Razib Khan One-stop-shopping for all of my content

October 21, 2012

The arcane art of ancient admixture

Filed under: Anthroplogy,Human Evolution,Human Genetics — Razib Khan @ 9:29 pm


I have mentioned the PLoS Genetics paper, The Date of Interbreeding between Neandertals and Modern Humans, before because a version of it was put up on arXiv. The final paper has a few additions. For example, it mentions the generally panned (at least in the circles I run in) PNAS paper which suggested that ancient population structure could produce the same patterns which were earlier used to infer admixture with Neandertals (the authors also point to Yang et al. as a support for the proposition of admixture rather than structure). The primary result, dating the admixture between Neandertals and anatomically modern humans ~40-80,000 years before the present, is reiterated.

An interesting aspect is that their method is to utilize linkage disequilibrium (LD) decay. It’s interesting because tens of thousands of years is a hell of a long time to be able to detect an admixture event via LD! In particular because there’s likely a palimpsest effect where there are intervening admixtures and other assorted demographic events (e.g., bottlenecks and selective sweeps can also generate LD). So how’d they do it? Basically the authors figured out a way to ...

October 16, 2012

Neandertal one stop shopping

Filed under: Human Evolution,Neandertals — Razib Khan @ 11:46 pm

If you have a hard time following all the Neandertal genomics findings from the last few years, and their implications, National Geographic has a really thorough piece up. It’s a good digest of all the news you can use. One thing I would like to add: from what I can tell the probability of the signals of admixture in non-Africans being genuinely Neandertal seem to be increasing as we progress. In other words, you should weight the “other side” (ancient population structure, where some African populations were closer to Neandertals before they left Africa) less than you did in 2010.

Of course one of the more inevitable aspects of the admixture story has been the humanization of Neandertals. I don’t know how I feel about this. Should our own affinity to Neandertals alter our view of their behavior or anatomy? Plenty of behaviorally anatomically modern humans were beastly after all.

October 15, 2012

Don’t trust an archaeologist about genetics, don’t trust a geneticist about archaeology

Filed under: Anthroplogy,Evolutionary Genetics,Human Evolution — Razib Khan @ 1:38 pm

Who to trust? That is the question when you don’t know very much (all of us). Trust is precious, and to some extent sacred. That’s why I can flip out when I realize after the fact that someone more informed than me in field X sampled biased their argument in a way they knew was shady to support a proposition they were forwarding. What’s the point of that? Who cares if you win at a particular bull-session? You’re burning through cultural capital. And not that most of my interlocutors care, but I’m likely to never trust them again on anything.

In any case, this came to mind when I ran across a James Fallows’ post at The Atlantic. Here’s a screenshot of the appropriate section, with my underlines:


The PNAS link is wrong. The correspondent is actually linking to an article in Quaternary International. And they do point out that there are possible problems with draft quality sequences due to contamination. But I didn’t find the paper too persuasive. There are two issues. First, the Denisova genome is very good quality. So you can be more ...

October 12, 2012

I believe in the blank slate!

Filed under: Anthroplogy,Human Evolution — Razib Khan @ 11:21 am

Well, not really…but in some ways close enough judged against the initial reference point of where I started on certain questions. Dienekes contends:

This will help us understand both: the ancestors of non-Africans did not come forth fully formed, like Athena from Zeus’s head, having spent millennia of perfecting their craft and honing their minds by perforating shells and scratching lines in some South African cave. Instead, they may been plain old-style hunter-gatherers who stumbled into Asia by doing what they always did: following the food. At the same time, the UP/LSA revolution may not have been effected by a new and improved type of human bursting into the scene and replacing Neandertals and assorted dummies, but rather as a cultural revolution that spread across a species that already had the genetic potential for it, and was already firmly established in both Africa and Asia.

The former position, that the Out-of-Africa population were genetically endowed supermen who blitzkrieged other humans ~50,000 years ago was probably the most common position ~10 years ago. It’s outlined by Richard Klein in The Dawn of Human Culture. A contrasting argument was put forth at about the same time by Stephen Oppenheimer in

I believe in the blank slate!

Filed under: Anthroplogy,Human Evolution — Razib Khan @ 11:21 am

Well, not really…but in some ways close enough judged against the initial reference point of where I started on certain questions. Dienekes contends:

This will help us understand both: the ancestors of non-Africans did not come forth fully formed, like Athena from Zeus’s head, having spent millennia of perfecting their craft and honing their minds by perforating shells and scratching lines in some South African cave. Instead, they may been plain old-style hunter-gatherers who stumbled into Asia by doing what they always did: following the food. At the same time, the UP/LSA revolution may not have been effected by a new and improved type of human bursting into the scene and replacing Neandertals and assorted dummies, but rather as a cultural revolution that spread across a species that already had the genetic potential for it, and was already firmly established in both Africa and Asia.

The former position, that the Out-of-Africa population were genetically endowed supermen who blitzkrieged other humans ~50,000 years ago was probably the most common position ~10 years ago. It’s outlined by Richard Klein in The Dawn of Human Culture. A contrasting argument was put forth at about the same time by Stephen Oppenheimer in

I believe in the blank slate!

Filed under: Anthroplogy,Human Evolution — Razib Khan @ 11:21 am

Well, not really…but in some ways close enough judged against the initial reference point of where I started on certain questions. Dienekes contends:

This will help us understand both: the ancestors of non-Africans did not come forth fully formed, like Athena from Zeus’s head, having spent millennia of perfecting their craft and honing their minds by perforating shells and scratching lines in some South African cave. Instead, they may been plain old-style hunter-gatherers who stumbled into Asia by doing what they always did: following the food. At the same time, the UP/LSA revolution may not have been effected by a new and improved type of human bursting into the scene and replacing Neandertals and assorted dummies, but rather as a cultural revolution that spread across a species that already had the genetic potential for it, and was already firmly established in both Africa and Asia.

The former position, that the Out-of-Africa population were genetically endowed supermen who blitzkrieged other humans ~50,000 years ago was probably the most common position ~10 years ago. It’s outlined by Richard Klein in The Dawn of Human Culture. A contrasting argument was put forth at about the same time by Stephen Oppenheimer in

October 10, 2012

There may be no gene which is essential for our humanity

Filed under: Anthroplogy,Human Evolution — Razib Khan @ 11:39 pm

The always informative Ann Gibbons has a piece in Slate, The Neanderthal in My Family Tree. There is almost nothing new for regular readers of this weblog, but it’s rather awesome that Slate is now publishing stuff like this. Many people are simply unaware of the new paleogenomics. Case in point, a good friend who has a doctorate in chemical physics, and was totally unaware a year after the seminal Science paper on Neandertal admixture of the likelihood of Neandertal admixture!

Nevertheless, I think it is important for me to be repetitive and highlight a disagreement I have with the Gibbons’ piece. She says:

…But the differences in the genomes of Denisovans, Neanderthals, and modern humans are also revealing the genetic traits that set us apart from them—the traits that made us human. “I’ve been comparing it to the pictures of Earth that came back from Apollo 8. The Neanderthal genome gives us a picture of ourselves, from the outside looking in,” says paleoanthropologist John Hawks of the University of Wisconsin in Madison, in his blog on paleoanthropology, genetics, and evolution. “We can see, and now learn about, the essential genetic changes that make us human—the things that made ...

September 29, 2012

The Others, in black and white

Filed under: Anthroplogy,Human Evolution — Razib Khan @ 12:18 am

New Scientist has a piece up, Europeans did not inherit pale skins from Neanderthals, based on a paper I blogged last month. One thing that I hadn’t though about in detail…how did anatomically modern humans of various shades perceive Neandertals of various shades? For example, it seems highly likely that there were swarthy Neandertals and pale Neandertals. Similarly, there were swarthy modern humans, and soon enough pale ones. Skin color is a very salient trait. Very different populations phylogenetically, Sub-Saharan Africans, Melanesians, and South Asians, have been defined as “black.” Did modern humans perceive Middle Eastern Neandertals, who may have been relatively dark, as much closer to humanlike status because of their similar complexion to anatomically modern Middle Eastern humans? Did they perceive European Neandertals, who may on average have been much lighter, as fundamentally different?

When doing physical reconstructions it seems to me that the gross morphology of Neandertals has been more emphasized. Their brow ridges, large prominent noses, and stocky body plans. But in this manner perhaps they’re like our imaginings of ancient Greek temples as alabaster white. In reality the temples of antiquity and many public buildings were festooned with color. Similarly, Neandertals came in all shades.

September 23, 2012

Humanity isn’t, it becomes

Filed under: Anthroplogy,Human Evolution,Neandertals — Razib Khan @ 6:55 pm

John Hawks prompts to reemphasize an aspect of my thinking which has undergone a revolution over the past 10 years. I pointed to it in my post on the Khoe-San. In short, the common anatomically modern human ancestors of Khoe-San and non-Khoe-San may not have been people. Rather, people may have evolved over the past 100-200,000 years ago. Of course the term “people” is not quite as scientific as you might like. In philosophy and law you have debates about “personhood”. Granting the utility of these debates I am basically saying that the common ancestor of Khoe-San and non-Khoe-San may not have been persons, as well understand them. Though, as a person myself, I do think they were persons. At this point I am willing to push the class “person” rather far back in time.

As I suggested earlier there is an implicit assumption that personhood is a shared derived trait of our species. Or at least it is a consensus today that all extant members of H. sapiens are persons. Since Khoe-San are persons, the common ancestor of Khoe-San and non-Khoe-San must also be ...

September 18, 2012

The brambly bush of humanity

Over at Haldane’s Sieve there are more than preprints posted, there are commentaries from the authors as well. For example, for The genetic prehistory of southern Africa, the first author, Dr. Joseph K. Pickrell, has a extended comment up.

But occasionally you get contributions & perspectives from non-authors which are very interesting. And it is to one of these I want to draw your attention, Thoughts on: The date of interbreeding between Neandertals and modern humans. It’s a comment on The date of interbreeding between Neandertals and modern humans. In the post Dr. Graham Coop contends:

At this point you are likely saying: well we know that Neandertals existed as a [somewhat] separate population/species who are these population X you keep talking about and where are their remains? Population X could easily be a subset of what we call Neandertals, in which case you’ve been reading this all for no reason [if you only want to know if we interbred with Neandertals]. However, my view is that in the next decade of ancient human population history things are going to get really interesting. We have already seen this from the Denisovian papers [1,2], and the work ...

September 3, 2012

The pruned tree

Filed under: Anthroplogy,Human Evolution — Razib Khan @ 9:45 pm

Dienekes Pontikos has a long post up on how reticulation within phylogenetic trees may distort our perception of human natural history when we force the data into a more conventional tree (i.e., bifurcation after bifurcation). The concrete reason for this rethinking is the high probability of “archaic admixture” into the dominant genetic signal of anatomically modern African humanity, both within Africa and outside of it.

Dienekes proposes that when ancient DNA from early modern Eurasians is analyzed then a large portion of the portrait will be unmasked. For example, if high levels of admixture were present very early on then you would see very divergent regional populations because of persistence and continuity of local hominin population substructure. The pre-African Eurasians from each given region would have contributed substantially to the genetic makeup of the first modern humans who flourished in Europe and East Asia. On the other hand, if admixture was minimal, then the early Europeans and Asians would be far less distinct than their modern descents.

This is where I want to highlight one aspect of Dienekes’ model which is implicit, but I think needs to be strongly emphasized. ...

August 28, 2012

Not all genes are created the same

The map to the right shows the frequencies of HGDP populations on SLC45A2, which is a locus that has been implicated in skin color variation in humans. It’s for the SNP rs16891982, and I yanked the figure from IrisPlex: A sensitive DNA tool for accurate prediction of blue and brown eye colour in the absence of ancestry information. Brown represents the genotype CC, green CG, and blue, GG. Europeans who have olive skin often carry the minor allele, C. While SLC24A5 is really bad at distinguishing West Eurasians from each other, SLC45A2 is better. Though both are fixed in Northern Europe, the former stays operationally fixed in frequency outside of Europe, in the Near East. As I stated earlier the proportions of the ancestral SNP in the Middle Eastern populations in the HGDP seem to be easily explained by the Sub-Saharan admixture you can find in these groups.

In contrast major SNPs in SLC45A2 are closer to disjoint between Europeans and South Asians. For example I’m a homozygote for the C allele. And yet even here we need ...

August 27, 2012

Europeans got less shaded in stages

The Pith: the evolution of lighter skin is complex, and seems to have occurred in stages. The current European phenotype may date to the end of the last Ice Age.

A new paper in Molecular Biology and Evolution, The timing of pigmentation lightening in Europeans, is rather interesting. It’s important because skin pigmentation has been one of the major successes of the first age of human genomics. In 2002 we really didn’t know the nature of normal human variation in skin color in terms of specific genes (basically, we knew about MC1R). This is what Armand Leroi observed in Mutants in 2005, wondering about our ignorance of such a salient trait. Within a few years though Leroi’s contention was out of date (in fact, while Mutants was going to press it became out of date) . Today we do know the genetic architecture of pigmentation. This is why GEDmatch can predict that my daughter’s eyes will be light brown from just her SNPs (they are currently hazel). This genomic yield was facilitated by the fact that pigmentation seems to be a trait where most human variation is ...

August 26, 2012

Eat smarter, don’t work out harder?

Filed under: Anthroplogy,Human Evolution — Razib Khan @ 4:53 pm

There have been several recent studies reemphasizing diet over exercise (timely because Americans are kind of fat, on average). A new piece in The New York Times looking at the Hadza of Tanzania, who are hunter-gatherers, seems to reiterate this point, Debunking the Hunter-Gatherer Workout:

We found that despite all this physical activity, the number of calories that the Hadza burned per day was indistinguishable from that of typical adults in Europe and the United States. We ran a number of statistical tests, accounting for body mass, lean body mass, age, sex and fat mass, and still found no difference in daily energy expenditure between the Hadza and their Western counterparts.

How can the Hadza be more active than we are without burning more calories? It’s not that their bodies are more efficient, allowing them to do more with less: separate measurements showed that the Hadza burn just as many calories while walking or resting as Westerners do.

We think that the Hadzas’ bodies have adjusted to the higher activity levels required for hunting and gathering by spending less energy elsewhere. Even for very active people, physical activity accounts for only a small portion of daily energy expenditure; most energy is ...

August 19, 2012

On phylogenetic instrumentalism

Filed under: Genomics,Human Evolution,Human Genetics,Human Genomics,phylogenetics — Razib Khan @ 4:40 pm

ADMIXTURE and STRUCTURE tests aren’t formal mixture tests. Yes! In fact, in the “open science” community this issue is repeated over and over and over, because people routinely get confused (our audience does not consist of population geneticists and phylogeneticists by and large). So sometimes it is necessary to lay it out in detail as in the post above. The key point to always remember is that population genetic & phylogenetic statistics and visualizations are a reduction and summary of reality in human palatable form. They tell us something, but they do not tell us everything. A common issue is that for purposes of mental digestion it is useful to label ancestral elements “European,” or on PCA refer to a “European-Asian” cline, as if the population genetic abstractions themselves are the measure of what European or Asian is. But European and Asian are themselves human constructions, and subject to debate (e.g., do Turks count as Europeans? Indians as Asians?) The population genetic statistics are not themselves subjective, but the meanings we give them are.


Let’s illustrate this with a concrete example. The Cape Coloured population of South Africa is a compound of Khoisan, Bantu, South Asian, Southeast Asian, and ...

August 18, 2012

The origins of modern humanity: 2012

Filed under: Anthroplogy,Human Evolution — Razib Khan @ 5:26 pm

Matt Ridley has a column up, Did Your Ancestor Date a Neanderthal? In it he juxtaposes the two recent papers which got some attention on the relationship of modern humans to Neandertals. To be frank I think it took too much of the “two sides/opposing views/views differ” tack. From what I can gather the scientific consensus is moving further toward admixture, rather than ancient structure. Additionally, as John Hawks states flat out the PNAS paper which casts doubt on the strength of the admixture hypothesis is not the strongest of contributions to the field(in line with David Reich and Nick Patterson’s assessments, and others who shall remain nameless).

But it’s hard to keep track of all the threads, isn’t it? One of the most tragic aspects of the death of classic “Out of Africa” is that we lost an exceedingly simple narrative which had the positives of clarity and precision. The basic outlines were reducible to one sentence: all humans today descend from a small group of modern humans alive ~100,000 years ago. At this time we do not have such an elegant replacement framework. In fact, we may never have such an elegant model which ...

August 14, 2012

Neanderthal admixture & the ecology of academe

Yesterday I pointed out that David Reich had a moderately dismissive attitude toward the new paper in PNAS, Effect of ancient population structure on the degree of polymorphism shared between modern human populations and ancient hominins. Here’s what Reich said:

…But Reich believes that the discussion would have been different if it had happened in the open. The PNAS paper questioning the Neanderthal admixture addresses issues swirling around two years ago, but not Reich and Slatkin’s latest work. “It’s been an issue for several years. They were right to work on this,” says Reich. But now, “it’s kind of an obsolete paper,” he says.

Here’s what Nick Patterson, Reich’s colleague told me via email:

Ancient structure in Africa was considered when we wrote the Green et al. paper, and we were aware that this could explain D-statistics. But the hypothesis is no longer viable as the major explanation of Neandertal genetics in Eurasia. This was discussed in the recent paper of Yang et al. (MBE, 2012). (Not referenced by the PNAS paper).

A very simple argument, that convinces me, is that the allelic frequency spectrum of Neandertal alleles in Eurasia falls off very quickly. A bottleneck flattens out the ...

August 12, 2012

Human-on-human sex

Filed under: Human Evolution,Neandertal — Razib Khan @ 11:27 pm

Dienekes tips me off to the fact that the long-awaited Reich lab paper on Neandertal admixture dating has finally been put on arXiv! The date of interbreeding between Neandertals and modern humans:

Comparisons of DNA sequences between Neandertals and present-day humans have shown that Neandertals share more genetic variants with non-Africans than with Africans. This could be due to interbreeding between Neandertals and modern humans when the two groups met subsequent to the emergence of modern humans outside Africa. However, it could also be due to population structure that antedates the origin of Neandertal ancestors in Africa. We measure the extent of linkage disequilibrium (LD) in the genomes of present-day Europeans and find that the last gene flow from Neandertals (or their relatives) into Europeans likely occurred 37,000-86,000 years before the present (BP), and most likely 47,000-65,000 years ago. This supports the recent interbreeding hypothesis, and suggests that interbreeding may have occurred when modern humans carrying Upper Paleolithic technologies encountered Neandertals as they expanded out of Africa.

This isn’t the only group working on the Neandertal genomic admixture story. From reading his blog you probably know that John Hawks is working in this area, but there are other ...

July 30, 2012

Human version 2.001

Filed under: Human Evolution — Razib Khan @ 6:09 pm

Dienekes reflects on the seemingly simultaneous appearance of behavioral modernityin South Africa and Europe and Australia, pending the acceptance of the most recent finds. This part is very important in my opinion:

The San people still live in several countries of southern Africa, and until the latter part of the 20th century were still mainly hunter-gatherers. But Dr. Stringer cautioned not to think of them as “living fossils,” unchanged by time. “Their genes, cultures and behaviors have undoubtedly continued to evolve in the intervening millennia,” he said.

I see no reason to think that these were the ancestors of the San. Over 45,000 years I think the most likely option is that genetic and cultural continuity will not be maintained, and these are probably a sister group to the modern peoples of Southern Africa. In any case, to address Dienekes’ confusion, I think this is one case where his non-American background shows. We know exactly what happened so long ago to kick-start modern humanity. The answer has been with us for over 40 years.

July 19, 2012

The expanding crest of modern humanity

Filed under: Human Evolution — Razib Khan @ 11:46 pm

If you are interested in genomics and human evolution, a new review paper in PLoS Genetics is a must read, Genomic Data Reveal a Complex Making of Humans. A must read not because you need to agree with the thrust of the authors’ arguments, but because it provides a thorough bibliography for the last 2 to 3 years. Here is the abstract:

In the last few years, two paradigms underlying human evolution have crumbled. Modern humans have not totally replaced previous hominins without any admixture, and the expected signatures of adaptations to new environments are surprisingly lacking at the genomic level. Here we review current evidence about archaic admixture and lack of strong selective sweeps in humans. We underline the need to properly model differential admixture in various populations to correctly reconstruct past demography. We also stress the importance of taking into account the spatial dimension of human evolution, which proceeded by a series of range expansions that could have promoted both the introgression of archaic genes and background selection.

The main problem I have at this point is the general mode of range expansions, whereby population A expands as a demographic wave across a substrate of population B. These sorts ...

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