July 31, 2012

On the age of Y-chromosome haplogroup R1b-M343

Continuing my exploration of the human Y-chromosome, on the basis of 1000 Genomes data, I turned my attention to Y-haplogroup R1b-M343, one of the most populous lineages in extant Europeans. A total of 109 Y-chromosomes possessed the mutation diagnostic of this haplogroup.

At first, I calculated the histogram of pairwise TMRCA between all these 109 Y-chromosomes:
Most times are around 6-7 thousand years ago, but there is an outlier bump at around 15 thousand years ago. To further investigate this bump, I carried out multidimensional scaling of the collection of Y-chromosomes:

It is clear that the group of high pairwise TMRCAs correspond to the individual on the left of the figure that emerges as a clear outlier vis a vis the rest. The ID of that individual is HG00640 (from PUR population). One possibility is that this individual is M343+ due to sequencing error and belongs to a different lineage altogether. However, HG00640 is also R1-S1+ and R1b1-L278+ but R1b1a-P297-.

It will appear therefore that the HG00640 Puerto Rican belongs to the R1b1-L278 clade, but not to the R1b1a-P297 subclade. He thus represents an earlier split from the tree than the R1b1a2-M269 (frequent in West Eurasia), as well as the R1b1a1-M73 (frequent in Central Asia). It seems that I have chanced upon a real relic Y-chromosome!

The estimate of the age difference between HG00640 and the remaining M343+ chromosomes that cluster on the right is: 15,426 years. We now have direct evidence that haplogroup R1b1 is quite old, and R1b-M343 itself must have emerged sometime between 23,657 years (the TMRCA of R1a vs. R1b) and 15,426 years.

This little exercise reinforces my belief, first expressed in the outliers article, that there are real relic Y chromosomes in the world today, and we neglect them at our own peril.

Most European and European-derived men from the 1000 Genomes Project who belong to the R1b-M343 clade share patrilineal descent within the last 7,000 years or so. But, not all of them do, and outliers like HG00640 can only be caught with very large worldwide sample sizes and full genome sequencing.

* * *

Addendum: There appears to be a R1b1(xP297) DNA Project. There appear to be a quite rich collection of men with SNP results similar to HG00640, including R1b1c-V88+ (as suggested by Roy King in the comments), but also of V88- individuals. I see great utility in such projects, because if one can detect very aberrant Y-STR haplotypes (which can be done with a simple histrogram or MDS plot, as in this post), then one can identify candidate Y chromosomes for full sequencing.

* * *

I have also assessed all PUR individuals with the world9 calculator. This can be found here. HG00640 does not appear to be unusual in terms of his overall genomic ancestry.

Redating of Later Stone Age brings it in line with Upper Paleolithic

Two new papers in PNAS document that the Later Stone Age (LSA), the period of African prehistory corresponding to the Upper Paleolithic in Europe, began earlier than previously thought (c. 44ka BP), and contained elements of the material culture of present-day San populations.

There really seems to have been a Big Bang of sorts during that time that has now been shown to have affected most of the world: early modern humans in Europe were replacing Neandertals and starting the Aurignacian, fishing in the open seas in East Timor, and, now it seems, hunting and living in a very modern way in South Africa.

Intriguingly, the evidence for archaic admixture in Africa (Lachance et al. 2012; Hammer et al. 2011) point to about the same time. And, the 37,000 year old Hofmeyr skull from South Africa is most similar to early Upper Paleolithic European specimens. Together with new evidence about the human Y-chromosome phylogeny, it seems inescapable that something very big was taking place all over the world around the same time, something quite akin to the spread of a new people and not only to a spread of a new technology or way of thinking.

While precursors to modern human behavior have been documented in earlier contexts in Southern Africa and even among European Neandertals, these pale in comparison to the MP/MSA to UP/LSA transition. Here, we have near-simultaneous appearance of fully modern human behavior all over the planet, the appearance of fully modern skull forms with unmistakeable long range links, the rooting of most major Y-chromosome haplogroups, evidence for archaic admixture/disappearance. It was a real quantum leap in both human creativity and in the spread of human physical presence around the globe.

I have previously expressed the opinon that the "trigger" for this remarkable phenomenon can be found a few thousand years earlier, when the Sahara-Arabia belt entered a dry phase that would have driven its population outwards. But, really, the near simultaneous appearance of the same phenomenon all over the planet makes it difficult to find its ultimate source. These are exciting times for human origins research!

Press releases: Later Stone Age got earlier start in South Africa than thoughtModern culture 44,000 years ago
Coverage elsewhere: NY Times.

UPDATE I: From d' Errico et al.:
Contrary to lithic technology, which shows at Border Cave agradual evolution toward the ELSA starting after 56 ka (21), organic artifacts unambiguously reminiscent of LSA and San materialculture emerge relatively abruptly, highlighting an apparent mismatch in rates of cultural change. Our results support the view that what we perceive today as modern behavior is the resultof nonlinear trajectories that may be better understood whendocumented at a regional scale (7, 12–14, 21, 54).
Villa et al. also have a section on whether or not the MSA persisted longer than the arrival of the LSA:

Did MSA Technology Survive Until 26–20 ka in South Africa? Several sites in South Africa Lesotho and Swaziland are dated to the interval between 40 and 20 ka and defined as MSA or transitional MSA–LSA (11–15, 63). However, many assemblages have uncertain stratigraphy or small and undiagnostic inventories or are poorly dated or unpublished. A few have only preliminary descriptions. 
At Rose Cottage three layers (DY, DC, and RU) dated between ca. 30.8 and 27 ka are defined as final MSA (64). They are described as having bladelets produced by the bipolar technique but also having “MSA” types of formal tools (11). 
Strathalan Cave B (Eastern Cape) has two main layers dated between 29 and 25.7 ka. Their inventory, defined as late MSA, includes single and multiplatform cores, some blades, many irregular flakes, and very few retouched blades and flakes (65). At Boomplas Cave (Western Cape) the uppermost MSA level (BP), dated to 34–32 BP, is unpublished. Layer LPC contains an assemblage classified as LSA, with two bone points and few bladelets, dated to ca. 21 ka (2, 14). Systematic technological analyses and more dates are needed to break the impasse (63). 
It does seem that part of the reason why the MSA/LSA transition was dated later was that it did not happen simultaneously overnight. There is also very good reason to think that if the simultaneous appearance of modern behavior around the world was related to the spread of modern humans, then the modern San are not simple direct descendants of the Border Cave population, since their divergence from Eurasians greatly exceeds 100,000 years. A simpler explanation might be that at 44kya there was a migration of behaviorally modern people (evidenced e.g., by links between Hofmeyr and Eurasians), but that in Africa this set of people admixed with more divergent African populations; there is evidence of deep links between South and East Africans, as well as of more recent links between South  and West African farmers and East African pastoralists. Clearly, things were going on in the region in the last 40,000 years, as they seem to have done elsewhere.

PNAS doi: 10.1073/pnas.1202629109

Border Cave and the beginning of the Later Stone Age in South Africa

Paola Villa et al.

The transition from the Middle Stone Age (MSA) to the Later Stone Age (LSA) in South Africa was not associated with the appearance of anatomically modern humans and the extinction of Neandertals, as in the Middle to Upper Paleolithic transition in Western Europe. It has therefore attracted less attention, yet it provides insights into patterns of technological evolution not associated with a new hominin. Data from Border Cave (KwaZulu-Natal) show a strong pattern of technological change at approximately 44–42 ka cal BP, marked by adoption of techniques and materials that were present but scarcely used in the previous MSA, and some novelties. The agent of change was neither a revolution nor the advent of a new species of human. Although most evident in personal ornaments and symbolic markings, the change from one way of living to another was not restricted to aesthetics. Our analysis shows that: (i) at Border Cave two assemblages, dated to 45–49 and >49 ka, show a gradual abandonment of the technology and tool types of the post-Howiesons Poort period and can be considered transitional industries; (ii) the 44–42 ka cal BP assemblages are based on an expedient technology dominated by bipolar knapping, with microliths hafted with pitch from Podocarpus bark, worked suid tusks, ostrich eggshell beads, bone arrowheads, engraved bones, bored stones, and digging sticks; (iii) these assemblages mark the beginning of the LSA in South Africa; (iv) the LSA emerged by internal evolution; and (v) the process of change began sometime after 56 ka.


PNAS doi: 10.1073/pnas.1204213109

Early evidence of San material culture represented by organic artifacts from Border Cave, South Africa

Francesco d’Errico et al.

Recent archaeological discoveries have revealed that pigment use, beads, engravings, and sophisticated stone and bone tools were already present in southern Africa 75,000 y ago. Many of these artifacts disappeared by 60,000 y ago, suggesting that modern behavior appeared in the past and was subsequently lost before becoming firmly established. Most archaeologists think that San hunter–gatherer cultural adaptation emerged 20,000 y ago. However, reanalysis of organic artifacts from Border Cave, South Africa, shows that the Early Later Stone Age inhabitants of this cave used notched bones for notational purposes, wooden digging sticks, bone awls, and bone points similar to those used by San as arrowheads. A point is decorated with a spiral groove filled with red ochre, which closely parallels similar marks that San make to identify their arrowheads when hunting. A mixture of beeswax, Euphorbia resin, and possibly egg, wrapped in vegetal fibers, dated to ~40,000 BP, may have been used for hafting. Ornaments include marine shell beads and ostrich eggshell beads, directly dated to ~42,000 BP. A digging stick, dated to ~39,000 BP, is made of Flueggea virosa. A wooden poison applicator, dated to ~24,000 BP, retains residues with ricinoleic acid, derived from poisonous castor beans. Reappraisal of radiocarbon age estimates through Bayesian modeling, and the identification of key elements of San material culture at Border Cave, places the emergence of modern hunter–gatherer adaptation, as we know it, to ~44,000 y ago.


July 30, 2012

Estimating the age of Y-chromosome Adam (again)

UPDATE (August 1): The dates in this post have been superseded by the ones in Dates of major clades of the Y-chromosome phylogeny.

I have used the official phase1 chrY SNP data instead of the working data used in my first experiment. The histogram of pairwise TMRCA values looks much sharper now; not sure what the difference between the two datasets was:

In any case, the divergence of the most basal African clade is very evident here on the right, corresponding to an age for the human Y-MRCA of 159,298 years.

Also of interest are the other peaks in the distribution of pairwise TMRCAs which correspond to 6.5, 40.0, 66.3 thousand years. I think we are getting some good signals corresponding to Out-of-Arabia (66.3ky?) where a hyper-arid phase in Arabia may very well have caused a bottleneck in the population of modern humans, and full behavioral modernity/UP revolution (40.0ky?) where modern humans start turning up all over Eurasia, and even some Africans look like UP Europeans.

Perhaps, I'll spend some more time assigning the Y-chromosomes to haplogroups so that I can give a more complete estimate of the major clades of the Y-chromsome phylogeny.

UPDATE: Node Ages

I will add various node ages as I calculate them. Thanks to ISOGG for a convenient correspondence between haplogroups and SNP genetic positions.

Age (years)
(B-M247 vs. CT-M294)
(C1-P122 vs. C3-Z1453)
(C-M130 vs. F-P137)
(DE-M145 vs. CF-P143)
(D-Page3 vs. E-P169 )
(E1-P147 vs. E2-M75)
(E1b1a-V38 vs. E1b1b-M215)
(E1b1b1a1a-V12 vs. E1b1b1a1b-V13)
(E1b1b1a1a-V12 vs. E1b1b1a1c-V22)
(E1b1b1a1b-V13 vs. E1b1b1a1c-V22)
(I1-L75 vs. I2-L68)
(I2a1a-M26 vs. I2a1b-S328)
(I1-L75 vs. J-L60)
(IJ-P125 vs. K-P131)
(J1-M267 vs. J2-M172)
(J2a-L212 vs. J2b-M102)
(N-M231 vs. O-P191)
(O1a-M119 vs. O2-M268)
(O1a-M119 vs. O3-P198)
(O2-M268 vs. O3-P198)
(O3a1-L465 vs. O3a2-P201)
(Q-M242 vs. R-P224)
(R1a-M420 vs. R1b-M343)
(R1b1a2a1a1a5a-Z156 vs. R1b1a2a1a1a5b-Z301)

(*) This is, strictly speaking, the common ancestor of J1 and J2, since J*(xJ1, J2) chromosomes have also been observed.
(**) This is also the common ancestor of R1a and R1b, since R1* chromosomes have also been observed
(***) Paragroup DE* chromosomes have also been observed
(****)  Paragroup E* chromosomes have also been observed, so this is, strictly speaking, the common ancestor of E1 and E2; this is only a small underestimate, given that the DE node (62,205 years) is only marginally older
(*****) There is also the paragroup I2a1* and I2a1c

(x) Due to absence of published bifurcating structure within K-M9, I estimated this using the same model-free method used for Y-MRCA. This result in an "older peak" of pairwise K-M9 TMRCAs of 36,389 years. This seems appropriate as it lies between IJK (41,910 years) and P (33,043 years)

July 29, 2012

Stephen J. Gould and his legacy

I tend to the opinion that Stephen Jay Gould's legacy, at least in the field of anthropology, was mostly a negative one. I am also less inclined to attribute his mishandling of the Morton affair to "unconscious bias" on his part; conscious data manipulation in the interest of a strongly held political opinion seems more likely. If a living scientist had treated another's reputation in the way that Gould treated Morton, the end result would more likely be retraction and ejection from academia, rather than hagiography.

Nonetheless, Gould is important, primarily because he has shaped and continues to shape the thought of many, both professional scholars in some disciplines, but also of regular people who might have had the (mis?)fortune of learning their zoology and basic anthropology through his popular books. And, while I don't have the distinction of more than glancing through his massive posthumous magnum opus, it may very well be the case that there are hidden gems in so prolific a writer. So, the availability of full-length video of the presentations at a recent meeting dedicated to his legacy, titled Stephen J. Gould's Legacy: Nature, History, Society, is very welcome.

A playlist of the all the talks can be found here.

A couple that may be of interest is one by Niles Eldredge documenting the origin of Gould's arguably most famous idea of "punctuated equilibria":

A second video by Ian Tattersall discusses Gould's legacy to anthropology:

David Reich gives us some more hints

From 7:24 onwards:
For example people often think that Europeans are homogeneous group that arrived in a simple way there maybe 40 or 50 thousand years ago maybe based on the archaeology and just kind of sat there until they became the Europeans they are today, but that's probably not true: the Europeans today are a replacement population who came in much more recently and replaced the people who were there originally 40 thousand years ago. 

People in Africa certainly very diverse, but in fact there is very deep strands of variation in Africa and for example West Africans, people, the primary ancestral group of African Americans today, are actually turn out to be mixtures of very differently diverged groups that go very deep in time. So this is all very interesting, also true for East Asians, people in China today are not the same people who were there from the first time 40 thousand years ago, in fact they are a replacement population largely, that arrived after the first people there. So you see this history of more complex population movements than people think at first.
Previous hints about Europeans: onetwo.

All these themes ought to be familiar to readers of the blog, and I personally can't wait to sink my teeth into the new research results when they finally see the light of day.

Estimating the age of Y chromosome Adam

I took chrY SNP data from the 1000Genomes Project, with the goal of estimating the age of the root of the Y chromosome phylogeny. I used the mutation rate of 3x10^-8 mutations/nucleotide/generation of Xue et al. (2009), and a generation length of 25 years.

I decided to use a rather unconventional model-free approach, not building a phylogeny, but simply observing the distribution of pairwise TMRCA between all 526 Y chromosomes. A histogram thereof can be seen below:

My assumption is that the most basal split in the tree will correspond to the local peak on the right. I used MCLUST to cluster the observations, and, as is visually apparent, the right-most local peak forms a cluster with a mean of ~184 thousand years. This is a bit older than the 142 thousand year old date of Cruciani et al. (2011) which was based on a 200kb region of the MSY.

In any case, a re-rooting of the Y chromosome phylogeny is apparently in the works, so we're bound to know much more in the near future; we are long overdue for a systematic revision of node split times using the SNP counting method.

It is also imperative that African outliers in Eurasia be better studied to determine whether they have shallow or deep divergences with their African cousins. Much will depend on this, since the argument for recent Out-of-Africa crucially depends on Eurasia harboring a subset of African variation, a proposition which relies on the dismissal of apparently African outliers in Eurasia as recent migrants rather than relics.

UPDATE (July 30): I have now updated my age estimate using a newer cleaner version of the 1000 Genomes chrY data.

July 28, 2012

Complex Y chromosome structure in East Tyrol (and more IE thoughts)

Cultural diversity can disappear in a few generations, but genetic diversity -barring major genocides or disasters- usually persists.

The East Tyrol region in Austria has been Germanic-speaking since the Middle Ages, but historical evidence documents the presence of Romance, Germanic, and Slavic groups in its territory. How can we untangle the origin of the different groups when they are all jumbled up together now, and all Germanic-speaking? Previous research has shown that patrilineal groups can be isolated on the basis of surnames, but in the case of East Tyrol, the wide adoption of surnames happened after the region had become linguistically Germanic.

The authors of the new paper exploited the structure of local toponyms, in particular pasture names. The figure on the left shows the concentrations of Slavic (panel A), Romance (panel B), and Germanic (panel C) pasture names. While Germanic pasture names are evenly distributed, there is a contrast between those of Slavic and Romance origin. From the paper:
From the 853 analyzed pasture names in East Tyrol 71% were derived from Germanic (Bavarian) etymons, 17% from Slavic etymons, and 12% from Romance etymons. While pasture names with Germanic etymons were evenly distributed in high density within the whole study area the names with Slavic etymons were spatially focused in the east and north of East Tyrol (Fig. 2). Geographically, these are the lower Drau, Isel, Kals, Virgen and the Defereggen valleys (Fig. 1). No names with Slavic etymons were found in the southwestern Puster valley (Fig. 2). The pasture names with Romance etymons focus mainly in the southern part of East Tyrol (Gail, Puster, and Villgraten valley, Fig. 2). The slight northeastward trend observed in the distribution of Romance etymons is solely caused by the Kals valley, a medieval Romance linguistic enclave, which was separated from the Romance main territory in the 10th century [36]. On the basis of these results, East Tyrol was divided into two regions of former Romance (Puster, Gail, and Villgraten valley; region A) and Slavic (Isel, lower Drau, Defereggen, Virgen, and Kals valley; region B) main settlement (Fig. 2).
The authors dissected the occurrence of different haplogroups in the two contrasting regions (A: Romance, and B: Slavic) in some great detail:

Splitting the East Tyrolean population sample into regions A and B resulted in a partitioning of haplogroups E-M78, R-M17, R-M412/S167*, and R-S116*. E-M78, R-M17 and R-S116* Y chromosomes were exclusively found in region B whereas samples assigned to R-M412/S167*, R-U106/S21, and R-U152/S28 reached higher frequencies in region A (Fig. 3, Table S7). When attributing the samples to the fathers' and grandfathers' places of birth/residence, as reported by the participants, practically identical patterns were obtained for most of the haplogroups (Fig. 3). 
Y chromosomes belonging to haplogroups G-P15, I-M253, and J-M304 showed much lower regionalization in their frequencies (Fig. 3) at all three generation levels.

The non-localization of the G-P15, I-M253, and J-M304 seems reasonable as these may represent what is common in these populations (and one could indeed speculate -on the basis of current ancient DNA knowledge- that they correspond to Neolithic, Paleolithic, and Bronze Age processes respectively)

Two of the most interesting findings are:
Haplogroup R-M412/S167* was found at low frequencies in the combined East Tyrolean sample. However, the R-M412/S167* chromosomes were sorted by the subdivision of the study area and reached in region A levels of ~14% whereas their frequency in region B was well below the 5% threshold. At the probands and fathers level of analysis region A featured approximately fourfold higher frequencies of these chromosomes than region B. This ratio changed to about nine when placing the samples at the grandfathers' places of birth/residence. These contrasts remained statistically significant after correcting for multiple comparisons [22] at the fathers and grandfathers analysis level.
The western border of the geographic expansion of haplogroup R-M17 Y chromosomes is to be found in Central Europe and largely follows the political border separating present-day Poland (57%) and Germany (East: ~30%, South: ~14%, West: ~10%) [42]. Frequencies of about 15% and 10% were also found for Austria [18] and North-East Italy [48], respectively. In South Italy and in West Europe R-M17 chromosomes are not present at informative frequencies. 
In this study, the proportion of Y chromosomes carrying the derived M17 allele was 14.1%, a value that nearly perfectly matched those reported for West Austria (North Tyrol, 15.4%) and South Germany (Munich; 14.3%) [18], [42]. However, haplogroup R-M17 was completely absent in the East Tyrolean sub-sample from region A, but made up to 16% in region B. This result remained practically unchanged when assigning the probands to their respective fathers' or grandfathers' places of birth/residence (Fig. 3).
The new study reinforces my belief that R-M17 was not originally present in the Italo-Celtic branch of Indo-European. Together with the paucity of the same lineage in Albanians (~5%), Armenians (less than 5%), and its quite uneven distribution in Greeks, it is becoming increasingly clear that R-M17 may represent a late entrant that affected minimally southern and western Europe.

The fountain of its spread was probably a trans-Caspian (?) Central Asian staging point that followed a counter-clockwise route into Europe that spawned the northern (Germanic and Balto-Slavic) groups of Europe and the Indo-Iranians, who remained longer in their BMAC homeland, finally breaking down during the 2nd millennium BC. This would also harmonize with the increasing evidence for complementary R-M17 distributions in Europe and Asia, associated with the Z93 marker. 

It might appear that Z93+ chromosomes may track the later expansion of the Indo-Iranian world. I have observed before that R-M17 seems distributed in a long arc north and east of the Caspian, and it is perhaps in different points along this arc that the dominant European (NW) and Asian (SE) types emerged out of the early Neolithic population.

Combining this insight with an analysis of Y chromosome variation within the Graeco-Armeno-Aryan group, it appears that Graeco-Armenian is characterized predominantly by J2+R1b related lineages, while Indo-Iranian by J2+R1a related lineages. The evidence for Tocharian would involve J2+R1b related lineages.  Overall, it would appear that the earliest J2 core of PIE affected two different groups of populations living on complementary sides of the Caspian:

  • The trans-Caspian R-M17 population followed an early (3rd, or late 4th millennium BC?) north-west trajectory into Europe (associated with northern European groups such as Balto-Slavic and Germanic) as well as a later expansion (2nd millennium BC? associated with climatic deterioration in BMAC) that brought Iranian speakers to the steppe, as well as to Iran, and Indo-Aryans to South Asia.
  • The cis-Caspian, trans-Caucasian R-M269 population followed an early (late 4th millennium, early 3rd millennium?) expansion into Europe, probably together with J2 in the Balkans (Graeco-Phrygian, perhaps Thracian), and arriving in the form of Bell Beakers in Western Europe (Italo-Celtic), as well as a later (2nd-1st millennium BC?) expansion to the east (Tocharians)
This long excursus was necessary as a preamble to an explanation on what happened in Europe itself, which brings us back to the topic of the current paper:

  • The lack of structure between regions A and B with respect to haplogroup J, together with the great difference in levels of this haplogroup between Italy and the Celtic world,  suggests that Italian J-related lineages  may have been inflated in proto-historical and historical times. There are candidates a-plenty: Greeks, Etruscans, Trojans to name but three. Excess of J in Italy, relative to the Celtic world, clearly relates to the abundant traditions of eastern origins for the historical groups of Italy.
  • It would appear that during proto-history, most of Europe was dominated by three sets of IE people (R-M269 in the west, who had transmitted Proto-Celto-Italic; R-M17 in the northeast of Proto-Balto-Slavic speech, and Proto-Germanic in-between, participating in both worlds, and --appropriately-- often linked with either Italo-Celtic or Balto-Slavic linguistically)
  • There were other (now-extinct) groups as well: the Illyrians vs. Thracians in the Balkans with complementary Y chromosome distributions, the former including an extra chunk of aboriginal legacy (haplogroup I), no doubt due to the much more difficult terrain of the western Balkans. These are contrasted with our final group, the Greeks who straddled three worlds (the Paleo-Mediterranean world of the first farmers, the Thraco-Phrygian world linked to the Indo-Iranians at a deeper level, and the Anatolian world)
The boundaries between these various groups were a little blurred in the course of history. But, apparently, they were still a little clearer during the Middle Ages, and probably much clearer before the Völkerwanderung of the Germans, and the expansion of the Slavs.

Geneticists are executing a remarkable pincer movement, zeroing in on the period of European ethnogenesis from both the remote past and the present: through a study of ancient DNA from the dawn of history, they are beginning to understand how Europe was peopled, layer after layer of settlement; and through the study of surnames and toponyms they are drilling ever deeper into the pre-genealogical past. Together with much anticipated technological progress related to full genome sequencing and ancient DNA extraction, it will not be long before the history of Europe will be laid bare in remarkable detail.

PLoS ONE 7(7): e41885. doi:10.1371/journal.pone.0041885

Pasture Names with Romance and Slavic Roots Facilitate Dissection of Y Chromosome Variation in an Exclusively German-Speaking Alpine Region

Harald Niederstatter et al.

The small alpine district of East Tyrol (Austria) has an exceptional demographic history. It was contemporaneously inhabited by members of the Romance, the Slavic and the Germanic language groups for centuries. Since the Late Middle Ages, however, the population of the principally agrarian-oriented area is solely Germanic speaking. Historic facts about East Tyrol's colonization are rare, but spatial density-distribution analysis based on the etymology of place-names has facilitated accurate spatial mapping of the various language groups' former settlement regions. To test for present-day Y chromosome population substructure, molecular genetic data were compared to the information attained by the linguistic analysis of pasture names. The linguistic data were used for subdividing East Tyrol into two regions of former Romance (A) and Slavic (B) settlement. Samples from 270 East Tyrolean men were genotyped for 17 Y-chromosomal microsatellites (Y-STRs) and 27 single nucleotide polymorphisms (Y-SNPs). Analysis of the probands' surnames revealed no evidence for spatial genetic structuring. Also, spatial autocorrelation analysis did not indicate significant correlation between genetic (Y-STR haplotypes) and geographic distance. Haplogroup R-M17 chromosomes, however, were absent in region A, but constituted one of the most frequent haplogroups in region B. The R-M343 (R1b) clade showed a marked and complementary frequency distribution pattern in these two regions. To further test East Tyrol's modern Y-chromosomal landscape for geographic patterning attributable to the early history of settlement in this alpine area, principal coordinates analysis was performed. The Y-STR haplotypes from region A clearly clustered with those of Romance reference populations and the samples from region B matched best with Germanic speaking reference populations. The combined use of onomastic and molecular genetic data revealed and mapped the marked structuring of the distribution of Y chromosomes in an alpine region that has been culturally homogeneous for centuries.


July 26, 2012

New evidence for archaic admixture in African hunter gatherers (Lachance et al. 2012)

At the end of last year I predicted that full genome sequencing would begin turning up evidence for more archaic admixture in Africa. Halfway into the year, it appears that my prediction has proven to be correct: a new study in Cell by Lachance et al. documents the existence of such admixture between an archaic hominin and Pygmies from Cameroon, and the East African Hadza and Sandawe.

Archaic admixture in Biaka and San was previously detected by Hammer et al. Hence, we now have evidence for archaic admixture from several regions that encompass all major regions within sub-Saharan Africa. It seems that my old idea about layers of Palaeoafricans being absorbed by early modern humans in Africa was basically correct, and that some of these layers correspond to archaic African populations.

But not all agree. The New York Times coverage of the paper suggests that there is a controversy surrounding the new study:
All human fossil remains in Africa for the last 100,000 years, and probably the last 200,000 years, are of modern humans, providing no support for a coexistent archaic species. 
Paleoanthropologists like Dr. Klein consider it “irresponsible” of the geneticists to publish genetic findings about human origins without even trying to show how they may fit in with the existing fossil and archaeological evidence. Dr. Akey said he agreed that genetics can provide only part of the story. “But hopefully this is just a period when new discoveries are being made and there hasn’t been enough incubation time to synthesize all the disparities,” he said.
This is of course completely wrong; as Chris Stringer mentions in the NY Times piece, there is ample evidence for archaic Africans down to quite recent times in the form of Iwo Eleru and Ishango, and there is more evidence besides. Indeed, it does not appear at all that there was a punctuational event that replaced archaic hominins with a new Homo sapiens species. If anyone wants to criticize the new study, complaining about it being in disharmony with physical anthropology is not a good way to go about it. Nor is it, of course, "irresponsible" to report the new findings.  And, apparently, there is more on the way:

In a report still under review, a third group of geneticists says there are signs of Neanderthals having interbred with Asians and East Africans. But Neanderthals were a cold-adapted species that never reached East Africa.
Things are bound to become quite interesting.

From the paper:

A striking finding in our data set is that compelling evidence exists that extant hunter-gatherer genomes contain introgressed archaic sequence, consistent with previous studies (Hammer et al., 2011; Plagnol and Wall, 2006; Reich et al., 2010; Shimada et al., 2007; Wall et al., 2009). We note that unambiguous evidence of introgression is difficult to obtain in the absence of an archaic reference sequence, which currently does not exist and may never be feasible given the rapid decay of fossils in Africa. Although we carefully filtered our data set in an attempt to analyze only high-quality sequences (Supplementary Information), it is possible that unrecognized structural variants or other alignment errors could generate a spurious signature similar to introgression. Encouragingly, we did not see an enrichment of structural variation calls in our candidate introgression regions. Additionally, through extensive simulations and analysis of European whole-genome sequences (Supplementary Information), we have demonstrated that the signatures of introgression that we observed are unlikely to be entirely accounted for due to other aspects of population demographic history, natural selection, or sequencing errors. Moreover, we did not find strong evidence that introgressed regions were clustered in the genome more often than expected by chance (p > 0.05; Supplemental Information). Nor did we find significant evidence that introgressed regions were enriched in genic regions (p > 0.05); rather, genic regions were significantly depleted for introgression in several populations (Supplemental Information). Therefore, the simplest interpretation of these data is that introgressed regions in extant human populations represent neutrally evolving vestiges of archaic sequences. In short, we find that low levels of introgression from an unknown archaic population or populations occurred in the three African hunter-gatherer samples examined, consistent with findings of archaic admixture in non-Africans (Reich et al., 2010). 

What are the implications of the new research? Where did modern humans actually originate and how can their archaic admixture be explained?

One possible explanation, consistent with multi-regional evolution (MRE) theory, is that modern humans didn't originate anywhere in particular; they emerged out of Homo populations that lived everywhere. And, certainly, the discovery of archaic admixture of a local origin is quickly reducing the number of places where the common ancestors of modern humans could have begun their expansion. Western Eurasia is out due to Neandertals; East Eurasia and Oceania is out due to Denisovans; the entirety of Sub-Saharan Africa seems to also be out. North Africa and Southwest Asia appear to be the only remaining candidates.

I don't particularly agree with MRE; one of its predictions (about the relevance of archaic hominins to the human story) has proven to be correct: it increasingly seems that there never was a new Homo sapiens species that was in reproductive isolation from the rest of the Homo genus. On the other hand, the existence of local admixture with different sets of archaic hominins, together with the relative homogeneity of our species is indicative of a range expansion that largely replaced archaic humans -- but not completely.

There does seem to have been a Big Bang of modern humans which caused the demographical explosion of a particular subset of genetic variation. This Big Bang is often associated with Out-of-Africa, but there are good reasons to doubt the traditional 60,000-year old Out-of-Africa theory, according to which humans from South or East Africa crossed into Arabia and followed the coast to populate the world. We now have more reasons to doubt this: evidence of archaic admixture in both the postulated homelands: South Africa, often cited as the region where the first signs of behavioral modernity appear, and East Africa, where the earliest anatomically modern human fossils appear.

My money continues to be on the "two deserts" theory I have proposed some time ago:

  • A green Sahara pumping the ancestors of modern humans pre-100 thousand years ago, and 
  • a deteriorating green Arabia pumping them post-70 thousand years ago, with some back-migration into Africa.
This would relate the two regions where no evidence (yet?) for archaic humans exist (North Africa and South West Asia), explain the causes of their dispersal (climate change), and harmonize with the evidence for archaic admixture, since the expanding wave of modern humans would partially absorb pre-existing hominins in both Sub-Saharan Africa and across Eurasia.

It must be noted that scientists have been rather conservative in their estimates of archaic admixture in the absence of ancient DNA sequence. Recombination obliterates traces of really old admixture, because introgressed segments become ever smaller, resulting in a pastiche of modern and archaic sequence that no longer looks statistically archaic. But, hopefully, the ever-solidifying case for archaic admixture in our species will finally deal the death blow to tree models, and reveal a much more interesting story of our origins.

Other coverage of the new paper: Nature, Science, ScienceDaily, EurekAlert, Washington Post, SciAm.

Cell doi:10.1016/j.cell.2012.07.009

Evolutionary History and Adaptation from High-Coverage Whole-Genome Sequences of Diverse African Hunter-Gatherers

Joseph Lachance et al.

To reconstruct modern human evolutionary history and identify loci that have shaped hunter-gatherer adaptation, we sequenced the whole genomes of five individuals in each of three different hunter-gatherer populations at >60x coverage: Pygmies from Cameroon and Khoesan-speaking Hadza and Sandawe from Tanzania. We identify 13.4 million variants, substantially increasing the set of known human variation. We found evidence of archaic introgression in all three populations, and the distribution of time to most recent common ancestors from these regions is similar to that observed for introgressed regions in Europeans. Additionally, we identify numerous loci that harbor signatures of local adaptation, including genes involved in immunity, metabolism, olfactory and taste perception, reproduction, and wound healing. Within the Pygmy population, we identify multiple highly differentiated loci that play a role in growth and anterior pituitary function and are associated with height.


A look at Y chromosomes of Romania via Count Dracula

In short: researchers tried to see whether they could identify a specific Y chromosome lineage associated with the House of Basarab in Romania, the most famous member of which is Vlad the Impaler, an inspiration for the mythical Count Dracula. To do this, they tested Basarab-surnamed individuals, as well as the general Romanian population.

The whole exercise was, in a sense, a failure, since it neither disclosed a Basarab-specific lineage, nor resolved the historical question about the origin of the House of Basarab (Vlach or Cuman). But, it gave us some wonderful new data on Romania that is, of course, quite welcome.

This seems like a good candidate for a future ancient DNA study, assuming of course, that Vlad and his family are still in their final resting place, and there are brave enough researchers to disturb them (j/k).

On a more serious note, the authors correctly state that even if the Basarab house was originally Turkic, they could still have carried West Eurasian chromosomes, since incoming Turkic groups in Europe were not purely Mongoloid like their more remote ancestors. On the other hand, I note that most of the Basarab-surnamed individuals belonged to E-V13, I-P37.2, J-M241 all of which are almost certainly native Romanian. If one of them carries the original chromosome, then the odds are in favor of a Romanian origin, although nothing short of ancient DNA work can resolve the issue, assuming that's possible.

Table S1 contains the new Romanian data, and Table S2 data from surrounding populations (Hungary, Bulgaria, Ukraine).

PLoS ONE 7(7): e41803. doi:10.1371/journal.pone.0041803

Y-Chromosome Analysis in Individuals Bearing the Basarab Name of the First Dynasty of Wallachian Kings

Begoña Martinez-Cruz et al.

Vlad III The Impaler, also known as Dracula, descended from the dynasty of Basarab, the first rulers of independent Wallachia, in present Romania. Whether this dynasty is of Cuman (an admixed Turkic people that reached Wallachia from the East in the 11th century) or of local Romanian (Vlach) origin is debated among historians. Earlier studies have demonstrated the value of investigating the Y chromosome of men bearing a historical name, in order to identify their genetic origin. We sampled 29 Romanian men carrying the surname Basarab, in addition to four Romanian populations (from counties Dolj, N = 38; Mehedinti, N = 11; Cluj, N = 50; and Brasov, N = 50), and compared the data with the surrounding populations. We typed 131 SNPs and 19 STRs in the non-recombinant part of the Y-chromosome in all the individuals. We computed a PCA to situate the Basarab individuals in the context of Romania and its neighboring populations. Different Y-chromosome haplogroups were found within the individuals bearing the Basarab name. All haplogroups are common in Romania and other Central and Eastern European populations. In a PCA, the Basarab group clusters within other Romanian populations. We found several clusters of Basarab individuals having a common ancestor within the period of the last 600 years. The diversity of haplogroups found shows that not all individuals carrying the surname Basarab can be direct biological descendants of the Basarab dynasty. The absence of Eastern Asian lineages in the Basarab men can be interpreted as a lack of evidence for a Cuman origin of the Basarab dynasty, although it cannot be positively ruled out. It can be therefore concluded that the Basarab dynasty was successful in spreading its name beyond the spread of its genes.

The social network of the Iliad is highly realistic

From the paper:
In an attempt to place the three mythological networks on the spectrum from the real to the fictitious, we compared their properties to actual and imaginary social networks. Table 2 summarises the broad properties of the different types of networks. Of the three myths, the network of characters in the Iliad has properties most similar to those of real social networks. It has a power-law degree distribution (with an exponential cut-off), is small world, assortative, vulnerable to targeted attack and is structurally balanced. This similarity perhaps reflects the archaeological evidence supporting the historicity of some of the events of the Iliad.

arXiv:1205.4324v2 [physics.soc-ph]

Universal Properties of Mythological Networks

Pádraig Mac Carron, Ralph Kenna

(Submitted on 19 May 2012 (v1), last revised 18 Jul 2012 (this version, v2))

As in statistical physics, the concept of universality plays an important, albeit qualitative, role in the field of comparative mythology. Here we apply statistical mechanical tools to analyse the networks underlying three iconic mythological narratives with a view to identifying common and distinguishing quantitative features. Of the three narratives, an Anglo-Saxon and a Greek text are mostly believed by antiquarians to be partly historically based while the third, an Irish epic, is often considered to be fictional. Here we show that network analysis is able to discriminate real from imaginary social networks and place mythological narratives on the spectrum between them. Moreover, the perceived artificiality of the Irish narrative can be traced back to anomalous features associated with six characters. Considering these as amalgams of several entities or proxies, renders the plausibility of the Irish text comparable to the others from a network-theoretic point of view.


July 25, 2012

Genographic 2.0 launched

The Genographic Project at National Geographic has announced their new Genographic 2.0 test. This is a new test which tests about 150,000 SNPs and gives you information about your ancestry:
  • Ancestral breakdown (admixture)
  • Hominid (Neandertal/Denisova) admixture
  • Y chromosome haplogroup (apparently on the order of 10,000 SNPs)
  • mtDNA haplogroup
I participated in a pre-launch online presentation of the test about a month ago, and it seems that the creators of the test have paid some thought into identifying their set of SNPs. The number of SNPs is about right for ancestry comparisons, but it will be interesting to see how many of them intersect the many publicly available datasets that already exist.

If you take the test and receive your raw data, drop me a line -but don't send me the data, right away!- because I would be interested in seeing the format in which the data can be downloaded, for possible inclusion of Geno 2.0 data in my own Dodecad Project. It might be a good idea for a technical description of the new array to be posted on the website.

Overall, it is a great idea to update the Genographic test that was previously based only on Y chromosomes and mtDNA, and I will be following any further developments closely. Your Genetic Genalogist and The Genetic Genealogist have many more details on this.

(I do not personally endorse any particular testing company or product).

The long, drawn-out road to us

Timothy Weaver has an intellectually challenging recent article in the Journal of Human Evolution. He proposes that there was no punctuational "rise of modern humans", but rather a long, drawn-out continuous process since our split with our closest cousins, the Neandertals.

The argument for "no bottleneck" leading up to modern humans in Africa was recently made by Sjödin et al. Weaver examines critically three of the arguments of the "recent Out of Africa" model:

  • the shallow coalescence of mtDNA Eve
  • the emergence of anatomically modern traits in Africa c. 200ky ago
  • the idea that these modern traits are quite different from the ones that preceded them -the idea that a new species was born at the time.

With respect to mtDNA, Weaver makes the argument that the fact that mtDNA Eve coalesces to about 200ky ago (actually 177ky according to the latest estimate) does not mean that there was some bottleneck at the time associated with the rise of modern humans; the same coalescence age could occur under quite different scenaria: perhaps there were bottlenecks all the time, and nothing special happened at that time; or, there were no bottlenecks at all: if the effective population size was constant, then mtDNA would still coalesce at some time, depending on what that effective size was.

This of course raises the question: if we know what the human effective population size is, could we estimate when mtDNA ought to coalesce. First, coalescence theory does not provide a hard time for the coalescence, but rather an expected value; coalescence at 177ky is compatible with lots of different effective sizes, and different effective sizes are compatible with a coalescence at 177ky.

(More importantly, and contrary to popular belief and recent commentary: we have absolutely no idea what the human ancestral effective population size is. Figures like 10,000 people are sometimes quoted around, but we must remember where they come from: there is a triangle of doom between the human-chimp divergence date, the effective population size, and the mutation rate, and you need to know two of these to infer the other. Actually, we are beginning to get a hold of the mutation rate -thanks to the ability to sequence full genomes- but we have absolutely no clue when human-chimp divergence actually happened, at least not within a few million years.)

There is a different blow that can be directed to the idea of using mtDNA to infer a "rise of modern humans": if we look at Denisova and Neandertal hominins, they are autosomally about equidistant to us, but Denisova carries an mtDNA lineage that is about half a million years more ancient. If that doesn't stop us from repeating the "recent mtDNA Eve = recent African origin" meme, I don't know what is.

Getting back to the Weaver article, the author argues that the appearance of cranial modernity is expected if we only make an assumption about the narrow-sense heritability of human traits; that is, working backwards from the present, and taking into account drift and mutation, we expect that "modern traits" will start appearing in the anthropological record at the time of the supposed "rise of modern humans". This is simply a consequence of the fact that anthropologists label traits as modern or archaic with respect to extant human variation; so, there is nothing special about the fact that such "modern" traits appear on the record, since they are expected to do so by the mere fact that the people who lived 100-200ky ago are ever-more related to us.

The final aspect of the Weaver article has to do with the supposed punctuation in the appearance of modern humans in Africa. He makes a good point here, that the African record is so fragmentary that we hardly know what people were like before the supposed rise of modern humans. It's tough to argue about the emergence of a new species when you have no good comparative base. I would also add that even after the supposed emergence, "modern" and "ancient" traits co-exist, with no clear overall pattern discernible in the data. If modern humans suddenly arose in Africa and replaced pre-existing African hominins, the evidence for this sudden emergence and replacement is lacking.

Overall, I would say that Weaver makes a good argument against the idea of us being something special in the grand scheme of things. Perhaps we're not mutant world conquerors after all, but rather the latest phase in a long and drawn-out evolution of Homo. It's a less dramatic and more mellow theory about our origins, but one that may very well be true.

Journal of Human Evolution
Volume 63, Issue 1, July 2012, Pages 121–126

Did a discrete event 200,000–100,000 years ago produce modern humans?

Timothy D. Weaver


Scenarios for modern human origins are often predicated on the assumption that modern humans arose 200,000–100,000 years ago in Africa. This assumption implies that something ‘special’ happened at this point in time in Africa, such as the speciation that produced Homo sapiens, a severe bottleneck in human population size, or a combination of the two. The common thread is that after the divergence of the modern human and Neandertal evolutionary lineages ∼400,000 years ago, there was another discrete event near in time to the Middle–Late Pleistocene boundary that produced modern humans. Alternatively, modern human origins could have been a lengthy process that lasted from the divergence of the modern human and Neandertal evolutionary lineages to the expansion of modern humans out of Africa, and nothing out of the ordinary happened 200,000–100,000 years ago in Africa.

Three pieces of biological (fossil morphology and DNA sequences) evidence are typically cited in support of discrete event models. First, living human mitochondrial DNA haplotypes coalesce ∼200,000 years ago. Second, fossil specimens that are usually classified as ‘anatomically modern’ seem to appear shortly afterward in the African fossil record. Third, it is argued that these anatomically modern fossils are morphologically quite different from the fossils that preceded them.

Here I use theory from population and quantitative genetics to show that lengthy process models are also consistent with current biological evidence. That this class of models is a viable option has implications for how modern human origins is conceptualized.


Khoisan genetic prehistory (Pickrell et al. 2012)

This appears to be the first paper using the specialized Affymetrix chip, which was announced some time ago, and used in some of my previous experiments. The new array has been dubbed "Affymetrix Human Origins array" and has been composed by intersecting panels of SNPs ascertained in individuals from several world populations.

It is of course great to see that this paper has appeared as a preprint in arXiv, and hopefully this is a trend that will continue; biology should be like physics, with papers appearing immediately online for commenting, and not hidden away in authors', editors', and reviewers' drawers for months if not years before they become available to all.

I will highlight some points of particular interest to me:

Some caveats of interpretation here are warranted. First, all the Khoisan populations have some level of admixture with non-Khoisan populations. There is thus no single \split time" in their history, and any method (like the one used here) that estimates a single such time will actually be estimating a composite of several signals. Second, we have made the modeling assumption that history involves populations splitting in two with no gene  ow after the split. More complex demographies are quite plausible, but render the interpretation of a split time nearly meaningless (if populations continue to exchange migrants after \splitting", they arguably have not split at all). We thus consider strong interpretations of split times estimated from genetic data to be impossible, but we nonetheless and the estimates to be useful in constraining the set of historical hypotheses that are consistent with the data. 

This echoes (somewhat) my sentiments about split times being a tug-of-war in the presence of admixture. Another interesting bit from the paper:

Interestingly, a few of the Khoe-speaking populations have slightly positive f4 statistics in this com- parison, and in the Shua the f4 statistic is significantly greater than zero. We speculate that some of the Khoe-speaking populations have a low level of east African ancestry, and that the relevant east African population was itself admixed with a western Eurasian population. The Shua also show a detectable signal of admixture LD, though we estimate the admixture date as much older (44 generations). This signal of east African ancestry specifically in Khoe-speaking populations is of particular interest in the light of the hypoth esis that the Khoe-Kwadi languages were brought to southern Africa by a pre-Bantu pastoralist immigration from eastern Africa [Guldemann, 2008] 

The authors also announce an improvement on TreeMix:

In the original TreeMix algorithm, one first builds the best-tting tree of populations. However, this approach is not ideal if there are many admixed populations (as in our application here, where all of the Khoisan populations are admixed). To get around this, we allow for known admixture events to be incorpo- rated into this tree-building step. Imagine that there are several populations that we think a priori might be unadmixed (in our applications, these are the Chimpanzee, Yoruba, Dinka, Europeans, and East Asians). We  first build the best tree of these unadmixed populations using the standard TreeMix algorithm. Now assume we have an independent estimate of the admixture level of each Khoisan population, and imagine we know the source population for the mixture. 
I don't think that Sub-Saharan African populations can any longer be considered unadmixed. When one used SNPs ascertained in Eurasian individuals, many Sub-Saharan populations appear symmetrically related to Eurasians, because they lack variation at sites where new polymorphism appeared outside Africa. 

This is not, however, the case when one uses SNPs ascertained in African individuals, and a clear pattern of differential affiliation with West Eurasians across the continent is evident. As I have said before, I strongly suspect that this is due to fairly late back-migration of Eurasians into Africa, carrying Y-haplogroup DE chromosomes. Within haplogroup CT, both its major subclades CF and DE are represented in Eurasia, and both D,E, and DE* as well. In Africa, as far as we know, only DE* and E are native. On balance, the weight of the evidence would suggest a Eurasian origin of the DE-YAP haplogroup.

(I would perhaps be as bold as to extend this into the even more basal clades of the phylogeny which turn up with surprising regularity in Eurasian datasets, and are usually discounted as the result of recent admixture. I'm not so sure; if recent admixture was at fault, then the African signal in Eurasia would be absolutely dominated by E-related lineages: but the A's and B's turn up in quite unexpected places. Are they really all recent Africans, or could they share a much deeper common ancestry? If I had deep pockets, I'd surely invest in genome sequencing the collection of such Eurasian erratics)

As a parting thought, I hope that the data used in this paper will become publicly available in time, perhaps when the article appears in journal form. True open science depends not only in the public availability of research results, but also of the data that produced them.

UPDATE: Here is the ADMIXTURE analysis from the paper (Figure 7):

It would have been nice if the Fst values between ancestral populations were reported in the paper; also, if an East Eurasian group was added in the analysis. In any case, there does appear a pattern of differential affiliation with the French population (K=2). At K=3 the main Sub-Saharan (blue) component emerges, and a few populations continue to exhibit an excess of West Eurasian affiliation.

arXiv:1207.5552v1 [q-bio.PE]
The genetic prehistory of southern Africa

Joseph K. Pickrell et al.

The hunter-gatherer populations of southern and eastern Africa are known to harbor some of the most ancient human lineages, but their historical relationships are poorly understood. We report data from 22 populations analyzed at over half a million single nucleotide polymorphisms (SNPs), using a genome-wide array designed for studies of history. The southern Africans-here called Khoisan-fall into two groups, loosely corresponding to the northwestern and southeastern Kalahari, which we show separated within the last 30,000 years. All individuals derive at least a few percent of their genomes from admixture with non-Khoisan populations that began 1,200 years ago. In addition, the Hadza, an east African hunter-gatherer population that speaks a language with click consonants, derive about a quarter of their ancestry from admixture with a population related to the Khoisan, implying an ancient genetic link between southern and eastern Africa.


R1b1a2 variants in 1000G data

It's nice to see a group of independent researchers documenting their work using 1000 Genomes data. I've been following on-and-off developments in this field, and I have to say that it requires deep commitment from the persons involved to keep a mental picture of the ever-deepening phylogeny.

But, in a sense, that is what's great about the efforts of citizen scientists tackling a scientific problem: they are deeply invested in understanding their little part of the human Y-chromosome phylogeny, because it's their part and every SNP discovery in it represents a small victory. Thus, they can expend the time and effort to push the discovery process to its technological limits.

It's only too sad that this can at present be done only using 1000 Genomes data, a.k.a. the global collection of full genome data that completely ignores the part of the world between  Italy and China/India. Hopefully, sometime in the future, the ever-better-understood twig of R1b1a2 will be placed within its wider Eurasian context.

PLoS ONE 7(7): e41634. doi:10.1371/journal.pone.0041634

Discovery of Western European  R1b1a2 Y Chromosome Variants in 1000 Genomes Project Data: An Online Community Approach

Richard A. Rocca1*, Gregory Magoon2, David F. Reynolds3, Thomas Krahn4, Vincent O. Tilroe5, Peter M. Op den Velde Boots6, Andrew J. Grierson7

The authors have used an online community approach, and tools that were readily available via the Internet, to discover genealogically and therefore phylogenetically relevant Y-chromosome polymorphisms within core haplogroup R1b1a2-L11/S127 (rs9786076). Presented here is the analysis of 135 unrelated L11 derived samples from the 1000 Genomes Project. We were able to discover new variants and build a much more complex phylogenetic relationship for L11 sub-clades. Many of the variants were further validated using PCR amplification and Sanger sequencing. The identification of these new variants will help further the understanding of population history including patrilineal migrations in Western and Central Europe where R1b1a2 is the most frequent haplogroup. The fine-grained phylogenetic tree we present here will also help to refine historical genetic dating studies. Our findings demonstrate the power of citizen science for analysis of whole genome sequence data.


July 24, 2012

Broken Hill humerus: date unknown

Recently it was hinted that the Broken Hill skull is younger than has been thought before. Now, a brief communication by Erik Trinkaus in AJPA suggests that the BH humerus which has featured in debates about the evolution of human postcranial morphology lacks proper stratigraphic context, and is from a location where modern human disturbance is likely. The conclusion: it should be avoided in studies about the evolution of humans until it is securely dated.

Redating fossils is a problem that has plagued anthropology for a while. For example, H. sapiens idaltu (Herto) was given a Linnaean moniker and recognized as a precursor of modern humans because of its mix of modern and archaic traits, but shortly thereafter the Omo skulls were re-dated to tens of thousands of years earlier (~195ka), indicating that the more modern morphology of Omo I actually preceded the more archaic one of Herto Man.

When an older fossil is redated to a younger age, what was once seen as showing signs of evolutionary trends leading up to modern humans ends up being an embarrassing survival of archaic traits in a period where they are supposed to have been on their way to replacement. The once popular story of modern humans shedding their archaic traits and attaining modernity in Africa, and then populating the world is increasingly unbelievable, both because the 60,000-year-old coastal migration is bunk, but also because archaic traits persist in some African populations down to the Holocene. I strongly suspect that the story of our origins may be much more interesting than anyone had imagined.

AJPA DOI: 10.1002/ajpa.22118

Brief communication: The human humerus from the broken hill mine, kabwe, zambia

Erik Trinkaus et al.

The distal half of a right human humerus (E.898), recovered ex situ in 1925 by Hrdlicka at the Broken Hill Mine, Kabwe, Zambia, has figured prominently in assessments of Middle Pleistocene Homo postcranial variation and of the phylogenetic polarity and functional anatomy of Pleistocene Homo upper limb morphology. Reassessment of distal humeral features that distinguish modern human and some archaic Homo humeri, especially relative olecranon breadth and medial and lateral pillar thicknesses, confirm previous studies placing it morphologically close to recent humans, as well as possibly to Early Pleistocene Homo. However, it completely lacks stratigraphic context, and there is faunal and archeological evidence for human activity at Broken Hill from the Middle Pleistocene to the Holocene. Given its uncertain geological age and modern human morphology, the Broken Hill E.898 humerus should not be used in analyses of Pleistocene humans until it is securely dated. Am J Phys Anthropol, 2012. © 2012 Wiley Periodicals, Inc.


Volcanic ash didn't kill Neandertals, modern humans did

Related story by Michael Balter:
The team collected samples containing CI cryptotephra from four central European caves where stone tools and other artifacts typical of Neandertals and modern humans have been found. They also gathered the particles from a modern human site in Libya and from marshland and marine sites in Greece and the Aegean Sea. The results, the team argues in a paper published online this week in the Proceedings of the National Academy of Sciences, are incompatible with the hypothesis that the CI was responsible for Neandertal extinction, at least in central Europe. The CI cryptotephra lie above, and so postdate, the transition from Neandertal to modern human stone tool types at all four central European sites, indicating that modern humans had replaced Neandertals before the catastrophic events of 40,000 years ago.
It's a little strange that modern humans arrive in Europe by the late 40,000s cal BP, replace the Neandertals, and shortly -in geological terms- thereafter, a massive volcano goes off on them. Perhaps, a little nemesis?

PNAS doi: 10.1073/pnas.1204579109

Volcanic ash layers illuminate the resilience of Neanderthals and early modern humans to natural hazards

John Lowe et al.

Marked changes in human dispersal and development during the Middle to Upper Paleolithic transition have been attributed to massive volcanic eruption and/or severe climatic deterioration. We test this concept using records of volcanic ash layers of the Campanian Ignimbrite eruption dated to ca. 40,000 y ago (40 ka B.P.). The distribution of the Campanian Ignimbrite has been enhanced by the discovery of cryptotephra deposits (volcanic ash layers that are not visible to the naked eye) in archaeological cave sequences. They enable us to synchronize archaeological and paleoclimatic records through the period of transition from Neanderthal to the earliest anatomically modern human populations in Europe. Our results confirm that the combined effects of a major volcanic eruption and severe climatic cooling failed to have lasting impacts on Neanderthals or early modern humans in Europe. We infer that modern humans proved a greater competitive threat to indigenous populations than natural disasters.


Admixture matters (for polar bears too!)

In Admixture matters, I argued, inter alia, that "admixture can also deflate divergence, if there is subsequent gene flow between the diverged populations."

Interestingly, polar bears are now providing us with a wonderful example of this process in action. It has been abundantly clear for a while now, that polar bears are an arctic-adapted form of non-polar bears, bow how far back in time can there evolutionary relationship be pushed?

A new open access paper in PNAS answers this question:

We first used a simple isolation model (15), comparing pairs of genomes under the assumption of allopatric speciation. However, for all comparisons, we obtained estimates of very recent split times and very large ancestral effective population sizes (Ne ), consistent with mis-specification of the demographic model and suggesting that the true demographics involved are not simple splits but instead initial splits followed by prolonged periods with structured populations and gene flow. WWe therefore applied an extended model estimating an initial split time followed by a period of gene flow before a complete split (SI Appendix). We estimated an initial split between black bears and their sister lineage 4 to 5 Mya followed by gene flow until 100 to 200 kya (Fig. 3)
There you have it: low split times/high effective sizes are inferred in a tree model ("simple isolation model"), but when one does not take into account gene flow between the diverged populations, split times balloon and effective sizes shrink.

Of course in this case, we actually do have extant brown/black/polar samples to work with. But, leaving zoology and going back to anthropology, we only have on extant species (H. sapiens) within the genus Homo and only two (H. Neandertalensis and "Denisovans") of several archaic hominins that once roamed the planet, in some cases, apparently until very recently. Both the cases we do have indicate differential admixture levels with modern human groups.

I think we need to open ourselves to the possibility that shallow divergence times and higher effective population sizes in some human populations may not be the result of Biblical-level bottlenecks as small tribes of humans "conquered the earth", but of thorough and long-term gene flow between populations within the genus Homo.

PNAS doi: 10.1073/pnas.1210506109

Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change

Webb Miller et al.

Polar bears (PBs) are superbly adapted to the extreme Arctic environment and have become emblematic of the threat to biodiversity from global climate change. Their divergence from the lower-latitude brown bear provides a textbook example of rapid evolution of distinct phenotypes. However, limited mitochondrial and nuclear DNA evidence conflicts in the timing of PB origin as well as placement of the species within versus sister to the brown bear lineage. We gathered extensive genomic sequence data from contemporary polar, brown, and American black bear samples, in addition to a 130,000- to 110,000-y old PB, to examine this problem from a genome-wide perspective. Nuclear DNA markers reflect a species tree consistent with expectation, showing polar and brown bears to be sister species. However, for the enigmatic brown bears native to Alaska's Alexander Archipelago, we estimate that not only their mitochondrial genome, but also 5–10% of their nuclear genome, is most closely related to PBs, indicating ancient admixture between the two species. Explicit admixture analyses are consistent with ancient splits among PBs, brown bears and black bears that were later followed by occasional admixture. We also provide paleodemographic estimates that suggest bear evolution has tracked key climate events, and that PB in particular experienced a prolonged and dramatic decline in its effective population size during the last ca. 500,000 years. We demonstrate that brown bears and PBs have had sufficiently independent evolutionary histories over the last 4–5 million years to leave imprints in the PB nuclear genome that likely are associated with ecological adaptation to the Arctic environment.


Purifying selection and measures of population differentiation

From the paper:
Because allele frequencies are known to be lower at positions under stronger purifying selection (Subramanian and Kumar 2006), we examined the relationship between population differentiation estimates and minor allele frequencies (MAF). They are also highly positively correlated (Fig. 3A; P less than 10-15). 
Our results suggest that interpreting and comparing results from population genomic studies now should consider this dependence of FST on the frequency of the allele as well as the functional importance (evolutionary rate) of the position. For example, estimates of FST at sites on the Y chromosome and at sites in the mitochondrial genome are sometimes compared to detect the difference in male vs. female migration rates (e.g., Seielstad et al. 1998). In such examinations, we now need to compare FST at sites with similar MAF across populations to detect the difference in migration rates. It is also important when we compare FST at sites among different populations. For example, African populations are known to have higher MAF across populations than non-African populations (Tishkoff and Kidd, 2004). Without consideration of MAF before comparing FST estimates at different positions in the two may lead to incorrect inference of higher degree of population differentiation among one set of populations as compared to the other set of populations.   
I can't say that I am very comfortable with the technical details of this paper, but from my first reading, it would appear that African populations have higher minor allele frequency (MAF) than non-African ones, so measures of population divergence for Africans may be inflated relative to non-Africans, and be reflective of lower levels of purifying selection in African populations.

This would of course have monumental implications for the reconstruction of human prehistory, as it would suggest that high Fst values between different African populations and between Africans and Eurasians may be, at least partially, driven by lower levels of purifying selection in the former. It is also possible, as I've suggested, that excess variation (manifesting itself as higher minor allele frequency) may be the result of admixture between divergent Homo populations.

Biology is a mess, but hopefully statistical geneticists are up to the task!

Mol Biol Evol (2012) doi: 10.1093/molbev/mss187

Purifying selection modulates the estimates of population differentiation and confounds genome-wide comparisons across single nucleotide polymorphisms

Takahiro Maruki et al.

An improved understanding of the biological and numerical properties of measures of population differentiation across loci is becoming increasingly more important because of their growing use in analyzing genome-wide polymorphism data for detecting population structures, inferring the rates of migration, and identifying local adaptations. In a genome-wide analysis, we discovered that the estimates of population differentiation (e.g., FST, θ, and Jost’s D) calculated for human single nucleotide polymorphisms (SNPs) are strongly and positively correlated to the position-specific evolutionary rates measured from multispecies alignments. That is, genomic positions (loci) experiencing higher purifying selection (lower evolutionary rates) produce lower values for the degree of population differentiation than those evolving with faster rates. We show that this pattern is completely mediated by the negative effects of purifying selection on the minor allele frequency at individual loci. Our results suggest that inferences and methods relying on the comparison of population differentiation estimates (FST, θ, and Jost’s D) based on SNPs across genomic positions should be restricted to loci with similar minor allele frequencies and/or the rates of evolution in genome-scale surveys.


Archaeometallurgy in the Mediterranean

Continuing a discussion on metallurgical innovation which I began here.

Some interesting excerpts from a book chapter:
Tin bronze first appeared in Mesopotamia and Anatolia during the third millennium B.C., or Early Bronze Age (Pare 2000a:6–7). In the Mediterranean,the transition from arsenical to tin bronze took place during the course of the Middle Bronze Age (late third to early second millennium B.C.in the eastern Mediter-ranean, somewhat later in the west). The implication (Renfrew 1972:313–319) that tin bronze was an independent development in the northeast Aegean is contradicted by lead isotope analyses which show that most copper or bronze objects from sites such as Troy, Poliochni, and Kastri were not produced from local ores (Muhly and Pernicka 1992; Pernicka 1998:140–141). Exactly what caused the transition from arsenical to tin bronze is not well understood: as an alloy, tin bronze is not mechanically superior to arsenical copper (Pernicka 1998:135–136).Unlike arsenic, moreover, tin is not widely available as a mineral, and new trade networks would have been required to enable its distribution. However, it may have been easier to control the quality of tin bronze, and the production of tin bronze would have overcome the problem of working with toxic arsenic fumes (Charles 1978:30;Pare 2000a:7).

Given the limited number of tin deposits in the region, the source(s) of tin usedin the prehistoric eastern Mediterranean has always been a highly controversial issue. The suggestion that Afghanistan served as a prime source of tin for Bronze Age eastern Mediterranean societies is based in part on the existence of its rich tin resources (Muhly and Pernicka 1992:315;Weeks 1999:60–61).Muhly (1999:21) recently argued that Afghanistan or central Asia provided the tin that supplied the bronze industries of Mesopotamia, Anatolia, and the eastern Mediterranean, including Cyprus. Cuneiform documents from the early second millennium B.C., moreover, point to a trade network that brought tin from the east to the early states of Anatolia and Mesopotamia (Maddin et al.1977:41:Weeks 1999),and thence to the Mediterranean. Weisgerber and Cierny (2002,with fuller references) now maintain that prehistoric tin mining (second millennium B.C.), attested at the sites of Karnab (Uzbekhistan) and Musciston (Tajikistan), provided an important source of tin for Anatolia and Mesopotamia, if not for the Mediterranean. In contrast, Yener and Vandiver (1993) have argued that (very limited) tin deposits in the Taurus Mountains of southern Turkey were exploited during the Early Bronze Age. Their argument has been challenged by several scholars (e.g.,Muhly 1993;Weisgerberand Chierny 2002:180–181;papers in Journal of Mediterranean Archaeology 5[1995]) who maintain that the archaeological evidence is unclear,and far too limited to demonstrate anything beyond local use. Even if tin from the Taurus were mined during the Early Bronze Age, it now seems more likely that central Asia provided at least some of the tin used during the Middle-Late Bronze Ages,when tin bronze was far more widely produced, traded, and consumed in the Mediterranean. 
By the Late Neolithic period (ca.4800–3100 B.C.), most people living in the Mediterranean region produced their own food, lived the year round in sedentary communities and increasingly were involved in intricate social and economic exchanges. By the beginning of the Bronze Age, certain alliances, special-interest groups, or even individual local leaders came to control access to raw materials in demand: obsidian, precious or semi-precious stones, metals such as gold, silver, copper, and tin, and a range of more perishable goods. From about 3000 B.C.onward – corresponding to the Chalcolithic period (Argaric culture) in Spain, the Final Neolithic in Italy, and the Early Bronze Age in the Aegean and eastern Mediterranean – the production and trade in metals increasingly became a key factor in promoting social change (Giardino 2000b;Knapp 1990a;Levy et al.2002;Manning 1994;Ruiz Taboada and Montero Ruiz 1999).  
Technological innovations may be seen as progressive by managers and elites, but for the people who mined ores or smelted metals they were also potentially disruptive, forming the backdrop for social change as well as social abuse (Heskel andLamberg-Karlovsky 1980:260–261;Stollner 2003:427–429). Miners and metal-smiths often use ideology as a means to maintain, resist,or change their power base within society. Because elites who control and organize metallurgical produc-tion often use material culture to restructure relations of power (Gamble 1986:39), we may also expect such transformations to be visible in the archaeological record. 
Consequently, there is little room to doubt that innovations in technology had deep-seated and long-lasting social and ecological effects, placing constraints as well as conferring benefits on Bronze Age mining and metallurgical production. In social terms, whereas the intensified production of copper employing an advanced technology did not preclude a strong sense of local community, such factors served to increase social distinctions between those at the top of the control structure and those at the bottom (Hardesty 1988:102,116;Knapp 1986b;2003). 
The trade in metals during the Chalcolithic period was carried out on a very limited scale, and most metals were certainly consumed in the same area where they were produced (cf.Gale 1991). During the Early Bronze Age (third millennium B.C.), technological innovations like the longboat and sail facilitated the bulk transport of raw materials or manufactured goods on a much larger scale than ever before (Broodbank 1989). 
Metals and metallurgy wielded an immense impact on Mediterranean Bronze Age societies, clearly evident in all the fundamental changes seen in the archaeological record from the end of the Chalcolithic period (Copper Age) onward. During the Bronze Age,innovations in maritime transport and the earliest cultivation of olives and vines stimulated the economy of the Mediterranean region and spurred some of its inhabitants to produce metals, take part in maritime trade, manufacture distinctive artifacts, and build domestic and public structures that represented the earliest towns and ceremonial complexes in the Mediterranean. The advent and spread of metallurgy promoted greater social distinctions,as certain individuals or groups acquired new wealth and prestige items. Because tin had to be imported in order to produce bronze, long-distance trade was stimulated. Duringthe second millennium B.C., gold, silver, copper, and tin came to represent what Sherratt (2000:83) has termed “convertible”value, both in an economic sense and in the literal sense that they could be consumed, stored, redistributed, or recycled in diverse forms and for various symbolic or ideological ends.Such documentary evidence as exists, exclusively in the eastern Mediterranean, is frequently preoccupied with these self-same metals (Liverani 1990:205–223,247–266;Moran,inKnapp 1996:21–25).

A remarkable series of social and economic changes thus were linked closely to all the innovative developments in extractive and metallurgical technologies,and tothe increasingly widespread and intensified production and distribution of metalsand metal objects. These changes include but are not limited to: (1) the proliferation of settlements and the emergence of town centers;(2) the development and expansion in interregional trade;(3) the growth of palatial regimes and city-state kingdoms,with their attendant writing systems (notably in the eastern Mediterranean);(4) the development and refinement of craft specialization and the spread of an iconographic koine;(5) the elaboration of mortuary rituals and burials with large quantities of precious metal goods;(6) the widespread occurrence of metal hoards and the related trade in recycled and scrap metal. The circulation of goods, ideas, and ideologies across geographic,cultural,and economic boundaries represents a social transaction,one that entangled producers, distributors, and consumers in wider relations of alliance and dependence, patronage and privilege, prestige and debt (Thomas 1991:123–124). Certain occupational identities came to be focused around metallurgical production and trade, and Cyprus even gave its name to the island’s most prominent product: copper ore (Muhly 1973:174–175).The coming of the Age of Iron, subsequent to all the developments discussed in this study, itself relied on extractive and smelting technologies developed during theBronze Age,together with the use of carburization, all of which are linked directly(albeit over the millennia) to the dramatic social and economic changes that ushered in the Industrial Revolution and the beginnings of the modern era.If it is indeed the case that “metals make the world go round” (Pare 2000b),nowhere can this slogan be better and more widely illustrated than in the prehistoric Bronze Age of the Mediterranean.

Archaeometallurgy in the Mediterranean: The Social Context of Mining, Technology, and Trade

Vasiliki Kassianidou and A.Bernard Knapp