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.

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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!]

Canine DNA analysis

When we adopted our latest rescue dog, Guinness, the people at the shelter told us that he was a Black Lab/Akita mix.  He certainly looks like it:

But I've heard from a lot of people that the assessments made at shelters are guesses at best, so a few months ago we had him DNA tested.  The results:

He is neither Black Lab nor Akita.

The test gave us the following results, most of which seem spot-on.  The largest portion of his ancestry is Staffordshire Terrier, which is one of the breeds from which Pit Bulls are bred.  He has the broad chest and blocky head of a pitty for sure.  The next three on the list were Husky, Chow, and Dalmatian.  He's got a curly tail and a thick, sleek coat, so those make some sense as well.  The only one I'm not buying is the last one on the list, which is Bichon Frisé, which (for the non-doggy people in the audience) is a small white dog that looks like a cross between a poodle and a cotton ball.

Maybe the white splotch on his chest and the tips of his toes are from his Bichon ancestry, I dunno.  Or maybe one just ran into him at some point, and that's the splat mark.

So okay, maybe the DNA tests have their issues, too.  But at least the majority of it makes sense, from his appearance and personality, the latter of which is seventy pounds of spring-loaded bounce.  He has two settings: full throttle and off.  Our mellow old coonhound, Lena, frequently looks at him with this expression that says, "Dude, you have got to switch to decaf."

This all comes up because of a study out of Arizona State University that appeared in PLoS-One a couple of weeks ago.  Titled, "More Than a Label: Shelter Dog Genotyping Reveals Inaccuracy of Breed Assignments," the researchers took DNA samples from nine hundred shelter dogs and ran a full genotypic analysis on them.  The results were startling; they found ancestry from 125 different breeds, and the accuracy of the breed assignment by the shelter was only ten percent.

It shouldn't be surprising; the handful of genes that codes for basic body shape and features like coat color, eye color, ear shape, and so on, and relatively responsive to selective breeding, and since that's what we're basing our assessment on, it stands to reason we'd get misled.  If you keep selecting the same thing over and over in two unrelated lineages, you'll eventually end up with their progeny looking like each other.  (This is called convergent evolution and is why the marsupial sugar glider and the flying squirrel are so strikingly similar; it's also why distantly-related groups of humans who live near the equator all have dark skin despite not sharing recent ancestry.)

"Breed identification has quite an outsize role in people's perceptions of dogs," said Clive Wynne, professor of psychology and head of the Canine Science Collaboratory at ASU, and co-author of the study.  "'What breed is he?' is often the first question people ask about a dog, but the answer is often terribly inaccurate."

As far as Guinness, I did ask what breed he was, but it was more out of curiosity than any kind of deciding factor regarding our potentially adopting him.  I fell for him right away, and he's turned out to be a sweetheart, despite being (and I say this with the utmost affection) a big galoot.  (Which my wife tells me in Latin translates to "galooteus maximus."  We are all about multilingual wordplay in this family.)

But it's still interesting how far wrong they were.  I get why they thought "Black Lab," with his shiny, thick, jet-black coat; it never really occurred to me to question it.  When I got the test results back, I was pretty stunned.

I guess it's no wonder, though, with a 90% fail rate.

So anyhow, keep adopting rescue animals -- it's the best way to go.  We've always gotten rescues and never gone wrong.  But don't necessarily believe what they tell you about the breed.

Now, I gotta go, because Guinness is ready to play his sixth round of "fetch the rubber ball over and over."  Simple pleasures, y'know.  And maybe I can get him to run off some of his ya-yas.  As the trainer told us, "A tired dog is a good dog."

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This week's recommendation is a classic.

When I was a junior in college, I took a class called Seminar, which had a new focus/topic each semester.  That semester's course was a survey of the Book Gödel, Escher, Bach: An Eternal Golden Braid by Douglas Hofstadter.  Hofstadter does a masterful job of tying together three disparate realms -- number theory, the art of M. C. Escher, and the contrapuntal music of J. S. Bach.

It makes for a fascinating journey.  I'll warn you that the sections in the last third of the book that are about number theory and the work of mathematician Kurt Gödel get to be some rough going, and despite my pretty solid background in math, I found them a struggle to understand in places.  But the difficulties are well worth it.  Pick up a copy of what my classmates and I came to refer to lovingly as GEB, and fasten your seatbelt for a hell of a ride.

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

Alien DNA test

Online Critical Thinking course -- free for a short time!

This week, we're launching a course called Introduction to Critical Thinking through Udemy!  It includes about forty short video lectures, problem sets, and other resources to challenge your brain, totaling about an hour and a half.  The link for purchasing the course is here, but we're offering it free to the first hundred to sign up!  (The free promotion is available only here.)  We'd love it if you'd review the course for us, and pass it on to anyone you know who might be interested!

Thanks!

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Today we're going to take a break from subatomic physics and the Big Bang, not to mention the current state of political affairs (and I'm using that in both senses of the word) in the United States, to consider:

DNA tests that are designed to see if you have alien ancestry.

As with so many of the topics I address here at Skeptophilia, I owe this one to Reddit, that amazing clearinghouse for ideas from profound to ridiculous to completely baffling.  The post on Reddit that clued me in to the fact that alien DNA testing is a thing lands toward the "baffling" end of that continuum, although to be fair, the person who found it posted it on r/Skeptic, so they clearly didn't believe it themselves.

It was accompanied by a screencap of the offer on eBay, which I include below:

Being that the print is a little small, let me list the salient features:

• It sounds like your typical DNA analysis kit, wherein you spit into a test tube and send it in.  I did one of these (23 & Me) just out of curiosity, not that there's anything particularly in question about my own ancestry.  My heritage is French, Scottish, German, Dutch, and English, and my DNA came back: French, Scottish, German, Dutch, and English.  At least it speaks well for the accuracy of the analysis, not to mention my genealogical research and the low incidence of infidelity in my family.  (Incidentally, my DNA profile allowed me to connect with four different people whom I had not known before, and who turned out to be fairly close cousins.)
• The difference here is that instead of telling you your ethnic makeup, this test purports to tell you how much of it doesn't originate on planet Earth.  Note that it is accompanied by a highly scary-looking artist's representation of an individual who, if your test turns out to be positive, is apparently your Great-Great-Great Grandpa G'zork.
• It originates in Canada, and you can't have it shipped to the United States.  I find this a little suspicious.  I mean, it could be because it would require the transportation of bodily fluids across national boundaries, which could be a serious issue vis-à-vis disease transmission, but I prefer the hypothesis that it's because here in the United States, they'd prefer it if we don't find out we're actually aliens.  So far, apparently they're keeping Rudy Giuliani in the dark, and he looks a lot more like the aforementioned G'zork than most of the humans I've seen.
• It costs only $15.95 (Canadian).  This is a hell of a deal, especially given what it purports to do.  My 23 & Me test set me back eighty bucks, which I spent to find out what I more or less already knew.  (It did tell me that I have about three hundred "Neanderthal gene markers," which probably explains why I like my steaks on the rare side, and periodically feel like hitting people with a club, especially the ones who walk really slowly while blocking the entire aisle in the grocery store.)

So to any of my Canadian readers who don't mind sacrificing sixteen bucks for a little empirical research, I encourage you to buy a kit, and let us know here at Skeptophilia headquarters about the results.

Having a background in genetics, however, I have to wonder what they're using for their basis of comparison.  I know that in the historical documentary The X Files, the government had lots of deep-frozen alien babies in a lab somewhere, which (of course) Mulder found and (of course again) Scully didn't get to see.  So did they do a genetic analysis of the alien babies?

More importantly, why am I putting so much effort into analyzing this?

My general feeling is that even if alien intelligence exists, it's extremely unlikely that it will have a similar biology to ours, and even less likely that it will encode its genetic material the same way.  (Witness the fact that even related terrestrial species, who have fairly recent common ancestry, can't interbreed.)  So the chance of human/alien hybridization is nil, and that's even assuming they have naughty bits that are of the right size and shape to be compatible with ours.

Anyhow, that's our dip in the deep end for today.  And if you turn out to have alien DNA, I'm sorry if I sounded scornful.  I don't mean to insult your family.

Although I'd make an exception in the case of Rudy Giuliani.

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This week's featured book is a wonderful analysis of all that's wrong with media -- Jamie Whyte's Crimes Against Logic: Exposing the Bogus Arguments of Politicians, Priests, Journalists, and Other Serial Offenders.  A quick and easy read, it'll get you looking at the nightly news through a different lens!