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. 

Disentangling the histories of mtDNA haplogroups M1 and U6

mtDNA haplogroups M1 and U6 are often mentioned in terms of Eurasian back-migration in Africa. The former is the only clade of the Asian haplogroup M which occurs in Africa at all; the latter is the only clade of the West Eurasian haplogroup U that does the same. These haplogroups also tend to co-exist in North and East Africa, although they are largely absent in sub-Saharan Africa. Different ideas have been offered for their occurrence, including a "Paleolithic" spread or a more recent one associated with the spread of Afroasiatic languages.

The new paper offers useful new data on this debate. The most important conclusion is that despite their oft-mentioned association, these two haplogroups appear to have distinct histories. One argument for this is their separate geographic distribution:

M1 (on panel A) is much more common in Northeast Africa and the Near East (including the Caucasus), whereas U6 (panel B) is more confined in Africa, and has its stronger peak in NW Africa, being rare in NE Africa.

An interesting aside, is that all the mysterious M1 from the Caucasus belongs to subclade M1a, while the smaller M1b clade tends to co-occur with M1a in other parts of Africa and the Near East. This indicates a founder effect for the origin of Caucasian M1a, but leaves open the issue of the immediate origins of M1. Hopefully it will become possible to place this haplogroup within the broader M phylogeny in the future.

The Bayesian skyline plots also contrast M1 and U6 in terms of their demographic histories:

The authors argue that these histories are inconsistent with either a very early dispersal history with the Dabban industry, as well as a more recent spread with Afroasiatic. From the paper:

The transition from the Middle Palaeolithic to Upper Palaeolithic in North Africa is characterised by the appearance of the “Dabban”, an industry that is restricted to Cyrenaica in northeast Libya and represented at the caves of Hagfet ed Dabba and Haua Fteah [19]. Whilst a techno-typological shift occurred within the Dabban ~33 KYA [19], starker changes in the archaeological record occurred throughout North Africa and Southwest Asia ~23-20 KYA, represented by the widespread appearance of backed bladelet technologies. The appearance of these backed bladelet industries more or less coincides with the timing of the Last Glacial Maximum (LGM) (~23-18 KYA), including: ~21 KYA in Upper Egypt [20]; ~20 KYA at Haua Fteah with the Oranian [21]; the Iberomaurusian expansion in the Jebel Gharbi ~20 KYA [22]; and the first Iberomaurusian at Tamar Hat in Algeria ~20 KYA [23]. The earliest Iberomaurusian sites in Morocco appear to be only slightly younger ~18 KYA [24].

A disassociation of these haplogroups from the UP in North Africa might be consistent with my idea that the UP was in part a cultural revolution that spread not only with people, but often with ideas across a species that already had the "biological machinery" for behavioral modernity and was already established in both Africa and the Near East.

As for the connection to Afroasiatic, the authors detect a linguistic correlation with M1a, which, however, appears too old to have been involved directly in the spread of this language family:

Concerning haplogroup M1 individually, a significant correlation with languages was observed. Furthermore, within M1, it appears that the correlation is mostly due to M1a. However, given the small sample size of M1b, any potential signal correlating with language might not be detectable. Interestingly, M1a has a likely East African origin, but its coalescent age of ~21 KYA still largely predates that of the proto-AA. Maybe a sub-clade of M1a would still give a similar correlation, but there are not sufficient samples to allow splitting M1a into its various sub-clades, and to test for a correlation. Although we found a correlation, limited sample sizes do not allow drawing unambiguous connection between genes and languages. Furthermore, it is also possible that this putative sub-clade of M1 does not testify for the expansion of AA speaking people, but was already present among the people who inhabited the area before the spread of the AA languages.

Personally, I am in favor of an East African origin of Afroasiatic, as this makes sense of various lines of evidence, one of which is the African shift of the "Southwest_Asian" component that is modal in Semitic populations. I envision that M1 was geographically circumscribed in a NE African population after its much earlier arrival from Asia and piggy-backed onto the expansion of Afroasiatic speakers, thus explaining the observed correlation. A good analogy would be with the expansion of, say, haplogroup H in the Americas which piggybacked on the European colonization, even though the coalescence age of H predates the arrival of Europeans in the New World by many millennia.

BMC Evolutionary Biology 2012, 12:234 doi:10.1186/1471-2148-12-234


Divorcing the Late Upper Palaeolithic demographic histories of mtDNA haplogroups M1 and U6 in Africa

Erwan Pennarun et al.

Abstract (provisional)
Background
A Southwest Asian origin and dispersal to North Africa in the Early Upper Palaeolithic era has been inferred in previous studies for mtDNA haplogroups M1 and U6. Both haplogroups have been proposed to show similar geographic patterns and shared demographic histories.

Results
We report here 24 M1 and 33 U6 new complete mtDNA sequences that allow us to refine the existing phylogeny of these haplogroups. The resulting phylogenetic information was used to genotype a further 131 M1 and 91 U6 samples to determine the geographic spread of their sub-clades. No southwest Asian specific clades for M1 or U6 were discovered. U6 and M1 frequencies in North Africa, the Middle East and Europe do not follow similar patterns, and their sub-clade divisions do not appear to be compatible with their shared history reaching back to the Early Upper Palaeolithic. The Bayesian Skyline Plots testify to non-overlapping phases of expansion, and the haplogroups' phylogenies suggest that there are U6 sub-clades that expanded earlier than those in M1. Some M1 and U6 sub-clades could be linked with certain events. For example, U6a1 and M1b, with their coalescent ages of ~20,000-22,000 years ago and earliest inferred expansion in northwest Africa, could coincide with the flourishing of the Iberomaurusian industry, whilst U6b and M1b1 appeared at the time of the Capsian culture.

Conclusions
Our high-resolution phylogenetic dissection of both haplogroups and coalescent time assessments suggest that the extant main branching pattern of both haplogroups arose and diversified in the mid-later Upper Palaeolithic, with some sub-clades concomitantly with the expansion of the Iberomaurusian industry. Carriers of these maternal lineages have been later absorbed into and diversified further during the spread of Afro-Asiatic languages in North and East Africa.

Link