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Category: Human Evolution
Neanderthals came in all colors
There’s a report in Science about a new short paper about Neandertal pigmentation genetics. The context is this. First, in 2007 an ingenuous paper was published which inferred that it may be that Neandertals had red hair, at least based on an N = 2 from two divergent locations. The new study looks at three Croation samples, and reports genotypes which are correlated with a swarthier phenotype in modern populations. But the results are neither here nor there: everyone interviewed in the paper assumes that like modern Europeans Neandertals were a polymorphic set of populations when it comes to pigmentation. There are lots of reasons for this agreement, despite issues one might take with this paper.
The report on the paper in Science has two sections which I want to zoom in on. First, “Nearly 60% of the formula’s predictions matched the subjects’ actual physical appearance, the authors say. The team considers that accuracy rate satisfactory, given the complexity of the genetics behind skin color and other physical traits.” Do you consider 60 percent satisfactory? What curve are you grading on? I’m willing to bet that the reporter didn’t consider 60 percent satisfactory, and neither do I. If you look in the paper you’ll see that their method predicts that a Yoruba in the HGDP sample has blue eyes and red hair. Several of the Papuans are predicted to have blue eyes.
Beyond trees and European trees
Submitted for your approval, a very important post and preprint from Dr. Joseph Pickrell, Identifying targets of natural selection in human and dog evolution. If you read the preprint there’s a lot of good stuff. Dienekes highlighted the most relevant aspect: representation of genetic relationships with phylogenetic trees mask the likely reality of gene flow and admixture. In the guts of the paper though Pickrell et al. use their framework to identify some novel patterns. For example, that Cambodians may be descended in small part from some basal Eurasian lineage (~15 percent), perhaps their equivalent of “Ancient South Indians”? Using ADMIXTURE and such it has long been evident that there’s something funny there. My own working assumption was that the relatives of “Ancient South Indians” could be found in Southeast Asia, though these results (preliminary as they are) might imply something even more interesting. Second, there is a tidbit which might lend support to the fans of the Solutrean model, or can be interpreted in that way (I suspect that it does not, but it could be spun in such a fashion).
Extraordinary claims require a lot of evidence
Several people have emailed me about the Solutrean hypothesis. The trigger is the publication of Across Atlantic Ice: The Origin of America’s Clovis Culture. To my surprise this has received a lot of media attention. The Washington Post, io9, and The New Scientist. Granted, the coverage has been appropriately skeptical. But it still gets to the truth of it that all publicity is good publicity, and here I am talking about a model which I believe is pretty much bunk.
Jerry Coyne on race: a reflection of evolution
After my post on the ‘race question’ I thought it would be useful to point to Jerry Coyne’s ‘Are there human races’?. The utility is that Coyne’s book Speciation strongly shaped my own perceptions. I knew the empirical reality of clustering before I read that book, but the analogy with “species concept” debates was only striking after becoming more familiar with that literature. Coyne’s post was triggered by a review of Race?: Debunking a Scientific Myth and Race and the Genetic Revolution: Science, Myth, and Culture. He terms the review tendentious, and I generally agree.
In the early 20th century Western intellectuals of all political stripes understood what biology told us about human taxonomy. In short, human races were different, and the white European race was superior on the metrics which mattered (this was even true of Left-Socialist intellectuals such as H. G. Wells and Jack London). In the early 21st century Western intellectuals of all political stripes understand what biology teaches us about human taxonomy. Human races are basically the same, and for all practical purposes identical, and equal on measures which matter (again, to Western intellectuals). As Coyne alludes to in his post these are both ideologically driven positions. One of the main reasons that I shy away from modern liberalism is a strong commitment to interchangeability and identity across all individuals and populations as a matter of fact, rather than equality as a matter of legal commitment. In a minimal government scenario the details of human variation are not of particular relevance, but if you accept the feasibility of social engineering (a term I am not using in an insulting sense, but in a descriptive one) you have to start out with a model of human nature. So this is not just an abstract issue. For whatever reason many moderns, both liberals and economic conservatives, start out with one of near identity (e.g., H. economicus in economics).
I want to highlight a few sections of Coyne’s post:
Ötzi the Iceman and the Sardinians
Well, the paper is finally out, New insights into the Tyrolean Iceman’s origin and phenotype as inferred by whole-genome sequencing. In case you don’t know, Ötzi the Iceman died 5,300 years ago in the alpine region bordering Austria and Italy. His seems to have been killed. And due to various coincidences his body was also very well preserved. This means that enough tissue remained that researchers have been able to amplify his DNA. And now they’ve sequenced it enough to the point where they can make some inferences about his phenotypic characteristics, and, his phylogenetic relationships to modern populations.
The guts of this paper will not be particularly surprising to close readers of this weblog. The guesses of some readers based on what the researchers hinted were correct: Ötzi seems to resemble mostly closely the people of Sardinia. This is rather interesting. One reason is prosaic. The HGDP sample used in the paper has many Northern Italians (from Bergamo). Why is it that Ötzi does not resemble the people from the region that he was indigenous to? (we know that he was indigenous because of the ratio of isotopes in his body) A more abstruse issue is that it is interesting that Sardinians have remained moored to their genetic past, enough so that a 5,300 year old individual clearly can exhibit affinities with them. The distinctiveness of Sardinians jumps out at you when you analyze genetic data sets. They were clearly set apart in L. L. Cavalli-Sforza’s The History and Geography of Human Genes, 20 years ago. One reason that Sardinians may be distinctive is that Sardinia is an isolated island. Islands experience reduced gene flow because they’re surrounded by water. And sure enough, Sardinians are especially similar to each other in relation to other European populations.
Neandertal population structure
There’s a new paper out, Partial genetic turnover in neandertals: continuity in the east and population replacement in the west. The primary results are above. Basically, using 13 mtDNA samples the authors conclude that it looks as if there was a founder effect for Neanderthals in Western Europe ~50 K years ago, generating a very homogenized genetic background for this particular population before the arrival of modern humans. Perhaps it’s just me, but press releases with headlines such as “European Neanderthals Were On the Verge of Extinction Even Before the Arrival of Modern Humans” strike me as hyperbolic. I’m also confused by quotes like the one below:
Adam's end was never in the cards
There has been a lot of talk in the media about a new paper which reports that the Y chromosome is not deteriorating, as had been previously inferred from the data. In the 2004 Bryan Sykes wrote Adam’s Curse: A Future Without Men which used this model as a framing device (and naturally elicited great general interest). You can read some earlier critiques at Gene Expression Classic. I never paid attention to this debate in the details because it seemed ludicrous on the face of it. Bryan Sykes’ was predicting the extinction of males in ~100,000 years. Right, we just happen to be living right before the genomic Götterdämmerung. I don’t think so. Sometimes absurd results which fly in the face of plain history and robust theory are profoundly insightful. But most of the time they’re just false leads.
Out of who knows where
In The New York Times, DNA Turning Human Story Into a Tell-All:
The tip of a girl’s 40,000-year-old pinky finger found in a cold Siberian cave, paired with faster and cheaper genetic sequencing technology, is helping scientists draw a surprisingly complex new picture of human origins.
The new view is fast supplanting the traditional idea that modern humans triumphantly marched out of Africa about 50,000 years ago, replacing all other types that had gone before.
Instead, the genetic analysis shows, modern humans encountered and bred with at least two groups of ancient humans in relatively recent times: the Neanderthals, who lived in Europe and Asia, dying out roughly 30,000 years ago, and a mysterious group known as the Denisovans, who lived in Asia and most likely vanished around the same time.
Their DNA lives on in us even though they are extinct. “In a sense, we are a hybrid species,” Chris Stringer, a paleoanthropologist who is the research leader in human origins at the Natural History Museum in London, said in an interview.
First, for reasons of novelty we are emphasizing the exotic tendrils of the human family tree. Even Chris Stringer, the modern paleontological father of “Out of Africa,” is claiming we’re hybrids! But let’s not forget that non-Africans are the product of a very rapid radiation out of the margins of the Afrotropic ecozone within the last ~50-100,000 years. I am not entirely sure that this is as true of Africans (recall how extremely basal Bushmen are to the rest of humanity; they seem to have diverge well before the “Out of Africa” pulse).
Out of Africa and out of Siberia
The latest edition of The American Journal of Human Genetics has two papers using “old fashioned” uniparental markers to trace human migration out of Africa and Siberia respectively. I say old fashioned because the peak novelty of these techniques was around 10 years ago, before dense autosomal SNP marker analyses, let alone whole genome sequencing. But mtDNA, passed down the maternal line, and Y chromosomes, passed from father to son, are still useful. Prosaically they’re useful because the data sets are now so large for these sets of markers after nearly 20 years of surveying populations. More technically because these two regions of the genome do not recombine they lend themselves to excellent representation as a tree phylogeny. Finally, mtDNA in particular is particularly amenable to estimates via molecular clock methodologies (it has a region with a higher mutational rate, so you can sample a larger range of variation over a given number of base pairs; you can use STRs, which mutate rapidly, for Y chromosomes, but there seems to be a lot of controversy in dating).
The papers are The Arabian Cradle: Mitochondrial Relicts of the First Steps along the Southern Route out of Africa and Mitochondrial DNA and Y Chromosome Variation Provides Evidence for a Recent Common Ancestry between Native Americans and Indigenous Altaians. Dienekes has already commented on the first paper. I am not going to take a detailed position on either, but I have to add that we need to be very careful of extrapolating from maternal or paternal lineages, and, assuming that population turn over is low enough that we can make phylogeographic inferences about the past from the present. For example, if you look at mtDNA South Asians as a whole strongly cluster with East Asians and not Europeans, while if you look at Y chromosomes you see the reverse. The whole genome gives a more mixed picture. Additionally, ancient DNA analyses in Northern Eurasia are showing strong discontinuities between past and present populations. So coalescence back to last common ancestor between two different lineages in two different regions may actually be due to diversity in a common source population more recently, which entered into demographic expansion and replaced other groups.
If you need the papers, email me. Some of you know the alphabet soup of haplogroups better than I do. Below are two figures which I think give the top line results.
When Eve met Creb
The excellent site io9 has a piece up today which is a fascinating indicator of the nature of popular science publications as a lagging indicator. It is a re-post of a piece published last April, How Mitochondrial Eve connected all humanity and rewrote human evolution. In it you have an encapsulation of a particular period in our understanding of human natural history through evolutionary genetics. Notice for example the focus on maternally transmitted lineages, mtDNA and Y chromosomes. And the citations on genealogy date to the middle aughts. The science is mostly correct as far as it goes in the details (or at least it is defensible, last I checked there was still debate as to the validity of the molecular clocks used for Y chromosomal lineages), but it misses the big picture of how we’ve reframed our understanding of the human past over the last few years. The distance between 2011 and 2009 is far greater in this sense than between 2009 and 1999 (or even 2009 and 1989!). The io9 piece is a reflection of the era before the paradigmatic rupture.
How the Amhara breathe differently
I have blogged about the genetics of altitude adaptation before. There seem to be three populations in the world which have been subject to very strong natural selection, resulting in physiological differences, in response to the human tendency toward hypoxia. Two of them are relatively well known, the Tibetans and the indigenous people of the Andes. But the highlanders of Ethiopia have been less well studied, nor have they received as much attention. But the capital of Ethiopia, Addis Ababa, is nearly 8,000 feet above sea level!
Another interesting aspect to this phenomenon is that it looks like the three populations respond to adaptive pressures differently. Their physiological response varies. And the more recent work in genomics implies that though there are similarities between the Asian and American populations, there are also differences. This illustrates the evolutionary principle of convergence, where different populations approach the same phenotypic optimum, though by somewhat different means. To my knowledge there has not been as much investigation of the African example. Until now. A new provisional paper in Genome Biology is out, Genetic adaptation to high altitude in the Ethiopian highlands:
The erectus within?
The Pith: More caveman admixture in modern humans, especially Melanesians!
A new paper on archaic adaptive introgression among Melanesians has been discussed elsewhere. But I think it is worth reviewing, because it’s probably a foretaste of what’s to come. Researchers are combing through the human genome, as more and more genomes come on line, in the search of weird and unexpected variation. The paper is in Molecular Biology and Evolution, and is titled Global genetic variation at OAS1 provides evidence of archaic admixture in Melanesian populations (why is it that this journal doesn’t even allow supplemental information to be free to the public?). The two primary figures from this paper do a good job of illustrating the main result.
The first figure is a phylogenetic tree of haplotypes at the OAS1 locus, with pie charts showing the proportion of individuals from a set of populations which contribute to the total number for that haplotye. So you see above that the “deep lineage” is relatively distant from a cluster of other haplotypes (as measured by mutational differences which are proportional to depth of common ancestry), and, that deep linage is exclusively found in Papuans in this set. The second figure shows the frequency of the deep lineage haplotype over a larger set of populations. I cut off the section which shows that Africans are at zero percent. The haplotype is found almost exclusively in Melanesian populations, except for the fact out of over 200 South Asians they sampled, 3 of them carried it (2 Pakistanis, 1 Sri Lankan). There is aspect though not evident in the figures above, but which is clear in the abstract that you need to know:
Reconstructing a generation unsampled
In the near future I will be analyzing the genotype of an individual where all four grandparents have been typed. But this got me thinking about my own situation: is there a way I could “reconstruct” my own grandparents? None of them are living. The easiest way to type them would be to obtain tissue samples from hospitals. This is not totally implausible, though in this case these would be Bangladeshi hospitals, so they might not have saved samples or even have a good record of hem. Another way would be to extract DNA from the burial site. This is not necessarily palatable. But assuming you did this, if you have access to a forensic lab it might be pretty easy (though I think most forensic labs using VNTRs, rather than SNP chips, so I don’t know if they’d touch every chromosome), I’m not sure that the quality would be optimal for more vanilla typing operations, especially for older samples which are likely to be contaminated with a lot of bacteria.
For me the simplest option is to look at relatives. Each of my grandparents happens to have had siblings, so there are many sets of relatives related to just each of those individuals of interest. I also have many cousins, so pooling all the genotypes together and using the information of a pedigree one could ascertain which chromosomal segments are likely to derive from a particular grandparent. To give a concrete example, my mother has a maternal cousin to whom she is quite close. By typing my mother and her cousin one could infer that the segments shared across the two individuals derive from the common maternal grandparents. Of course there’s a problem that cousins have a coefficient of relatedness of only 1/8th, so there is going to be a lot of information missing. But, if you had lots of cousins you could presumably reconstruct the genotypes far better.
Between the desert and the sea
There is a new paper in PLoS Genetics out which purports to characterize the ancestry of the populations of northern Africa in greater detail. This is important. The HGDP data set does have a North African population, the Mozabites, but it’s not ideal to represent hundreds of millions of people with just one group. The first author on this new paper is Brenna Henn, who was also first author on another paper with a diverse African data set. Importantly the data was posted online. Unfortunately though most of the populations didn’t have too many markers. This isn’t an issue in an of itself, but it becomes a big deal when trying to combine it with other data sets. If you limit the markers to those which intersect across two data sets you start to thin them down a lot, to the point where they’re not useful. Though the the results of the paper are worth talking about, the authors claim that they’ll be putting the data online. This is important because they used a large number of markers, so the intersections will be nice (I can, for example, envisage exploring the relationship between the North Africans and the IBS Iberian sample in the near future).
As for the paper itself, Genomic Ancestry of North Africans Supports Back-to-Africa Migrations:
Read More
PGD:2010s::IVF:1980s
Get ready for PGD, the acronym for preimplantation genetic diagnosis. We don’t really talk about “test tube babies” anymore. It’s “IVF,” and as American as apple pie (OK, perhaps as Israeli as falafel). Here’s the Ngrams result:
Human behavior over the ages
Over at Scientific American Eric Michael Johnson has a very long post up, The Case of the Missing Polygamists. It is a re-post of something he already published at Psychology Today a few years ago. Though provisionally a review of Sex at Dawn, Johnson covers a lot of ground, and also has extensive quotations from Sarah Blaffer Hrdy.
I’m reflecting upon the post for a second time because it is very rich in ideas, and lays out may different general concepts and specific propositions. The bottom line from what I can gather is that Johnson agrees with those thinkers who believe that agriculture and the Neolithic revolution to a great extent reshaped social relations, and give us a skewed perception of “normal” human societies. I’m not going to rehash all of the points in the piece, but will focus on just a few which I think I can extend upon fruitfully.
Science evolves
I missed this piece in Edge from Chris Stringer in November, Rethinking “Out of Africa”. He sums up his current thinking at the end:
We’ve got the lineage of the hobbit, ‘Homo floresiensis’ (in quotation marks because its human status in not yet clear), perhaps diverging more than two million years ago, evolving in isolation in southeast Asia, and apparently going extinct about 17,000 years ago.
We’ve got Homo erectus, most likely originating in Africa, giving rise to lineages which continue in the Far East in China and Java, but which eventually go extinct. In Europe, it perhaps gave rise to the species Homo antecessor, “Pioneer Man,” known from the site of Atapuerca in Spain. Again, going extinct.
In the western part of the Old World, we get the development of a new species, Homo heidelbergensis, present in Europe, Asia and Africa. We knew heidelbergensis had gone two ways, to modern humans and the Neanderthals. But we now know because of the Denisovans that actually heidelbergensis went three ways—in fact the Denisovans seem to represent an off-shoot of the Neanderthal lineage.
North of the Mediterranean, heidelbergensis gave rise to the Neanderthals, over in the Far East, it gave rise to the Denisovans. In Africa heidelbergensis evolved into modern humans, who eventually spread from Africa about 60,000 years ago, but as I mentioned, there’s evidence thatheidelbergensis populations carried on in Africa for a period of time. But we now know that the Neanderthals and the Denisovans did not go genetically extinct. They went physically extinct, but their genes were input into modern humans, perhaps in western Asia in the case of the Neanderthals. And then a smaller group of modern humans picked up DNA from the Denisovans in south east Asia.
We end up with quite a complex story, with even some of this ancient DNA coming back into modern humans within Africa. So our evolutionary story is mostly, but not absolutely, a Recent African Origin.
Now, I know that Milford Wolpoff has still not totally buried the hatchet with Stringer, but their views are actually converging a great deal. What does that tell us? Well, paleoanthropology most definitely is a science, reality and results are dictating to the intellectual antagonists.
(Via Ruchira Paul)
Economic forecasters should put their $ where their mouth is
Economic forecasting is a mug’s game. There are simply too many unknowable factors that affect “the economy” for anyone to make accurate predictions. The Fukushima earthquake and nuclear disaster, for instance, had a noticeably negative macroeconomic impact around the world, and nobody knows what lurks inside the hearts of central bankers. Plus, if I did possess the secrets to the future, I’d be making a fortune as a speculator, not telling you about it.
There are plenty of financial types who have funds where investment is contingent upon expectation of macroeconomic conditions. You know what they think because you know how they invest, and they’ll tell you what they think as well. What’s the point of journalists and academics even offering predictions if they don’t have “skin the game”? You can basically just say anything to be contrary, perhaps like in a publication such as Slate.
The bush & the bramble of the human family
I wonder if in future years we’re going to look at “species debates” in the context of human evolution like we look at counting angels on the head of a pin. Over at BBC News Clive Finlayson has a rambling opinion piece up, Has ‘one species’ idea been put to bed? Finlayson, the author of The Humans Who Went Extinct: Why Neanderthals Died Out and We Survived, doesn’t seem to have a tightly focused point and the end of it all (I think warranted, considering how unsettled this area is). But he does conclude:
And a major conference is planned for September next year when experts from all over the world will meet in Gibraltar to revise our ideas about “the human niche”. After decades of bad press we are finally getting round to humanizing the enigmatic Neanderthals.
The sons of Adam: spirit, not blood
Hominin increase in cranial capacity, courtesy of Luke Jostins
A few years ago a statistical geneticist at Cambridge’s Sanger Institute, Luke Jostins, posted the chart above using data from fossils on cranial capacity of hominins (the human lineage). As you can see there was a gradual increase in cranial capacity until ~250,000 years before the present, and then a more rapid increase. I should also note that from what I know about the empirical data, mean human cranial capacity peaked around the Last Glacial Maximum. Our brains have been shrinking, even relative to our body sizes (we’re not as large as we were during the Ice Age). But that’s neither here nor there. In the comments Jostins observes:
The data above includes all known Homo skulls, but none of the results change if you exclude the 24 Neandertals. In fact, you see the same results if you exclude Sapiens but keep Neandertals; the trends are pan-Homo, and aren’t confined to a specific lineage….
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