African genetics international conference (video)

A bunch of talks from the African Genetics International Conference have been posted.

You can refer to this list of talks.

I haven't watched any of the videos yet; feel free to comment on any interesting nuggets of information in them.

A few that I plan to watch:

(UPDATE: A very interesting bit at around 42')

Beyond Eden: The Significance of Archaic Human Genetic Sequences in African Populations

Michael Hammer, University of Arizona



The following video has been pixelized, presumably because it includes pictures of unpublished data (?)

Paleoanthropological Origins of Human Genetic Diversity: The Significance of humanity’s African Roots

Chris Stringer, Natural History Museum, London



Technological Innovations Impacting Genomic Science

George Church, Harvard & MIT

Science special issue on Human Conflict

The content is free for registered users (not necessarily subscribers).

Major new paper on Y chromosome haplogroup G (Rootsi et al. 2012)

Haplogroup G is of substantial interest to prehistorians, because it has been sampled on multiple Neolithic locations from across Europe. A new paper updates the phylogeny of this important haplogroup (left), and studies its distribution. You can find information about the frequency of different haplogroup G subclades in the freely available supplementary material (Table 1).

From the paper:

First, we calculated haplogroup diversity using data in Supplementary Table S1 for the 52 instances when total population sample size exceeded 50 individuals and Z5 hg G chromosomes were observed. Then we applied a 10% overall hg G frequency threshold and the additional specification that both haplogroup G1 and G2 lineages also be present. In the ten remaining populations, haplogroup diversity spanned from a low of 0.21 in Adyghes, to highs of 0.88 in Azeris (Iran) and 0.89 in eastern Anatolia and 0.90 in Armenia. We estimate that the geographic origin of hg G plausibly locates somewhere nearby eastern Anatolia, Armenia or western Iran. The general frequency pattern of hg G overall (Figure 2a) shows that the spread of hg G extends over an area from southern Europe to the Near/Middle East and the Caucasus, but then decreases rapidly toward southern and Central Asia.

It is certainly interesting that the estimated region of origin of haplogroup G intersects my so-called "womb of nations", out of which I believe flowed populations after the inception of the Neolithic. The rapid diminution of this haplogroup in Central/South Asia may be compatible with the relative lack of the K=7 "Southern" autosomal component in populations of the area, in contrast to a couple of Neolithic European farmers (the Tyrolean Iceman and Gok4). The Iceman himself belonged to haplogroup G, and so did individuals from Derenburg LBK, and Treilles.

A couple of lineages of interest are M527 which is a low-frequency haplogroup which the authors associate with Greek colonization and the Sea Peoples, and L497 which they associate with the LBK. It would certainly be interesting to test for the latter in some of the existing ancient DNA samples.

Finally, the following is of interest:

Concerning the presence of hg G in the Caucasus, one of its distinguishing features is lower haplogroup diversity in numerous populations (Supplementary Table S1) compared with Anatolia and Armenia, implying that hg G is intrusive in the Caucasus rather than autochthonous. Another notable feature is its uneven distribution. Hg G is very frequent in NW Caucasus and South Caucasus, covering about 45% of the paternal lineages in both regions2 in this study. Conversely, hg G is present in Northeast Caucasus only at an average frequency of 5% (range 0–19%). Interestingly, the decrease of hg G frequency towards the eastern European populations inhabiting the area adjacent to NW Caucasus, such as southern Russians and Ukrainians,18,40 is very rapid and the borderline very sharp, indicating that gene flow from the Caucasus in the northern direction has been negligible.

Unfortunately, we currently lack ancient Y-DNA samples from West Asia. But, certainly, the samples we do have from Europe are indicative of shifts in West Asia as well, since the predominance of Y-haplogroup G in Neolithic Europe is hardly compatible with a haplogroup composition in the eastern source areas similar to today's.

Rather, it begins to appear that there once was a (roughly speaking) western-eastern-southern distribution of the G/R1/J2 lineages in the territory of West Asia; this would be compatible with both the Neolithic European G dominance, the paucity of G in Central/South Asia, and its NW/S vs. NE Caucasus differentiation.

European Journal of Human Genetics advance online publication 16 May 2012; doi: 10.1038/ejhg.2012.86

Distinguishing the co-ancestries of haplogroup G Y-chromosomes in the populations of Europe and the Caucasus

Siiri Rootsi et al.

Haplogroup G, together with J2 clades, has been associated with the spread of agriculture, especially in the European context. However, interpretations based on simple haplogroup frequency clines do not recognize underlying patterns of genetic diversification. Although progress has been recently made in resolving the haplogroup G phylogeny, a comprehensive survey of the geographic distribution patterns of the significant sub-clades of this haplogroup has not been conducted yet. Here we present the haplogroup frequency distribution and STR variation of 16 informative G sub-clades by evaluating 1472 haplogroup G chromosomes belonging to 98 populations ranging from Europe to Pakistan. Although no basal G-M201* chromosomes were detected in our data set, the homeland of this haplogroup has been estimated to be somewhere nearby eastern Anatolia, Armenia or western Iran, the only areas characterized by the co-presence of deep basal branches as well as the occurrence of high sub-haplogroup diversity. The P303 SNP defines the most frequent and widespread G sub-haplogroup. However, its sub-clades have more localized distribution with the U1-defined branch largely restricted to Near/Middle Eastern and the Caucasus, whereas L497 lineages essentially occur in Europe where they likely originated. In contrast, the only U1 representative in Europe is the G-M527 lineage whose distribution pattern is consistent with regions of Greek colonization. No clinal patterns were detected suggesting that the distributions are rather indicative of isolation by distance and demographic complexities.

Link

ORBIS: The Stanford Geospatial Network Model of the Roman World

A very useful new tool.

Screenshot:

Example output:


The fastest  journey from Roma to Constantinopolis in January takes 20.7 days, covering 2951 kilometers.
Prices in denarii, based on the use of a faster sail ship and a civilian river boat (where applicable), and on these road options:
 * Per kilogram of wheat (by donkey): 4.37
 * Per kilogram of wheat (by wagon): 4.99
 * Per passenger in a carriage: 580.42

Y chromosome diversity in Native Mexicans (Sandoval et al. 2012)

From the paper:

The first dimension of the CoA (60.53%) separates Q-M3 from the rest, and the second dimension (39.47%) C-M130 from the rest. In agreement ith the known distribution of haplogroup C, we observed that the two northernmost populations of this panel (Chippewa and Sioux) cluster next to C-M130 and the rest of populations show varying proportions of Q-M242 and Q-M3. It is noteworthy that Native Mexicans are the only regional group with populations represented next to both the Q-M242 cluster and the Q-M3 cluster. In contrast, all Central and South American samples were grouped significantly closer to the Q-M3 haplogroup (Fig. 3).

Am J Phys Anthropol DOI: 10.1002/ajpa.22062

Y-chromosome diversity in Native Mexicans reveals continental transition of genetic structure in the Americas

Karla Sandoval et al.

The genetic characterization of Native Mexicans is important to understand multiethnic based features influencing the medical genetics of present Mexican populations, as well as to the reconstruct the peopling of the Americas. We describe the Y-chromosome genetic diversity of 197 Native Mexicans from 11 populations and 1,044 individuals from 44 Native American populations after combining with publicly available data. We found extensive heterogeneity among Native Mexican populations and ample segregation of Q-M242* (46%) and Q-M3 (54%) haplogroups within Mexico. The northernmost sampled populations falling outside Mesoamerica (Pima and Tarahumara) showed a clear differentiation with respect to the other populations, which is in agreement with previous results from mtDNA lineages. However, our results point toward a complex genetic makeup of Native Mexicans whose maternal and paternal lineages reveal different narratives of their population history, with sex-biased continental contributions and different admixture proportions. At a continental scale, we found that Arctic populations and the northernmost groups from North America cluster together, but we did not find a clear differentiation within Mesoamerica and the rest of the continent, which coupled with the fact that the majority of individuals from Central and South American samples are restricted to the Q-M3 branch, supports the notion that most Native Americans from Mesoamerica southwards are descendants from a single wave of migration. This observation is compatible with the idea that present day Mexico might have constituted an area of transition in the diversification of paternal lineages during the colonization of the Americas.

Link

Y chromosomes in Haiti and Jamaica (Simms et al. 2012)

The paper investigates the different signals of patrilineal ancestry in two Caribbean islands, finding the expect signals of European and African ancestry, as well as minor other signals from the New World, East Asia, and even South Asia.

I will just point out the presence of a DE* chromosome in Jamaica. Such chromosomes have occasionally turned up in both Asia and Africa, and they ought to be an object of further study, preferrably with full Y-chromosome sequencing technology, since a better resolution of the DE-YAP haplogroup's structure will go a long way towards solving many puzzles about prehistory.

Am J Phys Anthropol. 2012 May 11. doi: 10.1002/ajpa.22090.

Y-chromosomal diversity in Haiti and Jamaica: Contrasting levels of sex-biased gene flow.

Simms TM, Wright MR, Hernandez M, Perez OA, Ramirez EC, Martinez E, Herrera RJ.

Abstract

Although previous studies have characterized the genetic structure of populations from Haiti and Jamaica using classical and autosomal STR polymorphisms, the patrilineal influences that are present in these countries have yet to be explored. To address this lacuna, the current study aims to investigate, for the first time, the potential impact of different ancestral sources, unique colonial histories, and distinct family structures on the paternal profile of both groups. According to previous reports examining populations from the Americas, island-specific demographic histories can greatly impact population structure, including various patterns of sex-biased gene flow. Also, given the contrasting autosomal profiles provided in our earlier study (Simms et al.: Am J Phys Anthropol 142 (2010) 49-66), we hypothesize that the degree and directionality of gene flow from Europeans, Africans, Amerindians, and East Asians are dissimilar in the two countries. To test this premise, 177 high-resolution Y-chromosome binary markers and 17 Y-STR loci were typed in Haiti (n = 123) and Jamaica (n = 159) and subsequently utilized for phylogenetic comparisons to available reference collections encompassing Africa, Europe, Asia (East and South), and the New World. Our results reveal that both studied populations exhibit a predominantly South-Saharan paternal component, with haplogroups A1b-V152, A3-M32, B2-M182, E1a-M33, E1b1a-M2, E2b-M98, and R1b2-V88 comprising 77.2% and 66.7% of the Haitian and Jamaican paternal gene pools, respectively. Yet, European derived chromosomes (i.e., haplogroups G2a*-P15, I-M258, R1b1b-M269, and T-M184) were detected at commensurate levels in Haiti (20.3%) and Jamaica (18.9%), whereas Y-haplogroups indicative of Chinese [O-M175 (3.8%)] and Indian [H-M69 (0.6%) and L-M20 (0.6%)] ancestry were restricted to Jamaica.

Link

4,000 year old rock art from Mongolia

4000-year-old rock art discovered in Mongolia

Eighteen rock art sites dating back over 4,000 years have been discovered by archaeologists in northern China's Inner Mongolia autonomous region. The prehistoric art was discovered in the Yinshan Mountains in Urad Middle Banner (an administration division of the Inner Mongolia Autonomous Region), said Liu Binjie, head of the Cultural Relics Bureau of Urad Middle Banner.

...

Liu said that carvings of faces found on Yinshan Mountains cliffs are similar to those in the Helan Mountains, located on the boundary between Ningxia and Inner Mongolia. They are also similar to those in eastern Russia, showing close connections with ancient peoples' migration patterns, showing similar worship ceremonies.

Can a Chinese reader dig up some pictures of these faces? I've seen a few stories about these discoveries in various outlets, but only a very small picture as of yet. This has some information on the Rock Painting of Yinshan Mountains. Also: The Rock Art of Inner Mongolia & Ningxia (China).

Unknown language discovered in tablet from the Governor’s Palace in Tušhan

The Independent covers this:

Archaeologists have discovered evidence for a previously unknown ancient language – buried in the ruins of a 2800 year old Middle Eastern palace.

The discovery is important because it may help reveal the ethnic and cultural origins of some of history’s first ‘barbarians’ – mountain tribes which had, in previous millennia, preyed on the world’s first great civilizations, the cultures of early Mesopotamia in what is now Iraq.

Evidence of the long-lost language - probably spoken by a hitherto unknown people from the Zagros Mountains of western Iran – was found by a Cambridge University archaeologist as he deciphered an ancient clay writing tablet unearthed by an international archaeological team excavating an Assyrian imperial governors’ palace in the ancient city of Tushan, south-east Turkey.

The tablet revealed the names of 60 women – probably prisoners-of-war or victims of an Assyrian forced population transfer program. But when the Cambridge archaeologist – Dr. John MacGinnis - began to examine the names in detail, he realized that 45 of them bore no resemblance to any of the thousands of ancient Middle Eastern names already known to scholars.

...

Typical names, born by the women – the evidence for the lost language – include Ushimanay, Alagahnia, Irsakinna and Bisoonoomay.

Journal of Near Eastern Studies
Evidence for a Peripheral Language in a Neo-Assyrian Tablet from the Governor’s Palace in Tušhan (pp. 13-20) John MacGinnis DOI: 10.1086/664450 Stable URL: http://www.jstor.org/stable/10.1086/664450

Agriculture arrived in Cyprus 10,600 years ago

PNAS doi: 10.1073/pnas.1201693109

First wave of cultivators spread to Cyprus at least 10,600 y ago

Jean-Denis Vigne et al.

Early Neolithic sedentary villagers started cultivating wild cereals in the Near East 11,500 y ago [Pre-Pottery Neolithic A (PPNA)]. Recent discoveries indicated that Cyprus was frequented by Late PPNA people, but the earliest evidence until now for both the use of cereals and Neolithic villages on the island dates to 10,400 y ago. Here we present the recent archaeological excavation at Klimonas, which demonstrates that established villagers were living on Cyprus between 11,100 and 10,600 y ago. Villagers had stone artifacts and buildings (including a remarkable 10-m diameter communal building) that were similar to those found on Late PPNA sites on the mainland. Cereals were introduced from the Levant, and meat was obtained by hunting the only ungulate living on the island, a small indigenous Cypriot wild boar. Cats and small domestic dogs were brought from the mainland. This colonization suggests well-developed maritime capabilities by the PPNA period, but also that migration from the mainland may have occurred shortly after the beginning of agriculture.

Link

Patrilineal signals of Austronesian expansion in mainland Southeast Asia

There was a recent paper on the spread of Austronesian in Island Southeast Asia, and now here's one on its spread in mainland Southeast Asia. Information about sampled populations can be found in Table 1. Haplogroup frequencies below:

PLoS ONE 7(5): e36437. doi:10.1371/journal.pone.0036437

Patrilineal Perspective on the Austronesian Diffusion in Mainland Southeast Asia

Jun-Dong He et al.

The Cham people are the major Austronesian speakers of Mainland Southeast Asia (MSEA) and the reconstruction of the Cham population history can provide insights into their diffusion. In this study, we analyzed non-recombining region of the Y chromosome markers of 177 unrelated males from four populations in MSEA, including 59 Cham, 76 Kinh, 25 Lao, and 17 Thai individuals. Incorporating published data from mitochondrial DNA (mtDNA), our results indicated that, in general, the Chams are an indigenous Southeast Asian population. The origin of the Cham people involves the genetic admixture of the Austronesian immigrants from Island Southeast Asia (ISEA) with the local populations in MSEA. Discordance between the overall patterns of Y chromosome and mtDNA in the Chams is evidenced by the presence of some Y chromosome lineages that prevail in South Asians. Our results suggest that male-mediated dispersals via the spread of religions and business trade might play an important role in shaping the patrilineal gene pool of the Cham people.

Link

Late glacial recolonization of Europe from Near Eastern refugia

A couple of quick comments on this important new paper:

• It is important to confirm the hypotheses put forward with ancient DNA data. For example, haplogroup V is said to be traced to Paleolithic SW Europe, and yet it is lacking in ancient DNA data. Looking at Jean Manco's ancient Eurasian DNA compendium, I only find a very late Neolithic hunter-gatherer sample from Pitted Ware in Sweden (2,800-2,000BC); if J/T subclades had entered Europe prior to the Neolithic, their almost complete absence in ancient DNA data is puzzling.
• Both this and the recent "Copernican" paper provide age estimates for the same nodes of the tree using the mutation rate of Soares et al. (2009). The estimaets of Pala et al. (2012) appear to be older by several thousand years than those of Behar et al. (2012) for different nodes. I don't know whether this is due to a different methodology or different dataset, but, in any case, it is a warning to avoid very close correlations between archaeological-geological events and age estimates.

UPDATE: A press release on the article.

The American Journal of Human Genetics, Volume 90, Issue 5, 915-924, 4 May 2012 doi:10.1016/j.ajhg.2012.04.003

Mitochondrial DNA Signals of Late Glacial Recolonization of Europe from Near Eastern Refugia

Maria Pala et al.

Human populations, along with those of many other species, are thought to have contracted into a number of refuge areas at the height of the last Ice Age. European populations are believed to be, to a large extent, the descendants of the inhabitants of these refugia, and some extant mtDNA lineages can be traced to refugia in Franco-Cantabria (haplogroups H1, H3, V, and U5b1), the Italian Peninsula (U5b3), and the East European Plain (U4 and U5a). Parts of the Near East, such as the Levant, were also continuously inhabited throughout the Last Glacial Maximum, but unlike western and eastern Europe, no archaeological or genetic evidence for Late Glacial expansions into Europe from the Near East has hitherto been discovered. Here we report, on the basis of an enlarged whole-genome mitochondrial database, that a substantial, perhaps predominant, signal from mitochondrial haplogroups J and T, previously thought to have spread primarily from the Near East into Europe with the Neolithic population, may in fact reflect dispersals during the Late Glacial period, ∼19–12 thousand years (ka) ago.

Link

Genetic structure of North-East Sardinia (Pardo et al. 2012)

European Journal of Human Genetics , (29 February 2012) | doi:10.1038/ejhg.2012.22

Dissecting the genetic make-up of North-East Sardinia using a large set of haploid and autosomal markers

Luba M Pardo et al.

Abstract

Sardinia has been used for genetic studies because of its historical isolation, genetic homogeneity and increased prevalence of certain rare diseases. Controversy remains concerning the genetic substructure and the extent of genetic homogeneity, which has implications for the design of genome-wide association studies (GWAS). We revisited this issue by examining the genetic make-up of a sample from North-East Sardinia using a dense set of autosomal, Y chromosome and mitochondrial markers to assess the potential of the sample for GWAS and fine mapping studies. We genotyped individuals for 500K single-nucleotide polymorphisms, Y chromosome markers and sequenced the mitochondrial hypervariable (HVI–HVII) regions. We identified major haplogroups and compared these with other populations. We estimated linkage disequilibrium (LD) and haplotype diversity across autosomal markers, and compared these with other populations. Our results show that within Sardinia there is no major population substructure and thus it can be considered a genetically homogenous population. We did not find substantial differences in the extent of LD in Sardinians compared with other populations. However, we showed that at least 9% of genomic regions in Sardinians differed in LD structure, which is helpful for identifying functional variants using fine mapping. We concluded that Sardinia is a powerful setting for genetic studies including GWAS and other mapping approaches.

Link

Horse domestication mystery solved (?)

I will add the abstract of the paper later when it is "live" on the PNAS site. For the moment, a link to the press release:

New research indicates that domestic horses originated in the steppes of modern-day Ukraine, southwest Russia and west Kazakhstan, mixing with local wild stocks as they spread throughout Europe and Asia. The research was published today, 07 May, in the journal PNAS.

For several decades scientists puzzled over the origin of domesticated horses. Based on archaeological evidence, it had long been thought that horse domestication originated in the western part of the Eurasian Steppe (Ukraine, southwest Russia and west Kazakhstan); however, a single origin in a geographically restricted area appeared at odds with the large number of female lineages in the domestic horse gene pool, commonly thought to reflect multiple domestication "events" across a wide geographic area.

In order to solve the perplexing history of the domestic horse, scientists from the University of Cambridge used a genetic database of more than 300 horses sampled from across the Eurasian Steppe to run a number of different modelling scenarios.

Their research shows that the extinct wild ancestor of domestic horses, Equus ferus, expanded out of East Asia approximately 160,000 years ago. They were also able to demonstrate that Equus ferus was domesticated in the western Eurasian Steppe, and that herds were repeatedly restocked with wild horses as they spread across Eurasia.

ScienceNOW also covers the new research, and reports on a contrasting viewpoint:

Not all researchers are convinced, however. Archaeologist Marsha Levine of the University of Cambridge thinks using modern genetic samples to retrace horses' evolution is a dead end. "There's been mixing of cultures and mixing of horses in this region for many thousands of years," she says. "And so when you're looking at any modern horse, you just don't know where it's from."

Bringing together many kinds of evidence is what will ultimately answer the whens and wheres of horse domestication, Levine says. "What we need to be doing is using material from excavations, sequencing ancient genes, and combining that with what we know from archaeological evidence about how animals were used in the past."

I agree with the idea that ancient DNA will ultimately confirm/reject the model presented in the paper. Of course, it may be the case that the west Eurasian steppe was the place where horse domestication happened, but it is also the place where local horses may be descended from European, West Asian, and Central Asian breeds. I'll have to read the paper to see how the problem of possible admixture between western and eastern horse breeds on the steppe is accounted for in the paper.

PNAS doi: 10.1073/pnas.1111122109

Reconstructing the origin and spread of horse domestication in the Eurasian steppe

Vera Warmuth et al.

Despite decades of research across multiple disciplines, the early history of horse domestication remains poorly understood. On the basis of current evidence from archaeology, mitochondrial DNA, and Y-chromosomal sequencing, a number of different domestication scenarios have been proposed, ranging from the spread of domestic horses out of a restricted primary area of domestication to the domestication of numerous distinct wild horse populations. In this paper, we reconstruct both the population genetic structure of the extinct wild progenitor of domestic horses, Equus ferus, and the origin and spread of horse domestication in the Eurasian steppes by fitting a spatially explicit stepping-stone model to genotype data from >300 horses sampled across northern Eurasia. We find strong evidence for an expansion of E. ferus out of eastern Eurasia about 160 kya, likely reflecting the colonization of Eurasia by this species. Our best-fitting scenario further suggests that horse domestication originated in the western part of the Eurasian steppe and that domestic herds were repeatedly restocked with local wild horses as they spread out of this area. By showing that horse domestication was initiated in the western Eurasian steppe and that the spread of domestic herds across Eurasia involved extensive introgression from the wild, the scenario of horse domestication proposed here unites evidence from archaeology, mitochondrial DNA, and Y-chromosomal DNA.

Link

Bell Beakers from Germany: Y-haplogroup R1b

Just in time with my recent speculations about post-Neolithic events affecting Europe, we now have a paper of a Bell Beaker sample from Germany. Like with earlier Neolithic samples there are two camps in trying to explain the Bell Beaker phenomenon: one of them saw only a cultural phenomenon epitomized by burials with the eponymous Bell Beaker pottery; the other saw a true invading population. This is how Carleton Coon described them:

The Dinaric type, with which the Rhenish Bell beakers are associated, is one which entered the western Mediterranean by sea from the east, and eventually moved, by some route yet to be determined in an accurate manner, to the north, and eventually to central Europe.

As such, the Bell Beaker phenomenon is a test case for the pots-not-people paradigm. There is ample physical anthropological evidence that the people of Beaker burials had a distinctive physical type which contrasted with the long-headed type typical of the era, so I have always been on the "people" side of the conflict.

I will update this entry when I read the paper.

American Journal of Physical Anthropology DOI: 10.1002/ajpa.22074

Emerging genetic patterns of the european neolithic: Perspectives from a late neolithic bell beaker burial site in Germany†

Esther J. Lee et al.

Abstract

The transition from hunting and gathering to agriculture in Europe is associated with demographic changes that may have shifted the human gene pool of the region as a result of an influx of Neolithic farmers from the Near East. However, the genetic composition of populations after the earliest Neolithic, when a diverse mosaic of societies that had been fully engaged in agriculture for some time appeared in central Europe, is poorly known. At this period during the Late Neolithic (ca. 2,800–2,000 BC), regionally distinctive burial patterns associated with two different cultural groups emerge, Bell Beaker and Corded Ware, and may reflect differences in how these societies were organized. Ancient DNA analyses of human remains from the Late Neolithic Bell Beaker site of Kromsdorf, Germany showed distinct mitochondrial haplotypes for six individuals, which were classified under the haplogroups I1, K1, T1, U2, U5, and W5, and two males were identified as belonging to the Y haplogroup R1b. In contrast to other Late Neolithic societies in Europe emphasizing maintenance of biological relatedness in mortuary contexts, the diversity of maternal haplotypes evident at Kromsdorf suggests that burial practices of Bell Beaker communities operated outside of social norms based on shared maternal lineages. Furthermore, our data, along with those from previous studies, indicate that modern U5-lineages may have received little, if any, contribution from the Mesolithic or Neolithic mitochondrial gene pool.

Link

Nature special issue on "Peopling the Planet"

Special issue: Peopling the planet

Not long ago, the story was simple. A vanguard of modern humans left their African birthplace 50,000–60,000 years ago and quickly conquered Asia. They turned left into Europe some 40,000 years ago, later crossing the Bering Strait and marching southward into the Americas. With their advance, Neanderthals and other earlier peoples dwindled and vanished.

But in the past five years, the picture has grown more complex — and more interesting.

Few question the idea that modern humans are all emigrants from Africa. But when their journey began, when it ended and what they did along the way makes for a deepening mystery, explored in this issue of Nature.

Discoveries on the Arabian peninsula, for example, show that modern humans were camped on the doorstep of Asia more than 100,000 years ago, nearly twice as long ago as anyone thought. If they went farther at that early date — and some archaeologists insist that they must have — their presence would explain a smattering of ambiguous artefacts and fossils around Asia (see page 24).

Elsewhere, humans definitely arrived ahead of schedule. Sensitive new radiocarbon-dating techniques show that the first modern humans reached Europe thousands of years earlier than was thought, implying a lengthy coexistence with Neanderthals there (see page 27). And the picture of big-game hunters following an inland route from Asia to the Americas 13,000 years ago has been obliterated by a barrage of reports of older sites. Archaeologists are studying DNA, ancient and modern, for clues to when and how the first Americans arrived (see page 30).

The most dramatic change, however, concerns the archaic peoples whose world we inherited. In the past two years, ancient-DNA researchers have deciphered the full genome sequences of Neanderthals and a hitherto unknown group called Denisovans, then compared them with modern human genomes. The startling upshot: genetic traces of our vanished cousins live on in people today (see page 33). Just where and how the ancient trysts took place is yet to be revealed, as researchers continue to unravel the human story.

Nature 485, 23 (03 May 2012) doi:10.1038/485023a

Link

Drawing the human Y chromosome tree with SNPs

Terry, (tdrobb@gmail.com), a poster at GENEALOGY-DNA-L reported age estimates for various nodes of the Y-chromosome tree based on SNPs. These can be found in this PDF file and here (scroll down for UPDATE10). He used 1000 Genomes data and SNP counting to reach these estimates.

It will be nice to see others join in on the SNP bandwagon, because that is really the way forward in age estimation for Y-chromosome lineages. SNPs have an extremely low (=negligible) rate of back-mutation, but they occur at a much lower rate than Y-STR step mutations. On the other hand, there are at most a few hundred Y-STRs and only ~100 tested by commercial companies, while scientific datasets generally include at most a few dozen of them. The Y chromosome includes millions of mutable sites and these will be generally reported both by the 1000 Genomes Project, and the plethora of full genome sequences that is about to become available.

Y-SNP based age estimation has the potential of greatly improving estimates by tightening confidence intervals substantially; there will, of course, be lingering uncertainty of parameters such as generation length, but Y chromosome mutation rates are likely to become very secure once full genome sequencing becomes so cheap that it can be applied to a number of father-son pairs.

Looking at the inferred tree, what is striking is the great distance between haplogroup A1b and the rest of the tree, or about 100,000 years. Note that these are not "relative" estimates as were published by the 1000 Genomes Project (based on "archaeologically" calibrating a node and estimating ages of other nodes by counting the relative number of SNPs), but "absolute" ones (dividing SNPs with a mutation rate).

(UPDATE: There is apparently an even more basal clade than A1b currently investigated; I have removed the link to an announcement regarding this clade, since there are issues regarding the release of this information)

Going back to the age estimates, I cannot help but notice the concordance between Terry's age estimates for DE/CF split (55ky) with the mtDNA estimates for most mtDNA L3 subclades. Terry labels DE "African" and CF "Eurasian", but, in fact DE is Afrasian and "CF" Eurasian. Together with the absence of any evidence for a post-70ka Out-of-Africa, I'd say that it is becoming increasingly clear that while modern humans can be ultimately traced to the Middle Stone Age in Africa, their major expansion that went on to colonize the entire world originated in Asia, and included a major episode of back-migration into Africa.

I also earnestly hope that the next set of Y chromosome papers on recent populations will forego the cost of testing hundreds of samples on Y-STRs and invest in full Y-chromosome sequencing of a few samples after an initial Y-SNP screening.