test showed the following ethnic breakdown, picking up both my Native and African heritage:

I particularly like these results because the X chromosome is included, and seeing Native on the X chromosome, which has a unique inheritance path is a very important piece of data.

Family Tree DNA Version 1

Family Tree DNA’s first version of their Family Finder product produced results stating that I am 100% European, split between western and northern, shown below (minus the map.)

Dr. Doug McDonald

Doug McDonald, a retired physical chemistry professor, compiles contributed raw data and compares the raw data locations with both reference populations and the contributor results. This is not a commercial endeavor but a private research project which has been ongoing for years. His analysis of my raw data results from 23andMe and Family Tree DNA showed that they are primarily European. His first analysis was without Middle Eastern populations and the results showed European except for a total of about 3% East Asian, Oceana and American. However, in a second run including the Pakistan and Middle Eastern populations, the results now showed 88% European, about 1% Oceanic and American and the balance Middle Eastern and Pakistani.

A small amount of Middle Eastern heritage is not unexpected since I do have confirmed Turkish ancestors.

Dr. McDonald indicated that this was slightly more, 1-2%, than most Europeans, and that I was generally planted firmly in the middle of the “English” area in his data. His results showed no African.

Standard deviation (statistical noise) is about 1%. He can achieve these low deviation numbers by using such a large number of markers (536,904 to be exact)[1] for his comparison. I am grateful to Dr. McDonald for his contribution, not only to me, but to this field.

The graph below shows that my primary ancestry falls in the English/French region.

The second graph maps these results on my chromosomes. The American, bright green, is found on chromosomes 1 and 2, and the X chromosome shows South Asian.

Doug indicates that the Native American is found at about the .5% level. Interestingly, on my mother’s graphs and charts (below), the Native segments are nearly identical, but my first grey South Asian segment on my X is Mideast on her chart.

It’s also interesting to note that my Native American on chromosome 2 is larger than my mother’s which may well reflect Native heritage on my father’s side. Ironically, the oral history of Native ancestry was on my father’s side, not my mothers.

Doug’s analysis has been updated several times over the years and these results are the most current. The vendors have made upgrades too. In 2012, both 23andMe and Family Tree DNA underwent upgrades to their ethnicity software and the Genographic Project version 2.0 test was released.

23andMe 2012 Updated Version

The new 23andMe software offers different confidence levels.

The standard estimate, or confidence level, shows that I have about .5% Native American. This is consistent with Dr. McDonald’s findings.

A second view is available which paints the chromosomes. A split view is also available if one of your parents has been tested at 23andMe as well. That is not an option for me.

The conservative estimate, below, shows less Native at .2%.

The speculative level below shows the Native back to .5% but adjusts the European regions significantly.

Although 23andMe does not provide participants with the start and stop locations, through alternative means, meaning a very smart friend, Rebekah Canada, who is a Java programmer, start and stop locations can be discerned.

CeCe Moore documented Rebekah’s technique for those who will be following along with their own results through this process.

In a future segment of this series, we’ll look at alternative ways to discern Native segments. Thanks to Rebekah’s technique, I can tell you that 23andMe shows my Native segments as follows:

Chromosome 1 – 165,658,091 to 175,711,116

Chromosome 2 – 86,316,174 to103,145,426

23andMe also provides a Neanderthal percentage. What fun!!!

Family Tree DNA Updated 2012 Version

My mother was deceased before chip based autosomal testing was available, but I ordered the Family Finder test for her as soon as it was available. Thankfully her DNA was stored at Family Tree DNA and was still viable.

Mother’s original results are shown above and her most recent results are shown below. Her results shifted within Europe and her margin of error doubled.

My current results from Family Tree DNA’s updated software are shown below.

National Geographic Genographic 2.0

I was very surprised to see my National Geographic results. They were very unexpected, in particular the high percentages of Mediterranean and Southwest Asian, totaling 54%.

It made more sense when I read the information. It’s true, reading is fundamental.

These results are, in essence, more anthropological in nature.

Of course, one of the fun parts of the Genographic results are the Neanderthal and Denisovan percentages.

These are somewhat different than the 23andMe results, although if you add the Neanderthal and Denisovan values together, the resultant 2.2% is very close to 23andMe’s 2.5%.

Ancestry.com

In 2012, Ancestry introduced an autosomal DNA test as well. What it provides is very limited, with limited tools, but it does provide percentages of ethnicity in addition to matches. Recently, Ancestry announced that the percentages may change over time. They have been severely beaten within the genetic genealogy community for quality issues with this product, including percentages of ethnicity that are highly erroneous. Their stated time reference is 500 years ago.

Recently this new page was added before you can see your detailed results.

Ancestry shows my heritage as only British and Scandinavian.

Ironically, Ancestry has mapped the birth locations of my ancestors in Europe on the map above, based on my family tree submitted. Interesting that Germany doesn’t show in Ancestry’s ethnicity list but many of my family lines originated in Germany and Holland, and none in Scandinavia.

Testing Provider Summary

Where do we stand now?

A summary of the various test results is shown below compared to my pedigree analysis.

Test Results Chart

I have included Dr. McDonald’s analysis here, not because he’s a testing provider in the sense of the testing companies, but because his offering was available in this timeframe, and because he worked with Family Tree DNA to develop their Population Finder code.

You can see that the results are relatively consistent between testing companies. There is certainly no question about majority ancestry, but the minority admixture which hovers someplace near 1%, give or take 5% in either direction, is much less consistent and not always reported. If I were to have tested with only one company and taken the results as gospel, I could certainly have been left believing that I had no Native or African admixture. For many people, it’s this small amount of minority admixture that they are seeking. So in answer to the question of which testing company is “best,” the answer is, if you’re looking for trace amounts of anything, the compendium of all the testing companies (minus Ancestry) would provide the best set of results. We will be using the match information as well in the next sections, so certainly nothing has been “wasted” testing with multiple companies, again, except Ancestry. I am hopeful that Ancestry will in the future release our raw data (which they have promised to do) in a useable format, fix their misleading ethnicity results and add chromosome painting tools so that we can fully utilize our data.

In Part 5 of the series, we’ll take a look at third party tools and how they can continue to refine and add to our knowledge of our admixture.

1. Genealogy-DNA Rootsweb posting by Doug McDonald on 7-26-09 and personal correspondence.

2. 71.5% western European, 28.4% Northeastern European

3. Inferred that Asian is actually Native in an American with no history of Asian ancestry.

4. No category, inferred.

5. 78.6% Northern European, 1.8% Southern European, 18.7% Nonspecific European

6. 54.6% Northern European, .3% Southern European, 43% Nonspecific European

7. 91.7% Northern European, 3% Southern European, 3.3% Nonspecific European

8. 75.18% West Europe (French and Orcadian), 24.82 Europe (Romanian, Russian, Tuscan and Finnish). Note that my mother’s results are almost identical except the Finnish is missing from hers.

9. 43% North Europe and 36% Mediterranean

10. 80% British, 12% Scandinavian

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Decoding and Rethinking Neanderthals

Posted on January 10, 2013 by Roberta Estes

On January 9, 2013, PBS ran a wonderful documentary, Decoding Neanderthals, about Neanderthals, what we have recently discovered about them, and what it means to us as humans. There has been a lot of discussion about this topic spurred by both the 23andMe and the Geno2.0 tests that provide a percentage of Neanderthal to participants. Geno2.0 also provides a percentage of Denisovan.

Program Description:
Over 60,000 years ago, the first modern humans—people physically identical to us today—left their African homeland and entered Europe, then a bleak and inhospitable continent in the grip of the Ice Age. But when they arrived, they were not alone: the stocky, powerfully built Neanderthals had already been living there for hundreds of thousands of years. So what happened when the first modern humans encountered the Neanderthals? Did we make love or war? That question has tantalized generations of scholars and seized the popular imagination. Then, in 2010, a team led by geneticist Svante Paabo announced stunning news. Not only had they reconstructed much of the Neanderthal genome—an extraordinary technical feat that would have seemed impossible only a decade ago—but their analysis showed that “we” modern humans had interbred with Neanderthals, leaving a small but consistent signature of Neanderthal genes behind in everyone outside Africa today. In “Decoding Neanderthals,” NOVA explores the implications of this exciting discovery. In the traditional view, Neanderthals differed from “us” in behavior and capabilities as well as anatomy. But were they really mentally inferior, as inexpressive and clumsy as the cartoon caveman they inspired? NOVA explores a range of intriguing new evidence for Neanderthal self-expression and language, all pointing to the fact that we may have seriously underestimated our mysterious, long-vanished human cousins.

I’m going to share some of the highlights of the program, but this is in no way a spoiler, as the program contains lots of visual information that just can’t be conveyed by a review.

Chris Stringer from the Natural History Museum in London introduced us to the Neanderthals. It turns out that our perception of what a Neanderthal looks like is a result in large part of skeleton that was reconstructed improperly due to advanced arthritis, causing the individual to appear to walk hunched over, much like, well, our stereotypical view of a caveman. Just goes to show what bad PR can cause.

Neanderthal skeletons can be positively identified. Their facial structure is different than that of modern man, with an identifiable brow ridge and bones that push forward in the nose and mouth region, as compared to our flatter faces today.

Neanderthals lived a short life, most were dead by age 30. They were large and strong. They participated in up-close and personal hunting, using spears, which meant they had to come in close contact with their prey.

Neanderthals began living in Europe about 300,000 years ago, having exited from Africa. They evolved to fit the European, colder, climate. It had been thought up until recently that they lacked the brainpower of humans, had no spoken language, or the ability for such, no personal ornamentation, art or evidence of ritual or religion. These are the functions that make us uniquely human and separate us from the non-human world, and we fully believed that Neanderthals lacked these defining characteristics.

We have learned differently, much as a result of genetic discoveries that tell a different story of Neanderthals.

Homo sapiens left African about 40,000 years ago, and within 10,000 years, Neanderthals, who had spread throughout most of Europe and much of Asia were gone. The map below shows the locations where fossilized Neanderthal remains have been found.

The assumption has been made that Homo Sapiens were responsible for the Neanderthals demise, either by killing them off or providing too much competition for scarce resources, outnumbering them 10 to 1.

Svante Paabo, a Swedish geneticist now at the Max Planck Institute for Evolutionary Anthropology forever changed the genetic world, how we perceive Neanderthals, and paradoxically, how we think of ourselves.

Pääbo is known as one of the founders of paleogenetics, a discipline that uses the methods of genetics to study early humans and other ancient populations.

In August 2002, Paabo published findings about the “language gene”, FOXP2, which is lacking or damaged in some individuals with language disabilities. This research would prove critical, later, in the humanization of the Neanderthal.

In 2006, he announced a plan to reconstruct the entire genome of Neanderthals. In 2007, Pääbo was named one of TIME Magazine’s 100 most influential people of the year.

In February 2009, at the Annual Meeting of the American Association for the Advancement of Science (AAAS), it was announced that the Max Planck Institute for Evolutionary Anthropology had completed the first draft version of the Neanderthal genome. Over 3 billion base pairs were sequenced in collaboration with the 454 Life Sciences Corporation. This project, led by Pääbo, shed and will continue to shed new light on the recent evolutionary history of modern humans.

In March 2010, Pääbo and his coworkers published a report about the DNA analysis of a finger bone found in the Denisova Cave in Siberia; the results suggest that the bone belonged to an extinct member of the genus Homo that had not yet been recognized, the Denisova hominin.

In May 2010, Pääbo and his colleagues published a draft sequence of the Neanderthal genome in the journal Science. Below, a scientist at Max Plank extracting Neanderthal DNA.

Paabo shared in the program that many times during the Neanderthal sequencing project, he himself “despaired many times of being able to do it”, doubting that it could be done. It took a total of 4 years. The team found good candidates, 3 well-preserved female bone fragments from the Vindija Cave in Croatia.

Because of the age of the fragments, and because they had been in the ground for so long, much of the DNA recovered wasn’t Neanderthal, but that of bacterial organisms and fungus. The team developed a method to eliminate the bacteria, leaving only Neanderthal DNA. However, those genetic fragments still had to be reassembled, piece by piece, like a huge jigsaw puzzle with no picture on the box, into the Neanderthal genome.

Four long years later, the puzzle was finished. I hope the team had a very big celebratory party!

Ed Green, a scientist on Paabo’s team said that the first thing the scientists looked for was to determine whether or not Neanderthals had the FOXP2 gene for language, and if so, is it identical to the human version, or is it different. The answer was that it was identical to the language gene carried by Homo Sapiens, modern humans. This tells us not only that Neanderthals had the capabilities for language, but that this gene evolved in Africa, before Neanderthals left, 300,000 years ago.

The next question, of course, was whether or not modern humans carried any DNA that could be labeled as Neanderthal. In other words, the question of inter-species breeding arose. It was believed that this was impossible, because two different species cannot have fertile offspring. This was proven to be an inaccurate assumption relative to Neanderthal and Homo Sapiens.

Paabo’s team sequenced the DNA of 5 individuals from different parts of the world. They isolated parts of the Neanderthal DNA that were measurably different from that of modern humans. In other words, those sequences could be positively identified as Neanderthal. Compared against the DNA of the 5 contemporary individuals, only the person from Africa had none of the Neanderthal DNA.

Paabo didn’t believe the results, thought they might be an artifact of statistical error or the result of not enough data, so he had his team repeat the exercise with different people, again, and again, and again, and every time, the results came back the same. Neanderthals and humans inbred, and to the degree that there is Neanderthal DNA in every population on every continent outside of Africa today.

John Hawks, an anthropologist at the University of Wisconsin used jelly beans to illustrate Neanderthal DNA in worldwide populations today. It turns out that the Chinese have the least amount, with about 1% and the people of Tuscany have the most, with about 4%. So the mountainous areas of Europe and Italy were a hotbed of Neanderthal activity and human interbreeding.

This caused other experts to think again about the Neanderthals in what could be called a radical shift in perspective. All of a sudden, when we realized that they were part of us, they became more human to us. They could and probably did have speech, so they could and probably did other “human” things too.

Joao Zilhao, a paleolithic archaeologist at the University of Bristol, also a flintknapper, spent years reconstructing the process of making Neanderthal tools, what were once believed to be scraps of flint with sharp edges. He proved, among other things, that obtaining these “scraps” involved a complex process of very specific flintknapping strokes. This skill was far from the previously perceived unintelligent caveman, and furthermore, it likely required language instruction.

Another early technology, in use 250,000 years ago, involved a complex process to create a type of pitch to secure spearheads to spear shafts.

The Neanderthals began evolving before our very eyes.

Michael Walker, a professor of Zoology and Physical Anthropology at the University of Murcia, discovered indeed that Neanderthals likely did have ceremony and ritual, the hallmarks of religion, which involved the ability for complex thought and reasoning. Shells and bones, drilled or punched to be worn as ornaments have been identified, along with pigments believed to have been used as body paints.

We still do this today; look at the fans at any football game.

In addition, it appears that a burial may have been found in Spain, along with two panther paws. Michael mentioned them as a trophy, I thought more in terms of spiritual significance.

John Hawks discussed what the Neanderthal parts of our genome have done for humans. Many of the Neanderthal genes have no known purpose, but there is one significant exception. It’s somehow ironic that we may indeed have survived as a species in a foreign environment, colder Europe, thanks to inbreeding with the Neanderthals. Humans carry a very specific Neanderthal piece of DNA that is essential to the immune system’s ability to attack viruses and bacteria, the HLA or Human Leukocyte Antigen. Because individuals who carried HLA might well have survived when others didn’t, the HLA became naturally selected for, and therefore present in the descendant population, us, “saving lives to this day.’

As John said, we are just beginning to understand our debt to the Neanderthals. Not only that, we also are rethinking what extinction really meant. We have presumed that Neanderthals went extinct, or died out, because we could no longer find their remains in fossil evidence. Perhaps, as Mark Twain said “reports of my demise have been greatly exaggerated.”

Is the reason we could no longer find separate Neanderthals because they interbred and assimilated into the Homo Sapiens population who were probably the dominant species, outnumbering them ten to one? Was their extinction not a dying out at all, but an absorption? Perhaps that was simply the natural progression of things, or maybe they realized that their recipe for success, for long-term survival, was not to remain separate, but to become part of the larger population. In fact they do survive today in just that way, as a part of all of us outside of Africa.

Decoding Neanderthals is available to watch online at http://www.pbs.org/wgbh/nova/evolution/decoding-neanderthals.html

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