December 30, 2010

Study of Apidima 2 skull from Mani peninsula

Apidima 2 on the left, Petralona on the right. Apidima is a cave from southern-most Peloponnese, while Petralona is in northern Greece.

On the basis of the available evidence, the authors constrain the age of the skull between 115-105ka. They estimate his cranial capacity at 1,454cc, and note his very narrow face and high orbits.

Comparative analysis with H. sapiens, H. neandertalensis, H. heidelbergensis skulls suggests that the skull has Neandertal affinities. Below is the canonical variates analysis:

Apidima 2 is within the enclosing polygon of Neandertal specimens, being quite close to Guattari from neighboring Italy. It is also striking how close Petralona and Sima de los Huesos (attributed to H. heidelbergensis) are in this analysis, with La Ferassie 1 being particularly close to them.

Of particular interest is the position of Broke Hill (Kabwe/Rhodesian Man). Its relationship with European heidelbergensis is evident in its position along CV1, but I don't see how an especially close relationship with H. sapiens can be inferred. This seems consistent with the finding of H. sapiens beign separated from the heidelbergensis-neanderthalensis lineage, as well as the gist of a recent Tattersall paper which found it difficult to link modern Homo sapiens's derived morphological description to specimens usually called "archaic Homo sapiens". Kabwe is sometimes noted as an archaic H. sapiens representing an intermediate stage in the lineage that culminated in Omo and Herto.

The variability in the Skhul/Qafzeh specimens is also evident: Skhul 5 deviates strongly towards Neandertals/heidelbergensis while Qafzeh 6 is right in the middle of H. sapiens and Qafzeh 9 is intermediate. My own MCLUST analysis has Qafzeh 6 in the Australoid cluster while Skhul 5 is placed in the Neandertal cluster. This seems consistent with this CV analysis.

All in all, the authors of the current paper note the Neandertal affinities of Apidima 2, while noting that:
Contrary to our expectations, Apidima 2 did not show affinities with H. heidelbergensis (s.l.) or with the Petralona cranium in particular, but aligned more closely with our Neanderthal sample despite having been grouped a priori with H. heidelbergensis (s.l.). A brief comparison of the Apidima 2 frontal view to that of Petralona (Fig. 2) confirms several differences between the two specimens, including a more Neanderthal-like, relatively narrower face and higher cranium in Apidima (although the exact position and orientation of the two specimens could not be controlled and is not identical). However, Apidima 2 appears to lack the extremely derived Neanderthal nasal morphology, including the very high and protruding nasal bridge.

Journal of Human Evolution (in press)

Multivariate analysis and classification of the Apidima 2 cranium from Mani, Southern Greece

Katerina Harvati, Chris Stringer, Panagiotis Karkanas


How old is Y-chromosome Adam?

The presumed shallow time depth of the human Y-chromosome phylogeny is one of the main arguments of the recent Out-of-Africa theory. One of the major things I found while working on my Y-STR series is that point estimates from Y-STR variation are associated with huge confidence intervals, because of uncertainty about factors such as generation length, population history, mutation rates, even if the mutation model behaves "perfectly" in symmetrical stepwise fashion.

Trouble is, the deeper we go in time, the more uncertain we are about the behavior of our models. That is why I have generally avoided providing any age estimates for events prior to the Neolithic.

Nonetheless, it is interesting to see the state of the art in this area, because claims about the shallow time depth of the human Y-chromosome phylogeny are always flying around, but, if you follow the citation labyrinth, you will soon realize that the whole edifice is erected on sand.

Fortunately, I was recently reminded of a thoughtful post by Tim Janzen on the GENEALOGY-DNA-L from 2009 which is probably the "best thing" when it comes to Y-chromosome age estimation for deep clades of the phylogeny.

The most basal clade in the phylogeny is haplogroup A which is found in Africa. By comparing A chromosomes with those of the BT clade (everyone else), we can arrive at an estimate of Y-chromosome Adam. And, since BT clade contains much structure itself, we can compare A chromosomes with different subclades within BT, e.g., E or J or T.

This is essentially what Tim did: he compared a group of haplogroup A chromosomes with all the major clades of the BT group. Different age estimates produced by this method are not independent, because different haplogroups share more recent common ancestors: for example A vs I and A vs J both contain a common line of patrilineal descent (from the BT founder to the IJ founder). In any case, the different age estimates should all give approximately the same figure, as they are estimating the same quantity: if they do not, this is evidence about the inability of Y-STRs to provide good age estimates.

Tim went a step further, and he did his comparisons on different sets of markers: slow-evolving ones to fast-evolving ones. Again, age estimates with fast vs. slow-evolving markers should give similar age estimates. If they do not, then this means that an age estimate is a product not only of the true age of a lineage, but also of the particular mix of fast- and slow-evolving markers that one uses.

In short: age estimates by comparing haplogroup A with several other haplogroups and by using different sets of markers should be roughly similar. But, that is hardly what happened.

Below is Tim's table of age estimates in years. I have added an extra row and extra column: this contains the standard deviation of each column/row divided by the average (in %), and is useful to quantify how varied the age estimates are across different BT haplogroups and across different marker sets.

The standard deviation of the age estimates across haplogroups is reasonably small, but large enough to render any archaeological correlations useless. The real trouble is in the standard deviation of the age estimates across marker sets: they are higher than 100%!

What this means is that age estimates are largely a function of whether one uses slow- or fast- mutating markers.

Age estimates vary overall between 6,530 years and 535,755! It is obvious that fast/medium mutating markers provide unbelievably small age estimates (most of them are less than 20 thousand years). However, if we limit the analysis to slow mutating markers, most age estimates are in excess of 300,000 years!

In short, you can arrive at any age estimate you want, by choosing a particular mix of slow and fast mutating markers.

It could be argued that using all markers (50 markers column) would provide a better estimate, and, indeed, that estimate is in the order of 40-80ky, which is close to what is usually reported for human Y-chromosomes.

But that is equivalent to having a number of different clocks, some of which tell you that 3 seconds have transpired, and some which tell you that it's been a whole minute. The rational thing to do is not to take an average, but to throw the clocks in the garbage, or figure out what's wrong with them.


At present I am aware of no research that quantifies the depth of the human Y-chromosome phylogeny with anything bearing a semblance of accuracy. The 1000 genomes project has the potential to do this using using relatively well-behaved point mutations rather than Y-STRs, but, in the initial publication no actual age estimates were given, and the samples used to produce Supplementary Figure 7 lacked the most basal part of the tree (both clade A and the next most basal clade B).

UPDATE (Jan 2, 2011):

In a post in GENEALOGY-DNA-L, I show that by using slow- vs. fast-evolving markers using the Ballantyne et al. mutation rates and the tested haplogroup A and haplogroup C 67-marker haplotypes from the respective FTDNA projects, you can arrive at age estimates between 10-219ky.

This has confirmed to my mind that Tim Janzen's numbers about the dependence of age estimates on marker mutation rates are basically correct, and that age estimates about Y-chromosome Adam using Y-STRs are basically useless.

Let's hope that the 1000 Genomes Project will produce the data in the coming year that will allow us to make a better estimate, in terms of number of SNPs between A and non-A chromosomes presented as e.g., (i) a fraction of number of SNPs between human and chimpanzee, or (ii) by dividing with father-son Y-SNP mutation rates; the latter is already estimated but should become better fixed by looking at the father-son pairs included in 1000 genomes project

Cranial vault shape in fossil hominids

Homo sapiens is sometimes said to be derived from Homo heidelbergensis a species whose holotype is the Mauer mandible and which is sometimes extended to include the Broken Hill skull (Kabwe, Homo rhodesiensis) from Africa. This study seems to conflict with the earlier one which supported the grouping of H. heidelbergensis as an Afro-European taxon. Tim White suggested that Kabwe is ancestral to H. sapiens idaltu (Herto) which is ancestral to us. However, the Omo 1 skull is more ancient than idaltu and also more modern anatomically.

To say that the palaeoanthropological record is a mess would not be far from the truth...

Homo. 2010 Oct;61(5):287-313.

Cranial vault shape in fossil hominids: Fourier descriptors in norma lateralis.

Lestrel PE, Ohtsuki F, Wolfe CA.

Two major views of human evolution have elicited considerable controversy. These are: [1] the "out of Africa" hypothesis and [2] the "multiregional" hypothesis. This paper is an attempt to try to reconcile these two scenarios using hominid cranial vault data. Elliptical Fourier functions (EFFs) were used to describe, in visual and numerical terms, the shape of the human cranial vault in norma lateralis. Using jpeg images, contours of the cranial vault of a large sample of hominid specimens were pre-processed in Photoshop CS and rotated in 2D space (positional-orientation) so that a line drawn from nasion to porion was horizontal. The cranial vault image was then digitized with 72 closely-spaced points and submitted to a specially written routine that computed EFFs normalized by scaling (size-standardization). This ensured that the representation was invariant with respect to starting point, size and orientation. Statistically significant differences were found between the H. sapiens sample and both the H. erectus and H. neanderthalensis samples. In contrast, there were no statistically significant differences between the H. erectus and H. neanderthalensis groups, leading to three conclusions: [1] the similarity in cranial vault shape between H. erectus and H. neanderthalensis suggests a single gradually evolving lineage; [2] The taxon H. heidelbergensis can be embedded into the H. erectus→H. neanderthalensis line; and [3] H. sapiens seems to be a separate evolutionary development and is considered here either as a separate species or as a possible example of an allopatric semispecies (Grant, 1977). The results here suggest that human evolution over the last 2 Ma may turn out to be neither totally multiregional or simply out of Africa but rather represents a considerably more complicated picture.


December 29, 2010

Mauer site dated 609ka

Proc Natl Acad Sci U S A. 2010 Nov 16;107(46):19726-30. Epub 2010 Nov 1.

Radiometric dating of the type-site for Homo heidelbergensis at Mauer, Germany.

Wagner GA, Krbetschek M, Degering D, Bahain JJ, Shao Q, Falguères C, Voinchet P, Dolo JM, Garcia T, Rightmire GP.

The Mauer mandible, holotype of Homo heidelbergensis, was found in 1907 in fluvial sands deposited by the Neckar River 10 km southeast of Heidelberg, Germany. The fossil is an important key to understanding early human occupation of Europe north of the Alps. Given the associated mammal fauna and the geological context, the find layer has been placed in the early Middle Pleistocene, but confirmatory chronometric evidence has hitherto been missing. Here we show that two independent techniques, the combined electron spin resonance/U-series method used with mammal teeth and infrared radiofluorescence applied to sand grains, date the type-site of Homo heidelbergensis at Mauer to 609 ± 40 ka. This result demonstrates that the mandible is the oldest hominin fossil reported to date from central and northern Europe and raises questions concerning the phyletic relationship of Homo heidelbergensis to more ancient populations documented from southern Europe and in Africa. We address the paleoanthropological significance of the Mauer jaw in light of this dating evidence.


Is Homo heidelbergensis a distinct species?

J Hum Evol. 2009 Mar;56(3):219-46. Epub 2009 Feb 27.

Is Homo heidelbergensis a distinct species? New insight on the Mauer mandible

Mounier A, Marchal F, Condemi S.


The discovery of new fossils in Africa, Asia, and Europe, and the recognition of a greater diversity in the middle Pleistocene fossil record, has led to a reconsideration of the species Homo heidelbergensis. This nomen, formulated by Schoetensack in 1908 to describe the Mauer jaw (Germany), was almost forgotten during most of the past century. Numerous fossils have been attributed to it but no consensus has arisen concerning their classification. The holotype anatomical traits are still poorly understood, and numerous fossils with no mandibular remains have been placed in the taxon. Some researchers propose H. heidelbergensis as an Afro-European taxon that is ancestral to both modern humans and Neandertals whereas others think it is a strictly European species that is part of the Neandertal lineage. We focus on the validity of H. heidelbergensis, using the traditional basis of species recognition: anatomical description. We provide a comparative morphological analysis using 47 anatomical traits of 36 Pleistocene fossils from Africa, Asia, and Europe and 35 extant human mandibles. We re-examine the mandibular features of Mauer and discuss the specimen's inclusion in H. heidelbergensis, as well as alternative evolutionary theories. To lend objectivity to specimen grouping, we use multiple correspondence analysis associated with hierarchical classification that creates clusters corresponding to phenetic similarities between jaws. Our phenetic and comparative morphological analyses support the validity of H. heidelbergensis as a taxon. A set of morphological features can be statistically identified for the definition of the species. Some traits can be used to delimit H. heidelbergensis in an evolutionary framework (e.g., foramina mentale posteriorly positioned, horizontal retromolar surface). Those traits are also present on African (e.g., Tighenif) and European (e.g., Sima de los Huesos) specimens that show a close relationship with the Mauer mandible. Therefore, the definition of H. heidelbergensis is more precise and mainly supports the theory of an Afro-European taxon, which is the last common ancestor of H. neanderthalensis and H. sapiens. However, the results of this study fail to entirely discount the hypothesis that considers H. heidelbergensis as a chronospecies leading to the Neandertals.


December 28, 2010

400-200ka dental remains from Qesem Cave

The authors present three scenaria for the unique set of features of their discovered teeth:
  1. A local Homo population associated with the local Acheulo-Yabrudian cultural complex
  2. Neandertaloid traits (shoveling and lingual tubercle) may suggest a pre-Neandertal population, however, these traits are missing in the younger Skhul/Qafzeh specimens and re-appear in the later still Neandertals from the region
  3. Presence of multiple taxa in the sample; surprisingly earlier samples appear to be smaller and more modern than later ones
It is hard to evaluate the importance of this evidence, and it'd be nice to hear the opinion of dental/anthropology experts; my personal take-home lesson is that the finds are discordant with a simple model of heidelbergensis evolving into Neandertals and smaller and more modern morphology arriving from Africa.

American Journal of Physical Anthropology DOI: 10.1002/ajpa.21446

Middle pleistocene dental remains from Qesem Cave (Israel)

Israel Hershkovitz et al.


This study presents a description and comparative analysis of Middle Pleistocene permanent and deciduous teeth from the site of Qesem Cave (Israel). All of the human fossils are assigned to the Acheulo-Yabrudian Cultural Complex (AYCC) of the late Lower Paleolithic. The Middle Pleistocene age of the Qesem teeth (400–200 ka) places them chronologically earlier than the bulk of fossil hominin specimens previously known from southwest Asia. Three permanent mandibular teeth (C1-P4) were found in close proximity in the lower part of the stratigraphic sequence. The small metric dimensions of the crowns indicate a considerable degree of dental reduction although the roots are long and robust. In contrast, three isolated permanent maxillary teeth (I2, C1, and M3) and two isolated deciduous teeth that were found within the upper part of the sequence are much larger and show some plesiomorphous traits similar to those of the Skhul/Qafzeh specimens. Although none of the Qesem teeth shows a suite of Neanderthal characters, a few traits may suggest some affinities with members of the Neanderthal evolutionary lineage. However, the balance of the evidence suggests a closer similarity with the Skhul/Qafzeh dental material, although many of these resemblances likely represent plesiomorphous features.


Is multi-regional evolution dead?

A widely-circulated interpretation of the recent work on the genome of Neandertals and the Denisova hominins is that it proves the assimilation model of human origins. First, a reminder of the main models of human evolution from Stoneking et al.:

It is said that modern humans are mostly Out-of-Africa but there has been gene flow into regional Homo sapiens populations: Neandertal-related admixture affecting Eurasians and Denisovan-related admixture affecting Melanesians.

This naive interpretation of the evidence proposes that e.g., Melanesians are about 92% derived from Out-of-Africans and 8% derived from other hominins including both Neandertals and Denisovans.

It's important to state categorically that this only an interpretation of the evidence and in no way a disproof of the multiregional theory of human evolution.

Interbreeding happened

Let's begin by considering what we know to be true: interbreeding happened between widely divergent human populations. Otherwise the pattern of differential affiliation of modern human groups to archaic hominins would be impossible to explain: all humans should have the exact same relationship to the "side-branches" of the human family tree. But, this is clearly not the case.

If interbreeding happened then...

It's important to note how important this insight is. Modern human populations are mutually interfertile, but it is generally assumed that beyond a certain point of genetic divergence interbreeding is impossible for both anatomical and genetic incompatibility reasons.

But, if we accept the possibility of interbreeding even between very divergent populations, then where do we stop? It's possible that H. sapiens himself is the product of such interbreeding.

Admixture with archaics vs. Incomplete fusion

There are two ways of viewing the evidence:
  1. Different human populations have admixed with different archaic populations during the Out-of-Africa exodus
  2. Humans are descended from multiple archaic populations and have blended together, but the fusion is incomplete
Here is the Reich et al. model:

The alternative model is that Eurasian and African Homo can be envisioned as a mosaic of populations that did not speciate because gene flow between most of them was never interrupted.

Adaptive changes could flow freely in the lattice of populations: they could originate anywhere and spread across the entire species range in a few thousands of years.
  • Part of the regional variation spread and became part of the species-wide variation
  • Part of the regional variation was lost either because of drift or because it was maladaptive
  • Part of the regional variation remained in regional populations
It is this latter part that causes regional populations to show differential affiliation with archaic hominins.

A color analogy

Imagine a canvas painted with an orange color. It is not uniformly orange, however: parts of it are more "red" than average, and parts of it are more "yellow" than average.

One interpretation for this canvas is that the painter used an orange hue to paint it, but small amounts of red and yellow pigment were added in parts of the painting (Assimilation model)

A different interpretation is that the painter used red and yellow hues to paint it, but even though he moved his brush left-right and top-bottom, shuffling pigments around, there was an excess of red pigment at the spot where his brush first hit the canvas. (Multi-regional model)

What about the reduced genetic diversity of our species?

An argument for the recent Out of Africa model is that the reduced genetic diversity of our species necessitates a small effective population size and a recent genealogical time depth.

With respect to the latter, it should be noted that the genetic divergence between modern humans and Neandertals/Denisovans is about 1/3 more than between the most divergent humans (Papuans and San in Reich et al.). Hence, the shallow genealogical time depth is true, but it is not that different from our next-of-kin.

With respect to the reduced genetic diversity, one idea is that it is the result of genetic drift following a bottleneck in a small African population. But, the data can just as well be explained by species-wide selection which culled genetic variation.

The multi-regional hypothesis proposes that the reduced genetic diversity of our species is due to a pattern of selection. The evidence is not inconsistent with this hypothesis, as the human species shows a clear pattern of morphological change in the last 200 thousand years.

Indeed, the fact that at 100 thousand years ago the "chin" makes its appearance in the Levant and China could be interpreted as an Out-of-Africa migration, but it could just as well be interpreted as natural selection producing a chin in different Homo populations, without necessarily any large-scale population movements.

Aren't Africans more genetically diverse?

Another argument for the Out-of-Africa theory is that since Africans are more genetically diverse, that is where humans originated. But, different genes tell different stories; there are loci where Africans sport the greatest variation, and there are those with genealogies better explained by a Eurasian origin. Indeed, recently a paper suggested that some Indian groups may be more genetically diverse than African agriculturalists in a particular genomic region.

But, again, greater African genetic diversity does not necessitate an African origin of mankind, and could be partially explained by a pattern of admixture between divergent populations. Back-migration from Eurasia is rarely considered as a possibility, but there are good reasons to suspect it. For example, Yorubans are genetically closer to Chinese than they are to San, and back-migration to Africa is a possible explanation for this.

The Y-chromosome phylogeny presents strong evidence for back-migration. The basal clades of the phylogeny (A and B) are African, suggesting an African origin of extant human Y-chromosomes, but within the M168 major human lineage, haplogroup DE-YAP has mixed African and Eurasian affiliations, while F-M89 is Eurasian. A Eurasian origin of M168 is a strong possibility.

Another possibility is the larger effective population size in Africa, related perhaps to the fact that until recently our species was well-adapted to an African environment and lacked the know-how to thrive in latitudes further from the equator. In a larger population there are more new mutations and fewer alleles are lost due to drift, hence such a population may appear to be more genetically diverse irrespective of whether or not it is the parental population.

Did archaics contribute at most 8%?

Melanesians emerge as the most "archaic"-admixed population under the assimilation model, having Denisovan/Neandertal-related admixture of ~8%. But, there is reason to doubt this.

First of all, consider that between Green et al. and Reich et al. we went from 1-4% archaic contribution in Eurasia to 1-8%. It only took one additional hominin to find extra archaic admixture. What will happen when we sample another one?

But, the most important thing is to understand how these admixture estimates are arrived at: they are derived from sequence shared by archaics and non-Africans but not with Africans:
  • Sequence in which Africans are polymorphic and non-Africans are monomorphic may be due to archaic admixture in Africa
  • Sequence where everyone is polymorphic may derive from anywhere, not necessarily from Africa; the same is true for sequence where everyone is polymorphic and derived with respect to chimpanzee
  • Sequence where Eurasians are polymorphic and Aficans are monomorphic and in which Neandertals are monomorphic may derive from non-Neandertal non-African archaic hominins
In short, we should take the admixture ceiling of 8% with a huge grain of salt.


At the beginning of 2010 I would describe myself as fairly agnostic on the issue of human origins, but leaning towards the Recent Common Origin hypothesis due to:
  1. The Y-chromosome and mtDNA phylogeny
  2. The 100ky gap between Omo 1 and Qafzeh and the 50ky gap between Qafzeh and the later anatomically modern humans from Eurasia
  3. The greater African genetic diversity, and its clinal diminution from east Africa
  4. The lack of evidence for interbreeding between humans and archaic hominins
2010 has destroyed factors 2-4:
  • Zhirendong Cave gave us a chin in China, 100ky, and hence Qafzeh could no longer be interpreted as the early-Out-of-Africa that failed. The gap between anatomical modernity in Africa and in Eurasia narrowed.
  • Xing et al. narrowed the presumed gap in genetic diversity between Africans and Eurasians, and showed that the diversity decrease cline is spurious.
  • Reich et al., Green et al., and Krause et al. showed us that interbreeding between Homo sapiens and divergent Homo populations must've taken place.
As the beginning of 2011 approaches I am much less convinced of Out-of-Africa with Assimilation. Hopefully, in the coming years both the 1000 genomes project and ancient DNA work on early Homo sapiens or even other archaic hominins will add more data to the discussion.


Razib links to my post with some comments of his own. A few observations:
  • The importance of the Xing et al. paper is not so much in "disproving" the greater African genetic diversity. That conclusion cannot be reached from a single genetic region and without including African hunter-gatherers. Its importance is, however, in showing that the presumed smooth cline of decrease of genetic diversity from east Africa and across Eurasia is spurious; hence it weakens a crucial Out-of-Africa argument
  • Razib points out that recent selection tends to be regional (e.g., different genetic causes of light skin color in Europeans vs. Asians). That is true, but note that recent selection signatures in the last 10 thousand years should not be a guide to what happens in our species over 200-300 thousand years. Our ability to detect directional selection is time-limited: at its beginning it's lost in the noise, at its end, the selected allele is quasi-fixed. In a small and mobile population of Pleistocene hunter-gatherers, even one geographically as dispersed as Pleistocene Homo the entire process may take a few tens of thousands of years, depending on strength of selection. Hence, we are only detecting mostly recent signatures of selection that arose in dense and sedentary agricultural populations partly because older episodes of selection have already run their natural course.
  • The deep rooting of the Y-chromosome phylogeny in Africa is not in doubt, but the rooting of the major M168 clade, that accounts for surely over 90% of our species, and perhaps much more is in doubt. The point of the back-migration argument is not that Y-chromosomes did not originate in Africa (they did), but that African genetic diversity could be inflated by M168 back-migrants. I have yet to see a clear separation of African genetic diversity into what is indigenous and what can be accounted for by admixture. Hence, while the Xin et al. paper shows that the Eurasian cline of reduced diversity is not resilient to the addition of new populations, it is not at all clear to me that the greater genetic diversity of east Africans is not (at least in part) due to the trilateral admixed status of east Africans (natives, people from West Eurasia, and from deeper Africa).
  • Razib argues that we are unlikely to increase the archaic admixture percentage by much because there are only so many archaic hominins around. First of all, the multiregional model could be true even if we detected 0% archaic admixture, as long as fusion between different (not necessarily all) archaic populations was complete. But, also, we should remember that the genomic coverage of Pleistocene Homo is so geographically limited! Both Homo erectus soloensis and Homo erectus pekinensis are absent, as are the more recent hominins that might be directly relevant (e.g., Mungo Man, Dali, Zhiren). The same is true for Africa where recovery of ancient DNA seems extremely unlikely given present technology.
  • Razib points out that Fst distances between humans would be much higher under multiregional evolution, and that humans share a lot of common recent ancestry. First of all, genetic divergence dates for modern humans are about 400-600ky according to Reich et al. but we should remember that different genes tell different stories: there are both very old and very shallow coalescence times in the human genome, and a model of multiple archaic populations in Africa is a good fit for the data, as is an Out-of-Africa bottleneck 150ky, much earlier than previously thought. Add selection to the equation, and even greater time depths become plausible.
In short, I am not advocating either OoA with Assimilation or MRE at this point, but I would strongly argue that while Assimilation has become more plausible than Replacement after 2010, it's not the case that Assimilation has become more plausible than MRE.

The Human Evolution Wars have just begun...

December 23, 2010

Neandertals not cold-adapted (?)

There was a paper in 2008 which explained the wide nasal aperture in Neandertals in the context of their cold adaptation. That paper suggested that a combination of broad and long nose was the Neandertal solution to the cold.

Here comes a paper which argues against cold adaptation as the explanation for Neandertal facial morphology. On purely evolutionary grounds it's difficult to see why Neandertals would not be facially cold-adapted as they did live in extreme cold conditions. But, I'd have to look at the case the authors are making before voicing my opinion.

Journal of Human Evolution doi:10.1016/j.jhevol.2010.10.00

The Neanderthal face is not cold adapted

Todd C. Rae et al.

Many morphological features of the Pleistocene fossil hominin Homo neanderthalensis, including the reputed large size of its paranasal sinuses, have been interpreted as adaptations to extreme cold, as some Neanderthals lived in Europe during glacial periods. This interpretation of sinus evolution rests on two assumptions: that increased craniofacial pneumatization is an adaptation to lower ambient temperatures, and that Neanderthals have relatively large sinuses. Analysis of humans, other primates, and rodents, however, suggests that the first assumption is suspect; at least the maxillary sinus undergoes a significant reduction in volume in extreme cold, in both wild and laboratory conditions. The second assumption, that Neanderthal sinuses are large, extensive, or even ‘hyperpneumatized,’ has held sway since the first specimen was described and has been interpreted as the causal explanation for some of the distinctive aspects of Neanderthal facial form, but has never been evaluated with respect to scaling. To test the latter assumption, previously published measurements from two-dimensional (2D) X-rays and new three-dimensional (3D) data from computed tomography (CT) of Neanderthals and temperate-climate European Homo sapiens are regressed against cranial size to determine the relative size of their sinuses. The 2D data reveal a degree of craniofacial pneumatization in Neanderthals that is both commensurate with the size of the cranium and comparable in scale with that seen in temperate climate H. sapiens. The 3D analysis of CT data from a smaller sample supports this conclusion. These results suggest that the distinctive Neanderthal face cannot be interpreted as a direct result of increased pneumatization, nor is it likely to be an adaptation to resist cold stress; an alternative explanation is thus required.


Is the Denisova mtDNA sequence modern?

So says a paper that was posted in Nature Precedings. People more knowledgeable than myself about mtDNA sequence alignments and such are requested to chime in.

If true this would be very significant, because it would mean that the very archaic Denisova mtDNA reported in the new Nature paper is not really archaic.

Anyway, here's an excerpt from the paper:
The recognition of the Neandertal inserts in the Denisova sequence changes the reading considerably and indicates that the sequence before the insert at 16194, perhaps ending at 16181 is corrupt either from degradation or during preparation for sequencing. There may be another explanation for the lack of sequence alignment before that location and the substantial agreement after it. Nevertheless, this finding argues for modern human status of the Denisova sample and against a new species designation as suggested from the original analysis (Krause, et al., 2010). Variations in mtDNA in populations and their significance given the natural history of mitochondria have been noted by Ballard and Whitlock (2004) with a caution of their use to build phylogenetic relationships.

Niccolo Caldararo

The year of the great unraveling: a tale of seven caves

2010 is almost over, and how appropriate that the new Denisova paper would come right at its coda. Here we have what appears to be a sister clade of Neandertals, which apparently contributed their DNA to modern Melanesians. A link has been found between a tooth and a finger from a cave in the Altai (image source on the left) to people living a lot further to the south and east, in Papua and Bougainville?

That's 2 for 2 for Denisova surprising us: its mtDNA, reported earlier this year is discordant with the autosomal evidence: the Denisovans trace their mtDNA ancestry to a much earlier time than the division of humans and Neandertals. And, yet, the Denisova remains are about 50,000 years old, i.e., at a time close to the appearance of modern humans in Asia.

Who would have expected a fairly young specimen in South Siberia to have really archaic morphology and mtDNA, to tie itself to West Eurasian Neandertals on the one hand and to modern Melanesians on the other?

The other big paper of the year was the Neandertal one which tested Neandertal DNA from another cave, Vindija in Croatia (image on the right: Johannes Krause, Max Planck institute of evolutionary anthropology) threw another curveball at theories of human origins. Prior to the appearance of this paper there were two theories about possible Neandertal admixture in humans: one that there was none, and another that it might have affected West Eurasians (where Neandertals lived) and could be detected in either their genes (stories about the "red hair gene" that circulated a few years ago), or the morphology of late Upper Paleolithic anatomically modern humans from Europe.

And, yet, the Neandertal paper gave a startling conclusion: Neandertals were more related to non-Africans in general than they were to Africans. This evidence must be explored further: how is affinity to Neandertals distributed within Africa itself? Within Eurasia? In America?

No one would have expected this outcome: that people in the far east would be at least as related to Neandertals as Europeans are.

Speaking of the far east, it was another cave, Zhirendong that threw the third curveball on mainstream theories of human origins. Here we have palaeoanthropological remains that look especially modern, but with some archaic traits as well.

The story so far had been of a recent African Exodus of anatomically modern humans 40-60 thousand years ago. The presence of anatomically modern humans in other caves in the Levant such as Qafzeh around 100 thousand years ago was acknowledged, but it was usually brushed off, as the Out-of-Africa-that-failed, an early settlement of modern humans outside Africa that contributed little to the later pulse of humans that went on to populate the world.

The fossil evidence of Homo sapiens and pre-existing humans is notoriously difficult to make sense of. But, it certainly becomes more difficult to view Qafzeh as an experiment-that-failed when a similar mix of modern-and-archaic features can be found from roughly the same time all the way to the east in China.

Interpretation of these new findings will take some time, and the fact that we're getting regular DNA reads from samples that are a few myriad years old suggests to me that we should expect more surprises to come. I've voiced my opinions on many of these papers, but I'm ready to be surprised.

It was only a few decades ago that the notion of a common recent African descent of mankind was surprising and revolutionary (thanks to mitochondrial Eve & co.). The pendulum has begun to swing the other way, with all sorts of dead folks that were once considered to be irrelevant side-branches re-asserting themselves as our ancestors or kin.

Vindija, Denisova, Qafzeh, Zhiren, Vindija, Mezmaiskaya: expect these names to be passed around in scholarly discussions for years to come (and add Liang Bua cave, home of the "hobbits" to the company, to make them seven).

December 22, 2010

Post-glacial expansions of mtDNA haplogroups C and D in northern Asia

Table S1 has the C frequencies and Table S2 the D ones.

PLoS ONE 5(12): e15214. doi:10.1371/journal.pone.0015214

Origin and Post-Glacial Dispersal of Mitochondrial DNA Haplogroups C and D in Northern Asia

Miroslava Derenko et al.


More than a half of the northern Asian pool of human mitochondrial DNA (mtDNA) is fragmented into a number of subclades of haplogroups C and D, two of the most frequent haplogroups throughout northern, eastern, central Asia and America. While there has been considerable recent progress in studying mitochondrial variation in eastern Asia and America at the complete genome resolution, little comparable data is available for regions such as southern Siberia – the area where most of northern Asian haplogroups, including C and D, likely diversified. This gap in our knowledge causes a serious barrier for progress in understanding the demographic pre-history of northern Eurasia in general. Here we describe the phylogeography of haplogroups C and D in the populations of northern and eastern Asia. We have analyzed 770 samples from haplogroups C and D (174 and 596, respectively) at high resolution, including 182 novel complete mtDNA sequences representing haplogroups C and D (83 and 99, respectively). The present-day variation of haplogroups C and D suggests that these mtDNA clades expanded before the Last Glacial Maximum (LGM), with their oldest lineages being present in the eastern Asia. Unlike in eastern Asia, most of the northern Asian variants of haplogroups C and D began the expansion after the LGM, thus pointing to post-glacial re-colonization of northern Asia. Our results show that both haplogroups were involved in migrations, from eastern Asia and southern Siberia to eastern and northeastern Europe, likely during the middle Holocene.


mtDNA haplogroup U6 late Pleistocene expansion

BMC Evolutionary Biology 2010, 10:390doi:10.1186/1471-2148-10-390

Population expansion in the North African Late Pleistocene signalled by mitochondrial DNA haplogroup U6

Luisa Pereira et al.

Abstract (provisional)

The archaeology of North Africa remains enigmatic, with questions of population continuity versus discontinuity taking centre-stage. Debates have focused on population transitions between the bearers of the Middle Palaeolithic Aterian industry and the later Upper Palaeolithic populations of the Maghreb, as well as between the late Pleistocene and Holocene.

Improved resolution of the mitochondrial DNA (mtDNA) haplogroup U6 phylogeny, by the screening of 39 new complete sequences, has enabled us to infer a signal of moderate population expansion using Bayesian coalescent methods. To ascertain the time for this expansion, we applied both a mutation rate accounting for purifying selection and one with an internal calibration based on four approximate archaeological dates: the settlement of the Canary Islands, the settlement of Sardinia and its internal population re-expansion, and the split between haplogroups U5 and U6 around the time of the first modern human settlement of the Near East.

A Bayesian skyline plot placed the main expansion in the time frame of the Late Pleistocene, around 20 ka, and spatial smoothing techniques suggested that the most probable geographic region for this demographic event was to the west of North Africa. A comparison with U6's European sister clade, U5, revealed a stronger population expansion at around this time in Europe. Also in contrast with U5, a weak signal of a recent population expansion in the last 5,000 years was observed in North Africa, pointing to a moderate impact of the late Neolithic on the local population size of the southern Mediterranean coast.


Archaic Denisovans contributed to modern Melanesians

I love articles like this, because they force us to re-evaluate everything we thought we knew. I'll probably have much more to say on this paper once I read it, but for the moment I can't help but notice that the finding that the Denisova specimen belonged to a population that contributed DNA to modern Melanesians puts the description of various early Homo sapiens skulls as "Australoid" by various researchers in the past into a whole new perspective.

Indeed, I myself have used MCLUST to classify Upper Paleolithic skulls, and a number of them such as Markina Gora get the label of "Australoid". This is usually explained as an consequence of their greater robusticity, which links them to modern Australo-Melanesians, but the finding that a pre-modern population that lived in Eurasia did contribute genes to Melanesians, certainly raises all sorts of questions.


This is not a simple paper to read, if we also add the extensive supplementary material, so I will probably give my impressions and thoughts on it in piecemeal fashion.

The first interesting part comes from Table 1 in the paper. This contains values of the authors' D statistic D(H1,H2,archaic,chimpanzee) which shows how more frequently population H1 matches an archaic group than H2 does. A positive value suggests that H1 is more "archaic"-like.

The authors consider Neandertals (in the form of Vindija and Mezmaiskaya), as well as Denisova as the "archaic" groups of interest.

D values are consistently positive for H1=Papuans/Melanesians and H2 either African or Eurasian. This suggests indeed that Australo-Melanesians have archaic admixture from a population related to Denisova.


It is interesting that the authors are back-pedalling on the idea that specifically Neandertal admixture is responsible for the "archaic" genes found in Eurasians in the previous paper.

I think there are two reasons behind this: first of all, all Eurasians are closer to Denisova than Africans are. Melanesians are even more closer. But, Eurasians are closer to Neandertals than they are to Denisovans.

What this means is that Eurasians did not admix with Neandertals themselves but with a population that was closer to Neandertals than to Denisovans.

The second reason why I think that the idea of specifically Neandertal admixture is rejected is the fact that it makes no sense: the D statistic is 7.5 for Cambodians and 3.3 for Sardinian with standard errors of 1.2 and 1.5.

This means that Cambodians have more "Neandertal" admixture than Sardinians do, which makes absolutely no sense if specifically Neandertal admixture was the reason, as Neandertals were a West Eurasian-distributed species.

So, while not all is well for the Neandertal admixture theory, they also argue (in the supplementary material) that the alternative theory (which I've argued for, of archaic structure) is weakened by the new evidence. I'll think about their argument in a future update.


The authors did not consider the possibility of modern human to Denisova gene flow. Here is their reason (from the supplement):
Gene flow from modern humans into the ancestors of Denisovans is not only unsupported by the D-statistics, but is also historically implausible. The Denisova phalanx is more than 30,000 years old, and in our opinion is likely to be more that 50,000 years old (SI 12). The more ancient age estimate is older, and the more recent age estimate is only slightly younger than the age of the oldest confirmed modern human remains outside of Africa and the Levant. It is difficult to envision a plausible scenario in which the Denisovan population could have ancestry from a modern human group that experienced mixture in an area near where Melanesians live now, and then migrated to Siberia in just a few thousand years.

And, yet, we have evidence now of much older modern humans in South China, in the form of the Zhirendong mandible, which dates from ~100ky.


Looking at supplementary table S8.2 is quite interesting, because it gives the D statistics for intra-African "Neandertal" gene sharing.

The highest one is with H1=Yoruba and H2=Mbuti at 2%. What this means is, in essence, that Yoruba are more Neandertal-like than Mbuti are. How is this possible if a positive D value is reflective of admixture between Eurasians and Neandertals? There are no Neandertals in Nigeria to Neandertalize Yoruba with respect to Mbuti Pygmies.

This either means that Neandertal admixture is not the cause of the positive D statistics, or alternatively, that Yorubans are not pure Africans but have experienced back-migration of Neandertal-admixed Eurasians that Mbuti Pygmies did not experience to the same extent.

How interesting that Mbuti Pygmies (the least "Neandertal") and Papuans (the most "Denisovan") are the two most divergent living humans with an Fst of 0.377. Is it the case the different patterns of archaic admixture are contributing to this?


It is unfortunate that the authors did not sample East Africans yet again. The authors do not consider Z-scores below 3 (in absolute value) significant, so, the Yoruba/Mbuti score (for Neandertals) of 2.4 does not achieve significance, but it is almost there.

If the authors' theory is correct, then we expect to see no variation (or only variation attributed to noise) within native African populations with respect to their inferred "Neandertal admixture", as Neandertals were a Eurasian species.

It is perplexing why yet again East Africans were not sampled: if you are claiming Eurasian-African differences in archaic admixture, sampling East Africans who live in-between Eurasians and Africans is the natural thing to do!

Nature 468, 1053–1060 (23 December 2010) doi:10.1038/nature09710

Genetic history of an archaic hominin group from Denisova Cave in Siberia

David Reich et al.

Using DNA extracted from a finger bone found in Denisova Cave in southern Siberia, we have sequenced the genome of an archaic hominin to about 1.9-fold coverage. This individual is from a group that shares a common origin with Neanderthals. This population was not involved in the putative gene flow from Neanderthals into Eurasians; however, the data suggest that it contributed 4–6% of its genetic material to the genomes of present-day Melanesians. We designate this hominin population ‘Denisovans’ and suggest that it may have been widespread in Asia during the Late Pleistocene epoch. A tooth found in Denisova Cave carries a mitochondrial genome highly similar to that of the finger bone. This tooth shares no derived morphological features with Neanderthals or modern humans, further indicating that Denisovans have an evolutionary history distinct from Neanderthals and modern humans.

December 21, 2010

Y-chromosomes and mtDNA from Maharashtra

The paper has a nice map of the frequency of haplogroup J2a-M410, which is an update of the previous map from Sengupta et al. (2006)

The most recent gene flow paternal gene flow from West Asia corresponds largely to this haplogroup.

Unfortunately the authors used the "evolutionary mutation rate" which I and others have criticized, hence their age estimates are inflated. J2a and R1a1 have similar Y-STR variances in the two studied populations (0.36 and 0.34), and their ages are roughly a third of those reported (with wide uncertainty), or about ~4ky.

This is roughly consistent with the postulated arrival of the Indo-Aryans in India, and should probably be added to the enumeration of cases where the genealogical mutation rate correlates well with prehistory. It also seems consistent with my speculation about a West Asian origin of the Indo-Aryans.

Haplogroup R1a1 is more diverse in India-Pakistan than in west Eurasia, but there is variation in diversity in different South Asian groups. It's possible that a subgroup of it also migrated from the west, but that possibility must remain speculative in the absence of even more Y-SNP structure within it. Interestingly:
The network analysis of R1a with other Indian populations failed to provide any regional or linguistic clustering (Fig. S2).

The new Y-chromosome data from this paper can be found in Table S2.

PLoS ONE 5(12): e15283. doi:10.1371/journal.pone.0015283

The Influence of Natural Barriers in Shaping the Genetic Structure of Maharashtra Populations

Kumarasamy Thangaraj et al.

The geographical position of Maharashtra state makes it rather essential to study the dispersal of modern humans in South Asia. Several hypotheses have been proposed to explain the cultural, linguistic and geographical affinity of the populations living in Maharashtra state with other South Asian populations. The genetic origin of populations living in this state is poorly understood and hitherto been described at low molecular resolution level.

Methodology/Principal Findings
To address this issue, we have analyzed the mitochondrial DNA (mtDNA) of 185 individuals and NRY (non-recombining region of Y chromosome) of 98 individuals belonging to two major tribal populations of Maharashtra, and compared their molecular variations with that of 54 South Asian contemporary populations of adjacent states. Inter and intra population comparisons reveal that the maternal gene pool of Maharashtra state populations is composed of mainly South Asian haplogroups with traces of east and west Eurasian haplogroups, while the paternal haplogroups comprise the South Asian as well as signature of near eastern specific haplogroup J2a.

Our analysis suggests that Indian populations, including Maharashtra state, are largely derived from Paleolithic ancient settlers; however, a more recent (~10 Ky older) detectable paternal gene flow from west Asia is well reflected in the present study. These findings reveal movement of populations to Maharashtra through the western coast rather than mainland where Western Ghats-Vindhya Mountains and Narmada-Tapti rivers might have acted as a natural barrier. Comparing the Maharastrian populations with other South Asian populations reveals that they have a closer affinity with the South Indian than with the Central Indian populations.


Origin and history of horse mtDNA

PLoS ONE 5(12): e15311. doi:10.1371/journal.pone.0015311

Origin and History of Mitochondrial DNA Lineages in Domestic Horses

Michael Cieslak et al.


Domestic horses represent a genetic paradox: although they have the greatest number of maternal lineages (mtDNA) of all domestic species, their paternal lineages are extremely homogeneous on the Y-chromosome. In order to address their huge mtDNA variation and the origin and history of maternal lineages in domestic horses, we analyzed 1961 partial d-loop sequences from 207 ancient remains and 1754 modern horses. The sample set ranged from Alaska and North East Siberia to the Iberian Peninsula and from the Late Pleistocene to modern times. We found a panmictic Late Pleistocene horse population ranging from Alaska to the Pyrenees. Later, during the Early Holocene and the Copper Age, more or less separated sub-populations are indicated for the Eurasian steppe region and Iberia. Our data suggest multiple domestications and introgressions of females especially during the Iron Age. Although all Eurasian regions contributed to the genetic pedigree of modern breeds, most haplotypes had their roots in Eastern Europe and Siberia. We found 87 ancient haplotypes (Pleistocene to Mediaeval Times); 56 of these haplotypes were also observed in domestic horses, although thus far only 39 haplotypes have been confirmed to survive in modern breeds. Thus, at least seventeen haplotypes of early domestic horses have become extinct during the last 5,500 years. It is concluded that the large diversity of mtDNA lineages is not a product of animal breeding but, in fact, represents ancestral variability.


Fossil evidence for the origin of Homo sapiens

Debates in palaeoanthropology are often quite involved, and they become more arcane the further back we go in time. An modern human jawbone usually elicits a call to the police, but if you find an Upper Paleolithic jawbone, you can write paper upon paper on its anatomical minutiae.

Anthropologists who are intimately familiar with the ancient Homo record are not that many, so it is a pleasure to see a paper which tries to put their feuds and different perspectives into a historical context.

This is not easy reading, but you can skip the impenetrable anthrospeak about bipartite brows and penecontemporaneous specimens and appreciate the story at a higher level.

The paper is basically a polemic against "lumpers" who emphasize the unity of the Homo genus and even go as far as to propose that there is only a single Homo sapiens species that has gradually transformed over two million years.

From the paper:
What is most odd about this history is that anyone actually familiar with even a small portion of the human fossil record would ever even consider embracing Mayr's bizarrely influential assertions about human evolution. For, the signal of that record, even as it existed in the 1950s and 1960s, did not support Mayr's view at all. Nevertheless, most paleoanthropologists not only succumbed to Mayr's dictates but became intellectually constrained by them, apparently for the most part at least as a result of the weight of authority Mayr had gained, along with Dobzhansky and the paleontologist George Simpson, with the triumph of the “hardened” version of the Evolutionary Synthesis. This intellectual victory resulted in the almost complete suppression of competing evolutionary ideas, emanating primarily from Germany and the United Kingdom, that were in many ways much more “synthetic” (Schwartz, 2009a, b; Schwartz, in press) than the Synthesis itself. In the United States, especially, the prominent physical anthropologist S. L. Washburn (Washburn, 1951) was highly influential in publicizing the virtues of replacing old-fashioned “typology” with “population thinking” (e.g., Simpson, 1949). As a result, paleoanthropologists seem not to have noticed that the routine recognition and delineation of three different chronospecies of Homo was becoming ever more artificial and arbitrary as the hominid fossil record expanded.
Among the fossils that most of us were taught were uncontestable early representatives of our species are specimens from Qafzeh and Skhūl. From Qafzeh, the specimen most frequently cited and illustrated is the fairly complete skull Qafzeh 6. Yet this specimen lacks a bipartite brow, possessing instead a superoinferiorly somewhat tall brow that is anteriorly low and mounded, and continuous across an equally tall glabellar, region. Thus, although the neurocranium of Qazeh 6 is rather globular, and relative to it the face is not massive, this specimen conspicuously lacks the one particular apomorphy that would cement its allocation to H. sapiens (Schwartz and Tattersall, 1996b, 2000b) (Fig. 6).
With regard to other specimens that have been identified as “early anatomically modern” H. sapiens, we could confidently detect a glabellar butterfly only in the Liujiang cranium (>67 ka, possibly 101–227 ka) (Fig. 7). In the otherwise distinctive LH 18 (Ngaloba) calotte (108–129 ka) (Fig. 7), there appears to be something resembling this structure, the more robust and superoinferiorly thicker lateral portion forming an antero-obliquely facing plane (Schwartz and Tattersall, 2003). The variably complete crania of Omo Kibish I and II, Singa, and Jebel Irhoud I, and the Klasies River Mouth frontal fragment (Figs. 8 and 9), are broadly contemporaneous with, or older than, the Liujiang and LH 18 specimens and have been suggested as at least representing a precursor to anatomically modern H. sapiens. None of these specimens, however, displays a supraorbital configuration that could be described as bipartite, or as possessing a butterfly-shaped glabellar region.
Among chronologically younger specimens that have been considered definitively anatomically modern H. sapiens are the incomplete crania Border Cave 1 and Dar es Soltane II (Fig. 9). Although we have in the past agreed with this interpretation (Schwartz and Tattersall, 2003), our reassessment of these specimens has made us much more tentative now in both cases. Among the variably complete Pleistocene crania that we also viewed as morphological H. sapiens in our 2003 study, we still confidently include in our species the relatively recent specimens from Abri Pataud, Brno, Chancelade, Combe Capelle, Cro-Magnon, Dolni Věstonice, Engis (the adult), Grimaldi, Isturitz, Mladeč, Pavlov, Predmostí, Svitavka, Tuinplaas, Velika Pécina, Vogelherd, Wajak, Zhoukoudian Upper Cave, and Zláty Kůn (Fig. 10). Unaligned with typical H. sapiens on supraorbital conformation are the very recent specimens from Fish Hoek and Boskop (Schwartz and Tattersall, 2003) (Fig. 11). The latest estimate of 6891 ± 37 BP for Fish Hoek (Stynder et al., 2009) makes this atypicality all the more intriguing.

Am J Phys Anthropol. 2010;143 Suppl 51:94-121. doi: 10.1002/ajpa.21443.

Fossil evidence for the origin of Homo sapiens.

Schwartz JH, Tattersall I.


Our species Homo sapiens has never received a satisfactory morphological definition. Deriving partly from Linnaeus's exhortation simply to "know thyself," and partly from the insistence by advocates of the Evolutionary Synthesis in the mid-20th Century that species are constantly transforming ephemera that by definition cannot be pinned down by morphology, this unfortunate situation has led to huge uncertainty over which hominid fossils ought to be included in H. sapiens, and even over which of them should be qualified as "archaic" or as "anatomically modern," a debate that is an oddity in the broader context of paleontology. Here, we propose a suite of features that seems to characterize all H. sapiens alive today, and we review the fossil evidence in light of those features, paying particular attention to the bipartite brow and the "chin" as examples of how, given the continuum from developmentally regulated genes to adult morphology, we might consider features preserved in fossil specimens in a comparative analysis that includes extant taxa. We also suggest that this perspective on the origination of novelty, which has gained a substantial foothold in the general field of evolutionary developmental biology, has an intellectual place in paleoanthropology and hominid systematics, including in defining our species, H. sapiens. Beginning solely with the distinctive living species reveals a startling variety in morphologies among late middle and late Pleistocene hominids, none of which can be plausibly attributed to H. sapiens/H. neanderthalensis admixture. Allowing for a slightly greater envelope of variation than exists today, basic "modern" morphology seems to have appeared significantly earlier in time than the first stirrings of the modern symbolic cognitive system.


Patrilocal Spanish Neandertals

It's great to see what amounts to an ancient population study of a group of Neandertals.

PNAS doi: 10.1073/pnas.1011553108

Genetic evidence for patrilocal mating behavior among Neandertal groups

Carles Lalueza-Fox et al.

The remains of 12 Neandertal individuals have been found at the El Sidrón site (Asturias, Spain), consisting of six adults, three adolescents, two juveniles, and one infant. Archaeological, paleontological, and geological evidence indicates that these individuals represent all or part of a contemporaneous social group of Neandertals, who died at around the same time and later were buried together as a result of a collapse of an underground karst. We sequenced phylogenetically informative positions of mtDNA hypervariable regions 1 and 2 from each of the remains. Our results show that the 12 individuals stem from three different maternal lineages, accounting for seven, four, and one individual(s), respectively. Using a Y-chromosome assay to confirm the morphological determination of sex for each individual, we found that, although the three adult males carried the same mtDNA lineage, each of the three adult females carried different mtDNA lineages. These findings provide evidence to indicate that Neandertal groups not only were small and characterized by low genetic diversity but also were likely to have practiced patrilocal mating behavior.


December 20, 2010

A solution to the problem of Indo-Aryan origins

(Last Update: Dec 21)

Over at the Dodecad blog, I have been tracking a mysterious "Dagestan" genetic component in South Asia and Europe. This component is modal in populations of Dagestan: Dargins from Urkarah, Lezgins, and Kumyks from Stalskoe.

Dargins and Lezgins are Northeast Caucasian speakers, and while Kumyks are Turkic, this is probably due to a small East Eurasian component in their ancestry, and it's a fair guess that they too are natives to the region who underwent language shift.

Surprisingly, this component occurs at a high frequency in some South Asian populations, including Telugu and Tamil Brahmins from South India. These are believed to be descended from Indo-Aryan speakers from North India and to have maintained a genetic distinctiveness vis a vis the native inhabitants of South India.
There are two reasons why I think I am picking a really meaningful signal:
  • Differentiation between Tamil and Andhra Pradesh Brahmins and non-Brahmin populations from the same states
  • The levels of the component in India are as high as any other Eurasian populations save for the Dagestanis immediate neighbors in the Caucasus
Indeed, if you inspect the project members' results on this component, you will see that the "Dagestan" component is found at many South Asians who belong to other populations than those available in the public references. Without giving anything away, it's clear that the "Dagestan" component is found frequently in many parts of India.

Indo-Aryans outside India

The question of the origin of the Indo-Aryans is obviously very difficult, and attempts at tracing their origin use either a type of "geolinguistic trigonometry" to make them fit in the broader context of Indo-European dispersals, or rely on archaeological interpretation of the material culture of sites such as Arkaim or the BMAC.

I'll leave these speculations to those competent to make them, and I will turn to the concrete: the Mitanni of Syro-Anatolia. Here we have what seems to be Indo-Aryan personal/deity names, as well as numerals in what appears to have been a largerly Hurrian-speaking population.

The Kingdom of the Mitanni flourished in the 2nd millennium BC, a time also generally considered to be that of the earliest Indo-Aryan linguistic monument, the Rigveda.

What is most interesting, however, is that Hurrian, like Urartian are part of the Hurro-Urartian language family, which has been linked by some linguists to Northeast Caucasian.

I won't comment on whether such a link exists, but a relationship between Hurro-Urartian and Northeast Caucasian coupled with the known proximity of Indo-Aryans with Hurrians would immediately supply an explanation for the "Dagestan" component: it might be the legacy of an absorption of Hurrian elements by the ancestors of the Indo-Aryans while the latter were still in the Near East.

By the 2nd millennium BC, the Indo-Aryan element seems to have been well on its way to disappearance in the region, and we find no trace of it after the demise of the Mitanni. A millennium later came the disappearance of Urartian, replaced by various types of Indo-European (such as Armenian and Iranian), and Semitic. We are fortunate that the Indo-Aryans of Syro-Anatolia left traces of their existence before their demise.


The Bactria-Margiana Archaeological Complex was excavated by Viktor Sarianidi (here is a trailer for a documentary about it, and a Discover magazine article). According to Sarianidi, it is at least Indo-Iranian (if not specifically Indo-Aryan) and can be traced to the Syro-Anatolian region. The formation of the BMAC begins in the 3rd millennium BC, and it ends its existence in the 2nd, at around the time when Indo-Aryans are said to have made their appearance in the subcontinent. The geographical region of the BMAC (aka Oxus River civilization) is pictured on the left.

Whether we trace it to Anatolia, or, more modestly, to Iran, the likely western origin of the BMAC would almost certainly mean that it could have served as a conduit for the dispersal of the mystery "Dagestan" component to India.

Non-Indo-Europeans of Pakistan

The scenario I have outlined above derives the Indo-Aryans from the Transcaucasus where they pick up the "Dagestan" component, south of the Caspian, to the Oxus River civilization (BMAC) of Turkmenistan, to Afghanistan, and then via the Khyber Pass to Pakistan. The Mitanni are seen as Indo-Aryans who "stayed behind" and became thoroughly Hurrianized in the 2nd millennium BC.

We have one piece of evidence of the association of this component with Indo-Aryans: its presence in Brahmins and absence from low caste and tribal groups.

But, there is a different source of evidence that can potentially complete the argument: the non-Indo-European speakers of Pakistan: the Dravidian Brahui and the Burushaski speakers.

My theory predicts that they should have less of this component than Indo-Aryan and Iranian speakers from Pakistan such as Pathans, Sindhi, and Balochi. To test this, I repeated my South Asian experiment, but this time I added these two populations as well.

Below are the results:

In comparison to my previous experiment, the East Asian and Southeast Asian components have "folded back" into one, and the Burusho isolate has formed its own cluster.

But, here are the numbers that clinch the argument: the proportions of the Dagestan component #10 in South Asia:
As you can see, the component is minimized in tribals, low castes, and non-Indo-European groups of Pakistan (Burusho and Brahui).


I am not going to bet that all the details presented in this scenario are correct. But, this theory seems to make sense of many different pieces of evidence (such as the presence of Indo-Aryans in the Near East) and to harmonize with the genetic evidence.

UPDATE (Dec 21)

Since I've posted analysis of Europeans and South Asians separately, I decided to do a joint analysis.
Admixture proportions can be found in the spreadsheet. The "Dagestan" component is #1 (black) in this figure.

Here is the table of Fst distances between components:

The presence of component #1 in Uygurs and in Pathans may mean that it may have been carried by Indo-Iranians rather than specifically Indo-Aryans.

It would be wonderful to have samples from Kazakhstan, Turkmenistan, Afghanistan, Uzbekistan, or Tajikistan to fill the Central Asian gap between the Caucasus and China/South Asia. So, if you've chanced upon any people from those countries who happen to have tested with 23andMe, feel free to let them know about the Dodecad submission opportunity.

December 19, 2010

Survival of ancient DNA from teeth and bones

This is good news as it opens the way for more ancient DNA evidence, even from specimens that were thought not to contain usable DNA.

Journal of Archaeological Science doi:10.1016/j.jas.2010.11.010

Survival and recovery of DNA from ancient teeth and bones

C.J Adler et al.

The recovery of genetic material from preserved hard skeletal remains is an essential part of ancient DNA, archaeological and forensic research. However, there is little understanding about the relative concentrations of DNA within different tissues, the impact of sampling methods on extracted DNA, or the role of environmentally-determined degradation rates on DNA survival in specimens. We examine these issues by characterizing the mitochondrial DNA (mtDNA) content of different hard and soft tissues in 42 ancient human and bovid specimens at a range of fragment lengths (77–235 bp) using real-time PCR. Remarkably, the standard drill speeds used to sample skeletal material (c. 1000 RPM) were found to decrease mtDNA yields up to 30 times (by 3.1 × 105 mtDNA copies on average) compared to pulverization in a bone mill. This dramatic negative impact appears to relate to heat damage, and disappeared at very low drill speeds (e.g. 100 RPM). Consequently, many ancient DNA and forensic studies may have obtained false negative results, especially from important specimens which are commonly sampled with drills to minimize signs of damage. The mtDNA content of tooth cementum was found to be five times higher than the commonly used dentine (141 bp, p = 0.01), making the cementum-rich root tip the best sample for ancient human material. Lastly, mtDNA was found to display a consistent pattern of exponential fragmentation across many depositional environments, with different rates for geographic areas and tissue types, improving the ability to predict and understand DNA survival in preserved specimens.


December 16, 2010

Embalmed head of Henry IV found

BMJ 2010; 341:c6805 doi: 10.1136/bmj.c6805

Multidisciplinary medical identification of a French king’s head (Henri IV)

Philippe Charlier et al.

From the paper:
Since the desecration of the French kings’ graves in the basilica of Saint-Denis by the revolutionaries in 1793, few remains of these mummified bodies have been preserved and identified. After a multidisciplinary analysis, we confirmed that an embalmed head reputed to be that of the French king Henri IV and conserved in successive private collections did indeed belong to that monarch.
Now positively identified according to the most rigorous arguments of any forensic anthropology examination, the French king’s head will be reinterred in the royal basilica of Saint-Denis after a solemn funeral ceremony. Similar methods could be used to identify all the other kings’ and queens’ skeletons lying in the mass grave of the basilica, so that they can be returned to their original tombs.
Unfortunately, no "uncontaminated" mtDNA could be extracted. It would be interesting to compare his Y-chromosome to that of his descendant Louis XVI, but that doesn't seem to be possible.

Wikipedia article on Henry IV

(no abstract)

December 15, 2010

Human genetic variation: the first ? components

This is part III of my series on human genetic variation; it is based on the same dataset as part I: Human genetic variation: the first 50 dimensions and part II: Human genetic variation: 124+ clusters with the Galore approach

I have run ADMIXTURE on the 139-population/2,230-individual dataset, starting from K=3 and increasing K for as long as the Bayes Information Criterion increases. There was a temporary dip in the BIC at K=4, which, surprisingly, I had also encountered when analyzing a worldwide craniometric dataset (for an updated version of that analysis look here)

Below is a plot of the BIC as a function of K, the number of clusters:

The above plot should clarify the ? in the post's title. The BIC seems to increase law-like up to K=15, and I have no idea when it will plateau. Certainly many clusters I've encountered in previous analyses with subsets of these populations have yet to appear, so who knows?

As long as I have a functional computer and enough RAM I will continue this analysis, and the updated results will be posted in this blog post (although I think that after a certain K, I may have to invent a new color palette to represent them, or resort to just posting the numbers).


At K=3, Sub-Saharan Africans, West, and East Eurasians are distinguished

At K=4, Native Americans get their own cluster (dark green)


At K=5, Australoids (Papuans and Melanesians) get their own cluster (pink) which shows some affinity with populations from South Asia.

At K=6, the East Eurasian cluster is split into a North Eurasian/Central Asian (light blue) one and an East Asian (pink) one.

At K=7, a South Asian (light blue) cluster emerges.

At K=8, the Caucasoid cluster is split into European-centered (orange) and West Asian-centered (light blue) components

At K=9 the Mbuti, Biaka Pygmies, and San get their own cluster (Palaeofricans), with the Biaka showing some admixture with other Sub-Saharan Africans.

At K=10, a cluster (light green) centered on Koryak, Chukchi, Greenland emerges. Notice that this is also represented strongly among Athabask, much less in Pima and Maya from Mexico, and none at all in Karitiana and Surui, the southernmost Amerindian groups. This component is probably related to Y-haplogroup C3b-P39

It would be interesting to consider this in the light of the theory of a separate migration of Na Dene speakers (of which Athapaskans are a part) into North America and their inferred relationship with Kets. The absence of the "dark green" component which is present in Kets in Athabask does not really invalidate this hypothesis, as the "dark green" component may postdate the expansion of Na Dene speakers into the New World; however, the presence of the "light green" component in Athabask and its absence in other Amerindian groups is quite consistent with the two-migration model. No specific genetic relationship can be detected with Kets, however.

At K=11, the isolated Kalash of Pakistan get their own cluster, and this occurs at a high level in their neighbors


At K=12, a Southeast Asian cluster (red) emerges, highest in Malay and Cambodians, and well-represented in Chinese ethnic minorities such as Dai and Lahu. Notice also that the East Asian component in Melanesians also becomes "red", linking them to the Austronesians.


At K=13, a blue and a purple cluster supplant the previous West Asian cluster, with the blue one spilling to East Africa and the purple one to South Asia.

At K=14, the Karitiana, an Amerindian group from Brazil get their own cluster (pink), which spills into other Amerindian groups, but not substantially to the more northern Pima and Athabask.


At K=15 the Papuans and Melanesians are split into beige (?) and yellow population-specific clusters. Hence, the Melanesians, or at least the Nasioi from Bougainville where the HGDP sample is from, revealed in previous K to be associated with both Southeast Asians and Papuans, have actually acquired a genetic distinctiveness of their own.

Notice also that the Karitiana component that appeared at K=14 has "folded back" to the Amerindian component, while a "West Asian" and "Red Sea" component has appeared, the latter appearing on both Arabians and East Africans. As I've mentioned before, as K increases, ADMIXTURE has many roughly equiprobable choices in trying to represent the data.

At K=15 we are far from exhausting the available structure in modern humans.

Fst distances between components

Below is a table of genetic distances between the 15 inferred ancestral components:

As always, you should treat the chosen names for the components as helpful mnemonics; also, if a name used here has been used in a different ADMIXTURE analysis, with another set of populations and/or K, you should not assume that it reflects exactly the same entity.

Below is a dendrogram of hierarchical clustering of these 15 components with complete linkage. Once again, I emphasize that tree-like representations of human variation are not to be taken as anything other than a useful visualization of the data, as human populations did not evolve strictly tree-like, but have experienced lateral gene flow.

The tree shows clearly the four major divisions of mankind, which are separated quite distinctly from each other. From top to bottom: East Eurasians, West Eurasians, Australo-Melanesians, and Sub-Saharan Africans.

Once again, I emphasize that you should look at the table of Fst distances above, especially for closely related populations. For example, the Mediterranean component is joined to the Red Sea component in the dendrogram, but the table of distances shows that it is marginally closest to the North European (0.057), equidistant to the Red Sea and West Asian ones (0.062), the Indian (0.084) and the Kalash isolate (0.092). Do not rely on lossy representations like dendrograms when you can examine the actual distances themselves.

For completeness' sake, here is also a dendrogram of the hierarchical clustering using the average linkage method:

There is some internal re-arrangement of branches within the major races, and the Amerindian population becomes unattached from East Eurasians. Amerindians separated from East Eurasians fairly long ago, but their relationship to them is evidenced by the fact that they have their closest distances to East Asians and Siberians.

Finally, here is an MDS plot of the 15 components based on the inter-component Fst distances:

The maximum Fst in humans is between the Palaeoafrican ancestral population (Pygmies and San) and the Papuan one at 0.346, with a close second, that between Palaeoafricans and Amerindians (0.333).

The average Fst between the 15 components is 0.167. Notice that these are Fst distances between inferred ancestral populations, not between extant human populations. As such, they can be expected to be somewhat higher than conventionally given Fst distances for human populations.

However, the maximum distance also corresponds to distance between extant populations: guided by this analysis, I carried out a separate ADMIXTURE run using Papuans and Mbuti Pygmies from the HGDP set, arriving at Fst=0.377. This is probably not the limit of genetic differentiation within our species though, as Australian Aborigines, who are one further step removed from Africa than Papuans may be even more distant.


For anyone interested in exploring this data further, I've made a RAR file of the ADMIXTURE plots at a better resolution, as well as the raw admixture proportions behind them.

This also includes a file of Fst distances between components, and information about the samples (note that ancestral populations are labeled Pop0, Pop1, etc. and 1, 2, etc. in the distance file included in the RAR)