What do you think about this article re: Neanderthal genetics?

Question

https://getpocket.com/explore/item/genetics-spills-secrets-from-neanderthals-lost-history

Answer 1

Hi, Mark. I'm one of the nerds who is interested in this stuff, so thanks for posting.

The link is a reprint of an article originally published in Quanta Magazine September 2017. Its basis, as described in the piece, is a paper by Rogers, Bohlender, and Huff, published 2017 in PNAS: "Early history of Neanderthals and Denisovans."

In the paper, the authors write: "Our method extends an idea introduced by Reich et al." Citations for that statement were a September 2009 paper in Nature by Reich, Thangaraj, et al., "Reconstructing Indian population history," and Green, Krause, et al., "A Draft Sequence of the Neandertal Genome," Science, May 2010.

Also of some interest are the sources for the raw DNA Rogers and company used for their analyses. Both sets of data came from the Max Planck Institute for Evolutionary Anthropology. The Denisovan data was from sequencing done in 2012, and the Altai Neanderthal data was sequenced in May 2013.

Those dates are just on the cusp of big sequencing technology improvements that began circa 2014. There's no reason to believe the older data is incorrect, but more extensive sequencings have been done since, a good deal of it by David Reich's lab at Harvard.

If you're interested, a good follow-up read for general audiences is Reich's popular 2018 book, Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past. It's available at Amazon for a little over $10 in both Kindle and paperback formats.

Comments

Thanks for sharing this. I suspected there were many small, sub-populations. The focus seems to be on Gibraltar and parts of Germany, but people with relatively large amounts of Neanderthal DNA do not seem disproportionately heavily German or Spanish, granted their recent history may differ greatly than their genetic history from 50K years ago. You still would expect even the slightest inkling of a pattern within the current population around Gibraltar, but the only thing static is general European ancestry, and some Asian. They had to have been more spread out, as the article suggests, and I suspect there will be many more discoveries of Neanderthal bones in our lifetimes, but throughout Europe, and not just where they are initially focusing their interest.

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Thanks for the best-answer star, Tiah...and then Mark. 

When I saw the news a few minutes ago, I had to jump back over here just so I could make note of it: the Nobel Prize in Physiology or Medicine was awarded today to trailblazing Swedish population geneticist Svante Pääbo.

Among a long career of firsts and inspiring others, including David Reich, to pursue the genetics of ancient populations, Pääbo was a co-author on the May 2010 paper in Science I linked above, "A Draft Sequence of the Neandertal Genome." It was for his work in ancient genomics that the Nobel committee singled him out.

I also mentioned that the Denisovan and Altai Neanderthal DNA sequences used in Rogers's study are at the Max Planck Institute for Evolutionary Anthropology (and available to download, should anyone wish) where Dr. Pääbo became director in 1997.

Dr. Pääbo's CV is posted on the Institute's website at https://www.eva.mpg.de/genetics/staff/paabo/. A summary of the Nobel Prize award, along with a brief biography of Svante Pääbo, is available in a public article at Science: https://www.science.org/content/article/nobel-prize-physiology-or-medicine-2022.

Coincidences in timing are sometimes exceedingly odd, aren't they?

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1. By heart I made this timetable to show that there isn't any reason to expect more Neanderthal-DNA around Gibraltar. The mixing-up was many thousands year aerlier and the peopling with the ancestors of the modern Spaniards was many thousands years later. 

now: descendants of the people who now and then mixed up  with Neanderthal and Denisovian carry their genes for more than 60.000 years
3.000 bc: People of haplogroup R1b entering Spain 30.000 years after the Neanderthals became extinct
14.000 bp End of the glacial time; repeopling of the northern areas
20.000 BP the LGM Last Glacial Maximum: Neanderthals extinct; Denisovans nearly?
35.000 BP last Neanderthal populations in refugia like Gibraltar; no common offspring with these people
60.000 - (?) 30.000 BP:mixing up with Denisovans in Central;, East, South and Sout-East Asia.
70.000 BP Out of Africa II Homo sapiens; leaving Africa: now and then realtions between Neanderthal and H. sapiens, mainly in the Middle East
110 - 100 kY: rare encounters between H. Sapiens and Neanderthal in th Middle East (e.g. Karmel mountain); maybe the first common offspring.

Answer 2

According to 23 and Me I have more Neanderthal than 90% of their users.

Answer 3

It's interesting from an anthropological, or DNA, viewpoint, if that's what one is interested in. Like the 23andMe results detailing "Neanderthal ancestry", I don't find much relevance in it to the work that I do in genealogy. But everyone has different interests.

Please don't interpret this as a slight about posting the article, though! Keep posting things like this!

Comments

In the past I thought there likely is no relevance to ancient DNA and populations to our genealogy.  Now I believe ancient DNA really informs the human genome and identifies discreet populations that are unique which help to researchers to determine early migration patterns and the development and composition of the modern Homo Sapien.

As with dinosaurs and other early animals, DNA and archeological finds force us to evaluate and reconsider how and why our evolution and resulting ancestry developed as it did. What does it mean to us today?  Are there inherent qualities, behaviors, or attitudes that are informed by these ancient couplings?  

I personally believe it is quite interesting.  I have been listening to books on tape regarding early populations 400 AD into the 16th and 17th century that serves to identify attitudes, beliefs, prejudices, territorial conflicts, and alliances that bring us to migrations to the Americas and how attitudes have been informed over time.  Each territorial conflict / conquest resulted in a shift in how and why our early ancestors did what they did and why and how this led us to this point in our lineage today.  We carry all that came before us in who each of us are today.  To me, DNA helps to identify those major influences.

When I started working on my family history I had no idea about my lineage.  Learning that I had strong German and English lines on my father's side gave me several aha moments about who I and my family are and why.  The Eastern and Baltic DNA from my mother's family informs a very different world view and attitude.  

Neanderthal influences are there.  I am not sure how their DNA impacted what might have been otherwise, but there is no doubt there were serious and significant influences at the time that inform who we are today, no matter how subtle.  Time may better inform what they brought forward to us.  I have read studies regarding the understanding of who the Neanderthals actually were.  They were much more intelligent than what is appears to be generally accepted. 23andme shows that I have 2% Neanderthal DNA.  I am open to learn what that means to the person I am today.

Answer 4

I have more Neanderthal DNA than 94% of 23andMe users, which comes out to 288 variants. I've only seen 2 profiles with a higher amount than me (96%).

The descriptions the site gives about what it is supposed to mean don't seem accurate to me. For example, difficulty discarding rarely used possessions, worse sense of direction, and fear of heights not only don't apply to me in the slightest, but I also actually don't see how they apply to Neanderthals, given what science has been able to tell about them.

If you switch to facts from a variety of sources in general, then things start to get insightful. What strikes me the most is the more muscular bodies, propensity to tan, nicotine addiction, and allergies, to name a few. These things explain a lot about my life over the years, and hindsight is 20/20.

It's not that I have more muscle (and I doubt people with 2% Neanderthal DNA look more muscular in general), but it's something about the composition. All my life I've received comments like "Holy crap, you're strong!" It's not that I'm a body builder - it's that they didn't expect an average to slim sized young lady to do what she just did and not give it a second thought. I take on carrying and moving heavy things that many ladies would have some men come take care of. I actually just moved myself to a new apartment literally by myself, with not one person helping me, furniture and bed and all, from a third story apartment to a second story apartment, and it was just not a big deal. I have many more examples of this.

I also have some extremely unusual trait about tanning. I have fair Norwegian skin if I haven't been in the sun, but it ranges to an olive Italian shade if I've got some sun recently. But, I also admittedly have a tanning addiction and have had a membership at a high tech salon with these crazy machines for most my adult life. If I haven't tanned in a long time, I'll go in the machines for 10-12 minutes, then the next day I'll be red for maybe 10 hours, then the next day, I'm so dark you'd think I was from the Middle East. It's completely eerie what my skin does.

I'll also admit I'm a serious nicotine addict. I started smoking around age 13, and thankfully I got off the cigarettes as a young adult, but swapping it for hookah with my Arab friends, but I had to have one at home. Realizing that was not as bad as cigarettes, but still kind of bad, I swapped it for e-cigarettes (opting for the higher, at least 5% nicotine) about 5 years ago. I smoke these non-stop like a chimney. (Note: e-cigarettes are not "vapes," though often confused for them - they do not have the correlation with "popcorn lungs" that vapes do, which are based on a liquid pod.) Now, obviously, this is a very bad habit, but going from cigarettes to e-cigarettes, you reduce the number of chemicals from about 400 to about 3, depending. I don't feel like I'm doing something bad that I shouldn't do - I feel like I truly love nicotine, and I need it like air and water. It's weird.

As for allergies, I think I'm about a couple years away from becoming that girl on A&E locked in her basement with sealed walls, no windows, 20 air purifiers, and no one can enter without completing 5 hours of rituals to purify themselves first! I am allergic to everything, went through 5 years of immunotherapy with 12 shots per week, and still I'm on the verge of an ER trip every day of my life. I even have allergies no one has heard of, such as, for example, I'm literally allergic to cold temperature. My entire body can break out in hives from doing the dishes with cold water - not just my hands that touched the cold water. I used to live in Minnesota, and it was absolute torture. I had to spend the first couple hours of school every day in the nurse's office letting my hives wear off.

Now, is Neanderthal DNA the cause of all these things? Correlation does not imply causation, but...I will say, I've found nothing else that offers to explain all these strange things that make me different.

Comments

There is a theory I am researching that one reason that neanderthals were absorbed by homo sapiens was their comparative lack of empathy. They were never able to construct larger societal groups beyond immediate family and were thus unable to compete with much larger homo sapiens groups who supported each other in tribes or clans. Scientists have proven that certain kinds of empathy, to a  degree, have a genetic basis. (Quite recently scientists have identified a neanderthal genome that makes severe Covid more likely so we know these neanderthal genomes can affect human traits, strengths and weaknesses!) Therefore, it's possible that, in general, people with higher levels of neanderthal dna are more likely to have less empathy, but no one has mapped the "empathy" gene yet in either neanderthal or homo sapiens dna, so for now it is just an intriguing theory. I wonder if this empathy gene or genes has an affect on today's political divisions. Divisive issues like immigration, student debt forgiveness, homelessness, etc. seem to have their roots in empathy -- or the lack of it. Might we someday learn that Trump supporters have more neanderthal dna than Trump haters?

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Jerry, this is fascinating stuff. Thanks for your reply.

You may be onto something or other, but there's a couple issues here. I work in psychology and am ABD for my Ph.D. in philosophy, by the way.

One issue is when you say "they were never able to construct much larger societal groups." There's at least 2 issues with that. One, just because they didn't, doesn't mean they weren't "able" to...it only means they didn't. Secondly, it's only from the perspective of the group that did, that doing so is valued more, but that doesn't mean it's valued in the sense of absolutes.

Now, when it comes to empathy and a genetic basis, I thought it was already common knowledge out there that there is genetic basis for that, so I agree with you. But, there's just so much more to it than that. Isolating its genetic basis would be putting it in a vacuum. First, there are other reasons or inspirations for larger societal groups beyond empathy, driving people to create them. It could come down to a simple tit for tat. Second gets to the nurture versus nature debate. I'm not sure it's really a debate anymore, but at any rate, just because there is a genetic basis, doesn't mean there aren't environmental influences and factors as well, and just because there are genes involved, doesn't mean those genes are activated. There are active and inactive genes. (A further fascinating point is what activates an inactive gene because I hear it's not so simple as all your active genes being active since birth, but there are factors that can set them off during life.) What's more, genes aren't the be all and end all of empathy, even if empathy is localized in certain genes. With nurture also playing a factor, there is a whole field of research as to whether empathy can be taught. The only thing I see conclusive about this so far is that there are certain factors that may preclude empathy from being taught, such as antisocial personality disorder, which is as permanent and untreatable as mental retardation. Aside from those types of permanencies, there is indication both humans and other animals can learn empathetic behaviors.

There is also stigma attached to the notion of even "going there" to explore whether we can accomplish what we aim to accomplish in society without empathy. Anything emotional or touchy feely is generally held as sacred, and the exploration of how to achieve our goals with less of it is something that may not occur in our lifetimes. But, it may be the solution to all the crime and problems you mention, if those problems are to prevail and persist. If you can't beat them, join them (or, at least figure out how to defeat them from the standpoint of their own worldview).

Answer 5

Svante Paabo's Nobel Prize:  https://www.nobelprize.org/prizes/medicine/2022/press-release/