Human Phylogeography: The lessons learned, 1

June 4, 2019 • 9:10 am

by Greg Mayer

UPDATE. A couple of readers have drawn attention to the website, gcbias, of Graham Coop, a population geneticist at UC Davis. He has excellent discussions, with nice graphics, of issues in genetic genealogy, including calculation of the number of “genetic units” in particular generations. As an example, 7 generations back you have 256 ancestors, but only 286 genetic units produced by recombination, so although, on average, you will have a chunk from each of those 256, it is entirely plausible to have zero (since inheritance is stochastic). It’s well worth browsing, and this and this are good places to start. (Thanks to rich lawler and S. Joshua Swamidass for the pointers.)


In February, I posted the syllabus for a seminar class entitled “Human Phylogeography” that I was teaching with my colleague Dave Rogers. The seminar was based primarily on a close reading of David Reich’s (2018) Who We Are and How We Got Here (published by OUP in the UK). Well, the class has concluded now, and so I thought I’d report back on what happened.

First, I’d like to say that the class was a success. We had 16 students, double the most I’ve ever had in a number of similar seminar courses over the years, and the students were very successful in engaging with the subject in both written and oral contributions to the class. One of the students was a history major, and towards the end of the semester a colleague in computer science mentioned that, quite coincidentally, he was reading the book, so he joined the class for the last few meetings. In many ways, it was what college is supposed to be like (though too often isn’t). I hope the students learned a lot. I did, and here is the first of the three most striking things I learned.

1. Recombination is a lot rarer than you think.

If you think back to the last time you studied genetics, you’ll recall the phenomenon of recombination, one aspect of which is crossing over. Crossing over occurs during meiosis. Chromosomes come in homologous pairs (23 pairs in humans, for 46 total), and in meiosis the homologues can exchange pieces with one another. The chromosomes physically touch and cross one another, which is observable under the microscope, and are called, appropriately enough, chiasmata (chiasma, sing.)

Image result for crossing over meiosis
From BioNinja, https://ib.bioninja.com.au/standard-level/topic-3-genetics/33-meiosis/crossing-over.html

Recombination is important for a variety of reasons (for one, it increases genetic variability), but for our current purposes its importance is that it breaks up the nuclear genome from 23 genetic units into more, and smaller, units (as opposed to the mitochondrial genome, which has a number of genes, but all are inherited as a single genetic unit, since there is no recombination in mitochondria). In humans, it turns out, there are only 1-2 crossovers per chromosome per generation (1.2 per chromosome in fathers, 1.8 in mothers).

Now, I’d always thought that crossing over occurred frequently enough that we could think of the genome as essentially infinitely divisible. (There are 3 billion base pairs in the human genome, so, in the limit, there would be 3 billion genetic units, so not quite infinite!) But, it turns out that crossovers occur sufficiently infrequently that there is an appreciable chance that, if you go enough generations back, you share NO genes with your ancestor. This is because the number of ancestors goes up fast (2, 4, 8, 16, 32, 64, 128, 256, etc.), but the breaking up of the genome into smaller units by crossing over isn’t fast enough to ensure that the probability of sharing nothing is near zero.

Here’s a figure from Reich’s book showing how blocks of genes are broken up by recombination.

From Reich, 2018.

You start with an entirely Neanderthal chromosome (dark), which enters the anatomically modern human population by hybridization. A few generations later, the Neanderthal chromosome has been broken up, but it still occurs as largish blocks amongst the anatomically modern sections (gray). Still later, the blocks are smaller and fewer. (We’re assuming continued backcrossing into the anatomically modern population, so the % Neanderthal decreases; there could also be selection causing changes in the frequency of Neanderthal alleles). Finally, a present day individual has his Neanderthal DNA broken up into even smaller bits.

Here’s a figure from a talk by Svante Pääbo, showing in the top row for each chromosome (there are 22 listed, from 1-22) the entire genome of “Oase Boy” from 40K years ago in Romania. The green lines are Neanderthal sites in his genome. The five rows below Oase Boy are five modern human individuals; the colored lines are their “Neanderthal bits”. Note that for each chromosome, Oase boy has the biggest block of Neanderthal genes (green fluorescece):

From Pääbo , 2018. (Click to enlarge.)

Because of the age of the Oase sample, some of the black lines are missing data, and so Pääbo infers that there are seven large continuous blocks of Neanderthal genes (yellow bars above the Oase Boy line). Note that the modern individuals have less Neanderthal DNA, and it is not in large blocks.

Because the size of the blocks breaks up in a statistically predictable fashion, you can get a “recombination clock“, so that based on the size of the blocks you can estimate how many generations ago the hybridization occurred. For Oase Boy, Pääbo estimated that his Neanderthal ancestor occurred 4-6 generations back (his great great, or great great great, or great great great great grandfather).

From Pääbo , 2018, showing Oase’s Neanderthal ancestor (red) in the 5th generation (it could also be in the 4th or 6th).

Because the placement and frequency of crossing over is stochastic (random), the situation must be statistically modeled to derive sound estimates, and there will be a range of plausible estimates. And, since some of the fossils are well dated by other means, we can also estimate the long term human generation time, as was done by Priya Moorjani and her colleagues: it’s 26-30 years.

So, the low rate of recombination allows us to construct a “recombination clock”, and to estimate generation times. This is great stuff!

It also solved for me what was a puzzle. You may recall that last year Elizabeth Warren released the results of DNA tests showing that she had American Indian ancestry several generations back. This essentially confirmed what her family’s oral history said. The amount of her Indian ancestry was small (less than 1%), and a range of generations (6-10) was provided by the analysis (as was done by Pääbo for Oase Boy).

Now, there are a number of ways which these ancestry tests can be criticized, one of the most difficult for them being that there are very few North American Indian genotypes in the database used, and thus “American Indian” relationship is indicated by relationship to Central and South American Indians. Some critics of Warren, however, made erroneous criticisms. She did not contend, as some accused her of, of saying the results showed she was Cherokee—with few if any Cherokee in the database, the ancestry tests could not determine this. (And tribal membership is a legal matter, anyway, not directly dependent on genetic similarity.)

But some critics said that the data were consistent with her having no Indian ancestry at all. I wondered how they could say that– there are 3 billion bp, and 1 % of that is still a very large number. But now I realize my error. There are very many fewer genetic units– more than 23, but a lot less than 3 billion!– due to low rates of recombination. And, because of this, if you go back several generations, there is an appreciable probability of sharing no DNA with an indubitable ancestor. I now believe the critics must have looked at the latter fact, and realized Warren may not have DNA from all of her ancestors, and thus suggested she may have no Indian ancestry. But their error is that in saying she may lack DNA from an ancestor, say, 8 generations back, they are invoking an a priori probability. But in Warren’s case, her DNA was examined, and showed that she did have Indian ancestry.


Gravel, S. 2012. Population genetic models of local ancestry. Genetics 191:607-619. pdf

Ho, S. Y., Chen, A. X., Lins, L. S., Duchêne, D. A., & Lo, N. 2016. The genome as an evolutionary timepiece. Genome Biology and Evolution 8: 3006–3010. pdf

Huff, C.D. et mult. 2011. Maximum-likelihood estimation of recent shared ancestry (ERSA). Genome Research 21:768-774. pdf

Moorjani P, Sankararaman S, Fu Q, Przeworski M, Patterson N, Reich D. 2016. A genetic method for dating ancient genomes provides a direct estimate of human generation interval in the last 45,000 years. Proceedings of the National Academy of Sciences USA 113:5652-7. pdf

Pääbo, Svante. 3 October 2018. A Neanderthal Perspective on Human Origins. (video: embedded below)

Reich, D. 2018. Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past. Pantheon, New York.

Human Phylogeography

February 23, 2019 • 11:33 am

by Greg Mayer

For the spring semester, my colleague Dave Rogers and I are teaching a seminar class entitled “Human Phylogeography.” Phylogeography is the study of the history of the genetic variation, and of genetic lineages, within a species (or closely related group of species), and in the seminar we are looking at the phylogeography of human populations. DNA sequencing now allows a fine scale mapping of the distribution of genetic variation within and among populations, and, remarkably, the ability to sequence ancient DNA from fossil remains (including Neanderthals). The seminar is based primarily on a close reading of David Reich’s (2018) Who We Are and How We Got Here (published by OUP in the UK).

A Krapina, Croatia, Neanderthal woman, photo by Jerry.

Although rarely under that rubric, human phylogeography has been a frequent topic of discussion here at WEIT, by Jerry, Matthew, and myself, including our several discussions of Neanderthals (or Neandertals) and Denisovans. So it may be of interest for WEIT readers to follow along. Below the fold I’ve placed the course syllabus, which includes the readings, and links to many newspaper articles of interest, and online postings, including many here at WEIT, and also from John Hawks Weblog, a site we’ve recommended on a number of occasions when discussing human evolution. (The newspaper links appear as images; just click to go to the story.) We just finished our third meeting, and I’ve been quite impressed by the students’ discussion and writing. We’re fortunate to have some students from anthropology or with some anthro background.

Please read along with us, or browse what seems interesting below. If you have questions or comments, post them here, and I’ll be looking in.

Continue reading “Human Phylogeography”

Nature paper suggests humans inhabited North America 130,000 years ago

April 27, 2017 • 5:43 pm

by Greg Mayer

As Jerry noted yesterday, in a new paper in Nature, Steven R. Holen and colleagues report finding the remains of a butchered 130,000 year old mastodon in San Diego. (If you haven’t already done so, do go take a look at Jerry’s post, which includes a video press release, and illustrations from the paper.)

The key words in the first sentence are ‘butchered’* and ‘San Diego’. The first word indicates that people had taken the bones of the 130,000 year old mastodon apart– which in itself would be a “neat, but what’s the fuss” result. It’s ‘San Diego’ that’s the cause of the fuss. The peopling of the Americas has been a contentious topic for some time, but virtually all the debate has concerned a relatively slim time interval– 12-30 kya (see here for a previous discussion at WEIT, and this news piece in Science about two recent papers with contrasting conclusions). The San Diego find is thus 100,000 + years earlier!

So what evidence do they have for this early arrival? First, they have the mastodon, whose bones were fractured in ways which they find inconsistent with damage by carnivores or the environment, but which appear consistent only with being struck with implements. They did a lot of breaking of elephant bones in order to try to simulate the damage to the mastodon, and concluded that tools alone could do the trick. The mastodon’s remains were radiometrically dated at 130.7 ± 9.4 kya. In addition to the mastodon, they also found stone tools, which they interpret as hammerstones and anvils.

These results would have many important implications for human evolutionary history; but first we must ask, are the results correct?

I must admit I’m dubious. The anvil and hammerstones are not the sorts of objects which are unquestionably manufactured– they are not like finely fluted spear points, whose human origin cannot be doubted. The breakage patterns in the bones do indicate that the breaks occurred perimortem, but I’m not sure the breaks could not be due to non-human causes. The dating is directly on the mastodon, which is good– they’ve not dated some possibly extraneous item which could have been redeposited from earlier strata. But, nonetheless, dating is subject to various artifacts.

As Carl Sagan used to say, “Extraordinary claims require extraordinary evidence.” What makes the current claim extraordinary is that there’s no other evidence of human presence in the Americas for ca. 100+ K years after this find. And it’s not like the late Quaternary of America is an unstudied or poorly known stretch of time! I don’t regard fracture patterns and crude tools to be sufficiently extraordinary evidence to overcome, in a single go, the weight of that 100,000 year absence. It is much more reasonable to think that the new data can be reconciled with all the past data in a way that does not require us to discount the past data. And, thinking, “they must have made a mistake somewhere with the new data”, is a perfectly plausible way of reconciling the two. This conservatism in the face of anomalies is a key part of the method of science– it properly proportions belief to the evidence.

On the other hand, the new data do not threaten to overturn any fundamental principles, merely a seemingly well-attested fact of evolutionary history, and such facts have been overturned before. So, we must ask, but what if they’re right?

The most interesting implication, to me, is that if there were people here 130 kya, they went completely extinct.  It means that human habitation of an entire hemisphere is an iffy thing. The real first Americans got wiped out by something– disease, predators, climate, competitors, whatever. Who would these now extinct people have been? Well, if they got to America not too long before the radiometric date, they would probably be Neanderthaloid (by which I mean the varied archaic Eurasian subspecies of Homo sapiens with which anatomically modern humans interbred after their spread from Africa). If they came much earlier, they might have been Homo erectus (which would make Harry Turtledove’s A Different Flesh, in which the first European settlers of America encounter not Indians, but “sims“, prophetic!).

There would also be a possibility that these first Neanderthaloid Americans survived, and that the anatomically modern human colonizers of ca. 20 kya, interbred with them in the course of replacing them, just as their forebears did in Asia. However, because American Indians are not, as far as I know, enriched for Neanderthaloid alleles relative to other Eurasians (who are 1-4% Neanderthaloid; a bit higher in Melanesia), this seems unlikely. (There are claims out there that Indians are enriched for Neanderthaloid genes, but I don’t know how that got started; East Asians, from which, at least generally, American Indians descend, are Neanderthaloid enriched relative to Western Europeans, which seems to indicate more than one episode of interbreeding on the course of their migration from Africa.)

* I use “butchered” here in the sense of “processed for eating”, as the bones were presumed broken apart to get at the marrow. The paper uses “butcher” in the narrower sense of “cut with a knife or similar implement”. The paper does not say the mastodon was cut with a knife or other sharp tool.


Holen, S. R., T. A. Deméré, D. C. Fisher, R. Fullagar, J. B. Paces, G. T. Jefferson, J. M. Beeton, R. A. Cerutti, A. N. Rountrey, L. Vescera, and K. A. Holen. 2017. A 130,000-year-old archaeological site in southern California, USA. Nature 544:479-483.

Why we should be excited by 100,000 year old human teeth from China

October 15, 2015 • 7:10 am

by Matthew Cobb

I told you all the other day – discoveries in recent human evolution are appearing at an astonishing pace. I just gave my final lecture of the year to the students on the first year Genes, Evolution and Development course at the University of Manchester; last night, at around 23:30, I had to change the lecture because of a discovery that had just been reported in Nature.

47 teeth, clearly from modern humans, have just been found in a massive cave system in southern China. They are dated to over 80,000 years ago – the date range is 80-120,000 years. There were no tools associated with the find, so the researchers asssume that people were not living in the cave system, but rather these teeth came from bodies that were dragged into the caves by large predators (hyena bones were also found). Here are the teeth – these could have been pulled from your mouth (although they probably show less decay than would be in your teeth – much less than in mine!).

Photo: S. Xing and X-J. Wu (Nature).

Why is this a big deal? Because we weren’t supposed to be there at that time. Although there was archaeological evidence of humans having left Africa at around this time – there are traces of 100,000 year old human settlements in Israel – it had been argued that the expansion never got any further, and that the key wave of migration took place around 50-60,000 years ago.

These 47 teeth show that humans successfully left Africa and colonised an important part of the planet, tens of thousands of years earlier than we thought.

This figure from Liu et al (2015) shows the location of the material in the cave system:

a, Location of the Daoxian site. Late Middle Pleistocene and Late Pleistocene localities with human remains that have been included in the morphological and/or metric comparison with Daoxian are also marked on the map. 2: Tianyuan Cave; 3: Huanglong Cave; 4: Liujiang; 5: Zhiren Cave; 6: Tubo; 7: Xujiayao; 8: Luna; 9: Chuandong; 10: Malu Cave; 11: Lijiang; 12: Longlin; 13: Huli Cave; and 14: Xintai. The map is adapted from the original Chinese map from National Administration of Surveying, Mapping and Geoinformation of China (http://219.238.166.215/mcp/index.asp). b, General view of the interior of the cave and the spatial relationship of regions IIA, IIB and IIC, with some of the layers marked. c, Plan view of the excavation area. d, Detail of the stratigraphic layers of region II of the Daoxian site. All human fossils come from layer 2.

The key question now is what happened to that first wave of migration – did they die out, or did they meet up with subsequent migrants and exchange their genes? For the moment, there is no DNA to be analysed from these teeth. Furthermore, if people went to China, why didn’t they also spread up into Europe at this earlier date? We are confident this is not the case, because all the archaeological evidence argues against it.

Maybe Western Eurasia was too full of Neanderthals at the time, and it was only later, around 50,000 years ago that it was ecologically possible for hunter-gatherers to spread northwards – this would suggest that when we did successfully colonise Western Eurasia, either the Neanderthal population had already diminished for unknown reasons, or we had decisive cultural advantages that enabled us to rapidly spread into their areas.

As I said in a previous post, if I had my time over again, this is the area of science I would study. It is simply amazing.

This infographic from Nature sums up the new way of thinking:

 

References:

Callaway (2015) ‘Teeth from China revea early human trek out of Africa’. Nature website

Liu, W. et al. ‘The earliest unequivocal modern humans in Southern China’ Nature http://dx.doi.org/10.1038/nature15696 (2015).

Yes, Neanderthals are us!

October 23, 2014 • 9:03 am

by Greg Mayer

In a paper published today in Nature, Qiaomei Fu and colleagues report a high quality genome sequence derived from a 45,000 year old, anatomically modern human femur found in western Siberia. “Ust’-Ishim Man” has provided the oldest known genome of an anatomically modern human (there are earlier genomes of archaic humans).

Usht'-Ishim Man's femur (from Nature).
Ust’-Ishim Man’s femur (from Nature).

So, why is this interesting? First, it is a marvelous technical achievement to be able to get a high quality sequence out of a bone of such great age recovered from a riverbank. Kudos to Fu and her colleagues for this achievement. Second, Ust’-Ishim Man proves to be very interesting phylogenetically. While definitely non-African in his genetic affinities, he appears to be equidistant from both modern Europeans and modern East Asians. Fu et al. interpret him as being at or near the point in time when the split occurred between these two branches of humanity, making him part of the lineage of modern humans that had left Africa, but had not yet split into European and East Asian sub-lineages.  Third, by being able to identify the genetic differences between Ust’-Ishim and modern man, they were able to estimate the mutation rate in both the nuclear and mitochondrial genomes. The autosomal mutation rate was about .5X10E-9 per site per year, the Y chromosome mutation rate was higher, about .75X10E-9 per site per year, and the mitochondrial rate much higher, about 2.5X10E-8 per site per year. These rates and their mutual relations are about exactly what we would expect, but it’s nice to have fairly direct estimates, over a long time base, to confirm estimates based on short term de novo mutation studies and comparison of contemporaneous sequences.

And, finally, there’s what we learn about the interbreeding between anatomically modern humans and Neanderthals. As Jerry, John Hawks, and I have all argued before (and as I recently summarized at The Dish—  see the update at end of Andrew’s post), Neanderthals and early non-African anatomically modern humans (along with Denisovans), were all parts of a group of interbreeding populations in nature, and thus were all members of the species Homo sapiens. Ust’-Ishim Man’s genome is about 2% Neanderthal, just like modern Europeans and East Asians. This means that the level of admixture characterizing modern populations was already in place by 45,000 years ago. This is not too surprising. Neanderthals were going or gone by about then, so whatever interbreeding occurred should have (mostly) occurred by then. So Neanderthals are us.

Figure 5: Regions of Neanderthal ancestry on chromosome 12 in the Ust’-Ishim individual and fifteen present-day non-Africans. The analysis is based on SNPs where African genomes carry the ancestral allele and the Neanderthal genome carries the derived allele. Homozygous ancestral alleles are black, heterozygous derived alleles yellow, and homozygous derived alleles blue. (From Fu et al. 2014).
Figure 5: Regions of Neanderthal ancestry on chromosome 12 in the Ust’-Ishim individual and fifteen present-day non-Africans. The analysis is based on SNPs where African genomes carry the ancestral allele and the Neanderthal genome carries the derived allele. Homozygous ancestral alleles are black, heterozygous derived alleles yellow, and homozygous derived alleles blue. (From Fu et al. 2014).

But that’s not all. Modern humans are separated by some tens of thousands of years, and thousands of generations, from the time our forebears interbred with one another. During this time, recombination between the chromosomes of our anatomically modern and Neanderthal ancestors will have broken up the originally contiguous chromosome segments, dispersing the two sets among one another. Since the great majority of our genome is from anatomically modern ancestors, this will most easily be seen in our Neanderthal genetic component, which will become scattered throughout the anatomically modern part. This is exactly what is seen in the 15 modern non-African genomes in the figure above– the yellow and blue Neanderthal segments are scattered throughout the black anatomically modern background.

But when interbreeding first occurs, the two genomes will be separate. The first “hybrid” child will have one set of Neanderthal chromosomes, and one set of anatomically modern chromosomes. When that child produces gametes, its chromosomes will undergo crossing over— an exchange of chromosome segments– during meiosis, so that its children will receive a chromosomal gemisch: each chromosome will consist of alternating stretches of Neanderthal and anatomically modern parts. In subsequent generations, crossing over occurs again, so the contiguous segments from the founding generation keep getting broken up into smaller and smaller bits. So, if we catch the genome fairly soon after the genetic admixture has occurred, we should see that the chromosome segments occur in larger, contiguous blocks– and that’s exactly what Fu and colleagues found!

Look at the top row in the figure above. That’s Ust’-Ishim Man– note that his Neanderthal DNA occurs in larger blocks, indicating that it has not yet been fully broken up by crossing over. His genome represents an earlier stage in the genetic admixture of Neanderthals and anatomically modern humans. The actual interbreeding has already occurred– he’s 2% Neanderthal– but his Neanderthal DNA still largely occurs in unrecombined blocks. Based on this, Fu and colleagues have been able to calculate about how long before Ust’-Ishim Man the interbreeding occurred, and come up with a figure of about 300 generations, or about 10,000 years before Ust’-Ishim Man. So, the interbreeding occurred on the order of 50-60,000 years ago.

You might also wonder why our genomes are mostly from anatomically modern humans. If they and Neanderthals interbred, shouldn’t it be 50-50? Well, no– it would be 50-50 only if there were an equal number of ancestors from the two groups, but that’s not necessarily the case (in fact, we know it’s not the case in this instance). Most of the “hybrids” must have backcrossed (i.e. had children) with anatomically modern humans. There are many instance in history of two modern human groups meeting and interbreeding, but with a rather unqequal genetic contribution to the descendant populations. In the case of Neanderthals, the ratio was about 1 to 49. It’s easy to imagine how this might happen– a lone Neanderthal being adopted into a modern group, with its descendants therefore breeding mostly with the numerically predominant moderns. Many other scenarios could be posited, but they would be mostly speculative.

Whenever I see interesting results in human evolution, I always check to see what John Hawks has to say, but he’s not posted on this yet; fortunately Carl Zimmer at the NY Times has been able to get a hold of John personally, and ask him what he thinks:

“It’s irreplaceable evidence of what once existed that we can’t reconstruct from what people are now,” said John Hawks, a paleoanthropologist at the University of Wisconsin who was not involved in the study. “It speaks to us with information about a time that’s lost to us.”

That’s absolutely right of course, but I’d like to hear more of what he has to say, and I hope he will post something on the new discoveries.

____________________________________________________________

Fu, Q., et al. 2014.Genome sequence of a 45,000-year-old modern human from western Siberia. Nature 514:445-449. abstract

When did the Neanderthals go extinct?

August 28, 2014 • 7:36 am

by Greg Mayer

In a recent paper in Nature (abstract only), Tom Higham of Oxford and several colleagues report on their effort to determine by radiocarbon dating when Neanderthals went extinct. Higham et al. conclude that it was about 40,000 years ago. It’s gotten a fair amount of media coverage—more on this below—but let’s look at the science first. What’s most interesting is that they strove very hard to get accurate dates not biased by contamination of their samples by younger carbon (developing new and refined methods along the way), and that they sampled a large number of sites across (mostly Western) Europe. Here’s the basic result.

a) Sites studied; b) dates of last occupation of the various sites (expressed as a probability distribution).
a) Sites studied; b) dates of last occupation of the various sites (expressed as a probability distribution); c) detail of the overall estimate of the end of Neanderthal culture (the Mousterian).

You can see that latest dates range from about 49 to 40 KYA, with a joint estimate of the end of the Mousterian culture at about 40 KYA. There are a few caveats. First, there’s no explanation in the paper for why there are no dates in panel (b) for the 7 southern Iberian localities. These sites are of special interest, because it has been argued in the past that the latest survival of Neanderthals (ca. 35 KYA) was in southern Spain. The Spanish localities are mentioned in the 160+ page supplement, and some are said to not have produced reliable data, but others did, and, maybe the answer’s buried somewhere in the enormous supplement, but I could not readily locate it. (This by the way, is yet another example of the bad practice, characteristic of Science and Nature, of having extremely short papers with monographic online supplements that contain not just the details, but critical parts of the work. If your work is that substantial, then you should publish a monograph, not a tiny summary in Science or Nature.)

Second, many of the sites have little in the way of human remains, so the datings are of a particular cultural style, and the associated type of human is assumed (Neanderthal in the case of the Mousterian), although on fairly robust empirical grounds.

And third, the geographic sampling is sparse outside Western Europe. A claimed late refuge in the Arctic, for example, was not sampled. (There was a very late refuge, until historic times, for mammoths in the Arctic.)

What about the media coverage? It’s been very confused– see examples here and here. Media reports hail the work as showing that Neanderthals went extinct earlier than previously thought; and that we now know Neanderthals and anatomically modern humans overlapped significantly in time, thus allowing opportunities for the genetic mixing that has been now well documented (and much discussed here at WEIT). But these two claims are contradictory– earlier extinction means less temporal overlap; and the second thing is something we’ve known for quite awhile.

So what are we to make of the media claims? Well, the new work doesn’t say much at all about genetic mixing– it occurred whether Neanderthals were all gone by 40 KYA (as this latest work proposes), or survived in Spain till 35 KYA (as some earlier authors had claimed). Higham et al. estimate that there was an overlap of several thousand years of Neanderthals and anatomically modern humans, plenty of time for interbreeding. If the Spanish localities really are a late survival of Neanderthals, that would just add a few thousand more years of opportunity. Now, it will be of great interest to learn (if we can) exactly when and where the interbreeding occurred, but the new paper just adds constraints to the timing– it doesn’t suddenly make interbreeding now seem plausible.

I normally go see what John Hawks has to say about paleoanthropological matters, especially as in this case, since I felt perhaps I was missing something. I looked, but he hasn’t posted in a few weeks– he must be on vacation. I expect he’ll have something to say when he returns.

____________________________________________________________

Higham, T et al. 2014. The timing and spatiotemporal patterning of Neanderthal disappearance. Nature 512:306-309. (abstract only)

h/t Barry Lyons

Neanderthals are us?

May 15, 2011 • 9:03 pm

by Greg Mayer

At least since Socrates explored the meaning of the Greek maxim “Know thyself”, and Alexander Pope added that “the proper study of Mankind is Man”, we have been interested in knowledge about ourselves. But who are we? A paper in press in the Proceedings of the National Academy of Sciences by Ron Pinhasi and colleagues raises this issue with regard to Neanderthals, an issue which Jerry considered a while back: are they us?

In several senses, they obviously are us: fellow mammals, fellow primates, fellow hominids, and fellow members of the genus Homo, and thus men in the generic sense (in both the vernacular and technical senses of generic). But are they members of the same species as us, Homo sapiens? Or members of a distinct species, Homo neanderthalensis?

Life reconstruction of a Neanderthal by John Gurche at the USNM.

The question of whether they are a different species from us is the question of whether or not we could interbreed with each other. And not just mate– but successfully produce fertile offspring. For most of the time since the first reported Neanderthal in 1856, reproductive compatibility could only be inferred based on morphological data, and opinions varied as to whether Neanderthals were a subspecies of H. sapiens or a separate species. The great Finnish paleontologist Bjorn Kurten proposed in his novel, Dance of the Tiger, that Neanderthals and modern H. sapiens could mate and produce offspring, but that the offspring, while showing somatic luxuriance (they were really smart and strong), were completely sterile (a form of post-mating reproductive isolation). Published in 1980 before there was any genetic evidence, a novel, rather than a scientific paper, was probably the right venue for Kurten’s reasoned but entirely speculative proposal.

Early genetic data from mitochondrial DNA indicated that Neanderthal mitochondria were well outside the variability of modern populations, supporting the ideas of those (such as Kurten) who supposed that Neanderthals were a separate species. More recently obtained nuclear DNA sequences, however, showed that 1-4% of the genome of modern Eurasians was derived from Neanderthals (modern Africans lack this admixture of Neanderthal DNA). Thus there was enough successful interbreeding to leave a noticeable signature in modern genomes. Even more recently, a previously unknown fossil Asian population called Denisovans, related to but distinct from Neanderthals, has been shown to have contributed about 5% of the genome of modern Melanesians. Thus, measurable interbreeding occurred between anatomically modern humans and more archaic Eurasian populations as the former spread out of Africa across the remainder of the Old World.

The paper by Pinhasi et al. revises the dating of Neanderthal fossils from the Caucasus, finding them to be older than previously thought (about 40,000 years BP). The authors also suggest that other younger dates are unreliable, and that it is unlikely that anatomically modern humans and Neanderthals coexisted for any substantial length of time. If they are correct, then the Neanderthal (and Denisovan) contribution to modern genomes speaks even more strongly of conspecficity, as the gene flow had to occur over shorter periods of time. There are, regrettably, quite a few historical instances where two peoples (both of course undoubted anatomically modern H. sapiens) met, and one quickly disappeared, with relatively little measurable gene flow having occurred, so the rapid demise of Neanderthals in the face of anatomically modern humans is no bar to their having been the same species. I would interpret the genetic evidence so far as indicating that the Neanderthals, indeed, are us.

In addition to the references below, John Hawks of the University of Wisconsin, Madison, has a fine blog in which he often comments on Neanderthals and other paleoanthropological topics. His take on the Pinhasi et al. paper, which deals more with the dating issues, is here; his view on the species question is here. [JAC: I also discussed the species problem in Neanderthals, reaching the same conclusion as Hawks.]

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Green, R.E. et al. 2010. A draft sequence of the Neandertal genome. Science 328:710-722.

Green, R.E., et al. 2008. A complete Neandertal mitochondrial genome sequence determined by high-throughput sequencing. Cell 134:416-426.

Kurten, B. 1980. Dance of the Tiger. Reissued by University of California Press, Berkeley, 1993.

Pinhasi, R., T.F.G. Highamb, L.V. Golovanovac, and V.B. Doronichev. 2011 Revised age of late Neanderthal occupation and the end of the Middle Paleolithic in the northern Caucasus. Proceedings of the National Academy of Sciences in press.

Reich, D., et al. 2010. Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature 468:1053-1060.

The bitterness goes way back

August 17, 2009 • 8:54 am

by Greg Mayer

In a soon to be published paper in the Royal Society’s Biology Letters (abstract only), Carles Lalueza-Fox of Universitat Pompeu Fabra ( website in Catalan!) in Barcelona and colleagues report that they have sequenced the gene TAS2R38 from a Neanderthal man (press coverage by the BBC and NY Times). The ability to sequence genes from fossil material is remarkable enough in itself, but this study has particular interest, and not just because it was done on one of our fossil relatives.  Variation in the gene they sequenced is responsible for the polymorphism in modern man for the ability to perceive bitter tastes (some people can tast bitter, some can’t). Determining the frequency of the two forms (or alleles) of the gene is a classic high school biology exercise, carried out by seeing who can taste the bitter chemical PTC.  People who have either one or two copies (humans are diploid, so most genes are present in each individual’s genome in two copies) of the taster allele can taste bitter; those with two copies of the non-taster allele cannot. Today, the two alleles are about equally frequent, so that about 25% of people have two taster alleles (i.e. they are homozygous for the taster allele), about 50% have one taster and one non-taster (they are heterozygotes), and 25% are homozygous for the non-taster allele.

The Neanderthal they sequenced was a heterozygote, and thus could taste bitter (and also [with sample of only 1, mind you] had the same allele frequencies as we do). The polymorphism thus goes back somewhere on the order of 40,000 years. But Neanderthals split from the lineage leading to modern humans on the order of 300,000 years ago, with little or no subsequent interbreeding. So the polymorphism probably goes back even further, predating the modern Homo sapiens/Neanderthal split. Although an exciting find, this is not a record for the antiquity of a modern polymorphism: some are known to predate the human/chimp split (abstract only), and that’s millions of years ago.