DNA Sequencing Megathread! Neanderthals, Denisovans and other ancient DNA!

[viper37]

!!!

Can those people find you?

Well yes and no.

Yes they can message you on Ancestry and you are free to ignore them.

But it is not like they are giving them your personal name or phone number or anything. Just your ancestry account

I mean if you are on Ancestry you are interested in collaboration for genealogy research.

I am sure you can opt out if that makes you paranoid or something.

"Lord Viper, 37th of the name,
Dear Sir, please find attached a list containing the real names of your 36 ancestors.

Here are the 36 others of your name.

Yours truly,

AncestorDNA"


That'd be awesome!

[Malthus]

My whole family has fallen down this rabbit hole.

All they talk about is the random distant relations they discovered through linking up over DNA profiles, and genealogical history.

Last time I went over to visit my parents, they had me looking over a self-published manuscript detailing family grave sites in Nova Scotia (an amazing number of them were of the sort 'some random unidentified bodies washed ashore, and were kindly buried in the McGregor family plot as an act of Christian charity'. This seems to have happened - a lot ... ). Cheerful! 

Edit: another very common one was 'Nineteenth century mother and her five children all died of the fever within a few days of each other'.

The waters around Nova Scotia and Magdelen Islands in the gulf are reputed to be treacherous - well, for 18th-19th century travelers.  Some high ground or such, moving underwater sand dunes and such.

I figured it had to be something of that sort. The descriptions certainly gave a pretty graphic feel for just how dangerous seafaring prior to the 20th century could be!

[Grey Fox]

Only Radar & Sonar really made the St-Lawrence gulf "safe" to ship travel.

[Caliga]

!!!

Can those people find you?

Yep.  One messaged me a week or so ago "Hi we are fifth cousins!"  um, so?  You have hundreds of thousands of fifth cousins, dude.

[viper37]

Only Radar & Sonar really made the St-Lawrence gulf "safe" to ship travel.

yeah, pretty much.  Lots of stories around here of boats who crashed on reefs.

[Kaeso]

On 23andme, I got contacted once by an woman from Michigan with whom I could be related and I contacted one person who turned out was related to me. But those are flimsy links.  I find the claim of connecting someone with her relatives a bit over the top considering it is people so distant on the family tree.

I wish I went through and got my father to participate, it would have been fun to see what I got from him. As for my eldest daughters, it would be interesting to see the amount of Basque and Native, I am just not convinced our data is safe... 90 $ for a test, it is hardly covering the shipping of the sample from Switzerland to the US with Fedex, so my data is for sure more valuable for them.

[Josquius]

The European lab is in the Netherlands IIRC.
It's true the data is more valuable to them than the money for the tests. But not your data in particular. Its bulk that makes their money. I don't see the issue with my genetic data being out there. Nobody is going to make a biological weapon just to kill me

[The Brain]

The European lab is in the Netherlands IIRC.
It's true the data is more valuable to them than the money for the tests. But not your data in particular. Its bulk that makes their money. I don't see the issue with my genetic data being out there. Nobody is going to make a biological weapon just to kill me

They're gonna know things about you that you don't even know yourself. And they will know things about your relatives that the relatives don't even know, and that the relatives haven't even chosen to give, you chose for them.

These may or may not all be OK, but there are many things to consider here IMHO.

[jimmy olsen]

Humans, like dogs, have self domesticated themselves

https://www.sciencenews.org/article/gene-facial-development-hints-humans-domesticated-themselves

By Tina Hesman Saey

DECEMBER 4, 2019 AT 2:36 PM

Domestic animals' cuteness and humans' relatively flat faces may be the work of a gene that controls some important developmental cells, a study of lab-grown human cells suggests.

Some scientists are touting the finding as the first real genetic evidence for two theories about domestication. One of those ideas is that humans domesticated themselves over many generations, by weeding out hotheads in favor of the friendly and cooperative (SN: 7/6/17). As people supposedly selected among themselves for tameness traits, other genetic changes occurred that resulted in humans, like other domesticated animals, having a different appearance than their predecessors. Human faces are smaller, flatter and have less prominent brow ridges than Neandertal faces did, for instance.

Domesticated animals look different from their wild counterparts as well. Shorter snouts, curly tails, floppy ears and spotted coats are all traits that tend to pop up in domesticated animals. But until recently, no one had an explanation for this "domestication syndrome."

Then in 2014, three scientists proposed that as people selected animals for tameness, they also happened to select for genetic changes that slightly hamper movement of some developmentally important cells (SN: 7/14/14). These neural crest cells are present early in embryonic development and migrate to different parts of the embryo where they give rise to many tissues, including bones and cartilage in the face, smooth muscles, adrenal glands, pigment cells and parts of the nervous system. The researchers' idea was that mild genetic changes might produce neural crest cells that don't move as well, leading to domestic animals' cuddlier look.


Sign Up For the Latest from Science News
Headlines and summaries of the latest Science News articles, delivered to your inbox

E-mail*
E-mail Address
GO
Both of those big domestication ideas have been just that, with not much hard evidence for or against either. Some studies have suggested that differences in some genes implicated in neural crest cell function might have been important in the domestication of cats (SN: 11/10/14), horses (SN: 4/27/17) and other animals (SN: 5/11/15). But none of those studies explained how those genetic differences led to altered behaviors or looks between wild and domesticated critters.

In the new study, researchers studied cells from people with developmental disorders to learn what makes neural crest cells tick. One gene, BAZ1B, is a neural crest cell boss, the team found, controlling 40 percent of genes active in those cells. Altering levels of BAZ1B's protein affects how quickly neural crest cells move in lab tests, the scientists report December 4 in Science Advances.

Genes under BAZ1B's direction are among those that changed both in animals during domestication and in modern humans as they evolved, the researchers also found. Some variants of those genes are found in nearly every modern human, but either weren't found or were not as prevalent in the DNA of their extinct Neandertal or Denisovan cousins (SN: 9/19/19), the team says.

That all adds up to one thing: "We're giving the first proof of self-domestication in humans," says neuroscientist Matteo Zanella of the University of Milan.

But Zanella and his colleagues' conclusion is a giant leap from their research on cells growing in laboratory dishes, says Kenneth Kosik, a neuroscientist at the University of California, Santa Barbara. "It's a very seductive paper," full of interesting ideas and reams of data, he says. But tying human evolution, domestication and development of facial features together based on the activity of one gene is an overinterpretation, Kosik says. "Those kinds of jumps just don't belong in a scientific paper."

The researchers made their discoveries by studying cells taken from people with two developmental disorders, each involving a big piece of DNA from chromosome 7 that contains 28 genes, including BAZ1B. People with Williams-Beuren syndrome are missing that piece of DNA from one copy of chromosome 7, leaving them with only one copy of BAZ1B and the other genes. People with the genetic disorder are characteristically talkative, outgoing and not aggressive, and also tend to have especially round faces with short noses, full cheeks and wide mouths with full lips. 

One the other hand, people with what's known as 7q11.23 duplication syndrome have an extra copy of that same piece of DNA, giving them three copies of BAZ1B and the other genes. People with the duplicated DNA have the opposite symptoms: They tend to be aggressive, sometimes have difficulty speaking and have autism-like characteristics that affect their ability to socialize. Their facial features are also exaggerated but different from Williams syndrome.

That combination of behavior extremes and exaggerated facial features seems to indicate that tameness and physical changes go hand in hand just as researchers have proposed for human self-domestication and domestication syndrome in other animals.

BAZ1B was already known to affect neural crest cell function. So probing its actions in cells from people with the syndromes seemed likely to reveal more about how modern human faces evolved, says neuroscientist and coauthor Alessandro Vitriolo, also of the University of Milan. The researchers reasoned that variations in BAZ1B and its protein may slightly impair their function or how much of the protein is produced, leading to slower neural crest cell movement and the characteristics of domestication. But first, the team needed to know whether altering amounts of the BAZ1B protein had any effect on neural crest cells. So the researchers reprogrammed skin cells from people with Williams or the duplication syndrome into stem cells. The scientists then grew the stem cells into neural crest cells.

For comparison, the team also made neural crest cells from people who develop normally and who have the usual two copies of BAZ1B and other 27 genes Also included were cells from a person with a mild form of Williams syndrome. That person was missing many of the genes in the region, but still had two copies of BAZ1B.

The team also used genetic tricks to reduce levels of the BAZ1B protein, to be sure that any effects were due to the BAZ1B gene and not one of the other nearby genes. When researchers reduced these protein levels in each of the different types of cells, the neural crest cells moved slower. Other genes' activities were also influenced by the dose of BAZ1B and its protein in cells, the researchers found.

Those results correlating the amount of BAZ1B protein with cellular biology is exactly what would be expected if a neural crest cell gene were responsible for domestication syndrome, says Adam Wilkins, an evolutionary biologist and one of the authors of the 2014 paper. The most convincing bit of evidence for him was the discovery that BAZ1B seems to affect the activity of some genes that have changed in modern humans from the forms seen in Neandertals and Denisovans.

Without that link, the data "would really be just an interesting set of correlations," says Wilkins, an independent researcher in Berlin. The researchers "have provided some genetic evidence for linking gene activity to paleoanthropological history." Still, he admits that he has some uneasiness about the study's sweeping conclusions, though he was not ready to articulate those doubts.

Other researchers are more enthusiastic. "This is the strongest test yet of the human self-domestication hypothesis, and seems to support the idea that humans, like many other animals, have evolved due to selection for friendliness that also shaped other features like our faces," says Brian Hare, an evolutionary anthropologist at Duke University.

[Josquius]

I've certainly ready a study in the past about how our brains shrunk when we domesticated dogs.

[The Brain]

I've certainly ready a study in the past about how our brains shrunk when we domesticated dogs.

And our right arms got weaker.

[Caliga]

Sinister.

[Tonitrus]

I blame women. 

[katmai]

Ancestry updated their genetic percentages.

[The Larch]

Not quite "ancient DNA", but interesting nevertheless.

VIKINGS MAY NOT BE WHO WE THOUGHT THEY WERE, DNA STUDY FINDS

HISTORY BOOKS TYPICALLY DEPICT VIKINGS as blue-eyed, blonde-haired, burly men sailing the North Atlantic coast to pillage wherever they set foot on land. While some of that may be true, a new genetic study of Viking DNA is flipping much of this history on its head.

In the largest genetic study of Viking DNA ever, scientists have found that Vikings — and their diaspora — are actually much more genetically diverse than we may have thought and were not necessarily all part of a homogenous background.

Sequencing the genomes of over 400 Viking men, women, and children from ancient burial sites, researchers found evidence of genetic influence from Southern Europe and Asia in Viking DNA dating back to before the Viking Age (750 - 1050 A.D.).

The authors also note that individuals not related to Vikings genetically, such as native Pictish people of Scotland and Ireland, sometimes received traditional Viking burials — suggesting that being a Viking was not so much about specific family roots but about a sense of internal identity.

In the study, published Wednesday in the journal Nature, an international team of researchers reports findings from their six-year-long study of 442 human remains from burial sites that date back between the Bronze Age (2400 B.C.) to the Early Modern period (1600 A.D.)

When comparing the genetic material of these ancient samples with 3,855 present-day individuals from regions like the United Kingdom, Denmark, and Sweden, and data from 1,118 ancient individuals, they discovered more intermixing of genetic material than they'd originally imagined, lead author and director of The Lundbeck Foundation GeoGenetics Centre at the University of Copenhagen, Eske Willerslev, said in a statement.

"We have this image of well-connected Vikings mixing with each other, trading and going on raiding parties to fight Kings across Europe because this is what we see on television and read in books — but genetically we have shown for the first time that it wasn't that kind of world," explains Willerslev.

"This study changes the perception of who a Viking actually was — no one could have predicted these significant gene flows into Scandinavia from Southern Europe and Asia happened before and during the Viking Age."

Based on these results, Willerslev says that even well-known imagery of Vikings being blonde and blue-eyed (like Chris Hemsworth's depiction of Thor) may not be totally true, especially for Vikings with Southern European roots. The authors write that their analysis also confirmed some long-held theories and hunches about the movement of Vikings during this time.

WHAT'D THEY FIND — One of the first hunches that the study was able to confirm was the final destination of different threads of Viking migration from modern-day Scandinavia.

The DNA of ancient Danish Vikings cropped up in England while Norwegian Viking DNA was found in Ireland, Iceland, and Greenland. Unexpectedly though, they also found evidence of DNA similar to present-day Swedish populations in the western edge of Europe and DNA similar to modern Danish populations further east.

The researchers write that this unexpected discovery suggests that complex settling, trading, and raiding networks during these times resulted in communities of mixed ancestry.


Even more, the study's analysis shows that this mixed ancestry was taking place even before the so-called Viking Age, explains Martin Sikora, a lead author on the study and associate professor at the Centre for GeoGenetics, University of Copenhagen.

"We found that Vikings weren't just Scandinavians in their genetic ancestry, as we analyzed genetic influences in their DNA from Southern Europe and Asia which has never been contemplated before," said Sikora. "Many Vikings have high levels of non-Scandinavian ancestry, both within and outside Scandinavia, which suggest ongoing gene flow across Europe."

And some "Vikings" weren't of genetic Viking descent at all, researchers found when analyzing a Viking burial site in Orkney, Scotland. Despite being put to rest in traditional Viking style (including swords and other Viking memorabilia,) when sequencing the DNA of these remains the authors found that the two individuals buried at this site were in fact of Pictish (or, early-Irish and early-Scottish) decent.

The researchers write that this discovery suggests that being a Viking was not necessarily about how far back your Nordic roots reached but instead had more to do with one's lived identity.

"The results change the perception of who a Viking actually was," said Willerev. "The history books will need to be updated."

In addition to providing a more nuanced look at this transformational period of history, this new genetic insight can also help scientists better understand how different traits, like immunity, pigmentation, and metabolism, are selected for across genetic groups.

TL:DR summary: Viking =/= Scandinavian.