The genes of the ancestors

When I had my DNA tested two years ago, I found out I have 330 distinctly Neanderthal markers in my genes.  This, apparently, is well above average for people of western European descent, and may explain why I like to run around half-naked and prefer my steaks medium-rare.

In all seriousness, most people of European descent have Neanderthal ancestry; it's less common in people of African and Asian ancestry, and in the indigenous peoples of Australia and North America.  It makes sense, once you know where they lived.  The Neanderthals were a predominantly European species (or sub-species; the experts differ, and honestly, the definition of species is so mushy anyhow that it's probably splitting hairs to argue about it).  They seem to have split off from the main population of hominins in the region something like five hundred thousand years ago.  The first unambiguously Neanderthal bones are 430,000 years old, and they persisted until 40,000 years ago -- and we still don't know why they died out.

What's certain is that it wasn't a lack of sophistication and intelligence by comparison with contemporaneous Homo sapiens, whatever you might have gleaned from Jean Auel's The Clan of the Cave Bear.  The Neanderthals were plenty smart.  They had culture, made paintings on cave walls, and created jewelry.  To judge by the Divje Babe flute they made music.  They ceremonially anointed their dead, and appear to have had some concept of an afterlife.  They had the same version of the FOX-P2 gene we do, suggesting they had spoken language.  So despite my earlier quip, Neanderthals were far from the slow, sluggish, stupid "cave men" we often picture when we hear the name.

[Image licensed under the Creative Commons Werner Ustorf, Neanderthal man reconstruction, Natural History Museum, London, CC BY-SA 2.0]

As my own ancestry indicates, there was a good bit of crossbreeding between Neanderthals and "modern" humans.  (I put modern in quotes not only because it's self-congratulatory, but because all organisms on Earth have exactly the same time duration of their ancestral lineages; words like primitive and modern really "less changed since the common ancestor" and "more changed since the common ancestor," but those are clunky.  So I'll continue to use primitive and modern, although with the caveat that they're not value judgments.)

What's interesting, though, is that the genetic input of the Neanderthals was asymmetrical.  Of the Neanderthal markers we carry around, none are on the Y chromosome, indicating that something blocked any contribution of Y-chromosomal genes from our Neanderthal forebears.  It's possible that the answer is simple -- that most inter-species matings were between "modern" human men and Neanderthal women.  But now a new study from The American Journal of Human Genetics, by Fernando Mendez, G. David Poznik, and Carlos Bustamante (of Stanford University), and Sergi Castellano (of the Max Planck Institute for Evolutionary Anthropology) has suggested another reason the Neanderthal Y chromosome didn't survive; mutations that caused male hybrid fetuses to spontaneously miscarry.

The authors write:

Sequencing the genomes of extinct hominids has reshaped our understanding of modern human origins.  Here, we analyze ∼120 kb of exome-captured Y-chromosome DNA from a Neandertal individual from El Sidrón, Spain.  We investigate its divergence from orthologous chimpanzee and modern human sequences and find strong support for a model that places the Neandertal lineage as an outgroup to modern human Y chromosomes—including A00, the highly divergent basal haplogroup.  We estimate that the time to the most recent common ancestor (TMRCA) of Neandertal and modern human Y chromosomes is ∼588 thousand years ago (kya)...  This is ∼2.1 times longer than the TMRCA of A00 and other extant modern human Y-chromosome lineages.  This estimate suggests that the Y-chromosome divergence mirrors the population divergence of Neandertals and modern human ancestors, and it refutes alternative scenarios of a relatively recent or super-archaic origin of Neandertal Y chromosomes.  The fact that the Neandertal Y we describe has never been observed in modern humans suggests that the lineage is most likely extinct.  We identify protein-coding differences between Neandertal and modern human Y chromosomes, including potentially damaging changes to PCDH11Y, TMSB4Y, USP9Y, and KDM5D.  Three of these changes are missense mutations in genes that produce male-specific minor histocompatibility (H-Y) antigens. Antigens derived from KDM5D, for example, are thought to elicit a maternal immune response during gestation.  It is possible that incompatibilities at one or more of these genes played a role in the reproductive isolation of the two groups.

Which is an interesting hypothesis.  It's possible, of course, that there was more than one thing going on, here; there may also have been a skewed distribution of genders in inter-species matings as well as a higher death rate in male children of male Neanderthals and female "modern" humans.   In fact, genetics and culture can sometimes create a feedback loop; the taboo in traditional Basque society against Basque women marrying non-Basque men is thought in part to have come from the high frequency amongst the Basques of the Rh negative blood group allele, resulting in children of Basque women (likely to be Rh negative) and non-Basque men (likely to be Rh positive) having a higher probability of dying of Rh incompatibility syndrome.

So sometimes cultural norms and genetics can intertwine in curious ways.

In any case, that's today's science story, tying together anthropology, genetics, and evolutionary biology, all particular fascinations of mine.  And the fact that it could well be talking about some of my own ancestry adds a nice twist.  Hopefully my forebears will forgive me for my jab about running around naked.  Maybe the most Neanderthal thing about me is that I play the flute.  Kind of turns the "cave man" trope upside down, doesn't it?

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Unity in diversity

It was in my evolutionary biology class in college that I ran into a concept that blew my mind, and in many ways still does.

It was the idea that race is primarily a cultural feature, not a biological or genetic one.  There is more genetic diversity amongst the people of sub-Saharan Africa -- people who many of us would lump together as "Black" -- than there is in the rest of the world combined.  A typical person of western European descent is, our professor told us, closer genetically to a person from Japan than a Tswana man is to the !Kung woman he lives right next door to in Botswana, even though both have dark skin and generally "African features."

To reiterate: I'm not saying race doesn't exist.  It certainly does, and the social, cultural, and political ramifications are abundantly clear.  It's just that what we often think of as race has very close to zero genetic support; we base our racial classifications on a handful of characteristics like skin and eye color, the shape of the nose and mouth, and the color and texture of the hair, all of which can so easily undergo convergent evolution that it triggers us to lump together very distantly-related groups and split ones that lie much closer together on the family tree.

The reason this comes up today is a couple of bits of recent research highlighting the fact that the subject is way more complicated than it seems at first.  The first looks at the fragmentation that happened in Africa, on the order of twenty thousand years ago, that resulted in the enormous genetic diversity still to be found in sub-Saharan Africa today.  By analyzing DNA from both living individuals and the remains of people from long ago, researchers at Harvard University found that this was about the time that our ancestors stopped (for the most part) making extended walkabouts to find mates, and settled into being homebodies.  What triggered this is a matter of conjecture; one possibility is that this was in the middle of the last ice age, it could be that the colder and drier conditions (even in equatorial regions) made food scarcer, so long trips into unknown territory were fraught with more danger than usual.

Whatever the cause, the isolation led to genetic drift.  A general rule of evolutionary biology is that if you prevent genetic mixing, populations will diverge because of the accrual of random mutations, and that seems to be what happened here.  The fact that a Tswana person and a !Kung person (to use my earlier example) are so distinct is because they've been genetically isolated for a very long time -- something facilitated by a tendency to stay at home and partner with the people you've known all your life.

Interestingly, some research last year suggested that there are "ghost lineages" in the human ancestry -- groups that are ancestral to at least some modern humans, but are as yet unidentified from the fossil record.  The one studied in last year's paper were ancestral to the Yoruba and Mende people of west Africa, in which between two and nineteen percent of the genomes come from this ghost lineage -- but the phenomenon isn't limited to them.  The authors found analogous (but different) traces of ghost lineages in people of northern and western European and Han Chinese descent, and the guess is that all human groups have mysterious, unidentified ancestral groups.

The other bit of research that was published last week was an exhaustive study of the genetics of people around the world, with an ambitious goal -- coming up with a genetic family tree for every group of people on Earth. "We have basically built a huge family tree, a genealogy for all of humanity that models as exactly as we can the history that generated all the genetic variation we find in humans today," said Yan Wong of the University of Oxford, who co-authored the study.  "This genealogy allows us to see how every person's genetic sequence relates to every other, along all the points of the genome."

The researchers analyzed 3,609 individual DNA samples representing 215 different ethnic groups, and used software to compare various stretches of the DNA and assemble them using the technique called parsimony -- basically, creating a family tree that requires the fewest random coincidences and ad hoc assumptions.  The result was an enormous genealogy containing 27 million reconstructed common ancestors.  They then linked location data to the DNA samples -- and the program identified not only when the common ancestors probably lived, but where they lived.

I find this absolutely amazing.  Using modern genetic analysis techniques, we can assemble our own family tree, with roots extending backwards tens of thousands of years and encompassing lineages for which we have no archaeological or paleontological records.  With the number of connections the research generated, I have no doubt we'll be studying it for years to come, and have only started to uncover the surprises it contains.

But all part of living up to the maxim inscribed in the Temple of Apollo at Delphi -- γνῶθι σεαυτόν.

"Know thyself."

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Genetic walkabout

Coming hard on the heels of yesterday's post about a woman who claims to be descended from Joseph of Arimathea, today we have some actual valid research, using mtDNA from two-millennium-old teeth in Syria to show that Mesopotamia deserves its moniker "the Cradle of Civilization" -- that same mtDNA signature shows up today as far away as Tibet.

Mitochondrial (mt) DNA is unique in that it always inherits through the matrilineal ancestry.  In other words, you contain the same mtDNA as your mother's mother's mother's etc., as far back as you like to go.  This takes out the role of recombination in your genetic makeup -- the random scrambling of the chromosomes in the nucleus every time they're passed on makes it damn near impossible that the same two parents could produce two genetically identical (non-twin) children.  But with mtDNA, the only differences occur from mutations, which are infrequent -- so this allows us to determine the relationships between different human populations, and track their movements back into prehistory.

My earliest-known matrilineal ancestor, Marie-Renée Brault (born in France in around 1616) had the mtDNA haplotype H13a1a, places her origin in western Europe (which we already knew), and the "H clade" to which she belongs is the commonest mtDNA in Europe.  So no big surprises there.

[Image licensed under the Creative Commons Vanesa Álvarez-Iglesias , Ana Mosquera-Miguel , Maria Cerezo, Beatriz Quintáns, Maria Teresa Zarrabeitia, Ivon Cuscó, Maria Victoria Lareu, Óscar García, Luis Pérez-Jurado, Ángel Carracedo, Antonio Salas, Spatial frequency distribution of different sub-lineages of mtDNA haplogroup H, CC BY 2.5]

Likewise, my two known Native American ancestors, both from the Abenaki tribe of Nova Scotia, were proven as such by their matrilineal descendants having a characteristic "A clade" mtDNA signature, which clearly demonstrates their ethnic heritage -- and their ultimate connection to other A-clade members in Siberia, Korea, and Japan.

The research that got me started on all this is not new, but was new to me; I was sent a link by a friend and loyal reader of Skeptophilia to a paper in PLOS-ONE called, "mtDNA from the Early Bronze Age to the Roman Period Suggests a Genetic Link between the Indian Subcontinent and Mesopotamian Cradle of Civilization," by Henryk W. Witas, Krystyna Jędrychowska-Dańska, and Tomasz Płoszaj (of the University of Łódź), Jacek Tomczyk (of Cardinal Stefan Wyszyński University), and Gyaneshwer Chaubey (of the Biocenter of Estonia).  And in this paper, we find out that an mtDNA type -- haplogroup M4 and M6, which currently are found only in India -- apparently are older than anyone realized, and came from what is now Syria:

Ancient DNA methodology was applied to analyse sequences extracted from freshly unearthed remains (teeth) of 4 individuals deeply deposited in slightly alkaline soil of the Tell Ashara (ancient Terqa) and Tell Masaikh (ancient Kar-Assurnasirpal) Syrian archaeological sites, both in the middle Euphrates valley.  Dated to the period between 2.5 Kyrs BC and 0.5 Kyrs AD the studied individuals carried mtDNA haplotypes corresponding to the M4b1, M49 and/or M61 haplogroups, which are believed to have arisen in the area of the Indian subcontinent during the Upper Paleolithic and are absent in people living today in Syria.  However, they are present in people inhabiting today’s Tibet, Himalayas, India and Pakistan.  We anticipate that the analysed remains from Mesopotamia belonged to people with genetic affinity to the Indian subcontinent since the distribution of identified ancient haplotypes indicates solid link with populations from the region of South Asia-Tibet (Trans-Himalaya).

The amazing part of this isn't so much in the details, but the method.  Mitochondrial DNA extraction from fossilized teeth can give us information about the movement of people back into prehistory. These ancestors of ours, about whom we know virtually nothing -- not their names, their faces, their professions, their cultures -- tell us about their travels by the genetic information carried in their bodies.

Which I find absolutely fascinating.  It's kind of mind-boggling that I carry a bit of DNA in my cells (lots of bits of it, in fact) that originated in the Middle East twenty-thousand-odd years ago, was carried from mother to daughter as these people moved into eastern Europe, crossing the Alps into France, and thence across the Atlantic Ocean to Nova Scotia for over a hundred years -- then back to France after they lost the French and Indian War and got kicked out -- and finally crossed the Atlantic again in 1785 to settle in southeastern Louisiana.

And each of you carry in your own cells pieces of DNA that have equally long, convoluted, and unexpected histories.

Makes you realize that we're all connected, down to the very instructions that built us, and are far more alike than we are different.

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These days, I think we all are looking around for reasons to feel optimistic -- and they seem woefully rare.  This is why this week's Skeptophilia book recommendation of the week is Hans Rosling's wonderful Factfulness: Ten Reasons We're Wrong About the World--and Why Things Are Better Than You Think.  

Rosling looks at the fascinating bias we have toward pessimism.  Especially when one or two things seem seriously amiss with the world, we tend to assume everything's falling apart.  He gives us the statistics on questions that many of us think we know the answers to -- such as:  What percentage of the world’s population lives in poverty, and has that percentage increased or decreased in the last fifty years?  How many girls in low-income countries will finish primary school this year, and once again, is the number rising or falling?  How has the number of deaths from natural disasters changed in the past century?

In each case, Rosling considers our intuitive answers, usually based on the doom-and-gloom prognostications of the media (who, after all, have an incentive to sensationalize information because it gets watchers and sells well with a lot of sponsors).  And what we find is that things are not as horrible as a lot of us might be inclined to believe.  Sure, there are some terrible things going on now, and especially in the past few months, there's a lot to be distressed about.  But Rosling's book gives you the big picture -- which, fortunately, is not as bleak as you might think.

[Note: if you purchase this book using the image/link below, part of the proceeds goes to support Skeptophilia!]

Aliens in the family tree

A frequent contributor to Skeptophilia sent me a link a couple of days ago with the note, "More grist for your mill."  As soon as I looked at the website address, I knew it was gonna be good, for two reasons.

The first is that the link was from The Daily Mail, a "news" source so sensationalized and tripe-filled that a lot of people call it The Daily Fail.  It seems to have replaced The National Enquirer as the go-to spot for information about celebrities, political sex scandals, and UFO sightings.

The second was that the title of the article was, "Humans Do NOT Come From Earth."

Upon opening the link, we find that a gentleman named Ellis Silver has written a book, coincidentally given the same title as the article.  Silver himself is a Ph.D.  How do I know?  Because on his book cover, which shows a picture of the Earth with Photoshopped black alien eyes, he calls himself "Ellis Silver Ph.D."

I'm always a bit put off when people do this.  It's a bit of a recursive appeal to authority.  My feeling is that if your ideas stood on their own merits, you wouldn't need to brag about your degree -- and that if what you're saying is ridiculous, the fact that you have a degree doesn't somehow make it sensible.  I wasn't able to find where his degree was from, but most of the sites that mention him call him "an American ecologist," so I suppose that must be what his doctorate is in.

Be that as it may, the review in The Daily Mail begins thusly:

A U.S. ecologist has claimed that humans are not from Earth but were put on the planet by aliens tens of thousands of years ago.

Dr Ellis Silver points to a number of physiological features to make his case for why humans did not evolve alongside other life on Earth, in his new book.

They range from humans suffering from bad backs - which he suggests is because we evolved in a world with lower gravity – to getting too easily sunburned and having difficulty giving birth.

Dr Ellis says that while the planet meets humans’ needs for the most part, it does not perhaps serve the species’ interests as well as the aliens who dropped us off imagined.

Well, this tells me two things right off: (1) Silver doesn't understand how evolution works; and (2) he hasn't spent much time looking at the problems other animals have.

Evolution is, at its heart, the law of "whatever works."  The fact that we are the only primate species that stands upright for long periods is what has resulted in our lower back problems -- our spines, which have the characteristic gentle s-bend in the middle, are a brilliant way to carry weight if you support yourself on your knuckles, but don't work so well if you are standing up.  (When was the last time you saw a front porch supported by a curved pillar?)  But the problems such a design engenders were, apparently, outweighed by the advantages conferred to our distant ancestors -- seeing further over tall grass and leaving our hands free to manipulate tools being two probable ones.

Secondly, we are hardly the only species that has trouble managing the vagaries of its environment.  Every species has traits that can backfire, or work well in some contexts and not so well in others.  Even the lowly brine shrimp of Great Salt Lake die by the millions of osmotic shock every time there's a sudden snow melt and subsequent influx of fresh water.

Maladaptive traits can exist for a variety of reasons.  One possibility is that they once were beneficial, but aren't any longer because circumstances changed -- a so-called "evolutionary misfire," like moths and other insects circling around light bulbs and ultimately getting fried.  (This behavior apparently originates from insects using distant light sources to navigate at night, and that strategy being confounded by nearby light sources.)  Others, like the peacock's unwieldy and cumbersome tail, probably evolved because of sexual selection pushing a trait to the point that it becomes a hindrance.  Still others crop up because of pleiotropy -- the fact that a single gene can have several different phenotypic manifestations, each carrying their own advantages and disadvantages.  The gene that causes seal-point coat color in Siamese cats, for example, can result in their having crossed eyes.

But Dr. Silver discounts all of the hundreds of examples of evolutionary compromise and outright maladaption in nature, and claims that humans are "the only ones who have these problems."  And his answer, according to The Daily Mail:  "He suggests that Neanderthals such as Homo erectus were crossbred with another species, perhaps from Alpha Centauri, which is the closest star system to our solar system, some 4.37 light years away from the sun."

Right.  "Neanderthals such as Homo erectus."  Which were two entirely different species, making that statement a little like saying, "Pigeons such as eagles."  And somehow, an alien species coming from an entirely different star system would have DNA that was compatible enough to proto-hominids (whatever species they were) that they could produce offspring at all?

Funny, isn't it, that there is a 98.7% overlap, genetically, between humans and our nearest relatives, the bonobos?  And that our bone structure shows 100% homology with other primates?  And that we give every evidence, in every respect, of being perfectly ordinary terrestrial animals, without a drop of green extraterrestrial blood?

Of course, this hasn't stopped woo-woo websites from picking up the story, and giving Dr. Ellis Silver Ph.D. all sorts of undeserved attention.  Besides his appearance in The Daily Mail, Silver has made Prison Planet, Above Top Secret, UFO Sightings Hotspot, Unexplained Mysteries, and a host of other "news" sources even less reputable.

Oh, and I forgot to mention why Silver thinks all of this happened.  "One reason for this," Silver says,"is that the Earth might be a prison planet, since we seem to be a naturally violent species and we're here until we learn to behave ourselves."

Well, that certainly seems to be working out well, doesn't it?

You know, I think this sort of thing springs from the same desire that drives a lot of the religious attitudes toward humanity vis-à-vis nature -- that we humans are somehow different, special, set apart.  I still see it in my biology classes, in which even bright kids will use phrases like "humans and animals," as if humans weren't animals themselves.  So I guess if you don't get your sense of species superiority from being a Unique Creation of God, you have to get it from being the Progeny of Aliens.

So that's our journey into the far side for today.  It's not, mind you, that I have any particular objection to the conjecture that life may exist elsewhere in the universe -- in fact, I think that to be so likely as to be a near certainty.  I just think that the chance of their being our great-grandparents contradicts everything we know about biology, human and otherwise, and that's even taking into account how odd my own family can be at times.