E-M81 in Morocco

Hum Biol. 2014 May;86(2):105-12.

Phylogeography of e1b1b1b-m81 haplogroup and analysis of its subclades in morocco.

Reguig A, Harich N, Barakat A, Rouba H.

Abstract

In this study we analyzed 295 unrelated Berber-speaking men from northern, central, and southern Morocco to characterize frequency of the E1b1b1b-M81 haplogroup and to refine the phylogeny of its subclades: E1b1b1b1-M107, E1b1b1b2-M183, and E1b1b1b2a-M165. For this purpose, we typed four biallelic polymorphisms: M81, M107, M183, and M165. A large majority of the Berber-speaking male lineages belonged to the Y-chromosomal E1b1b1b-M81 haplogroup. The frequency ranged from 79.1% to 98.5% in all localities sampled. E1b1b1b2-M183 was the most dominant subclade in our samples, ranging from 65.1% to 83.1%. In contrast, the E1b1b1b1-M107 and E1b1b1b2a-M165 subclades were not found in our samples. Our results suggest a predominance of the E1b1b1b-M81 haplogroup among Moroccan Berber-speaking males with a decreasing gradient from south to north. The most prevalent subclade in this haplogroup was E1b1b1b2-M183, for which diffferences among these three groups were statistically significant between central and southern groups.

Link

ISABS 2013 abstracts

From the book of abstracts (pdf):

MITOCHONDRIAL DNA AND PHYLOGENETIC ANALYSIS OF PREHISTORIC NORTH AFRICAN POPULATIONS

North Africa is located at a crossroad between Europe, Africa and Asia and has been inhabited since the Prehistoric time. In the Epipaleolithic period (23.000 years to 10.000 years BP), the Western North Africa has been occupied by Mecha- Afalou Men, authors of the Iberomaurusian industry. The origin of the Iberomaurusians is unresolved, several hypotheses have been forwarded. With the aim to contribute to a better knowledge of the Iberomaurusian settlement we analysed the mitochondrial DNA (mtDNA) of skeletons exhumed from the prehistoric site of Taforalt in Morocco (23.000-10.800 years BP) and Afalou in Algeria (11.000 to 15.000 BP -Algeria). Hypervariable segment 1 of mtDNA from 38 individuals were amplified by Real-Time PCR and directly sequenced. Sequences were aligned with the reference sequence to perform the mtDNA classification within haplogroups. Phylogenetic analysis based on mitochondrial sequences from Mediterranean populations was performed using Neighbor-Joining algorithm implemented in MEGA program. mtDNA sequences from Afalou and Taforalt were classified in Eurasiatic and North African haplogroups. We noted the absence of Sub-Saharan haplotypes. Phylogenetic tree clustered Taforalt with European populations. Our results excluded the hypothesis of the sub-Saharan origin of Iberomaurusians populations and highlighted the genetic flow between Northern and Southern cost of Mediterranean since Epipaleolithic period.

DISCONTINUITY SCREENING OF THE EARLY FARMERS’ MT-DNA LINEAGES IN THE CARPATHIAN BASIN

Discontinuous mitochondrial (mt) haplotype data between Central-Europe’s first farmers and contemporary Europeans have been described before. Hungary was a key-area of the Neolithisation, in the route of Neolithisation following the River Danube, and that was also the birthplace of the Linear Pottery Culture, which later colonised Western and Northern Europe. Neolithic and post-Neolithic human remains as well as contemporary population of Hungary is involved in our project to gain information on their mt-haplotype pattern and especially on the frequency of Asian haplotypes in the Carpathian Basin. HVS-I sequences from nt15977 to nt16430 of Neolithic specimens with sufficient mtDNA preservation among an extended Neolithic collection were analysed for polymorphisms, identifying 23 different ones. A novel, N9a, N1a, C5, D1/G1a, M/R24 haplogroups were determined among the pre-industrial Hungarians. The presence of Asian haplotypes in the ancient populations must be taken into consideration when reconstructing the population history of Europe and Asia, so a survey of the recent Asian haplotype frequency in Europe is unavoidable. The ancient and recent haplotype pattern of Hungary is definitely worth further investigation to test a theory on the continuous population history of Europe, wheter genetic gaps between ancient and recent human populations of Europe were more likely to be detected. 

ANTHROPOLOGIC AND MITOCHONDRIAL DNA ANALYSIS OF A MEDIEVAL GRAVEYARD FROM SOPOT (CROATIA)

Anthropologic and DNA analysis of human remains recovered from a graveyard in ©opot near Benkovac (Croatia) dating to the 14th/15th century was conducted in order to reconstruct the origin and life conditions of the people populating the region at that time. The dynamics of the population represented in this graveyard are important for understanding Croatian history because the deceased individuals were buried according to pagan ritual which was uncommon in a post Christianization period. Human remains from a total of 31 graves were analyzed, in which 47 individuals were found (9 female, 23 male and 15 children). Average age at death for adults was lower than expected (for female 28.9, male 32.4 years), suggesting that the living conditions of these individuals were poor. In addition, 10 antemortem traumas were visible on 6 adults, which is a higher rate than expected, and indicates potential violence within the population group. Finally, mitochondrial DNA (mtDNA) analysis was performed on hypervariable regions one and two for 46 of the individuals. Due to the age and condition of the remains, only 19 of the samples yielded full sequence profiles. Haplogroup analysis was performed for these 19 individuals, with the majority of the results falling within the most common groups in present-day Croatia. However, examination of the lesscommon haplogroups suggested a possible migration of individuals from Asia. Collectively, the physical and molecular results from this study provide evidence to suggest that individuals recovered from this gravesite are not from the current indigenous population.

MATERNAL GENETIC PROFILE OF A NORTHWEST ALGERIAN POPULATION

The North African population gene pool based on mitochondrial DNA (mtDNA) polymorphisms has been shaped by the back-migration of several Eurasian lineages in Paleolithic and Neolithic times. Recent influences from sub-Saharan Africa and Mediterranean Europe are also evident. The presence of East-West and North- South haplogroup frequency gradients strongly reinforces the genetic complexity of this region. However, this genetic scenario is beset with a notable gap, which is the lack of consistent information for Algeria, the largest country in the continent. To fill this gap, we analyzed a sample of 240 unrelated subjects from a northwest Algeria cosmopolitan population. mtDNA sequences analysis was performed on the regulatory hypervariable segment I region (HVSI). Haplogroup diagnostic mutations were analyzed using PCR-RFLPs and/or SNaPshot multiplex reactions. Of all North African populations, Eurasian lineages are the most frequent in Algeria (80%) while sub-Saharan Africa origin accounts for the remaining (20%). Within them, the North African genetic component U6 and M1 count for 20%. Indeed, the U6 haplogroup, highly distributed in Northwestern African populations, show a high frequency in Algeria (11.83%), while, the M1 frequency (7.1%) raises an anomalous peak in its decreasing Northeast - Northwest gradient. Moreover, the high frequency of HV subgroups (38.33%) point to direct maritime contacts between the European and North African western sides of the Mediterranean. Besides, the most common western H subgroups, H1 (47.8%) and H3 (10.1%), represent 60% of H lineages. These frequencies and HV0 (7.5%) lie well within the observed Northwestern to Northeastern African decreasing gradients.

MATERNAL GENETIC VARIATION OF THE SLOVENIAN POPULATION IN A BROADER EUROPEAN CONTEXT AND COMPARED TO ITS PATERNAL COUNTERPART

Slovenia is a European country situated at the crossroads of main European cultural and trade routes. It is geographically more linked to Central Europe, but history draws it closer together to its ex-Yugoslavian, Southeast European (SEE) neighbors. Slovenian maternal heritage has not been analyzed since 2003 and our aim was to analyze SNP markers of 97 Slovenian mtDNAs in high resolution to see where this population fits according to its maternal genetic variation. We compared the Slovenian sample with the neighboring SEE populations, as well as with other published European population datasets. Also, we compared the obtained mtDNA variation results with the available Slovenian Y chromosome data to see how these two uniparental marker systems correspond to each other. In the PC plot based on mtDNA haplogroups frequencies, Slovenian population has an outlying position mostly due to the increased prevalence of J (14.4%) and T (15.4%) clade and especially because of the abundance and diversity of J1c samples in Slovenia, represented with 8 haplotypes and in a percentage of >11%. Although in an outlying position, Slovenian mtDNA variation still shows a certain degree of affinity to SEE. On the contrary, Slovenia’s paternal genetic heritage yielded results that correspond to the population’s geographic location and groups Slovenian population considerably closer to Central European countries, based on increased prevalence of Northern/Central European R1a-M198 and decreased frequency of Balkan-specific I2a2-M423. Such differences in maternal and paternal marker systems could indicate that Slovenian genetic variation was influenced by sex-biased demographic events.

AN ASIAN TRACE IN THE GENETIC HERITAGE OF THE EASTERN ADRIATIC ISLAND OF HVAR

The Island of Hvar is situated in the central eastern Adriatic, and its relatively small rural population has been reproductively isolated thought history. Therefore, founder effects, genetic drift and inbreeding have had significant role in the shaping of current genetic diversity of Hvar Islanders. We analyzed Y-chromosome SNP markers of 412 Hvar islanders in high resolution, with the aim to investigate the current paternal genetic diversity. We found a relatively high frequency (6.1%) of unrelated male samples belonging to the Q*-M424 haplogroup, which is unusual for European populations. Interestingly, a previous study showed 9 individuals from Hvar with mitochondrial haplogroup F, which is almost absent in Europe. Both findings could indicate a certain connection with Asian populations, where these haplogroups are most common. This might be a result of several migratory events in the history, one of which could be linked to the ancient Silk Road, the other a consequence of the arrival of the Slavs, following the Avars, to the eastern Adriatic in the 6th century or due to the expansion of the Ottoman Empire in 16th to 18th century. The presence of these rare mitochondrial and Y-chromosome lineages are an example of founder effect and random genetic drift which, in this small island with a high degree of isolation and endogamy, had a strong impact on shaping the genetic diversity of the population. 

GENETIC PORTRAIT OF THE BESERMYAN ETHNIC GROUP BASED ON MTDNA HAPLOGROUP STUDY

Besermyan are a small ethnic group living in the Volga-Ural region of Russia. They belong to Finno-Ugric language group, but speak a special dialect. There are some Bulgar-Chuvash borrowings in their adverb vocabulary that are absent in other dialects of the Udmurt language. Besermyan live in the northwestern part of modern Udmurtia in the Cheptsa basin. In 2002 their number was about three thousand. The Besermyan origin is a very interesting issue. There is a view that the endonym Besermyan (beserman) is derived from the Turkic word which means flMuslim« in Arabic. This hypothesis, along with their language, hints at the origin of this ethnic group; however the genetic portrait of Besermyan has not been described yet. In our study we used the data of mitochondrial DNA (mtDNA) HVSI sequencing from 98 Besermyans representing 10 villages in Udmurtia Republic of Russia. The prevalence of Western Eurasian mtDNA lineages (91.7%) over Eastern Eurasian ones (9.2%) was shown in the studied population which is consistent with the structure of mtDNA pool of Finno-Ugric ethnic groups of the Volga-Ural region. Some Eastern Eurasian lineages in Besermyan are represented by haplogroups D4b, A4b and Z1a which are also common in Udmurts. It is important to note though that the share of Western Eurasian component in Udmurts according to previous study by Bermisheva et al. (2002) is about 74.5% so mtDNA haplogroup distribution in Besermyans is closer to other Finno-Ugric people of the Volga-Ural region: Mordvins and Maris.

COSMOPOLITAN CENTRAL ASIA: TAJIK MTDNA TRACES THE EASTWEST MOVEMENT OF ANCIENT NOMADS 

Tajikistan is a country in the mountains of southeast Central Asia. Due to its isolation, mtDNA variation in the Tajiks has been fragmentary studied on a limited number of samples. In 1997 saliva samples were collected from unrelated Tajiks across Tajikistan. After long-term preservation DNA was extracted from 2 mm FTA discs. Due to degradation mtDNA was amplified using the primary and secondary PCRs with nested primers in the multiplex format. The origin of 91 mitochondrial genomes from Tajikistan traced from western Eurasia (62.6%), eastern Eurasia (25.3%), south Asia (11.0%), and North Africa (1.1%). Significant population structure in the distribution of these mtDNA lineages was revealed within the regional groups in Tajikistan. The mtDNA variation was compared between the Tajiks and 45 populations of Eurasia. Pairwise Fst comparisons and the correspondence analysis revealed non-significant differences between the Tajik and Uzbek populations. Although both nations speak languages belonging to different linguistic groups, this result corresponds to their cultural and economic proximity. Surprisingly, after the Uzbeks, the Tajik mtDNA pool most closely resembles to the Ossetians, an Indo-Iranian people from the North Caucasus. The Tajiks also display intensive gene flow and admixture with some other populations of Central Asia and the Iranian Plateau living along the centers and crossroads of the earliest civilizations and belonging to different linguistic groups including the Uyghur, Kazakh, Karakalpak, Turkmen, Pathans, Iranian Arabs, and Gilaki. This study demonstrates an impact of ancient nomad migrations and invasions on the distribution of mtDNA variation in Eurasia. 

Origin of the Iberomaurusian

This seems to be in wonderful agreement with the coalescence ages of haplogroups M1 and U6. I would say that some type of Into-Africa migration makes the best sense of the totality of the evidence, now that we know that the Iberomaurusian appears after a hiatus in occupation.

Journal of Human Evolution doi:10.1016/j.jhevol.2013.06.003

Origins of the Iberomaurusian in NW Africa: New AMS radiocarbon dating of the Middle and Later Stone Age deposits at Taforalt Cave, Morocco

R.N.E. Barton et al. Recent genetic studies based on the distribution of mtDNA of haplogroup U6 have led to subtly different theories regarding the arrival of modern human populations in North Africa. One proposes that groups of the proto-U6 lineage spread from the Near East to North Africa around 40–45 ka (thousands of years ago), followed by some degree of regional continuity. Another envisages a westward human migration from the Near East, followed by further demographic expansion at ∼22 ka centred on the Maghreb and associated with a microlithic bladelet culture known as the Iberomaurusian. In evaluating these theories, we report on the results of new work on the Middle (MSA) and Later Stone (LSA) Age deposits at Taforalt Cave in Morocco. We present 54 AMS radiocarbon dates on bone and charcoals from a sequence of late MSA and LSA occupation levels of the cave. Using Bayesian modelling we show that an MSA non-Levallois flake industry was present until ∼24.5 ka Cal BP (calibrated years before present), followed by a gap in occupation and the subsequent appearance of an LSA Iberomaurusian industry from at least 21,160 Cal BP. The new dating offers fresh light on theories of continuity versus replacement of populations as presented by the genetic evidence. We examine the implications of these data for interpreting the first appearance of the LSA in the Maghreb and providing comparisons with other dated early blade and bladelet industries in North Africa.

Link

IBD sharing between Iberians and North Africans (Botigué et al. 2013)

An interesting new paper documents an excess of IBD sharing between Iberians (excluding Basques) and North African (and particular NW African) populations.

It would have been nice if the authors had used techniques such as rolloff and ALDER or those of Jin et al. (2012) to say something about the time/nature of the admixture event detected via IBD sharing; insteady, they use variance in admixture proportions, which gives a probably much noisier estimate, with the basic idea being that in the first few generations post-admixture there are individuals with much varying admixture proportions, but these tend to be homogenized over time.

The occurrence of North African-specific admixture in SW Europe has long been suspected on the basis of Y-chromosome/mtDNA work (e.g., the presence of E-M81 which is probably the best North African marker in existence). It also makes sense, because of the limited occurrence of Sub-Saharan markers in Iberia: such elements did not, presumably, fly over North Africa, but landed in Iberia via people who were themselves admixed.

A couple notes of caution:

(i) the use of ADMIXTURE as a means of estimating admixture proportions is dangerous in this case, because of the hybridity of "North Africans" themselves, which according to published estimates experienced Sub-Saharan African admixture in the last few thousand years. In my own experiments it is clear that "North Africans" are a mixture of three basic components related to Europe, Sub-Saharan Africa, and the Near East. Nonetheless, in my own experiments I do also get an excess of the component I've labeled "Northwest African" in Iberia that is not shared by Basques or French.

(ii) as I've emphasized before, IBD sharing between populations does not indicate the direction of gene flow. One would have to look at the ancestry of the shared segments to determine their origin. To give a simple example, an IBD segment shared by a Spaniard and a Mexican could be European, African, or Native American, and -thanks to historical knowledge- we can be fairly sure that the number of such segments is also in the given order.

Given that Iberia is the neighbor of NW Africa one would not be surprised if there was gene flow in both directions, and while North Africa gene flow into Iberia is one possible explanation, some of the gene flow may have gone the other way, e.g., with contacts during the Pax Romana, fleeing Iberian Muslim in the post-reconquista period, Barbary pirates attacking Christian ships and the like. In any case, it would be interesting to catalogue IBD shared segments between Iberia and NW Africa in terms of their geographical origin.

(iii) the sources and timing of admixture could potentially be determined by ancient DNA work. The three most recent time periods are related to the slave trade (both European of Africans and vice versa), the Islamic period, and the Roman Empire. Presumably, with the sampling of enough individuals, that type of admixture ought to manifest in populations living before/after each of these three events.

In any case, this is an interesting paper which is also accompanied by publicly accessible data.

PNAS doi: 10.1073/pnas.1306223110

Gene flow from North Africa contributes to differential human genetic diversity in southern Europe

Laura R. Botigué et al.

Human genetic diversity in southern Europe is higher than in other regions of the continent. This difference has been attributed to postglacial expansions, the demic diffusion of agriculture from the Near East, and gene flow from Africa. Using SNP data from 2,099 individuals in 43 populations, we show that estimates of recent shared ancestry between Europe and Africa are substantially increased when gene flow from North Africans, rather than Sub-Saharan Africans, is considered. The gradient of North African ancestry accounts for previous observations of low levels of sharing with Sub-Saharan Africa and is independent of recent gene flow from the Near East. The source of genetic diversity in southern Europe has important biomedical implications; we find that most disease risk alleles from genome-wide association studies follow expected patterns of divergence between Europe and North Africa, with the principal exception of multiple sclerosis.

Link

Origins of North African and Central/East European Jews

A couple of new papers appeared yesterday. I'll just post the abstracts for the time being, and add any further comments as an update when I find the time for them.

Some related analyses of mine:

• fastIBD analysis of Afroasiatic groups (Jews, Arabs, Assyrians, Berbers, Somalis, Amharas, etc.)
• fastIBD analysis of Iberia, France, Italy, Balkans, Anatolia and European Jews
• Admixture proportions for various populations (incl. various Jewish groups)

UPDATE (Aug 8):

Below is Fig. 3 from Campbell et al.:

One can see that Jewish groups have high degree of intra-population IBD sharing (A); many of the highest levels of IBD sharing is between Jewish groups (B and C).

This paper definitely shows that Jewish groups differ from non-Jewish North Africans. But, the lack of comparative samples from non-Jewish non-North Africans makes the interpretation of this result difficult. Both the PCA analysis, shown below, and the structure analysis indicates a significant Sub-Saharan component in North African non-Jewish populations.

So, it seems, based on these results, that Jewish groups are differentiated from North Africans due to their general lack of sub-Saharan admixture, and they also show a variable degree of affiliation to European groups; however, by "European" groups we go only as far as north Italy and Sardinia. What of the relationships of different Jewish groups to people from southern Italy, Greece, Anatolia, the Caucasus, or even Iranian speakers of the Near East?

Now, let's go to the Elhaik paper, which investigates a different problem altogether, trying to distinguish between the "Rhineland" and "Khazarian" hypotheses for the origins of Central-East European Jews. According to the paper:

Admixture calculations were carried out using a supervised learning approach in a structure-like analysis. This approach has many advantages over the unsupervised approach that not only traces ancestry to K abstract unmixed populations under the assumption that they evolved  independently (Chakravarti 2009; Weiss and Long 2009) but also problematic when applied to study Jewish ancestry, which can be dated as far back as 3,000 years (Figure 2). Admixture was calculated with a reference set of seven populations representing genetically distinct regions: Pygmies (Africa), French Basque (West Europe), Chuvash (East Europe), Han Chinese (Asia), Palestinians (Middle East), Turk-Iranians (Near East), and Armenians (Caucasus) (Figure 5).

But, Palestinians too have African admixture, so using them as a parental population conflates two separate issues: their old Near Eastern Semitic ancestors which could be reasonably inferred to be somewhat related to the Semitic ancestors of Jews, and their recent African admixture. Similarly, Turks have east Eurasian admixture, and Iranians have South Asian admixture.

The IBD sharing is probably the strongest piece of evidence in this paper for a Caucasian connection. Excess of IBD sharing with Caucasus and Palestinians relative to the other populations may indeed be a good indication of such admixture. On the other hand, the Khazarian Empire was primarily located in eastern Europe and the North Caucasus, not in Armenia and Georgia. Also, this analysis rejects the Greco-Roman hypothesis (whereby European Jews underwent admixture in Greco-Roman times when they were part of the Hellenistic and Roman Empires), but does not really include any Greco-Roman populations (for example, from Greece and Italy).

On the other hand, there may be something to the Khazar story (but in the sense of admixture, rather than replacement). High IBD sharing with Caucasians is one such piece of evidence. Another is the presence of Y-haplogroup Q and R-Z93+, both of which could in principle track a Central Asian Turkic influence (although Z93 could also track an Iranian influence). Then, there is the limited but persistent evidence for a little East Eurasian admixture present in Ashkenazi Jews and not in Sephardic Jews, which might also be consistent with a little Turkic influence.

Overall, I am convinced that most modern Jewish groups have some variable old Near Eastern Jewish ancestry, primarily on the basis of the elevated "Southwest Asian" that seems to correlate reasonably well with groups of Semitic speakers. But, it is difficult to say "how much" and to identify all the potential sources of admixture. Jews have been an international people for quite a long time, so I would guess that fragments of different peoples they encountered may remain in their genomes. Perhaps something akin to Ralph and Coop (2012) may give more information about the timing of these admixture events, as well as the date of the common ancestry of different Jewish groups.

PS: I started a small fastIBD analysis of different Jewish and non-Jewish groups with a fairly large assortment of populations, and will probably post it here in the next few days.

PNAS doi: 10.1073/pnas.1204840109

North African Jewish and non-Jewish populations form distinctive, orthogonal clusters

Christopher L. Campbell et al.

North African Jews constitute the second largest Jewish Diaspora group. However, their relatedness to each other; to European, Middle Eastern, and other Jewish Diaspora groups; and to their former North African non-Jewish neighbors has not been well defined. Here, genome-wide analysis of five North African Jewish groups (Moroccan, Algerian, Tunisian, Djerban, and Libyan) and comparison with other Jewish and non-Jewish groups demonstrated distinctive North African Jewish population clusters with proximity to other Jewish populations and variable degrees of Middle Eastern, European, and North African admixture. Two major subgroups were identified by principal component, neighbor joining tree, and identity-by-descent analysis—Moroccan/Algerian and Djerban/Libyan—that varied in their degree of European admixture. These populations showed a high degree of endogamy and were part of a larger Ashkenazi and Sephardic Jewish group. By principal component analysis, these North African groups were orthogonal to contemporary populations from North and South Morocco, Western Sahara, Tunisia, Libya, and Egypt. Thus, this study is compatible with the history of North African Jews—founding during Classical Antiquity with proselytism of local populations, followed by genetic isolation with the rise of Christianity and then Islam, and admixture following the emigration of Sephardic Jews during the Inquisition.

Link

arXiv:1208.1092v1 [q-bio.PE]

The Missing Link of Jewish European Ancestry: Contrasting the Rhineland and the Khazarian Hypotheses

Eran Elhaik

The question of Jewish ancestry has been the subject of controversy for over two centuries and has yet to be resolved. The "Rhineland Hypothesis" proposes that Eastern European Jews emerged from a small group of German Jews who migrated eastward and expanded rapidly. Alternatively, the "Khazarian Hypothesis" suggests that Eastern European descended from Judean tribes who joined the Khazars, an amalgam of Turkic clans that settled the Caucasus in the early centuries CE and converted to Judaism in the 8th century. The Judaized Empire was continuously reinforced with Mesopotamian and Greco-Roman Jews until the 13th century. Following the collapse of their empire, the Judeo-Khazars fled to Eastern Europe. The rise of European Jewry is therefore explained by the contribution of the Judeo-Khazars. Thus far, however, their contribution has been estimated only empirically; the absence of genome-wide data from Caucasus populations precluded testing the Khazarian Hypothesis. Recent sequencing of modern Caucasus populations prompted us to revisit the Khazarian Hypothesis and compare it with the Rhineland Hypothesis. We applied a wide range of population genetic analyses - including principal component, biogeographical origin, admixture, identity by descent, allele sharing distance, and uniparental analyses - to compare these two hypotheses. Our findings support the Khazarian Hypothesis and portray the European Jewish genome as a mosaic of Caucasus, European, and Semitic ancestries, thereby consolidating previous contradictory reports of Jewish ancestry.

Link

Maghrebi origin of early south Iberian Neolithic

Quaternary Research
Volume 77, Issue 2, March 2012, Pages 221–234

The Mesolithic–Neolithic transition in southern Iberia

Miguel Cortés Sánchez et al.

New data and a review of historiographic information from Neolithic sites of the Malaga and Algarve coasts (southern Iberian Peninsula) and from the Maghreb (North Africa) reveal the existence of a Neolithic settlement at least from 7.5 cal ka BP. The agricultural and pastoralist food producing economy of that population rapidly replaced the coastal economies of the Mesolithic populations. The timing of this population and economic turnover coincided with major changes in the continental and marine ecosystems, including upwelling intensity, sea-level changes and increased aridity in the Sahara and along the Iberian coast. These changes likely impacted the subsistence strategies of the Mesolithic populations along the Iberian seascapes and resulted in abandonments manifested as sedimentary hiatuses in some areas during the Mesolithic–Neolithic transition. The rapid expansion and area of dispersal of the early Neolithic traits suggest the use of marine technology. Different evidences for a Maghrebian origin for the first colonists have been summarized. The recognition of an early North-African Neolithic influence in Southern Iberia and the Maghreb is vital for understanding the appearance and development of the Neolithic in Western Europe. Our review suggests links between climate change, resource allocation, and population turnover.

Link

Back to (North) Africa (Henn et al. 2012)

A great new paper has just appeared, presenting new data, new conclusions about African prehistory, and new methodologies. I'll have to read it before I comment on it, but since it's open access you can read it for yourselves.

UPDATE I:


The new data are publicly available here, with information about samples here.
The new PCADMIX software is also available.

PLoS Genet 8(1): e1002397. doi:10.1371/journal.pgen.1002397 

Genomic Ancestry of North Africans Supports Back-to-Africa Migrations 

Brenna Henn et al.

 North African populations are distinct from sub-Saharan Africans based on cultural, linguistic, and phenotypic attributes; however, the time and the extent of genetic divergence between populations north and south of the Sahara remain poorly understood. Here, we interrogate the multilayered history of North Africa by characterizing the effect of hypothesized migrations from the Near East, Europe, and sub-Saharan Africa on current genetic diversity. We present dense, genome-wide SNP genotyping array data (730,000 sites) from seven North African populations, spanning from Egypt to Morocco, and one Spanish population. We identify a gradient of likely autochthonous Maghrebi ancestry that increases from east to west across northern Africa; this ancestry is likely derived from “back-to-Africa” gene flow more than 12,000 years ago (ya), prior to the Holocene. The indigenous North African ancestry is more frequent in populations with historical Berber ethnicity. In most North African populations we also see substantial shared ancestry with the Near East, and to a lesser extent sub-Saharan Africa and Europe. To estimate the time of migration from sub-Saharan populations into North Africa, we implement a maximum likelihood dating method based on the distribution of migrant tracts. In order to first identify migrant tracts, we assign local ancestry to haplotypes using a novel, principal component-based analysis of three ancestral populations. We estimate that a migration of western African origin into Morocco began about 40 generations ago (approximately 1,200 ya); a migration of individuals with Nilotic ancestry into Egypt occurred about 25 generations ago (approximately 750 ya). Our genomic data reveal an extraordinarily complex history of migrations, involving at least five ancestral populations, into North Africa.

Link

Human genetic variation: 124+ clusters with the Galore approach

The following uses the same 2,230-individual/139-population dataset described here, and analyzed with the Clusters Galore method introduced here, refined here, and applied to subsets of this data (HGDP and Behar et al. (2010)).

In short, this method exploits the clusteredness of individuals along different dimensions of the MDS representation of dense genotypic data. It uses a powerful model-based clustering algorithm (MCLUST) that can infer the existence of clusters of different size, shape, and orientation in the MDS space, and which automatically optimizes for the Bayes Information Criterion, balancing off detail with parsimony.

The only parameter that I need to specify to MCLUST is the number of MDS dimensions to retain (for a more detailed analysis, see here), as extra dimensions may add "clusteredness" but also noise. In order to decide on how many dimensions to retain, I empirically run MCLUST with a different number of dimensions (from 2 to 50).

Below is the number of clusters inferred by MCLUST as maximizing the Bayes Information Criterion, depending on how many MDS dimensions were retained. The maximum (124 clusters) was attained with 18 dimensions retained. I have allowed as many as 150 clusters to be considered.

The 124 clusters

The 2,230 individuals are assigned to 124 clusters. If we group them, a posteriori, with their populations, this results in a very sparse 139 by 124 matrix, where each i row and j column is the number of individuals from each (of the 139) population belonging to each (of the 124) clusters.

Number of individuals from each population assigned to each cluster (Google spreadsheet)

Alternatively, we can have an array of the same size with the percentage of individuals assigned to each cluster.

Percent of individuals from each population assigned to each of cluster (Google spreadsheet)

I won't even bother to post a screenshot of this table, as it is huge (17,236 elements) and very sparse (96.5% empty), which again confirms the impression that the algorithm is able to discover the population structure effectively.

K=124 is only the beginning

If you've followed previous Cluster Galore analyses, you will note that some populations that belong to the same cluster in this one (e.g., Sephardic and Ashkenazi Jews) were split in a previous one.

In the Dodecad blog, I also showed how Assyrians and Armenians who have never been split before by MCLUST, can, nonetheless be very nicely distinguished from each other if one does not rely on the Bayes Information Criterion (BIC) to guide choice of K, but does an analysis that includes only them with K=2.

It is important not to deify the BIC, and to consider it as a sort of a rough guide that tries to discover as many clusters as can be supported by the data. It's always possible that MCLUST infers some phantom clusters, e.g., between outliers. It's also possible that the BIC-optimal number of clusters misses some that actually exist.

A concrete example: splitting cluster #4

Cluster #4 in this analysis includes 2 of 10 Greeks, all 12 South Italians/Sicilians, 7 of 7 Ashkenazi Jews of the Dodecad Project, 17 of 21 Ashkenazi Jews from Behar et al. (2010), 12 of 16 Morocco Jews, and 18 of 19 Sephardic Jews from the same paper.

Yet, in the previous analyses, I was able to distinguish between almost all of these groups. Now, I will show that this is indeed possible, and it's a good idea to follow up on clusters that encompass multiple populations to uncover structure that may exist in them and the BIC-based optimization may miss.

Now, let's look at Greeks, South Italians/Sicilians, Ashkenazi, Morocco, and Sephardic Jews in a regional analysis. Here are the first two dimensions of the regional MDS:

Notice that dimension 1 splits a couple of Moroccan Jews from the rest; I'd venture that these are probably close relatives in the genetic sense. Let's apply MCLUST to these first 2 dimensions; 4 clusters are inferred, as we might guess by looking at the figure:

As you can see, Greeks, South Italians/Sicilians and Sephardic Jews fall in cluster #1, Morocco Jews in #2, Ashkenazi Jews in #3, and the 2 possibly related Morocco Jews to #4.

But, that is not the end of the story. The power of this approach is that we don't have to rely on our eyes to infer clusters. Let's try, instead of using only 2 dimensions, to vary the number of dimensions and see how the number of clusters inferred varies:

The number of clusters inferred can be as high as 9, with 7 MDS dimensions retained. Even, with 4 MDS dimensions retained, we get 8 clusters. Apparently, our monolithic cluster #4 has a lot of structure in it. So, let's look at what types of clusters are inferred with 7 MDS dimensions retained and 9 clusters:

There you have it: Cluster #1 is Greek/South Italian/Sicilian, and all the Jewish groups belong to largely disjoint sets of clusters, with even some within-group structure uncovered as well.

Rolling back

But, this is not the end of the story. If we don't prefer this level of detail, we can roll back, and examine the individuals with a smaller number of clusters. Here is what we get with the same 7 dimensions, but this time we fix 4 clusters.

There you go: cluster #1 is Greek/South Italian/Sicilian, cluster #2 is Sephardic, cluster #3 is Ashkenazi, and cluster #4 is Moroccan Jewish.

Conclusion

This is the first time, as far as I know that it has been shown that an excess of 100 clusters with strong correspondence to actual populations can be inferred from genotypic data of unlabeled humans.

The drilling of the populations participating in cluster #4 has shown that it is possible to increase this number by as much as an order of magnitude. Or, if you prefer, you can look at individuals at different levels of detail, to see both how populations group together, and also whether they have internal extremely fine-scale structure.

This type of analysis is very easy to do, and I encourage everyone to follow the instructions and try it.

The Mediterranean as barrier to gene flow (Athanasiadis et al. 2010)

A very limited number of markers, but a relatively wide assortment of populations.

BMC Evolutionary Biology 2010, 10:84doi:10.1186/1471-2148-10-84

The Mediterranean Sea as a barrier to gene flow: evidence from variation in and around the F7 and F12 genomic regions

Georgios Athanasiadis et al.

Abstract

Background
The Mediterranean has a long history of interactions among different peoples. In this study, we investigate the genetic relationships among thirteen population samples from the broader Mediterranean region together with three other groups from the Ivory Coast and Bolivia with a particular focus on the genetic structure between North Africa and South Europe. Analyses were carried out on a diverse set of neutral and functional polymorphisms located in and around the coagulation factor VII and XII genomic regions (F7 and F12).

Results
Principal component analysis revealed a significant clustering of the Mediterranean samples into North African and South European groups consistent with the results from the hierarchical AMOVA, which showed a low but significant differentiation between groups from the two shores. For the same range of geographic distances, populations from each side of the Mediterranean were found to differ genetically more than populations within the same side. To further investigate this differentiation, we carried out haplotype analyses, which provided partial evidence that sub-Saharan gene flow was higher towards North Africa than South Europe.

Conclusions
As there is no consensus between the two genomic regions regarding gene flow through the Sahara, it is hard to reach a solid conclusion about its role in the differentiation between the two Mediterranean shores and more data are necessary to reach a definite conclusion. However our data suggest that the Mediterranean Sea was at least partially a barrier to gene flow between the two shores.

Link

Y chromosome haplogroups from Tunisia and Morocco

As expected, the populations are dominated by haplogroups E (especially E-M81) and J1-M267. It used to be thought that J1 in North Africa represented the genetic impact of Arabs, and later of possible Neolithic origin.

While it is true that the expansion of the Arabs would have brought some J1 into North Africa, the discovery of J1 in pre-Arab expansion Canary Islands makes it likely that this lineage has a complex history, and it would be useful to discover additional markers to distinguish between various population movements into the West.

Forensic Science International: Genetics Supplement Series
Volume 1, Issue 1, August 2008, Pages 235-236
doi:10.1016/j.fsigss.2007.10.173

Y-chromosome markers distribution in Northern Africa: High-resolution SNP and STR analysis in Tunisia and Morocco populations

Valerio Onofri et al.

Abstract

At the beginning of 2006 more than 301,000 immigrants resident in Italy resulted to come from Tunisia and Morocco, 66% of which are male subjects; in addition, it is estimated that some other thousand are clandestine. Our data show that there is an increasing involvement of Tunisian and Moroccan individuals in paternity testing and in individual identification cases. For these reasons, the aim of this work was to enrich forensic Y-chromosome databases with Northern Africa data to better know markers frequency and their distribution across these populations (in YHRD there are 246 Tunisian samples and 0 Moroccans, access date to www.yhrd.org: August 2007). 103 Tunisian and Moroccan healthy male donors were typed by 17 microsatellites extended haplotype and 41 Y-SNPs. A high-resolution level database was created, including both haplotype and haplogroup for each sample. This study confirmed that precious informations might come both from Y-SNPs haplogroup distribution besides Y-STRs data.

Link

Ancestry informative marker set for determining continental origin (Nassir et al. 2009)

UPDATE: This PCA plot from the paper is very instructive:




In PC1 vs PC2 (top left), the five major races (Caucasoids, East Asian Mongoloids, Amerindians, Australoids, Negroids) are clearly separable, but their relationships are not very clear. Australoids are somewhere between Caucasoids and East Asians. If we were to go by this figure alone, we might even infer that they are some type of mix of the two. But, look at PC3 vs PC4 (top right). Here it is the case that Australoids are not intermediate between Caucasoids and Mongoloids, but occupy their own space, and we can conclude that they are not in fact such a mix.

Compare with Mexicans (bottom left), who occupy the same space as East Asians in PC1 vs PC2. Does that mean that they are East Asians? An alternative explanation is that they are a mix of Caucasoids and Amerindians, since they occupy an intermediate position between the two groups, which happens to coincide with the position of East Asians. But, if we look at PC3 vs P4 (bottom right), it is clear that Mexicans are indeed better explained as a Caucasoid-Amerindian mix, as they occupy an intermediate position between Caucasoids and Columbians/Quechuans (who are on the left), and not at all that of East Asians (who are on the right).

Next, consider African Americans. In PC1 vs PC2 they occupy an intermediate position between Negroids and Caucasoids (bottom left), as expected by their known ancestry. But, what if we didn't know about their history, and we wanted to infer their origin based on their genomes, as we did with Australoids? Unlike Australoids, in PC3 vs PC4, African Americans do not form a cluster of their own, but overlap with both Caucasoids and Negroids who occupy the same space in these two dimensions. Thus, we are more certain that they are indeed a Caucasoid-Negroid mixed population.

Next, consider Mozabites and South Asians, both of which deviate from Caucasoids, in a Negroid, and Mongoloid direction respectively (top left). North African Mozabites may indeed by Negroid-influenced, as is evident in the STRUCTURE analysis of this paper. South Asian Indians, however, who show "admixture" with the East Asian cluster at K=5 in the STRUCTURE analysis, are revealed to form a cluster of their own at higher K (pink), suggesting that they are not, in fact a Caucasoid-Mongoloid mixed population.

The important lesson from all of this, is to use as much information as possible when trying to examine population relationships from graphical plots, because things may not always be "what they seem", and a number of alternative explanations may result in identical two-dimensional plots.

BMC Genetics 2009, 10:39doi:10.1186/1471-2156-10-39

An ancestry informative marker set for determining continental origin: validation and extension using human genome diversity panels

Rami Nassir et al.

Abstract (provisional)

Background

Case-control genetic studies of complex human diseases can be confounded by population stratification. This issue can be addressed using panels of ancestry informative markers (AIMs) that can provide substantial population substructure information. Previously, we described a panel of 128 SNP AIMs that were designed as a tool for ascertaining the origins of subjects from Europe, Sub-Saharan Africa, Americas, and East Asia.

Results

In this study, genotypes from Human Genome Diversity Panel populations were used to further evaluate a 93 SNP AIM panel, a subset of the 128 AIMS set, for distinguishing continental origins. Using both model-based and relatively model-independent methods, we here confirm the ability of this AIM set to distinguish diverse population groups that were not previously evaluated. This study included multiple population groups from Oceana, South Asia, East Asia, Sub-Saharan Africa, North and South America, and Europe. In addition, the 93 AIM set provides population substructure information that can, for example, distinguish Arab and Ashkenazi from Northern European population groups and Pygmy from other Sub-Saharan African population groups.

Conclusion

These data provide additional support for using the 93 AIM set to efficiently identify continental subject groups for genetic studies, to identify study population outliers, and to control for admixture in association studies.

Link

mtDNA of Tunisians and Moroccans

Forensic Sci Int Genet. 2009 Jun;3(3):166-72

Polymorphisms of mtDNA control region in Tunisian and Moroccan populations: an enrichment of forensic mtDNA databases with Northern Africa data.

Turchi C, Buscemi L, Giacchino E, Onofri V, Fendt L, Parson W, Tagliabracci A.

Current forensic mitochondrial (mt)DNA databases are limited in representative population data of African origin. We investigated HVS-I/HVS-II sequences of 120 Tunisian and Moroccan healthy male donors applying stringent quality criteria to assure high quality of the data and phylogenetic alignment and notation of the sequences. Among 64 Tunisians, 56 different haplotypes were observed and the most common haplotype (16187T 16189C 16223T 16264T 16270T 16278T 16293G 16311C 73G 152C 182T 185T 195C 247A 263G 309.1C 315.1C; haplogroup (hg) L1b) was shared by four individuals. 56 Moroccans could be assigned to 52 different haplotypes where the most common haplotype was of West Eurasian origin with the hg H sequence motif 263G 315.1C and variations in the HVS-II polyC-stretch (309.1C 309.2C) shared by six samples. The majority of the observed haplotypes belong to the west Eurasian phylogeny (50% in Tunisians and 62.5% in Moroccans). Our data are consistent with the current phylogeographic knowledge displaying the occurrence of sub-Saharan haplogroup L sequences, found in 48.4% of Tunisians and 25% of Moroccans as well as the presence of the two re-migrated haplogroups U6 (7.8% and 1.8% in Tunisians and Moroccans, respectively) and M1 (1.6% in Tunisians and 8.9% in Moroccans).

Link

Intermarriage and the risk of divorce in the Netherlands

Prompted by my recent post on Constantinus Porphyrogenitus and inter-ethnic marriage.

From the paper:

We therefore introduce two hypotheses. The first hypothesis is the main-effects hypothesis, which argues that the more traditional the value orientation of a religious or national origin group, the lower the risk of divorce.

...

Our second hypothesis concerns the effect of the spouses’ religion and national origin, and argues that when the religions or national origins of the two spouses are dissimilar, the risk of divorce is higher.We call this the heterogamy hypothesis. Assumingthat the main-effects hypothesis is valid, we need to decide what constitutes evidence for the heterogamy hypothesis. If the divorce risk of a mixed marriage (between, say, a member of group A and a member of group B) is higher than the divorce risk of AA marriages but lower than the divorce risk of BB marriages, we argue that adaptation is taking place. The behaviour of those couples is in between the two groups, and one can argue that this is simply the average of the two group effects and not a heterogamy effect (Jones 1996). To analyse real heterogamy effects, we employ both a strong and a weak form of the heterogamy hypothesis. According to the strong heterogamy hypothesis, AB marriages will have a divorce risk that is higher than the maximum divorce risk of AA and BB marriages. For example, we expect that a marriage between a Catholic and an unaffiliated person will have a divorce risk that is higher than the (already) high risk for unaffiliated couples. According to the weak heterogamy hypothesis, AB marriages will have a divorce risk that is higher than the average risk of AA and BB marriages. In our example, the risk of the mixed group will be higher than the average of the low risk for Catholics and the high risk for unaffiliated couples.

The data is supportive of the strong heterogamy hypothesis, according to which an AB has a higher chance of a divorce than the highest of AA and BB:

Are there effects of heterogamy on the risk of divorce? Table 8 shows that the answer is clear: most mixed combinations have a risk of divorce that is higher than the highest level of divorce in the two homogamous groups. The average ratio is 2.02, indicating that mixed marriages have a risk of divorce twice as high as that of the maximum level of divorce in the two corresponding groups. This effect is quite strong and clearly supports the strong heterogamy hypothesis.

...

We also find variations in the magnitude of the effects that are consistent with our hypothesis about value orientations. Combinations of Dutch and Turkish or Moroccan persons reveal a stronger heterogamy effect than combinations involving Dutch and Western European persons. The effects for combinations involving Southern Europeans are in between the combinations with Turks or Moroccans and the combinations with Western Europeans. When looking at combinations involving
minority men, the differences are quite strong. The ratio is 4.7 for combinations involving Turkish men, 2.4 for combinations involving Moroccan men, and 1.5 for combinations involving Western European men. Because European groups are more similar than Moroccan and Turkish groups to the Dutch in values and lifestyle, this finding is consistent with theoretical interpretations of the heterogamy effect
in terms of value similarity.

The paper has detailed tables on the various combinations of intermarriage between different Dutch religious denominations and national origins. What seems clear is that Constantinus' ideas about religious and ethnic homogamy as more conducive to harmonious cohabitation seem to be supported by the data.

Population Studies, Vol. 59, No. 1, 2005, pp. 71-85

Intermarriage and the risk of divorce in the Netherlands: The effects of differences in religion and in nationality, 1974-94

Matthijs Kalmijn et al.

A textbook hypothesis about divorce is that heterogamous marriages are more likely to end in divorce than homogamous marriages. We analyse vital statistics on the population of the Netherlands, which provide a unique and powerful opportunity to test this hypothesis. All marriages formed between 1974 and 1984 (nearly 1 million marriages) are traced in the divorce records and multivariate logistic regression models are used to analyse the effects on divorce of heterogamy in religion and national origin. Our analyses confirm the hypothesis for marriages that cross the Protestant-Catholic or the Jewish-Gentile boundary. Heterogamy effects are weaker for marriages involving Protestants or unaffiliated persons. Marriages between Dutch and other nationalities have a higher risk of divorce, the more so the greater the cultural differences between the two groups. Overall, the evidence supports the view that, in the Netherlands, new group boundaries are more difficult to cross than old group boundaries.

Link

Major study of Iberian Y-chromosomes (Adams et al.)

with 2 Updates (latest: 9 Dec 08)

This article will be an invaluable resource for students of Iberian Y-chromosome diversity, due to the numerous 18-marker haplotypes from all regions contained in the supplement.

The authors modeled the Iberian population as a 3-way mix with "Basque", "Sephardic", and "North African". The main thesis is that the fairly substantial "Sephardic" and "North African" components identified are evidence of substantial religious conversion of Jews and Muslims.

The North African component may be roughly correct; it is similar to the 6% reported for Sicily, which was also occupied by Muslims. The Sephardic component is however suspect, as it may be of either Arabic or Italian origin, or indeed even earlier population movements from the Eastern Mediterranean.

Another point of contention is with the use of Basques as pre-Sephardic/Muslim Iberians. The Christian population of Iberia prior to the arrival of the Jews and Muslims, included non-Basque Celtiberians, Romance speakers, as well as a Visigoth/Germanic layer.

Nor is it clear that the North African component in Iberians stems from Muslim converts, since bidirectional movement of populations across Gibraltar may predate the occupation of Iberia.

UPDATE I

To see the reliability of this type of study, consider that what this study terms "Sephardic", is what another recent study termed "Phoenician". In the previous study Ibiza was considered Phoenician-influenced and compared with Mallorca and Minorca. In this one, Ibiza is assigned a hefty 33% "Sephardic Jewish" influence, while Minorca only -7.5%. At least, one would think they'd pick an admixture method that didn't result in negative contributions...

Choose your parental populations carefully, mix, shake, and get whatever result you please: Neolithic, Phoenician, Jewish, there's something for every taste.

UPDATE II (Dec 9)

Figure of frequencies added at the top of the post.

From the paper:

To formally assess the impact of North African and Sephardic Jewish contributions on the indigenous population, we carried out admixture analysis, employing the mY estimator and treating the study populations as hybrids of three parental populations. We chose the Basques as the Iberian parental sample. This is justified on the basis of a relative absence of Muslim occupation of the Basque region and supported by the genetic distinctiveness of the Basque and neighboring Gascon samples (Figure 3).

In plain English, the authors could just as well have written: "Basques are distinct from other Iberians. This may be due to either (i) the fact that there were indeed differences between Basques and other Iberians even before the Muslim occupation/Jewish settlement: after all they occupy their own region, not Iberia-at-large, and speak a different language. Or, (ii) it could be that the rest of the Iberians have undergone substantial admixture with Muslims and Jews. We arbitrarily choose hypothesis (ii) as our premise, and ¡qué sorpresa! our data backs up our pre-supposed idea."

More from the paper:

An additional factor that could lead to overestimation of Sephardic Jewish ancestry proportions is the effect of other influences on the Iberian Peninsula from eastern Mediterranean populations that might have imported lineages such as G, K*, and J. These influences fall into two different time periods: the Neolithic era, beginning in 10 KYA, the demographic effects of which are a matter for heated debate;1 and the last three millennia, the time period of Greek and Phoenician colonization.65 Effects in the second case are expected to be most marked in the eastern part of our sample area, but despite this, the apparent Sephardic Jewish ancestry proportions remain substantial in the west (Figure 4). The confounding effects of earlier population movement are likely to be particularly strong for Ibiza, Majorca, and Minorca, whose island natures make them more susceptible to influence by immigration and subsequent drift than inland sites. For example, history records that Ibiza, found to have a high apparent Sephardic Jewish ancestry proportion in our study, had an insignificant Jewish population compared to its neighbors66 yet had previously been an important Phoenician colony. Likewise, Minorca is recorded as having a substantial Jewish population,66 yet here, it shows no Sephardic Jewish ancestry.

It is true that Greek or Phoenician influence would be concentrated in particular regions. Whether Y-chromosomes "stay put" for a period of 2.5 thousand years is a different question. But, Neolithic Y-chromosomes certainly would have had ample time to be fairly uniformly distributed across the peninsula. And, the most important single aspect of Iberian history, i.e., the Roman conquest, which would have introduced not only the dominant language, but also a fair amount of genes is totally ignored.

In fact this is the single reference to the Roman period in this paper:

The Jewish presence was very long-established, with some evidence that it predated the Christian era; many Jews, however, are thought to have arrived during the Roman period

But, seriously, in the Roman period, not only Jews, but most importantly Romans settled in Iberia. And, by the way, they must have been numerous enough to change the language. But, let's ignore these pesky Romans and pretend that Iberians are a simple mix of Basques/Moroccan/Jews.

Bottom line: great data, subpar interpretation.

American Journal of Human Genetics doi:

The Genetic Legacy of Religious Diversity and Intolerance: Paternal Lineages of Christians, Jews, and Muslims in the Iberian Peninsula

Susan M. Adams et al.

Abstract

Most studies of European genetic diversity have focused on large-scale variation and interpretations based on events in prehistory, but migrations and invasions in historical times could also have had profound effects on the genetic landscape. The Iberian Peninsula provides a suitable region for examination of the demographic impact of such recent events, because its complex recent history has involved the long-term residence of two very different populations with distinct geographical origins and their own particular cultural and religious characteristics--North African Muslims and Sephardic Jews. To address this issue, we analyzed Y chromosome haplotypes, which provide the necessary phylogeographic resolution, in 1140 males from the Iberian Peninsula and Balearic Islands. Admixture analysis based on binary and Y-STR haplotypes indicates a high mean proportion of ancestry from North African (10.6%) and Sephardic Jewish (19.8%) sources. Despite alternative possible sources for lineages ascribed a Sephardic Jewish origin, these proportions attest to a high level of religious conversion (whether voluntary or enforced), driven by historical episodes of social and religious intolerance, that ultimately led to the integration of descendants. In agreement with the historical record, analysis of haplotype sharing and diversity within specific haplogroups suggests that the Sephardic Jewish component is the more ancient. The geographical distribution of North African ancestry in the peninsula does not reflect the initial colonization and subsequent withdrawal and is likely to result from later enforced population movement--more marked in some regions than in others--plus the effects of genetic drift.

Link

mtDNA of Berbers from Morocco and Egypt

Annals of Human Genetics doi: 10.1111/j.1469-1809.2008.00493.x

The Complex and Diversified Mitochondrial Gene Pool of Berber Populations

C. Coudray et al.

Abstract

The mitochondrial DNA variation of 295 Berber-speakers from Morocco (Asni, Bouhria and Figuig) and the Egyptian oasis of Siwa was evaluated by sequencing a portion of the control region (including HVS-I and part of HVS-II) and surveying haplogroup-specific coding region markers. Our findings show that the Berber mitochondrial pool is characterized by an overall high frequency of Western Eurasian haplogroups, a somehow lower frequency of sub-Saharan L lineages, and a significant (but differential) presence of North African haplogroups U6 and M1, thus occupying an intermediate position between European and sub-Saharan populations in PCA analysis. A clear and significant genetic differentiation between the Berbers from Maghreb and Egyptian Berbers was also observed. The first are related to European populations as shown by haplogroup H1 and V frequencies, whereas the latter share more affinities with East African and Nile Valley populations as indicated by the high frequency of M1 and the presence of L0a1, L3i, L4*, and L4b2 lineages. Moreover, haplogroup U6 was not observed in Siwa. We conclude that the origins and maternal diversity of Berber populations are old and complex, and these communities bear genetic characteristics resulting from various events of gene flow with surrounding and migrating populations.

Link

Forensic Science International: Genetics Supplement Series

Forensic Science International: Genetics Supplement Series has a whole bunch of very interesting population genetics papers in press. Some very exciting ones are:

• Mitochondrial DNA genetic relationships at the ancient Neolithic site of Tell Halula
• Tracing back ancient south Siberian population history using mitochondrial and Y-chromosome SNPs
• Y chromosome J2 subtyping in an Italian sample: Population and forensic implications
• Exploring mitochondrial DNA variation in the Italian Peninsula
• Recently introduced Y-SNPs improve the resolution within Y-chromosome haplogroup R1b in a central European population sample (Tyrol, Austria)
• Population genetics and DNA preservation in ancient human remains from Eastern Spain
• Haplogroup distribution of Hungarian population and the largest minority group
• mtDNA diversity in Sudan (East Africa)
• Y-chromosome markers distribution in Northern Africa: High-resolution SNP and STR analysis in Tunisia and Morocco populations
• Haplogroup H sub-lineages with mitochondrial SNPs
• Microgeographic variation of Y-chromosome haplotypes in Italy
• NRY haplogroups distribution in sub-Saharan Africa and Bantu expansion
• Results of Y-SNP typing in three different populations
• Microgeographic genetic variation of Y chromosome in a population sample of Ravenna's area in the Emilia-Romagna region (North of Italy)

Archaic Homo sapiens from Lake Eyasi, Tanzania

Wikipedia entry on Lake Eyasi. From the paper:

The best estimate of the burial age of EYJR 2 is an age range that encompasses the uncertainty in the model EU-ESR ages of EYJR 2: 88–132 ka. We use this estimate to infer the age of the associated finds, including EH06.

...

If the latter possibility is correct, EH06 shows an interesting continuation of the primitive features shown in Eyasi 1, in a period for which other areas have yielded, from a morphological standpoint, substantially more modern-looking specimens.


These modern-looking features are defined in broadly contemporary hominids by the expansion of the frontal area of the skull, with a more elevated and rounder slope of the frontal bone, together with a reduction of the supraorbital torus, supratoral area, and postorbital constriction. These are some of the features that morphologically differentiate Homo sapiens from earlier hominids. These features can be observed on the Omo and Herto crania (Ethiopia) and the Ngaloba (Tanzania), Jebel Irhoud (Morocco) and Florisbad (South Africa) crania, dated between 265,000 and 120,000 years ago ([Wolpoff, 1999], [White et al., 2003] and [McDougall et al., 2005]).

This ties in well with the idea of persistence of archaic features within African populations long after the appearance of more modern features, with the fully modern Omo coming before Homo sapiens idaltu from Herto, with its mix of archaic and modern traits, coming before more archaic EH06 from Lake Eyasi.

Journal of Human Evolution doi:10.1016/j.jhevol.2008.02.002

A new archaic Homo sapiens fossil from Lake Eyasi, Tanzania

M. Domínguez-Rodrigo et al.

(no abstract)

Link

Shared Y-chromosome heritage of Hindus and Muslims in India

A new study has looked at the Y-chromosome variation of a sample of Hindus and Muslims from Andhra Pradesh, finding them to be similar to each other. This indicates that at least in this case, the transmission of the Muslim religion was largely non-genetic.

Human Genetics (online early)

A shared Y-chromosomal heritage between Muslims and Hindus in India

Ramana Gutala et al.

Abstract Arab forces conquered the Indus Delta region in 711 AD and, although a Muslim state was established there, their influence was barely felt in the rest of South Asia at that time. By the end of the tenth century, Central Asian Muslims moved into India from the northwest and expanded throughout the subcontinent. Muslim communities are now the largest minority religion in India, comprising more than 138 million people in a predominantly Hindu population of over one billion. It is unclear whether the Muslim expansion in India was a purely cultural phenomenon or had a genetic impact on the local population. To address this question from a male perspective, we typed eight microsatellite loci and 16 binary markers from the Y chromosome in 246 Muslims from Andhra Pradesh, and compared them to published data on 4,204 males from East Asia, Central Asia, other parts of India, Sri Lanka, Pakistan, Iran, the Middle East, Turkey, Egypt and Morocco. We find that the Muslim populations in general are genetically closer to their non-Muslim geographical neighbors than to other Muslims in India, and that there is a highly significant correlation between genetics and geography (but not religion). Our findings indicate that, despite the documented practice of marriage between Muslim men and Hindu women, Islamization in India did not involve large-scale replacement of Hindu Y chromosomes. The Muslim expansion in India was predominantly a cultural change and was not accompanied by significant gene flow, as seen in other places, such as China and Central Asia.

Link

Polymorphism of the G1733A polymorphism in Mediterranean region

American Journal of Human Biology
Volume 17, Issue 6 , Pages 690 - 695

An unexpected wide population variation of the G1733A polymorphism of the androgen receptor gene: Data on the Mediterranean region

E. Esteban

Abstract

The androgen receptor (AR) has been proposed as a candidate gene for several cancers (breast, prostate, uterine endometrium, colon, and esophagus). Ethnicity is considered an associated risk factor for some of these cancers. Several case-control genetic studies have been focused in samples of the main ethnic groups, but little is known about the distribution of risk polymorphisms in current populations with accurate ethnic and/or geographic origins. The A allele of the G1733A polymorphism of the AR gene has been associated with increased risk of prostate cancer. We provide data from this marker in 12 samples from 7 Mediterranean countries such as Spain, Italy (Sardinia), Greece, Turkey, Morocco, Algeria, and Egypt. A sample from Ivory Coast has also been analyzed. The A allele distribution shows a frequency in the Ivory Coast population (65.17%) that contrasts with the low values found in Northern Mediterraneans (mean average value of 13.98%). North African populations present two-times higher frequencies (average value of 27.19%) than Europeans. The wide population variation range found for the A allele strengthens the potential interest of further screening as a baseline to the design of future preventive and population health programs.

Link

Prehistoric North Africans were Caucasoid

ANTHROPOLOGIE
Volume 43/1, 2005, pp. 1-11

Diversité mitochondriale de la population de taforalt(12.000 ans bp - maroc): une approche génétique a l'étude du peuplement de l'afrique du nord

KÉFI R., STEVANOVITCH A., BOUZAID E., BÉRAUD-COLOMB E.

ABSTRACT

The population exhumed from the archaeological site of Taforalt in Morocco (12,000 years BP) is a valuable source of information toward a better knowledge of the settlement of Northern Africa region and provides a revolutionary way to specify the origin of Ibero-Maurusian populations. Ancient DNA was extracted from 31 bone remains from Taforalt.The HVS1 fragment of the mitochondrial DNA control region was PCR-amplified and directly sequenced. Mitochondrial diversity in Taforalt shows the absence of sub-Saharan haplogroups suggesting that Ibero-Maurusian individuals had not originated in sub-Saharan region. Our results reveal a probable local evolution of Taforalt population and a genetic continuity in North Africa.

Link