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

[Razgovory]

It's the old joke.  A Jewish sailor is shipwrecked on a desert island a Jewish Robinson Crusoe.  Many years later he is found by a passing ship.  His rescuers notice that the sailor constructed three separate buildings, and inquire why. 

"That's my house, where I live" he says, pointed to the first one.
"What's the one next to that?" the rescuers ask. 
"That's the synaogue where I go to pray to God." 
"And the third?" 
"That's the synagogue I don't go to."

Well, thanks for sharing.

[Valmy]

It's the old joke.  A Jewish sailor is shipwrecked on a desert island a Jewish Robinson Crusoe.  Many years later he is found by a passing ship.  His rescuers notice that the sailor constructed three separate buildings, and inquire why. 

"That's my house, where I live" he says, pointed to the first one.
"What's the one next to that?" the rescuers ask. 
"That's the synaogue where I go to pray to God." 
"And the third?" 
"That's the synagogue I don't go to."

Always a good one. Though I thought it was 'the synagogue I would never step foot inside'

Raz: It is a reference to the contentious nature of the Jewish sects.

[The Minsky Moment]

The "lesson" is that making artificial divisions is core to human experience.  We just can't help ourselves.  Proximity or family connection often makes it worse, not better.

[Razgovory]

Oh okay.  I was just trying to figure out what it had to do with Neanderthal DNA.

[Valmy]

Oh okay.  I was just trying to figure out what it had to do with Neanderthal DNA.

It has lots to do with it.

[The Brain]

The "lesson" is that making artificial divisions is core to human experience.  We just can't help ourselves.  Proximity or family connection often makes it worse, not better.

If it's core, why was the sailor specifically Jewish?

[jimmy olsen]

Upward of 1,024 people are ancestors of mine, who cool is that for them.   

I find it rather disturbing that if I calculate my mathematical number of ancestors in the year 1400 it is well over twice the estimated population of the world at the time. Which means I am: extremely inbred.

The numbers and the genes say the most recent ancestor for all living people was 3400 years ago. Of course that number has been shortened by the massive migrations of the of the post 1492 exploration era. In 1400 the most recent ancestor was likely twice as distant or more due to the isolation of Australia, Americas and Pacific Islands from the majority of the population in Eurasia and Africa.

http://nautil.us/issue/56/perspective/youre-descended-from-royalty-and-so-is-everybody-else

You're Descended from Royalty and So Is Everybody Else

Anybody you can name from ancient history is in your family tree.

By Adam Rutherford
January 4, 2018

Charlemagne, Carolingian King of the Franks, Holy Roman Emperor, the great European conciliator; your ancestor. I am making an assumption that you are broadly of European descent, which is not statistically unreasonable but certainly not definitive. If you're not, be patient, and we'll come to your own very regal ancestry soon enough.

Along with Alexander and Alfred, Charlemagne is one of a handful of kings who gets awarded the post-nominal accolade "the Great." His early life remains mysterious and the stories are assembled from various sources, but it seems he was born around 742 A.D., just at the time when the Plague of Justinian was dispatching millions at the eastern edge of the moribund Roman Empire. The precise place of his birth is also unknown, but it's likely to be in a town such as Aachen, now in contemporary Germany, or Liège in Belgium. Even Einhard, his dedicated servant and biographer, wouldn't get drawn into the specifics of Charlemagne's early life in his fawning magnum opus, The Life of Charles the Great. The very fact that this account exists—probably the first biography of a European ruler—is testament to how important he was (or at least was seen to be). In many European languages, the word "king" is itself derived from Charlemagne's name.

He was the son of Pippin the Short, an aggressive ruler of France who expanded the Frankish kingdom until his death during the return journey from a campaign against the persistently rebellious realm of Aquitaine in 768. Charlemagne stepped up as his successor, and continued the expansion with aplomb. He battled the Saxons to the northeast, the Lombards in Italy, and Muslims in Spain. He capitalized on his father's good political relations with the Vatican, and in 800 was crowned the first Holy Roman Emperor by Pope Leo III in St Peter's Basilica, an event so momentous that Charlemagne marked it by giving Leo one of the great medieval relics as a thank you—the Holy Prepuce, better known as Jesus' foreskin.

Rutherford_BR-1

A fecund ruler, Charlemagne sired at least 18 children by motley wives and concubines, including nine by his second wife, Hildegard of Vinzgau. These kin included Charles the Younger, Pippin the Hunchback, Drogo of Metz, Hruodrud, Ruodhaid, Adalheid, Hludowic, and not forgetting Hugh, and he consolidated his reign by installing many of his sons in positions of power across the expanding empire. Royal lineages are historically the only ones to get documented well until the modern era, and Charlemagne's lineage is bountiful. We can trace a path directly from his fruitful loin: It begins with his son Louis the Pious, via Lothar, Bertha, Willa, Rosele, eight men called Baldwin, and so on through the ages until it reaches the 21st century in a Dutch family called the Backer-Dirks, whose family tree all the way back to the king is publicly available online.


This pedigree, by gorgeous chance, also contains Joachim Neumann, a 17th-century German Protestant preacher, who sought peace and meditation away from the political machinations and church hullabaloo of Dusseldorf in a small cave near the river Dussel. He had changed his name from Neumann to a Greek version with the same meaning: new man. He wasn't the only new man in that cave. This was the location of the very first new human to be identified, a century later, in the valley of Joachim Neander—Neanderthal man.


Sometime at the end of the 13th century lived a man or woman from whom all Europeans could trace ancestry.

What a lineage to behold! It comes as no great surprise that in the world of amateur genealogy, being descended from imperial royalty is considered of high cachet. In fact, descent from anyone actually named from history brings prestige, as the vast majority of humans have drifted into and out of existence leaving little or no historical footprint that shows they ever drew breath. To be drawn from the bloodline of a king, and not just any old Holy Roman Emperor, but the very first, must be momentous.


Christopher Lee—the great actor who among his roles counts Dracula; Tolkien's Saruman the White; the Man with the Golden Gun himself, Scaramanga; the fallen Jedi Count Dooku; and The Wicker Man's Lord Summerisle—claimed direct ancestry to King Charlemagne via the ancient house of his mother, Countess Estelle Marie (née Carandini di Sarzano):

The Carandini family is one of the oldest in Europe and traces itself back to the first century A.D. It is believed to have been connected with the Emperor Charlemagne, and as such was granted the right to bear the coat of arms of the Holy Roman Empire by Emperor Frederick Barbarossa.1

Maybe it was to enhance his august yet sinister screen image as having played some of the wickedest characters in film history. Most people don't have a coat of arms, but I can say with absolute confidence that if you're vaguely of European extraction, just like cinema's greatest Prince of Darkness, you are descended from Charlemagne too. Hail to the king!

We are all special, which also means that none of us is. This is merely a numbers game. You have two parents, four grandparents, eight great-grandparents, and so on. Each generation back the number of ancestors you have doubles. But this ancestral expansion is not borne back ceaselessly into the past. If it were, your family tree when Charlemagne was Le Grand Fromage would harbor around 137,438,953,472 individuals on it—more people than were alive then, now, or in total. What this means is that pedigrees begin to fold in on themselves a few generations back, and become less arboreal, and more a mesh or weblike. You can be, and in fact are, descended from the same individual many times over. Your great-great-great-great-great-grandmother might hold that position in your family tree twice, or many times, as her lines of descent branch out from her, but collapse onto you. The further back through time we go, the more these lines will coalesce on fewer individuals. "Pedigree" is a word derived from the middle French phrase "pied de grue"—the crane's foot—as the digits and hallux spread from a single joint at the bottom of the tibia, roughly equivalent to our ankle. This branching describes one or a few generations of a family tree, but it's wholly inaccurate as we climb upward into the past. Rather, each person can act as a node into whom the genetic past flows, and from whom the future spills out, if indeed they left descendants at all.

This I find relatively easy to digest. The simple logic is that there are more living people on Earth now than at any single moment in the past, which means that many fewer people act as multiple ancestors of people alive today. But how can we say with utter confidence that any individual European is, like Christopher Lee, directly descended from the great European conciliator?

The answer came before high-powered DNA sequencing and ancient genetic analysis. Instead it comes from mathematics. Joseph Chang is a statistician from Yale University and wished to analyze our ancestry not with genetics or family trees, but just with numbers. By asking how recently the people of Europe would have a common ancestor, he constructed a mathematical model that incorporated the number of ancestors an individual is presumed to have had (each with two parents), and given the current population size, the point at which all those possible lines of ascent up the family trees would cross. The answer was merely 600 years ago. Sometime at the end of the 13th century lived a man or woman from whom all Europeans could trace ancestry, if records permitted (which they don't). If this sounds unlikely or weird, remember that this individual is one of thousands of lines of descent that you and everyone else has at this moment in time, and whoever this unknown individual was, they represent a tiny proportion of your total familial webbed pedigree. But if we could document the total family tree of everyone alive back through 600 years, among the impenetrable mess, everyone European alive would be able to select a line that would cross everyone else's around the time of Richard II.

Chang's calculations get even weirder if you go back a few more centuries. A thousand years in the past, the numbers say something very clear, and a bit disorienting. One-fifth of people alive a millennium ago in Europe are the ancestors of no one alive today. Their lines of descent petered out at some point, when they or one of their progeny did not leave any of their own. Conversely, the remaining 80 percent are the ancestor of everyone living today. All lines of ancestry coalesce on every individual in the 10th century.

One way to think of it is to accept that everyone of European descent should have billions of ancestors at a time in the 10th century, but there weren't billions of people around then, so try to cram them into the number of people that actually were. The math that falls out of that apparent impasse is that all of the billions of lines of ancestry have coalesced into not just a small number of people, but effectively literally everyone who was alive at that time. So, by inference, if Charlemagne was alive in the ninth century, which we know he was, and he left descendants who are alive today, which we also know is true, then he is the ancestor of everyone of European descent alive in Europe today.

It's not even relevant that he had 18 children, a decent brood for any era. If he'd had one child who lived and whose family propagated through the ages until now, the story would be the same. The fact that he had 18 increases the chances of his being in the 80 percent rather than the 20 percent who left no 21st-century descendants, but most of his contemporaries, to whom you are all also directly related, will have had fewer than 18 kids, and some only one, and yet they are all also in your family tree, unequivocally, definitely, and assuredly.


DNA says exactly the same thing as mathematical ancestry: Our family trees are not trees at all, but entangled meshes.

At least that's the theory. With the advent of easy and cheap DNA sequencing came the possibility of testing this math. DNA is the bearer of biological ancestry, and you get all of your DNA from your two parents, pretty much a 50:50 split. They in turn got all of their DNA from their parents, so one quarter of your DNA is the same as a quarter of each of your grandparents. If you have a cousin, then you share around an eighth of your DNA, as you have a pair of grandparents in common. These shared bits of DNA are not the same sections though. And it doesn't keep halving perfectly as you meander up through your family tree. Remember that DNA gets shuffled when a sperm or egg is made, and every single shuffle is different, but it's quite clumsy shuffling. In the newly shuffled deck, that is, your own personal genome, big chunks of it are the same as your father or mother. The more closely related two people are, the more DNA they will share in big chunks. This is why identical twins are identical (all the chunks are the same), and why siblings and parents look similar (half of their DNA is the same as each other). In genetics, we call these sections of DNA identical by descent, and they are very useful for measuring the relatedness of two individuals.


In 2013, geneticists Peter Ralph and Graham Coop showed that DNA says exactly the same thing as Chang's mathematical ancestry: Our family trees are not trees at all, but entangled meshes. They looked for lengths of identical by descent DNA in 2,257 people from around Europe (to mitigate the influence of recent migration, all the subjects selected had four grandparents from the same region or country). By measuring the lengths of the shared DNA, they could estimate how long ago that deck got shuffled, and therefore how related any two people are. Computing and DNA have empowered this field, and this is shown in their dataset and the number crunching that follows.

Joseph Chang's mathematical calculation didn't account for something very obvious, which is that we don't mate randomly. We typically marry within socioeconomic groups, within small geographical areas, within shared languages. But with Coop and Ralph's genetic analysis, it didn't seem to matter that much. Ancestry is such that genes can spread very quickly over generations. It might seem that a remote tribe would have been isolated from others for centuries in, for example, the Amazon. But no one is isolated indefinitely, and it only takes a very small number of people to breed out with people from beyond their direct gene pool for that DNA to rapidly descend through the generations.

Chang factored that into a further study of common ancestry beyond Europe, and concluded in 2003 that the most recent common ancestor of everyone alive today on Earth lived only around 3,400 years ago.

He used two calculations, one that simply crunched the math of ancestry, and another that incorporated a simplified model of towns and migration and ports and people. In the computer model, a port has a higher rate of immigration, and growth rates are higher. With all these and other factors input, the computer calculates when lines of ancestry cross, and the number comes out at around 1400 B.C. It places that person somewhere in Asia, too, but that is more likely to do with the geographical center point from which the migrations are calculated. If this sounds too recent, or baffling because of remote populations in South America or the islands of the South Pacific, remember that no population is known to have remained isolated over a sustained period of time, even in those remote locations. The influx of the Spanish into South America meant their genes spread rapidly into decimated indigenous tribes, and eventually to the most remote peoples. The inhabitants of the minuscule Pingelap and Mokil atolls in the mid-Pacific have incorporated Europeans into their gene pools after they were discovered in the years of the 19th century. Even religiously isolated groups such as the Samaritans, who number fewer than 800 and are sequestered within Israel, have elected to outbreed in order to expand their limited gene pool.

You are of royal descent, because everyone is. You are of Viking descent, because everyone is.

When Chang factored in new, highly conservative variables, such as reducing the number of migrants across the Bering Straits to one person every 10 generations, the age of the most recent common ancestor of everyone alive went up to 3,600 years ago.

This number may not feel right, and when I talk about it in lectures, it often results in a frown of disbelief. We're not very good at imagining generational time. We see families as discrete units in our lifetimes, which they are. But they're fluid and continuous over longer periods beyond our view, and our family trees sprawl in all directions. The concluding paragraph of Chang's otherwise tricky mathematical and highly technical study is neither of those things. It's beautiful writing, extremely unusual in an academic paper, and it deserves to be shared in full:

Our findings suggest a remarkable proposition: No matter the languages we speak or the color of our skin, we share ancestors who planted rice on the banks of the Yangtze, who first domesticated horses on the steppes of the Ukraine, who hunted giant sloths in the forests of North and South America, and who laboured to build the Great Pyramid of Khufu.

You are of royal descent, because everyone is. You are of Viking descent, because everyone is. You are of Saracen, Roman, Goth, Hun, Jewish descent, because, well, you get the idea. All Europeans are descended from exactly the same people, and not that long ago. Everyone alive in the 10th century who left descendants is the ancestor of every living European today, including Charlemagne, and his children Drogo, Pippin, and, of course, not forgetting Hugh. If you're broadly eastern Asian, you're almost certain to have Genghis Kahn sitting atop your tree somewhere in the same manner, as is often claimed. If you're a human being on Earth, you almost certainly have Nefertiti, Confucius, or anyone we can actually name from ancient history in your tree, if they left children. The further back we go, the more the certainty of ancestry increases, though the knowledge of our ancestors decreases. It is simultaneously wonderful, trivial, meaningless, and fun.

The truth is that we all are a bit of everything, and we come from all over. Even if you live in the most remote parts of the Hebrides, or the edge of the Greek Aegean, we share an ancestor only a few hundred years ago. A thousand years ago, we Europeans share all of our ancestry. Triple that time and we share all our ancestry with everyone on Earth. We are all cousins, of some degree. I find this pleasing, a warm light for all mankind to share. Our DNA threads through all of us.

Ancestry is messy and difficult. Genetics is messy and mathematical, but powerful if deployed in the right way. People are horny. Lives are complex. A secret history is truly hidden in the mosaics of our genomes, but caveat emptor. No scientific test exists that will tell you where the DNA that you would come to inherit was precisely located in the past. Human history is replete with the fluid movement of people, and tribes and countries and cultures and empires are never, ever permanent. Over a long enough timescale, not one of these descriptions of historical people holds steadfast, and only a thousand years ago your DNA began being threaded from millions from every culture, tribe, and country. If you want to spend your cash on someone in a white coat telling you that you're from a tribe of wandering Germanic topless warriors, or descended from Vikings, Saracens, Saxons, or Drogo of Metz, or even the Great Emperor Charlemagne, help yourself. I, or hundreds of geneticists around the world, will shrug and do it for free: You are. And you don't even need to spit in a tube—your majesty.

[Grinning_Colossus]

The numbers and the genes say the most recent ancestor for all living people was 3400 years ago.

That seems very unlikely unless there are literally no pure blooded Aboriginals or Native Americans left.

[Valmy]

The numbers and the genes say the most recent ancestor for all living people was 3400 years ago.

That seems very unlikely unless there are literally no pure blooded Aboriginals or Native Americans left.

Yeah it is probably more like 20,000 years ago. I just figure if I go back to the Roman Empire I am descended from Pompey Magnus billions of different ways...and you are to!

[Ed Anger]

The numbers and the genes say the most recent ancestor for all living people was 3400 years ago.

That seems very unlikely unless there are literally no pure blooded Aboriginals or Native Americans left.

Yeah it is probably more like 20,000 years ago. I just figure if I go back to the Roman Empire I am descended from Pompey Magnus billions of different ways...and you are to!

Ewwwwww. Pompey. 

[Valmy]

Ewwwwww. Pompey. 

And Sulla! And maybe Marius...not sure if he had any living descendants after his son killed himself.

[Ed Anger]

Marius disgusts me.

[Barrister]

The numbers and the genes say the most recent ancestor for all living people was 3400 years ago.

That seems very unlikely unless there are literally no pure blooded Aboriginals or Native Americans left.

There probably aren't any.  There's been substantial intermixing in the last 500 years.

[mongers]

The numbers and the genes say the most recent ancestor for all living people was 3400 years ago.

That seems very unlikely unless there are literally no pure blooded Aboriginals or Native Americans left.

There probably aren't any.  There's been substantial intermixing in the last 500 years.

Indeed, that was a salient point in the article.

[jimmy olsen]

The numbers and the genes say the most recent ancestor for all living people was 3400 years ago.

That seems very unlikely unless there are literally no pure blooded Aboriginals or Native Americans left.

The population of these continents collapsed by 90% and were then overrun by migrants from Eurasia and Africa. I'd be very surprised if there are any left.