Genetic walkabouts

Today's topic comes to us from the One Thing Leads To Another department.

I got launched into this particular rabbit hole by a notice from 23 & Me that they'd refined their analysis of their test subjects' DNA, and now had a bigger database to extract from, allowing them to make a better guess at "percent composition" not only by general region, but by specific sub-region.

So I took a look at my results.  My DNA came out 63.5% French, 25.3% Scottish and English, 6.4% Ashkenazi, and the remaining 4.8% a miscellany.  This works out to be pretty much what I'd expect from what I know of my family tree.  My mom was close to 100% French, but a great-grandfather of hers, one Solomon Meyer-Lévy, was a French Jew from Alsace and is the origin of the Ashkenazic DNA.  My dad was a bit of a hodgepodge in which French, Scottish, and English predominate.

So like I said, no surprises.  I'm a white guy of western European descent, which if you look at my profile photo, is probably not going to come as any sort of shock.

What I thought was more interesting was the regional breakdown.  The Scottish and English bits were especially interesting because I only have a handful of records documenting where exactly my British Isles forebears were from.  Apparently I have a cluster of genetic relatives around Glasgow, the London area, and Yorkshire.  Other than my dad's paternal family (which was from the French Alps, near Mont Blanc and the border of Italy) and my Alsatian great-great-grandfather, my French ancestry is all in western France; this lines up with what I know of my mom's family, which came from Bordeaux, Poitou, the Loire Valley, and Brittany.

So all of this shores up their claims to accuracy, because this was ascertained purely by my DNA -- I didn't send them my family tree, or anything.  But then this got combined with another random thing, which is that I've been reading a book called The Ancient Celts by anthropologist Barry Cunliffe, and I was kind of surprised at how much of Europe the Celts once ruled -- not only the British Isles and all of France (then called Gaul), but what is now Switzerland, southern Germany, Austria, the northern half of Italy, the eastern half of Spain, and down into a big chunk of the Balkans.  They seem to have been nothing if not inveterate wanderers, and their walkabouts took them just about everywhere in Europe but Scandinavia.  They were there for a long while, too; it was only when the Romans got their act together and started to push back that the Celts retreated; they were shoved farther west when first the Germanic tribes, and then the Slavs, moved in from the east and kind of kept moving.

[Image is in the Public Domain]

This all got me thinking, "Okay, when I say my ancestry is on the order of 2/3 French, what exactly am I saying?"  So I started doing some research into "the ethnic origin of the French," and I found out that it's not simple.  The western parts of France (whence my mom's family originated) are mostly of Celtic (Gaulish) ancestry.  People in the southeast, especially the lowlands near Marseilles, have a lot of Roman and Etruscan forebears.  When you get over into Languedoc -- the southwestern part of France, near the border of Spain -- there's an admixture not only from the Moors of North Africa, but from the Basques, who seem to be the remnants of the earliest settlers of Europe, and are the only ones in western Europe who don't speak an Indo-European language.  In Normandy there's a good admixture of Scandinavian blood, from Vikings who settled there a thousand years ago -- in fact, "Normandy" means "North-man-land."  Despite the fact that the name of the country and its people comes from a Germanic tribe (the Franks), the only place there's a significant amount of Germanic ancestry in France is in the east -- from Burgundy north into Alsace, Lorraine, and Picardy.

Apparently the only reason the French are Frankish is because the Franks ruled the place for a few hundred years, a bit the way the Normans did in England.  The common people, your average seventeenth-century peasants in Bordeaux, probably were nearly 100% Gaulish Celt.

So when I say my mom's family is French, and a guy from Lille and a woman from Marseilles say the same thing, what exactly do we mean?

And there's nothing unusual about the French in that regard; I just use them as an example because I happen to know more about them.  The same is true pretty much anywhere you look except for truly insular cultures like Japan, which have had very little migration in or out for millennia.  We're almost all composites, and ultimately, all cousins.  I remember when I first ran into this idea; that the further back you go, the more our family trees all coalesce, and at some point in the past every human on Earth could be sorted into one of two categories -- people who were the ancestors of every one of us, and people who left no living descendants.

That point, most anthropologists believe, is way more recent than most of us would suspect.  I've heard -- to be fair, I've never seen it rigorously proven, but it sounds about right -- that the two-category split for those of us with western European ancestry happened in around 1,200 C.E.  So pick out anyone from thirteenth century western Europe, and (s)he's either my ancestor, or (s)he has no descendants at all.

This brings up a couple of things.  First, "royal blood" is an idiotic concept from just about whichever angle you choose.  Not only does royal ancestry not confer fitness for leading a country -- let's face it, a lot of those kings were absolute loonies -- I can pretty much guarantee that I descend from Charlemagne, and if you have European ancestry, so do you.  My wife actually descends from an illegitimate child of King Edward IV of England (something she likes to remind me about whenever I get uppity), but the truth is, all of us have royal blood and peasant blood pretty well mixed indiscriminately.

Second, racism, ethnicism, and xenophobia are all equally ridiculous, since (1) we're virtually all genetic mixtures, (2) regardless of our ethnicity, our genetic similarities far outweigh our differences, and (3) we're all cousins anyhow.  I find that rather cool, honestly -- that a Zulu woman living in Botswana and I have common ancestry if you go back far enough.  Race is a cultural construct, not a genetic one, which you can see with extraordinary vividness if you take a DNA test, or if you read anything about the migration patterns humanity has taken since first leaving the East African savanna something like 250,000 years ago.

Anyhow, those are my musings about ethnicity, DNA, ancestry, and so on.  It all goes to show that we're wonderfully complex creatures, and the determination of some of us to see the world as if it was straightforward black-and-white is not only inaccurate, it misses a great deal of the most interesting parts of it.  As the brilliant science fiction writer Ursula LeGuin put it, "I never knew anybody who found life simple.  I think a life or a time looks simple only if you leave out the details."

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

Neanderthal family reunion

Last year, I did a 23 and Me DNA test.

Besides the not-particularly-earthshattering conclusion that I'm mostly French, Scottish, German, and Dutch, I was amused to find that the test showed I have 284 Neanderthal markers.  This puts me in the 60th percentile as compared to the population overall, which probably explains why I like my steaks rare and run around half naked when the weather is warm.

What's fascinating is that some research released last week, a paper in Cell by David Enard of the University of Arizona and Dmitri A. Petrov of Stanford University called, "Evidence that RNA Viruses Drove Adaptive Introgression between Neanderthals and Modern Humans," has shown that some of these genes didn't get passed along the usual way, but by a process called transduction -- when viruses transmitted from one host to another carry novel genes with them.

The authors write:

After their divergence 500,000 to 800,000 years ago, modern humans and Neanderthals interbred at least twice: the first time ∼100,000 years ago and the second ∼50,000 years ago.  The first interbreeding episode left introgressed segments (IS) of modern human ancestry within Neanderthal genomes, as revealed by the analysis of ancient DNA from a single Altai Neanderthal individual sequenced by Prüfer et al. (2014).  This first interbreeding event appears not to have left any detectable segments of Neanderthal ancestry in extant modern human genomes.  In contrast, the second interbreeding episode left detectable IS of Neanderthal ancestry within the genomes of non-African modern humans. 

Recent advances in the detection of introgression have led to the discovery that the majority of genomic segments initially introgressed from Neanderthals to modern humans were rapidly removed by purifying selection.  Harris and Nielsen (2016) estimated that the proportion of Neanderthal ancestry in modern human genomes rapidly fell from ∼10% to the current levels of 2%–3% in modern Asians and Europeans.
This history of interbreeding and purifying selection against IS raises several important questions. First, among the introgressed sequences that were ultimately retained, can we detect which sequences persisted by chance because they were not as deleterious or not deleterious at all to the recipient species, and which persisted not despite natural selection but because of it—that is, which IS increased in frequency due to positive selection?  If any of the introgressed sequences were indeed driven into the recipient species due to positive selection, can we determine which pressures in the environment drove this adaptation? 

Recently we found that proteins that interact with viruses (virus-interacting proteins [VIPs]) evolve under both stronger purifying selection and tend to adapt at much higher rates compared to similar proteins that do not interact with viruses.  We estimated that interactions with viruses accounted for ∼30% of protein adaptation in the human lineage.   Because viruses appear to have driven so much adaptation in the human lineage, and because it is plausible that when Neanderthals and modern humans interbred they also exchanged viruses either directly by contact or via their shared environment, we hypothesized that some introgressed sequences might have provided a measure of protection against the exchanged viruses and were driven into the recipient species by positive directional selection.  Consistent with this model, several cases of likely adaptive introgression from Neanderthals to modern humans involve immune genes that are specialized to deal with pathogens including viruses.

Which is amazingly cool.  Viruses are parasites, and as such usually wreak havoc with our systems, but here we have viruses acting as carriers not only for genes that generate diversity, but that protect our cells from the damage viruses can cause.

Great-great grandpa Ugg [Image licensed under the Creative Commons Stefan Scheer, Neandertaler reconst, CC BY-SA 3.0]

"It's not a stretch to imagine that when modern humans met up with Neanderthals, they infected each other with pathogens that came from their respective environments," lead author David Enard said.  "By interbreeding with each other, they also passed along genetic adaptations to cope with some of those pathogens."

"Many Neanderthal sequences have been lost in modern humans, but some stayed and appear to have quickly increased to high frequencies at the time of contact, suggestive of their selective benefits at that time," Petrov said.  "Our research aims to understand why that was the case.  We believe that resistance to specific RNA viruses provided by these Neanderthal sequences was likely a big part of the reason for their selective benefits."

"One of the things that population geneticists have wondered about is why we have maintained these stretches of Neanderthal DNA in our own genomes," Enard added.  "This study suggests that one of the roles of those genes was to provide us with some protection against pathogens as we moved into new environments."

So having Neanderthal DNA isn't something to be ashamed of.  All of this highlights how incredibly cool the evolutionary model is, and the depth of its explanatory power.  Now, y'all'll have to excuse me.  I'm going to go get a snack.  I wonder if I have any roast mammoth left in the fridge?  Probably not.  I guess grilled cheese will have to do.

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

This week's Skeptophilia book recommendation is from the brilliant essayist and polymath John McPhee, frequent contributor to the New Yorker.  I swear, he can make anything interesting; he did a book on citrus growers in Florida that's absolutely fascinating.  But even by his standards, his book The Control of Nature is fantastic.  He looks at times that humans have attempted to hold back the forces of nature -- the attempts to keep the Mississippi River from changing its path to what is now the Atchafalaya River, efforts in California to stop wildfires and mudslides, and a crazy -- and ultimately successful -- plan to save a harbor in Iceland from a volcanic eruption using ice-cold seawater to freeze the lava.

Anyone who has interest in the natural world should read this book -- but it's not just about the events themselves, it's about the people who participated in them.  McPhee is phenomenal at presenting the human side of his investigations, and their stories will stick with you a long time after you close the last page.

[If you purchase the book from Amazon using the image/link below, part of the proceeds goes to supporting Skeptophilia!]