FastIBD detection of identity by descent

I referred to this paper earlier in my post on the ERSA software. The authors write:

If the input data are phased, GERMLINE is between 2 and 3 orders of magnitude faster than ten runs of fastIBD. Phasing data with BEAGLE takes time that is similar to one run of fastIBD, so in practice, the computation time for ten runs of fastIBD is approximately one order of magnitude larger than the computation time for GERMLINE when the phasing step is included. However, the greatly improved accuracy of fastIBD compensates for the increased computing time.

I was looking at GERMLINE recently, but I think I will switch my attention to fastIBD. A few test runs have convinced me that it's got a reasonable running time on a run-of-the-mill PC, and the extra accuracy is probably worth the time.

The American Journal of Human Genetics, Volume 86, Issue 4, 526-539, 18 March 2010
doi:10.1016/j.ajhg.2010.02.021

High-Resolution Detection of Identity by Descent in Unrelated Individuals

Sharon R. Browning, and Brian L. Browning

Detection of recent identity by descent (IBD) in population samples is important for population-based linkage mapping and for highly accurate genotype imputation and haplotype-phase inference. We present a method for detection of recent IBD in population samples. Our method accounts for linkage disequilibrium between SNPs to enable full use of high-density SNP data. We find that our method can detect segments of a length of 2 cM with moderate power and negligible false discovery rate in Illumina 550K data in Northwestern Europeans. We compare our method with GERMLINE and PLINK, and we show that our method has a level of resolution that is significantly better than these existing methods, thus extending the usefulness of recent IBD in analysis of high-density SNP data. We survey four genomic regions in a sample of UK individuals of European descent and find that on average, at a given location, our method detects IBD in 2.7 per 10,000 pairs of individuals in Illumina 550K data. We also present methodology and results for detection of homozygosity by descent (HBD) and survey the whole genome in a sample of 1373 UK individuals of European descent. We detect HBD in 4.7 individuals per 10,000 on average at a given location. Our methodology is implemented in the freely available BEAGLE software package.

Link

Human migration and cultural change in the origins of European farmers

Here is the press release, I'll update the post when the paper appears on the journal site.

Origins of Farming in Europe Result of Human Migration and Cultural Change, Study Suggests

It has long been debated as to whether the transition from a largely hunter-gatherer to an agricultural subsistence strategy in Europe was the result of the migration of farmers from the Near East and Anatolia, or whether this transition was primarily cultural in nature. A new study, co-authored by researchers at University College Cork and the University of Kent suggests that the prehistoric adoption of farming practices in outlying regions of Europe, Scandinavia, the Baltic, European Russia and the Ukraine, was the result of cultural diffusion.

Results provide evidence that indigenous hunter-gatherers in central Europe were largely replaced or assimilated by incoming Near-Eastern farmers in the core region of south-east and Central Europe. However, hunter-gatherer populations survived in outlying regions and adopted some of the cultural practices from neighbouring farming communities.

...

The new study published in the Proceedings of the Royal Society, B uses craniometric data from 30 Mesolithic and Neolithic populations to address these questions, as it has previously been shown that cranial measurements can be used as a reliable proxy for genetic information. The results show that while the initial transition to agriculture in central Europe was the result of migrating farmers from the Near-East and Anatolia, agricultural practices were adopted by indigenous hunter-gatherer populations in outlying regions of Europe. Therefore, instead of employing two competing and mutually exclusive models of biological versus cultural diffusion, a mosaic model of both biological and cultural diffusion is a more appropriate model for this demographic change across Europe as a whole

UPDATE:

Looking at the cranial distances table the distance between Çatal Höyük and Nea Nikomedeia 0.00001, which could very well be the smallest in the table leaves little doubt about the affinities of the Neolithic in Macedonia. It is unfortunate that other series from the rest of Greece were not included, but this may not be as important in the context of this paper, as the Neolithic cultures of the Balkans would be derived from those of northern Greece.

Another point of interest is to pay close attention to the different sites. For example, the Russian Neolithic is a late 2,400BC site from NW Russia belonging to the Pit-Comb Ware culture. This culture is labeled Neolithic on account of its use of pottery (one of the hallmarks of the Neolithic), but is essentially a boreal culture of pottery using hunter-gatherers.

Another point of interest is that the Dnieper-Donetz samples from Dereivka and Aleksandrija have close parallels to the Portuguese Mesolithic! This tends to reinforce the view that has emerged from the study of mtDNA of a fairly homogeneous pre-farming substratum that stretched from the Atlantic well to the east.

The Mesolithic and some Forest "Neolithic" samples of hunter-gatherers cluster together, described by the authors as follows:

In the circum-Baltic area, a number of ‘Forest Neolithic’ cultures emerged during the seventh millennium BP, continuing the Mesolithic hunting–gathering–fishing lifestyle by incorporating wild fauna and edible plant species into their diets but also living in semi-permanent locales [23,26].

Proc. R. Soc. B doi: 10.1098/rspb.2010.2678

Craniometric data support a mosaic model of demic and cultural Neolithic diffusion to outlying regions of Europe

Noreen von Cramon-Taubadel, and Ron Pinhasi


The extent to which the transition to agriculture in Europe was the result of biological (demic) diffusion from the Near East or the adoption of farming practices by indigenous hunter–gatherers is subject to continuing debate. Thus far, archaeological study and the analysis of modern and ancient European DNA have yielded inconclusive results regarding these hypotheses. Here we test these ideas using an extensive craniometric dataset representing 30 hunter–gatherer and farming populations. Pairwise population craniometric distance was compared with temporally controlled geographical models representing evolutionary hypotheses of biological and cultural transmission. The results show that, following the physical dispersal of Near Eastern/Anatolian farmers into central Europe, two biological lineages were established with limited gene flow between them. Farming communities spread across Europe, while hunter–gatherer communities located in outlying geographical regions adopted some cultural elements from the farmers. Therefore, the transition to farming in Europe did not involve the complete replacement of indigenous hunter–gatherer populations despite significant gene flow from the Southwest Asia. This study suggests that a mosaic process of dispersal of farmers and their ideas was operating in outlying regions of Europe, thereby reconciling previously conflicting results obtained from genetic and archaeological studies.

Link

Medieval DNA from Usedom, Germany

With respect to the Slavic/Germanic origin of the studied samples, I would like to point to a 2005 study on the differentiation between Germans and Poles. R-M458 should probably be assigned to the Slavic side, while E1b1b on the German. The absence of R1b (in the albeit limited sample) is interesting, and should be interpreted as further evidence for the Slavic side of the argument, as R1b strongly differentiates Germans from Slavs in today's populations and less than a millennium ago is probably too short a timespan to expect dramatic changes in haplogroup frequencies.

Related:

• Y chromosomes from 7th c. Ergolding (Bavaria, Germany)
• Ancient Y chromosome studies

Main title Die mittelalterlichen Skelette von Usedom
Subtitle Anthropologische Bearbeitung unter besonderer Berücksichtigung des ethnischen Hintergrundes
Title variations The mediaeval skeletons of Usedom
Subtitle for translated title Anthropological investigation in due consideration of the ethnical background
Author(s) Freder, Janine
Place of birth: Berlin
1. Referee Prof. Dr. Carsten Niemitz
Further Referee(s) Prof. Dr. Joachim Burger
Keywords Anthropology; osteometry; palaeodemography; Slavs; Danes; DNA; mitochondrial; Y chromosome
Classification (DDC) 570 Life sciences
Summary This study investigates 200 skeletons from an early Christian graveyard of the 12th to early 13th century in Usedom (Mecklenburg-Vorpommern, Germany). The city of Usedom was a notable maritime place of trade in a time of major political and social transformations. The Christianisation of the Slavic elite in 1128, the following raids of the Danes and the influx of German settlers starting in the 13th century were formative events.
The reconstruction of the living conditions of the Usedom population was achieved by means of well established anthropological and palaeodemographical methods. Age and sex distribution comply with other ordinary populations of that time frame: high proportion of children (32 %), comparatively few adolescents but many adults (59 %) as well as a slight surplus in men. Remarkably, a deficit in women in the mature age class is attended by an increased mortality of girls of the age class infans I. However, this may be due to a methodical error.
In order to clarify a possible Slavic, Danish or German background of the inhabitants of Usedom, eight skull measures, four skull indices and five measures of the long bones of the extremities were investigated typologically as well as statistically on the basis of their arithmetic means and compared to the measures of two series of Slavic or multiethnic/place of trade background (Sanzkow and Haithabu, respectively). The comparison of arithmetic means did yield statistically significant differences between the three populations. The men and women of Usedom seem to be more closely related to the Sanzkow population. However, they appear to take a position between the two other populations. Unfortunately, a comparison with Slavic and Germanic populations of the Neolithic till Early Middle Ages did not provide distinct results. The archaeologically based assumption of a mainly Slavic population cannot be rejected with anthropological means.
The analysis of mitochondrial and Y-chromosomal DNA, however, generated auspicious results despite adverse storage conditions. Results could be obtained from all four samples. Two individuals were of mtDNA haplogroup H and two of haplogroup K. Y-chromosome analysis yielded haplogroups E1b1b and R1a1a7, respectively, in two males. Future molecular research will see improved methods for the even more detailed reconstruction of human migration.

Link

Brown-eyed Oetzi the Iceman

Heike Engel-21Lux / Sdtiroler Archologiemuseum / National Geographic Deutschland

Iceman Oetzi gets a new face for 20th anniversary

BOLZANO, Italy — Iceman Oetzi, whose mummified body was famously found frozen in the Italian Alps in 1991, will get a new face for the 20th anniversary of his discovery.

As part of a new exhibit at the South Tyrol Museum of Archaeology in Bolzano (www.iceman.it), two Dutch experts -- Alfons and Adrie Kennis -- have made a new model of the living Oetzi, this time with brown eyes.

Indeed, recent research has shown the Iceman, now approaching the tender age of 5,300 years, did not have blue eyes as previously believed.

The Kennis model was created based on three-dimensional images of the mummy's skeleton as well as the latest forensic technology, and will go on display on March 1 until January 15, 2012.

The Bolzano museum is also planning to improve conservation of the mummy by using pure nitrogen, which should help it keep its relatively young appearance by eliminating oxidation.

Oetzi was discovered on September 19, 1991 by a German couple in a glacier in the Oetztal Alps in South Tyrol, northern Italy.

The Iceman, who is believed to have died around the age of 45, was about 1.60 metres (5 foot, 3 inches) tall and weighed 50 kilogrammes (110 pounds), about average for his time. If he had lived today, he would have worn size 38 shoes.

But Oetzi's notoriety has also been linked to a supposed curse surrounding the mummy, after several people -- authors, researchers, even mountain guides -- who came in contact with it died over the years.

One of the couple who discovered Oetzi was found dead after a mountain hike in 2004. A forensic expert, who had closely examined the find, meanwhile died in a car accident in 1992 on his way to a lecture about Oetzi.

Picture from an Italian story on the same topic

Y chromosome variation in Iranian religious groups

I am somewhat skeptical of the Y-chromosome results included in this paper:

For one thing, the extreme paucity of haplogroup J contradicts previous reports on the Iranian population and seems hardly consistent with the geographical position of Iran. On the other hand, the excess of Y* chromosomes (the two best candidates for what they represent are G and H) is also difficult to understand. 0/51 J in Shiraz Muslims and 1/37 in Zoroastrians seems difficult to believe. The low frequency of J in Assyrians (11%) also seems to contradict the results of the public information on that population; the admin of the Aramaic DNA project estimates a 33% occurrence of that haplogroup for Assyrians based on 23andMe, FTDNA, and SMGF samples, and this seems easier to reconcile than the 11% value.

The authors also cite Yonan et al. (2009), which, as far as I can tell, does not appear to be published anywhere (let me know if it is) except as an abstract in the linked site.

Ann Hum Biol. 2011 Feb 18. [Epub ahead of print]

Y chromosome diversity among the Iranian religious groups: A reservoir of genetic variation.

Lashgary Z, Khodadadi A, Singh Y, Houshmand SM, Mahjoubi F, Sharma P, Singh S, Seyedin M, Srivastava A, Ataee M, Mohammadi ZS, Rezaei N, Bamezai RN, Sanati MH.

Abstract

Background: Iran is ethnically, linguistically and religiously diverse. However, little is known about the population genetics of Iranian religious communities. Aim: This study was performed in order to define the different paternal components of the Iranian gene pool. Subjects and methods: Fourteen Y chromosome bi-allelic markers were analysed in 130 male subjects from Assyrian, Armenian and Zoroastrian groups in comparison with 208 male subjects from three Iranian Muslim groups. Results: Among the three Iranian Muslim groups, the Uromian people possessed a particularly close genetic relationship to the Armenian, whereas the Zoroastrian group was different from the Uromian, but had a close genetic relationship to the two other Muslim groups (Kermanian and Shirazian). The genetic results indicate a relationship between Armenian and Assyrian groups in Iran and a clear distinction of the former from the Zoroastrian group. However, Assyrians had elevated frequency (40%) of R*(xR1a) and low frequency (11%) of J. Conclusion: The results of this study may suggest that the Assyrian population either experienced Eurasian gene flow (possibly from Armenia) or that enforced relocations and expulsion of conquered people with different origin led to the integration of descendants with R haplogroup. This could also be due to genetic drift due to small population size and endogamy resulting from religious barriers.

Link

"Secrets of the Silk Road" @ Penn Museum

Here is the website of an exhibition that will run through March 28. There is also a weekly lecture series to accompany the event, the first few of which have been posted at the site. Here is the first one:

Introduction to the Silk Road by Nancy Steinhardt

The Tarim Basin Mummies by Victor Mair

UPDATE: Mair is mistaken when he states that Tocharian is the 2nd oldest language after Hittite.

Related:

• Y chromosomes and mtDNA in Bronze Age Tarim basin
• mtDNA evidence for Caucasoid-Mongoloid admixture in Xinjiang 2,500 years ago
• Mitochondrial DNA analysis of ancient Sampula population in Xinjiang

mtDNA discontinuity in the Nile Valley

From the paper:

The distribution of subsets of haplogroups U6 and M1 also suggests the presence of a discontinuity between Libya and Egypt, separating western North Africa from eastern North Africa. Even if both haplogroups are thought to have been carried by a back-to-Africa migration from the Near East, significant increased U6 frequencies have been detected in the West compared to the East. The network of all U6 sequences found in the database presents two nodes with star-like shape, U6a* and U6a1. In a similar way, M1a1 is the node with starlike topology in haplogroup M1, and the node where most of the eastern sequences are found. Time estimates of these nodes are 13.5 +/- 3.7, 13.0 +/- 5.7, and 13.1 +/- 7.0 kya for haplogroups U6a*, U6a1, and M1a1 respectively. The most plausible explanation of the frequency distribution of M1a, U6, and M1b1 lineages, their coalescence age estimates, and the star-like shape would be an early split in the back to Africa migration followed by a period of stability and a period of expansion. The split would have produced two different migration waves, one westward, represented by U6 and possibly M1b1 in lower frequencies, and the other southward, represented by M1a.

Am J Phys Anthropol DOI: 10.1002/ajpa.21472

Mitochondrial DNA structure in North Africa reveals a genetic discontinuity in the Nile Valley

Karima Fadhlaoui-Zid et al.

Human population movements in North Africa have been mostly restricted to an east-west direction due to the geographical barriers imposed by the Sahara Desert and the Mediterranean Sea. Although these barriers have not completely impeded human migrations, genetic studies have shown that an east-west genetic gradient exists. However, the lack of genetic information of certain geographical areas and the focus of some studies in parts of the North African landscape have limited the global view of the genetic pool of North African populations. To provide a global view of the North African genetic landscape and population structure, we have analyzed ∼2,300 North African mitochondrial DNA lineages (including 269 new sequences from Libya, in the first mtDNA study of the general Libyan population). Our results show a clinal distribution of certain haplogroups, some of them more frequent in Western (H, HV0, L1b, L3b, U6) or Eastern populations (L0a, R0a, N1b, I, J) that might be the result of human migrations from the Middle East, sub-Saharan Africa, and Europe. Despite this clinal pattern, a genetic discontinuity is found in the Libyan/Egyptian border, suggesting a differential gene flow in the Nile River Valley. Finally, frequency of the post-LGM subclades H1 and H3 is predominant in Libya within the H sequences, highlighting the magnitude of the LGM expansion in North Africa.

Link

A common ancestor of Indo-European and Hurrian

There is an interesting monograph by Fournet & Bomhard on the Indo-European Elements in Hurrian (pdf). I will leave the linguistic details to the experts, as I doubt that many people are competent in both Proto-Indo-European and Hurrian to assess the authors' thesis. However, this is the bit that captured my attention:

Hurrian cannot be considered an Indo-European language — this is so obvious that it barely needs to be stated. Traditional Indo-European languages, such as Sanskrit, Greek, Latin, Gothic, Old Irish, Old Church Slavic, Tocharian, etc., are clearly related to each other through many common features and shared innovations that are lacking in Hurrian.

However, that is not the end of the argument. In the preceding chapters, we presented evidence that Hurrian and Proto-Indo-European “[bear] a stronger affinity, both in the roots of verbs and in the forms of grammar, than could have been produced by accident; so strong that no philologer could examine [them] without believing them to have sprung from some common source.” In this chapter, we will discuss our views on what that common source may have been like. In so doing, we will have to delve deeply into prehistory, well beyond the horizon of what is traditionally reconstructed for Proto-Indo-European in the traditional handbooks.

...

Our discussion now comes to an end. In the course of this book, we have attempted to show, through a careful analysis of the relevant phonological, morphological, and lexical data, that Urarto-Hurrian and Indo-European are, in fact, genetically related at a very deep level, as we indicated at the beginning of this chapter by quoting from the famous Third Anniversary Discourse (1786) of Sir William Jones. We propose that both are descended from a common ancestor, which may be called “Proto-Asianic”, to revive an old, but not forgotten, term.

On the basis of genetic data I have recently proposed an origin of the Indo-Aryans in the Transcaucasus, based on their possession of a genetic component related to that of modern Northeast Caucasian speakers and the putative relationship of the latter with the Hurro-Urartian group. If the Hurrian-Indo-European "Proto-Asianic" hypothesis is true, then it would strengthen that hypothesis as it would place the Proto-Indo-Europeans in the vicinity of the Hurrians.

Earliest drinking skull-caps (15-12 thousand years ago)

I had no idea that skull-caps as drinking vessels is not an ethnographic oddity, but a widely attested practice. Besides the infamous Krum, and Herodotus' Scythians I did not have any other examples in mind. A new paper is a good primer on the subject, and it also presents evidence for the earliest known use of skull-caps from Gough's Cave in England.

From the paper:

At Gough's Cave there is unambiguous evidence for the intentional controlled production of skull-cups, resembling those from the Le Placard and Isturitz as well as modern ethnographic examples [8]. The distribution of cut and percussion marks, however, suggests that this meticulous shaping of the cranial vault was preceded by the processing of the cadavers for consumption of body tissues (including bone marrow from the mandible), with a pattern of cuts and impact damage that is identical to that found on other large mammals from the cave [26]–[27].

PLoS ONE 6(2): e17026. doi:10.1371/journal.pone.0017026

Earliest Directly-Dated Human Skull-Cups

Silvia M. Bello et al.

Abstract
Background
The use of human braincases as drinking cups and containers has extensive historic and ethnographic documentation, but archaeological examples are extremely rare. In the Upper Palaeolithic of western Europe, cut-marked and broken human bones are widespread in the Magdalenian (~15 to 12,000 years BP) and skull-cup preparation is an element of this tradition.

Principal Findings
Here we describe the post-mortem processing of human heads at the Upper Palaeolithic site of Gough's Cave (Somerset, England) and identify a range of modifications associated with the production of skull-cups. New analyses of human remains from Gough's Cave demonstrate the skilled post-mortem manipulation of human bodies. Results of the research suggest the processing of cadavers for the consumption of body tissues (bone marrow), accompanied by meticulous shaping of cranial vaults. The distribution of cut-marks and percussion features indicates that the skulls were scrupulously 'cleaned' of any soft tissues, and subsequently modified by controlled removal of the facial region and breakage of the cranial base along a sub-horizontal plane. The vaults were also ‘retouched’, possibly to make the broken edges more regular. This manipulation suggests the shaping of skulls to produce skull-cups.

Conclusions
Three skull-cups have been identified amongst the human bones from Gough's Cave. New ultrafiltered radiocarbon determinations provide direct dates of about 14,700 cal BP, making these the oldest directly dated skull-cups and the only examples known from the British Isles.

Link

Questioning the gap between anatomical and behavioral modernity

A central tenet of the consensus view on modern human origins is that anatomical modernity (first attested in the Omo skulls from Ethiopia, ~195ky) precedes behavioral modernity (clear signs of symbolic thinking, such as painting, decoration, burial, etc.) by about 150 thousand years. The latter is said to be most clearly attested in "Cro-Magnon"-type people from Europe, although precedents of this type are occasionally detected in older archaeological cultures.

A new paper challenges this prevailing view of the onset of behavioral modernity.

Here is what appears to be a dated quote from the paper:

Yet fossil morphology combined with studies of DNA both from fossils and from living humans now shows that Neanderthals and their associated archaeological record are largely irrelevant for models concerning early phases of H. sapiens evolution (Harvati, Frost, and McNulty 2004; Serre and Paabo 2006).

I would say that the recent 2010 articles on Neandertal/Denisovan intermixture with modern humans makes the notion of Neandertal irrelevance problematic. Indeed, while the author of the current paper argues for behavioral variability in anatomically sapiens populations predating the "Upper Paleolithic Revolution", I would say that an equally important aspect of variability is that related to non-sapiens populations such as Neandertals. That is, we should question not only the exclusion of chronologically older sapiens populations from behavioral modernity, but also contemporaneous non-sapiens ones.

Shea is dismissive of the Neandertal intermixture hypothesis, stating that:

Whatever one thinks about this issue, it is simply a fact that during the period under discussion, 50–200 kya, H. sapiens was an African primate.

I am not so sure about that. We have evidence for ~100ky anatomically modern humans in China, Arabia, the Levant (Qafzeh), and North Africa. A quite recent genetic study discounts the recent Out of Africa paradigm, opting instead for either a Multiple Archaic populations model, or an ancestral bottleneck 150 thousand years ago in Africa.

A significant part of the paper's argument is focused on the occurrence of different lithic technologies across time and space in Africa. The argument, as far as I can understand it, is that Mode 5 microlithic technologies of the European Upper Paleolithic type do not represent an innovation worthy of an idea of "progress" or particular newly-hatched cognitive skills:

Microlithic technologies occur in African contexts sporadically between 50 and 100 kya (Ambrose 2002). They become common and widespread after 20 kya, not just in Africa but also in Eurasia (Elston and Kuhn 2002). However, one ought not read too much into this difference. Small retouched stone tools are known from many Eurasian Lower and Middle Paleolithic contexts (Dibble and McPherron 2006; Zaidner, Ronen, and Burdukiewicz 2003). Small geometric-backed pieces are known from Last Interglacial (presumably Neanderthal) contexts in Germany (Conard 1990). Whatever cognitive capacities mode 5 microlithic technologies require were plainly ones that were either evolutionarily primitive or evolved convergently in the genus Homo.

While Shea questions the behavioral non-modernity of early East Africans such as Omo, Schwartz and Tattersall question the label of "archaic Homo sapiens", suggesting that recent Homo sapiens (of the period of the "Upper Paleolithic Revolution" and recent humanity) can be anatomically defined in a manner excluding of these earlier hominins. Another recent study gives me no great confidence that Rhodesian Man (Kabwe) commonly identified as ancestral to the Omo "archaic sapiens" deserves that position.

So, should we extend the definition of sapiens in both its anatomical and behavioral aspects to 200ky East Africans, or should we limit it (per S&T's suggestion) in both senses to humankind of the last few tens of thousands years?

My personal preference, stated several times in this blog, is to think in terms of a recent demographically dominant "Afrasian" population that absorbed other archaic humans in Africa ("Paleo-Africans") and Eurasia (Neandertals/Denisovans/?).

Recent genetic evidence (every time we sampled an "archaic" hominin we found that it can't be fit to a pure Out of Africa model) suggests to me that intermixture between deeply divergent human populations was the norm, rather than the exception, and assimilation models, or even multiregional evolution may be true, the latter.

As for the onset of "behavioral modernity" I envision two scenaria:

• An accretion of genetic changes across interbreeding hominins across the globe led to a demographic explosion, which led to more beneficial mutations in the ever-larger human population, which led to an even more successful human population (in both the behavioral and demographic senses)
• A cognitive leap allowed a portion of Homo (the Afrasians) to multiply, expand, and dominate over all other hominins, absorbing them in the process.

Whether one questions the concept of behavioral modernity or not, I think it's undeniable that something happened ~50ky ago leading to the extinction (via assimilation or competition) of so many not-modern looking populations across Eurasia.

Current Anthropology
Vol. 52, No. 1 (February 2011), pp. 1-35

Homo sapiens Is as Homo sapiens Was

John J. Shea

Abstract

Paleolithic archaeologists conceptualize the uniqueness of Homo sapiens in terms of “behavioral modernity,” a quality often conflated with behavioral variability. The former is qualitative, essentialist, and a historical artifact of the European origins of Paleolithic research. The latter is a quantitative, statistically variable property of all human behavior, not just that of Ice Age Europeans. As an analytical construct, behavioral modernity is deeply flawed at all epistemological levels. This paper outlines the shortcomings of behavioral modernity and instead proposes a research agenda focused on the strategic sources of human behavioral variability. Using data from later Middle Pleistocene archaeological sites in East Africa, this paper tests and falsifies the core assumption of the behavioral-modernity concept—the belief that there were significant differences in behavioral variability between the oldest H. sapiens and populations younger than 50 kya. It concludes that behavioral modernity and allied concepts have no further value to human origins research. Research focused on the strategic underpinnings of human behavioral variability will move Paleolithic archaeology closer to a more productive integration with other behavioral sciences.

Link

Y chromosomes of Libyan Tuareg

The gene pool of these samples seems quite simple composed entirely of E1b1a8-U175 (sub-Saharan), E1b1b1b-M81 (Northwest African), and R-V88. I find the absence of other clades of Middle Eastern or European origin as extremely interesting, pointing to the extreme value of this population as a key to North African prehistory.

Haplogroup U175 is most frequent in Sub-Saharan Africa and it belong to clade E-M2 which trace their descent to east Africa but became more frequent in Sub-Saharan Africa.

In the next Dodecad Project update, I will probably have a North African sample of more varied composition than the HGDP Mozabites and Behar et al. (2010) Moroccans. Note that North Africans are part of the current call for submissions in the project, so I would love to have more samples from that region of the world.

Am J Phys Anthropol DOI: 10.1002/ajpa.21473

Deep into the roots of the Libyan Tuareg: A genetic survey of their paternal heritage

Claudio Ottoni et al.

Recent genetic studies of the Tuareg have begun to uncover the origin of this semi-nomadic northwest African people and their relationship with African populations. For centuries they were caravan traders plying the trade routes between the Mediterranean coast and south-Saharan Africa. Their origin most likely coincides with the fall of the Garamantes who inhabited the Fezzan (Libya) between the 1st millennium BC and the 5th century AD. In this study we report novel data on the Y-chromosome variation in the Libyan Tuareg from Al Awaynat and Tahala, two villages in Fezzan, whose maternal genetic pool was previously characterized. High-resolution investigation of 37 Y-chromosome STR loci and analysis of 35 bi-allelic markers in 47 individuals revealed a predominant northwest African component (E-M81, haplogroup E1b1b1b) which likely originated in the second half of the Holocene in the same ancestral population that contributed to the maternal pool of the Libyan Tuareg. A significant paternal contribution from south-Saharan Africa (E-U175, haplogroup E1b1a8) was also detected, which may likely be due to recent secondary introduction, possibly through slavery practices or fusion between different tribal groups. The difference in haplogroup composition between the villages of Al Awaynat and Tahala suggests that founder effects and drift played a significant role in shaping the genetic pool of the Libyan Tuareg.

Link

Maximum likelihood estimation of recent shared ancestry (ERSA)

The ERSA software will be available at this address of the Jorde lab. They also used GERMLINE and fastIBD in BEAGLE, so it should be possible for genealogy-minded individuals to use it to confirm/disprove postulated relationships between individuals.

Genome Research doi:10.1101/gr.115972.110

Maximum-likelihood estimation of recent shared ancestry (ERSA)

Chad Huff et al.

Abstract

Accurate estimation of recent shared ancestry is important for genetics, evolution, medicine, conservation biology, and forensics. Established methods estimate kinship accurately for first- through third-degree relatives. We demonstrate that chromosomal segments shared by two individuals due to identity by descent (IBD) provide much additional information about shared ancestry. We developed a maximum-likelihood method for the estimation of recent shared ancestry (ERSA) from the number and lengths of IBD segments derived from high-density SNP or whole-genome sequence data. We used ERSA to estimate relationships from SNP genotypes in 169 individuals from three large, well-defined human pedigrees. ERSA is accurate to within one degree of relationship for 97% of first- through fifth-degree relatives and 80% of sixth- and seventh-degree relatives. We demonstrate that ERSA's statistical power approaches the maximum theoretical limit imposed by the fact that distant relatives frequently share no DNA through a common ancestor. ERSA greatly expands the range of relationships that can be estimated from genetic data and is implemented in a freely available software package.

Link

Mesolithic mtDNA haplogroup U5a from Luxembourg

Yet another U5a from pre-Neolithic Europe.

From the paper:

Le squelette mésolithique découvert à Reuland-
Loschbour (Fig. 1-2) est conservé au Musée national
d’histoire naturelle de Luxembourg, sous le numéro
20.5.1943. L’inhumation « LSB1 » de l’Homme de
Loschbour est une sépulture primaire datée d’environ 6 000 ans BC (Before Christ), par mesures radio - chronologiques sur le crâne [OxA-7338 : 7 205+/- 50BP (Before Present) soit 6 220-5 990 cal BC] et sur les 2 côtes d’aurochs accompagnant le squelette [GrN- 7115 : 7 115+/-45BP soit 6 070-5 890 cal BC].

This was a 1.6m tall, hyperdolichocephalic, robust, ~60kg male, with an age of 34-47 years. As the authors correctly point out:

Les haplogroupes U5 (65 %) et U4 sont les plus communs (>80%) parmi les chasseurs-cueilleurs d’Europe centrale et orientale (BRAMANTI et al. 2009). L’Homme de Loschbour, d’haplogroupe U5a, fait parfaitement le lien entre ceux-ci et l’Homme de Gough’s Cave (Cheddar Gorge, Somerset, Angleterre), daté de 7 150 BC et également d’haplogroupe U5a. Ces haplogroupes sont plus rares dans toutes ces régions, suite à l’arrivée des premiers agriculteurs de la Culture Linear Band Keramik (BRAMANTI et al. 2009), diffusant des Balkans, et probablement aussi pour d’autres raisons comme la dilution avec d’autres haplogroupes européens anciens présents au moins depuis l’expansion succédant au dernier maximum glaciaire. Actuellement, 11% de la population européenne globale appartiennent au clan U5. Les types U5, U5a et U5b ne représentent plus qu’environ 5 à 7 % de la population d’Europe occidentale, mais restent très fréquents (refuge ?) au Nord de l’Europe, principalement chez les Saami ou Lapons (40 % de la population), les Finlandais et les Estoniens ; ils ont également des représentants en Afrique du Nord (composante méridionale de l’expansion à la fonte des glaces ?) et au Proche Orient, probablement par migration inverse (voir MANCO 2009-2010 ; PONTIKOS 2010).

Bull. Soc. Préhist. Luxembourgeoise 31, 2009, 7-30.

De l’ocre sur le crâne mésolithique (haplogroupe U5a) de Reuland-Loschbour(Grand-Duché de Luxembourg) ?

Dominique Delsate, Jean Michel Guinet et Steven Saverwyns

Summary: A red colored area is present on the left portion of the frontal bone of the mesolithic man from Loschbour. After a preliminary report of the bio-anthropological study of the skeleton, with genetic typing of mitochondrial DNA, we present our attempts to determine the nature of the pigment, by the methods of Raman spectroscopy and elemental analysis by energy dispersive X-ray spectroscopy (EDX). Ochre is proven, and its presence is discussed.

Swedish population structure (Salmela et al. 2011)

From the paper:

In our earlier study [4], we saw that North European populations exhibited differing amounts of IBS similarity to East Asians so that Finns, especially Eastern Finns, were the most similar. Now we have observed the same phenomenon - though in a smaller degree - within Sweden, where Norrland showed the most of East Asian similarity and Götaland the least. This is consistent with earlier Y-chromosomal studies [13]. In strong contrast, however, neither Norrland nor Eastern Finns showed any increase in similarity to the Vologda Russians, and a similar lack of affinity between Finns and Russians can also be seen in separate datasets [6], [13]. Thus, if the current references are representative of Russians in this respect, the observed affinity to Eastern Asia would not be mediated by contacts with Russians but could reflect an ancient eastern influence predating the arrival of Slavic populations to Northeastern Europe in the end of the first millennium [23]. It remains unclear whether the eastern affinity observed in Sweden would date back to the same era, or rather reflect the amount of later Finnish contacts to the area.

PLoS ONE 6(2): e16747. doi:10.1371/journal.pone.0016747

Swedish Population Substructure Revealed by Genome-Wide Single Nucleotide Polymorphism Data

Elina Salmela et al.

Abstract

The use of genome-wide single nucleotide polymorphism (SNP) data has recently proven useful in the study of human population structure. We have studied the internal genetic structure of the Swedish population using more than 350,000 SNPs from 1525 Swedes from all over the country genotyped on the Illumina HumanHap550 array. We have also compared them to 3212 worldwide reference samples, including Finns, northern Germans, British and Russians, based on the more than 29,000 SNPs that overlap between the Illumina and Affymetrix 250K Sty arrays. The Swedes - especially southern Swedes - were genetically close to the Germans and British, while their genetic distance to Finns was substantially longer. The overall structure within Sweden appeared clinal, and the substructure in the southern and middle parts was subtle. In contrast, the northern part of Sweden, Norrland, exhibited pronounced genetic differences both within the area and relative to the rest of the country. These distinctive genetic features of Norrland probably result mainly from isolation by distance and genetic drift caused by low population density. The internal structure within Sweden (FST = 0.0005 between provinces) was stronger than that in many Central European populations, although smaller than what has been observed for instance in Finland; importantly, it is of the magnitude that may hamper association studies with a moderate number of markers if cases and controls are not properly matched geographically. Overall, our results underline the potential of genome-wide data in analyzing substructure in populations that might otherwise appear relatively homogeneous, such as the Swedes.

Link

Harappa Ancestry Project

Zack Ajmal has been doing some great work on the Harappa Ancestry Project, including posting some code and detailed instructions on how to process various source datasets. Zack contacted me only a couple of months ago for some tips about starting his own project, inspired by the Dodecad Project, and it's great to see that he is already outputting results.

This should be a good lesson to all people out there who possess (i) reasonable computer skills, (ii) reasonable understanding of genetics, (iii) reasonable computing power (my own platform most of the time is a virtual Linux box with 512MB of RAM), and (iv) time to spare on a hobby, that DIY genomics is a manageable endeavor. You will certainly learn a lot, both about genetics itself, and about the various genetics software. Most importantly, you will learn about human populations, and -if you have genetic data of your own- about yourself.

Sailing across the Pacific to settle Polynesia (Soares et al. 2011)

I always have a hard time following these easy archaeological interpretations on the basis of uniparental markers, both because I'm convinced that they are not supported by the wide confidence intervals of age estimates, and because, as I've argued countless times, age of colonization != age of most recent common ancestor of colonists' descendants.

With respect to the latter point, let me just reiterate that:

• The common founder of a set of lineages may postdate the colonization event, if the number of colonists was small enough so that attrition was high enough, and a founder that lived long after the colonization effect contributed most of the present-day population
• The common founder of a set of lineages may predate the colonization event, if the number of colonists was high enough, so that multiple related lineages with a founder who lived before the event, survived into the modern population.

We should all take modern genetic-archaeological-prehistorical correlations (including my own!) with a huge grain of salt. Polynesia seems like the last place on earth likely to yield ancient DNA of any antiquity, due to the combination of heat and moisture, but, on the whole, a single well-dated and authenticated ancient DNA sample carries much more weight than all the modern DNA put together.

From the press release:

Surprising new evidence which overturns current theories of how humans colonised the Pacific has been discovered by scientists at the University of Leeds, UK.

The islands of Polynesia were first inhabited around 3,000 years ago, but where these people came from has long been a hot topic of debate amongst scientists. The most commonly accepted view, based on archaeological and linguistic evidence as well as genetic studies, is that Pacific islanders were the latter part of a migration south and eastwards from Taiwan which began around 4,000 years ago.

But the Leeds research – published today in The American Journal of Human Genetics – has found that the link to Taiwan does not stand up to scrutiny. In fact, the DNA of current Polynesians can be traced back to migrants from the Asian mainland who had already settled in islands close to New Guinea some 6-8,000 years ago.

...

Professor Richards and co-researcher Dr Pedro Soares (now at the University of Porto), argue that the linguistic and cultural connections are due to smaller migratory movements from Taiwan that did not leave any substantial genetic impact on the pre-existing population.

The American Journal of Human Genetics, 03 February 2011
doi:10.1016/j.ajhg.2011.01.009

Ancient Voyaging and Polynesian Origins

Pedro Soares et al.

Abstract
The “Polynesian motif” defines a lineage of human mtDNA that is restricted to Austronesian-speaking populations and is almost fixed in Polynesians. It is widely thought to support a rapid dispersal of maternal lineages from Taiwan ∼4000 years ago (4 ka), but the chronological resolution of existing control-region data is poor, and an East Indonesian origin has also been proposed. By analyzing 157 complete mtDNA genomes, we show that the motif itself most likely originated >6 ka in the vicinity of the Bismarck Archipelago, and its immediate ancestor is >8 ka old and virtually restricted to Near Oceania. This indicates that Polynesian maternal lineages from Island Southeast Asia gained a foothold in Near Oceania much earlier than dispersal from either Taiwan or Indonesia 3–4 ka would predict. However, we find evidence in minor lineages for more recent two-way maternal gene flow between Island Southeast Asia and Near Oceania, likely reflecting movements along a “voyaging corridor” between them, as previously proposed on archaeological grounds. Small-scale mid-Holocene movements from Island Southeast Asia likely transmitted Austronesian languages to the long-established Southeast Asian colonies in the Bismarcks carrying the Polynesian motif, perhaps also providing the impetus for the expansion into Polynesia.

Link

The many faces of Moora

Here is a 2,600-year old bog woman from Lower Saxony, Germany as reconstructed by forensic scientists (Illustration courtesy Ursula Wittwer-Backofen, University of Freiburg).

And, here is a German language article on the same female which shows many different reconstructions.

By Caroline Wilkinson:

or, by Sabine Ohrlogge:

Multi-regionalism or assimilation?

In Is Multi-regional evolution dead? I argue that recent work on Neandertal/Denisovan admixture in modern humans has been misinterpreted as signifying only a limited contribution of archaic hominins to the dominant "Out of Africa" population. The main points of my argument are:

• Each non-modern specimen so far has yielded evidence of admixture; and since we have only examined only 2 types of archaic hominins in a relatively small part of Eurasia, it stands to reason that additional hominin populations (in Africa and the rest of Eurasia) may have also contributed their DNA to the modern human gene pool
• The uniformity of the common population element in modern humans should not be interpreted as exclusively African in origin. In a multi-regional model with gene flow we expect parts of the genome to be derived from different regions. The residual "admixture" with archaics may represent the constituent elements that have not gone global.

Ann Gibbons, writing in Science repeats the claim in favor of assimilationism:

New DNA data from archaic human species are providing a much higher resolution view of our past. When compared with the genomes of living people, the ancient genomes allow anthropologists to thoroughly test the competing models of human origins for the first time. The DNA data suggest not one but at least two instances of interbreeding between archaic and modern humans, raising the question of whether Homo sapiens at that point was a distinct species (see sidebar). And so they appear to refute the idea that modern humans came out of Africa, spread around the world, and completely replaced the archaic humans they met. But the genomic data also don't prove the classic multiregionalism model, which argues that a single, worldwide species of human, including archaic forms outside of Africa, met, mingled, and had offspring, and so produced Homo sapiens. They suggest only a small amount of interbreeding, presumably at the margins where invading moderns met archaic groups. The new picture most resembles so-called assimilation models, which got relatively little attention over the years.

This is a fallacious argument: even if we assume that the sub-10% admixture represents the entirety of non-African archaic admixture, this does not mean that there was a "small amount" of interbreeding "at the margins".

It may very well reflect differences in population sizes of different Pleistocene hominin populations.

Consider two species A and B, and a composite species C having 95% of genes derived from A and 5% of genes derived from B. This may either mean that there was sporadic and exceptional intermixture between A- with B-poeple. Alternatively, it may mean that there were many more A than B people, and even though nearly all B people were absorbed, they still did not affect the major group substantially.

This is not an insignificant point: occasional admixture at the fringes is quite a different phenomenon than wholesale admixture between demographically unequal populations.

I don't have any data on population sizes in the last 100-200 thousand years, but I would venture that before the technological advances of the last 50 thousand years ago, when full behavioral modernity arrived, northern Eurasians (Neandertals or Denisovans) did not have as great population densities and sizes as could be maintained in either the African homeland of Homo or more temperate climate zones in general. So, I would lean towards the idea that the observed levels of admixture signify substantial admixture between demographically unequal populations, rather than exceptional admixture.