Using mitochondrial DNA to test the hypothesis of a European post-glacial human recolonization from the Franco-Cantabrian refuge

Demographic, clinical, and ancestry characterization of a large cluster of mucopolysaccharidosis IV A in the Brazilian Northeast region

Mucopolysaccharidosis (MPS) IVA is a rare autosomal recessive disease with a highly variable distribution worldwide. Discrepancies in the incidence of MPS IVA among populations of different ethnicities are mostly attributed to founder effects. Demographic and clinical data from 28 MPS IVA patients, followed at a single center, and ancestry (Y chromosome and mitochondrial markers) of a subsample of 17 patients, most with the p.Ser341Arg (c.1023C>G) mutation were analyzed. Parental consanguinity was observed in 15/20 couples; a rare homozygous N-acetylgalactosamine-6-sulfatase (GALNS) mutation was found in 7/16 families with intra-familial phenotypic heterogeneity. Paternal ancestry was 94.2% (16/17) European, 5.8% (1/17) African, and 0% Amerindian. The European paternal haplogroups R1a, R1b, and R* accounted for 94.2% (16/17) of the patients. The R1b haplogroup, identified in 59% (10/17) of the patients, is frequently found in populations from the Iberian Peninsula. European, Amerindian, and African maternal ancestry was observed in 46.9% (8/17), 35.4% (6/17), and 17.7% (3/17) of the patients, respectively. Study of a cluster of MPS IVA patients from Northeastern Brazil, with high parental consanguinity and phenotypic heterogeneity showed predominantly European parental ancestry. This ancestry finding corroborates historical data on the local settlement, formed predominantly by European men.

Complete mitogenome data for the Serbian population: the contribution to high-quality forensic databases

Mitochondrial genome (mtDNA) is a valuable resource in resolving various human forensic casework. The usage of variability of complete mtDNA genomes increases their discriminatory power to the maximum and enables ultimate resolution of distinct maternal lineages. However, their wider employment in forensic casework is nowadays limited by the lack of appropriate reference database. In order to fill in the gap in the reference data, which, considering Slavic-speaking populations, currently comprises only mitogenomes of East and West Slavs, we present mitogenome data for 226 Serbians, representatives of South Slavs from the Balkan Peninsula. We found 143 (sub)haplogroups among which West Eurasian ones were dominant. The percentage of unique haplotypes was 85%, and the random match probability was as low as 0.53%. We support previous findings on both high levels of genetic diversity in the Serbian population and patterns of genetic differentiation among this and ten studied European populations. However, our high-resolution data supported more pronounced genetic differentiation among Serbians and two Slavic populations (Russians and Poles) as well as expansion of the Serbian population after the Last Glacial Maximum and during the Migration period (fourth to ninth century A.D.), as inferred from the Bayesian skyline analysis. Phylogenetic analysis of haplotypes found in Serbians contributed towards the improvement of the worldwide mtDNA phylogeny, which is essential for the interpretation of the mtDNA casework.

Forensically relevant phylogeographic evaluation of mitogenome variation in the Basque Country

The Basque Country has been the focus of population (genetic) and evolutionary studies for decades, as it represents an interesting evolutionary feature: it is the only European country where a non-Indo-European language is still spoken today and, for which there are no known living or extinct relatives. Early studies that were based on anatomical and serological methods, along with subsequent molecular genetic investigations, contain controversial interpretations of their data. Additionally, the analysis of mitochondrial DNA, which is maternally inherited and thus suitable for the examination of the maternal phylogeny of the population, was the focus of some studies. Early mtDNA studies were however restricted to the information provided by the control region or its hypervariable segments only. These are known to harbour little phylogenetic information, particularly for haplogroup H that is dominant in Westeurasian populations including the Basques. Later studies analysed complete mitogenome sequences. Their information content is however limited, either because the number of samples was low, or because these studies only considered particular haplogroups. In this study we present the full mitogenome sequences of 178 autochthonous Basque individuals that were carefully selected based on their familial descent and discuss the observed phylogenetic signals in the light of earlier published findings. We confirm the presence of Basque-specific mtDNA lineages and extend the knowledge of these lineages by providing data on their distribution in comparison to other Basque and non-Basque populations. This dataset improves our understanding of the Basque mtDNA phylogeny and serves as a high-quality dataset that is provided via EMPOP for forensic genetic purposes.

Environmental factors modulated ancient mitochondrial DNA variability and the prevalence of rheumatic diseases in the Basque Country

Among the factors that would explain the distribution of mitochondrial lineages in Europe, climate and diseases may have played an important role. A possible explanation lies in the nature of the mitochondrion, in which the energy generation process produces reactive oxygen species that may influence the development of different diseases. The present study is focused on the medieval necropolis of San Miguel de Ereñozar (13^th-16^th centuries, Basque Country), whose inhabitants presented a high prevalence of rheumatic diseases and lived during the Little Ice Age (LIA). Our results indicate a close relationship between rheumatic diseases and mitochondrial haplogroup H, and specifically between spondyloarthropathies and sub-haplogroup H2. One possible explanation may be the climate change that took place in the LIA that favoured those haplogroups that were more energy-efficient, such as haplogroup H, to endure lower temperatures and food shortage. However, it had a biological trade-off: the increased risk of developing rheumatic diseases.

The distribution of mitochondrial DNA haplogroup H in southern Iberia indicates ancient human genetic exchanges along the western edge of the Mediterranean

BACKGROUND

The structure of haplogroup H reveals significant differences between the western and eastern edges of the Mediterranean, as well as between the northern and southern regions. Human populations along the westernmost Mediterranean coasts, which were settled by individuals from two continents separated by a relatively narrow body of water, show the highest frequencies of mitochondrial haplogroup H. These characteristics permit the analysis of ancient migrations between both shores, which may have occurred via primitive sea crafts and early seafaring. We collected a sample of 750 autochthonous people from the southern Iberian Peninsula (Andalusians from Huelva and Granada provinces). We performed a high-resolution analysis of haplogroup H by control region sequencing and coding SNP screening of the 337 individuals harboring this maternal marker. Our results were compared with those of a wide panel of populations, including individuals from Iberia, the Maghreb, and other regions around the Mediterranean, collected from the literature.

RESULTS

Both Andalusian subpopulations showed a typical western European profile for the internal composition of clade H, but eastern Andalusians from Granada also revealed interesting traces from the eastern Mediterranean. The basal nodes of the most frequent H sub-haplogroups, H1 and H3, harbored many individuals of Iberian and Maghrebian origins. Derived haplotypes were found in both regions; haplotypes were shared far more frequently between Andalusia and Morocco than between Andalusia and the rest of the Maghreb. These and previous results indicate intense, ancient and sustained contact among populations on both sides of the Mediterranean.

CONCLUSIONS

Our genetic data on mtDNA diversity, combined with corresponding archaeological similarities, provide support for arguments favoring prehistoric bonds with a genetic legacy traceable in extant populations. Furthermore, the results presented here indicate that the Strait of Gibraltar and the adjacent Alboran Sea, which have often been assumed to be an insurmountable geographic barrier in prehistory, served as a frequently traveled route between continents.

Dissecting mitochondrial dna variability of balearic populations from the bronze age to the current era

OBJECTIVES

To determine ancient population influences on ancient and current Balearic populations and to reconstruct their mitochondrial DNA (mtDNA) gene pool evolution.

METHODS

We analyzed 239 individuals belonging to five archaeological populations from Majorca and Minorca, four dating to the transition between the Bronze Age and the Iron Age, and one Late Roman Majorcan population. Six additional individuals from Santa Teresa di Gallura from the Nuragic period were characterized and added to the existing samples from that culture to make comparisons with Talaiotic populations.

RESULTS

We characterized the haplogroups of 138 individuals and obtained 69 sequences from mtDNA hypervariable region I. In the intra-island study, the apparent differences in social and funerary rites between two contiguous Majorcan necropolises were correlated with genetic characteristics. Also, the likely occurrence of consanguinity in a population with a very particular burial pattern was supported by genetic data. Despite the uniqueness of each necropolis, the global comparison of the five necropolises revealed no significant differences between them, or between ancient and modern populations from the islands. Ancient Balearics showed a similar mtDNA gene pool to Ancient Catalans, had a Near Eastern component, and showed continuity with European populations since at least the Bronze Age.

CONCLUSION

We characterized five Balearic necropolises in the context of their geographic and cultural characteristics. The similarity between ancient Balearic and ancient Catalan gene pools reinforces their known historic interactions, while the lack of a consistent genetic continuity with Ancient Sardinians suggests that Talaiotic and Nuragic cultures arose in differentiated populations. Am. J. Hum. Biol. 29:e22883, 2017. © 2016 Wiley Periodicals, Inc.

Linking between genetic structure and geographical distance: Study of the maternal gene pool in the Ethiopian population

Background The correlation between genetics and geographical distance has already been examined through the study of the dispersion of human populations, especially in terms of uniparental genetic markers. Aim The present work characterises, at the level of the mitochondrial DNA (mtDNA), two new samples of Amhara and Oromo populations from Ethiopia to evaluate the possible pattern of distribution for mtDNA variation and to test the hypothesis of the Isolation-by-Distance (IBD) model among African, European and Middle-Eastern populations. Subjects and methods This study analysed 173 individuals belonging to two ethnic groups of Ethiopia, Amhara and Oromo, by assaying HVS-I and HVS-II of mtDNA D-loop and informative coding region SNPs of mtDNA. Results The analysis suggests a relationship between genetic and geographic distances, affirming that the mtDNA pool of Africa, Europe and the Middle East might be coherent with the IBD model. Moreover, the mtDNA gene pools of the Sub-Saharan African and Mediterranean populations were very different. Conclusion In this study the pattern of mtDNA distribution, beginning with the Ethiopian plateau, was tested in the IBD model. It could be affirmed that, on a continent scale, the mtDNA pool of Africa, Europe and the Middle East might fall under the IBD model.

The maternal perspective for five Slovenian regions: The importance of regional sampling

BACKGROUND

The Slovenian territory is geographically positioned between the Alps, Adriatic Sea, Pannonian basin and the Dinaric Mountains and, as such, has served as a passageway for various populations in different periods of time. Turbulent historic events and diverse geography of the region have produced a diverse contemporary population whose genetic analysis could provide insight into past demographic events.

AIM

The aims of this study were to characterize the Slovenian mitochondrial gene pool at the micro-geographic level and to compare it with surrounding populations.

SUBJECTS AND METHODS

A total of 402 individuals from five Slovenian regions were analysed in this study by typing HVR I, HVR II and coding region polymorphisms of mtDNA.

RESULTS

Analysis revealed 47 haplogroups and sub-haplogroups, the most common of which were H*, H1, J1c, T2 and U5a. Intra-population comparisons revealed a sharp gradient of the J1c haplogroup between Slovenian regions, with a peak frequency of 24.5% being observed in the population of the Littoral Region.

CONCLUSION

The sharp gradient of the J1c haplogroup between Slovenian regions is in line with the archaeological horizon known as Impressed Ware culture and could, therefore, represent a genetic trace of the early Neolithic expansion route along the East Adriatic coastal region.

Over the sands and far away: interpreting an Iberian mitochondrial lineage with ancient Western African origins

OBJECTIVES

There is an ongoing effort to characterize the genetic links between Africa and Europe, mostly using lineages and haplotypes that are specific to one continent but had an ancient origin in the other. Mitochondrial DNA has been proven to be a very useful tool for this purpose since a high number of putatively European-specific variants of the African L* lineages have been defined over the years. Due to their geographic locations, Spain and Portugal seem to be ideal places for searching for these lineages.

METHODS

Five members of a minor branch of haplogroup L3f were found in recent DNA samplings in the region of Asturias (Northern Spain), which is known for its historical isolation. The frequency of L3f in this population (≈1%) is unexpectedly high in comparison with other related lineages in Europe. Complete mitochondrial DNA sequencing of these L3f lineages, as well phylogenetic and phylogeographic comparative analyses have been performed.

RESULTS

The L3f variant found in Asturias seems to constitute an Iberian-specific haplogroup, distantly related to lineages in Northern Africa and with a deep ancestry in Western Africa. Coalescent algorithms estimate the minimum arrival time as 8,000 years ago, and a possible route through the Gibraltar Strait.

CONCLUSIONS

Results are concordant with a previously proposed Neolithic connection between Southern Europe and Western Africa, which might be key to the proper understanding of the ancient links between these two continents.

Echoes from Sepharad: signatures on the maternal gene pool of crypto-Jewish descendants

The majority of genetic studies on Jewish populations have been focused on Ashkenazim, and genetic data from the Sephardic original source, the Iberian Peninsula, are particularly scarce. Regarding the mitochondrial genome, the available information is limited to a single Portuguese village, Belmonte, where just two different lineages (a single one corresponding to 93.3%) were found in 30 individuals. Aiming at disclosing the ancestral maternal background of the Portuguese Jewry, we enlarged the sampling to other crypto-Jewish descendants in the Bragança district (NE Portugal). Fifty-seven complete mtDNA genomes were newly sequenced and - in contrast with Belmonte - a high level of diversity was found, with five haplogroups (HV0b, N1, T2b11, T2e and U2e) being putatively identified as Sephardic founding lineages. Therefore - in sharp contrast with Belmonte - these communities have managed to escape the expected inbreeding effects caused by centuries of religious repression and have kept a significant proportion of the Sephardic founder gene pool. This deeper analysis of the surviving Sephardic maternal lineages allowed a much more comprehensive and detailed perspective on the origins and survival of the Sephardic genetic heritage. In line with previously published results on Sephardic paternal lineages, our findings also show a surprising resistance to the erosion of genetic diversity in the maternal lineages.

The Carpathian range represents a weak genetic barrier in South-East Europe

Background

In the present study we have assessed whether the Carpathian Mountains represent a genetic barrier in East Europe. Therefore, we have analyzed the mtDNA of 128 native individuals of Romania: 62 of them from the North of Romania, and 66 from South Romania.

Results

We have analyzed their mtDNA variability in the context of other European and Near Eastern populations through multivariate analyses. The results show that regarding the mtDNA haplogroup and haplotype distributions the Romanian groups living outside the Carpathian range (South Romania) displayed some degree of genetic differentiation compared to those living within the Carpahian range (North Romania).

Conclusion

The main differentiation between the mtDNA variability of the groups from North and South Romania can be attributed to the demographic movements from East to West (prehistoric or historic) that differently affected in these regions, suggesting that the Carpathian mountain range represents a weak genetic barrier in South-East Europe.

Human maternal heritage in Andalusia (Spain): its composition reveals high internal complexity and distinctive influences of mtDNA haplogroups U6 and L in the western and eastern side of region

Background

The archeology and history of the ancient Mediterranean have shown that this sea has been a permeable obstacle to human migration. Multiple cultural exchanges around the Mediterranean have taken place with presumably population admixtures. A gravitational territory of those migrations has been the Iberian Peninsula. Here we present a comprehensive analysis of the maternal gene pool, by means of control region sequencing and PCR-RFLP typing, of autochthonous Andalusians originating from the coastal provinces of Huelva and Granada, located respectively in the west and the east of the region.

Results

The mtDNA haplogroup composition of these two southern Spanish populations has revealed a wide spectrum of haplogroups from different geographical origins. The registered frequencies of Eurasian markers, together with the high incidence and diversification of African maternal lineages (15% of the total mitochondrial variability) among Huelva Andalusians when compared to its eastwards relatives of Granada and other Iberian populations, constitute relevant findings unknown up-to-date on the characteristics of mtDNA within Andalusia that testifies a female population substructure. Therefore, Andalusia must not be considered a single, unique population.

Conclusions

The maternal legacy among Andalusians reflects distinctive local histories, pointing out the role of the westernmost territory of Peninsular Spain as a noticeable recipient of multiple and diverse human migrations. The obtained results underline the necessity of further research on genetic relationships in both sides of the western Mediterranean, using carefully collected samples from autochthonous individuals. Many studies have focused on recent North African gene flow towards Iberia, yet scientific attention should be now directed to thoroughly study the introduction of European genes in northwest Africa across the sea, in order to determine its magnitude, timescale and methods, and to compare them to those terrestrial movements from eastern Africa and southwestern Asia.

Evaluation of large-scale genetic structure in complex demographic and historical scenarios: the mitochondrial DNA and Y-chromosome pools of the Iberian Atlantic façade

Genetic structural patterns of human populations are usually a combination of long-term evolutionary forces and short-term social, cultural, and demographic processes. Recently, using mitochondrial DNA and Y-chromosome loci, various studies in northern Spain have found evidence that the geographical distribution of Iron Age tribal peoples might have influenced current patterns of genetic structuring in several autochthonous populations. Using the wealth of data that are currently available from the whole territory of the Iberian Peninsula, we have evaluated its genetic structuring in the spatial scale of the Atlantic façade. Hierarchical tree modeling procedures, combined with a classic analysis of molecular variance (AMOVA), were used to model known sociocultural divisions from the third century BCE to the eighth century CE, contrasting them with uniparental marker data. Our results show that, while mountainous and abrupt areas of the Iberian North bear the signals of long-term isolation in their maternal and paternal gene pools, the makeup of the Atlantic façade as a whole can be related to tribal population groups that predate the Roman conquest of the Peninsula. The maintenance through time of such a structure can be related to the numerous geographic barriers of the Iberian mainland, which have historically conditioned its settlement patterns and the occurrence of genetic drift processes.

Linguistic isolates in Portugal: insights from the mitochondrial DNA pattern

Miranda do Douro, located in the northeastern region of Portugal, has notable characteristics not only from a geographic or naturalistic point of view, but also from a cultural perspective. A remarkable one is the coexistence of two different languages: Portuguese and Mirandese, the second being an Astur-Leonese dialect. The current persistence of the Astur-Leonese dialect in this population falls on the singularity of the region: relative isolation, implying difficulties to communicate with other Portuguese regions, while the same location facilitated the establishment of social and commercial relationships with adjacent Spanish territories, origin of the Astur-Leonese language. The objective of this study was to characterize the population from Miranda through the analysis of maternal lineages in order to evaluate whether its mitochondrial DNA diversity fitted the patterns previously reported for other populations from the Iberian Peninsula. Viewing that, the entire control region of mitochondrial DNA from 121 individuals was examined. Miranda showed a haplogroup composition usual for a Western European population, in the sense that as high as 63.6% of sequences belonged to macro-haplogroup R0. Lineages ascribed to have an African (L2a and L1b) origin, were detected, but reaching an amount commonly found in Portugal. Miranda also presented a few haplogroups typically found in Jewish populations, while rarely observed in other Iberian populations. The finding can be explained by gene flow with crypto-Jew communities that since long are known to be established in the region where Miranda is located. In Miranda, both genetic and nucleotide diversities presented low values (0.9292 ± 0.0180 and 0.01101 ± 0.00614 respectively) when compared to populations from its micro-geographical framework, which constitute a sign of population isolation that certainly provided conditions for the survival of the Astur-Leonese dialect in the region.

The expanded mtDNA phylogeny of the Franco-Cantabrian region upholds the pre-neolithic genetic substrate of Basques

The European genetic landscape has been shaped by several human migrations occurred since Paleolithic times. The accumulation of archaeological records and the concordance of different lines of genetic evidence during the last two decades have triggered an interesting debate concerning the role of ancient settlers from the Franco-Cantabrian region in the postglacial resettlement of Europe. Among the Franco-Cantabrian populations, Basques are regarded as one of the oldest and more intriguing human groups of Europe. Recent data on complete mitochondrial DNA genomes focused on macrohaplogroup R0 revealed that Basques harbor some autochthonous lineages, suggesting a genetic continuity since pre-Neolithic times. However, excluding haplogroup H, the most representative lineage of macrohaplogroup R0, the majority of maternal lineages of this area remains virtually unexplored, so that further refinement of the mtDNA phylogeny based on analyses at the highest level of resolution is crucial for a better understanding of the European prehistory. We thus explored the maternal ancestry of 548 autochthonous individuals from various Franco-Cantabrian populations and sequenced 76 mitogenomes of the most representative lineages. Interestingly, we identified three mtDNA haplogroups, U5b1f, J1c5c1 and V22, that proved to be representative of Franco-Cantabria, notably of the Basque population. The seclusion and diversity of these female genetic lineages support a local origin in the Franco-Cantabrian area during the Mesolithic of southwestern Europe, ∼10,000 years before present (YBP), with signals of expansions at ∼3,500 YBP. These findings provide robust evidence of a partial genetic continuity between contemporary autochthonous populations from the Franco-Cantabrian region, specifically the Basques, and Paleolithic/Mesolithic hunter-gatherer groups. Furthermore, our results raise the current proportion (≈15%) of the Franco-Cantabrian maternal gene pool with a putative pre-Neolithic origin to ≈35%, further supporting the notion of a predominant Paleolithic genetic substrate in extant European populations.

Association between a MYH9 polymorphism (rs3752462) and renal function in the Spanish RENASTUR cohort

The MYH9 gene encodes a protein that is expressed in the kidney glomerular podocytes. MYH9 single nucleotide polymorphisms (SNPs) have been linked to the risk for chronic kidney disease (CKD) and end stage renal disease. Our aim was to determine whether MYH9 SNPs were associated with renal disease in Spanish Caucasians. The RENASTUR cohort consisted of 592 Spanish Caucasians, aged 55-85 years. They were genotyped for SNPs rs3752462 and rs4821480, which tagged haplotype E. The main values between individuals with a glomerular filtration rate (eGFR) <60 and ≥ 60 ml/min/1.73 m(2) were statistically compared. The next variables were significantly associated with the eGFR in the univariate analysis: age, gender, type 2 diabetes, total cholesterol, total LDL-cholesterol, and the MYH9 rs3752462 (TC+TT genotypes; p=0.003). This SNP remained significantly associated with the eGFR in the multivariate analysis. In conclusion, SNP rs3752462 was an independent predictor of reduced eGFR in the Spanish RENASTUR population. The genotyping of this MYH9 SNP could help to identify individuals at risk of developing CKD.

Introducing the Algerian mitochondrial DNA and Y-chromosome profiles into the North African landscape

North Africa is considered a distinct geographic and ethnic entity within Africa. Although modern humans originated in this Continent, studies of mitochondrial DNA (mtDNA) and Y-chromosome genealogical markers provide evidence that the North African gene pool has been shaped by the back-migration of several Eurasian lineages in Paleolithic and Neolithic times. More 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 Maghreb. To fill this gap, we analyzed a sample of 240 unrelated subjects from a northwest Algeria cosmopolitan population using mtDNA sequences and Y-chromosome biallelic polymorphisms, focusing on the fine dissection of haplogroups E and R, which are the most prevalent in North Africa and Europe respectively. The Eurasian component in Algeria reached 80% for mtDNA and 90% for Y-chromosome. However, within them, the North African genetic component for mtDNA (U6 and M1; 20%) is significantly smaller than the paternal (E-M81 and E-V65; 70%). The unexpected presence of the European-derived Y-chromosome lineages R-M412, R-S116, R-U152 and R-M529 in Algeria and the rest of the Maghreb could be the counterparts of the mtDNA H1, H3 and V subgroups, pointing to direct maritime contacts between the European and North African sides of the western Mediterranean. Female influx of sub-Saharan Africans into Algeria (20%) is also significantly greater than the male (10%). In spite of these sexual asymmetries, the Algerian uniparental profiles faithfully correlate between each other and with the geography.

Mitochondrial diversity patterns and the Magdalenian resettlement of Europe: new insights from the edge of the Franco-Cantabrian refuge

Phylogeography of the mitochondrial lineages commonly found in Western Europe can be interpreted in the light of a postglacial resettlement of the continent. The center of this proposal lies in the Franco-Cantabrian glacial refuge, located in the northern Iberian Peninsula and Southwestern France. Recently, this interpretation has been confronted by the unexpected patterns of diversity found in some European haplogroups. To shed new lights on this issue, research on Iberian populations is crucial if events behind the actual genetics of the European continent are to be untangled. In this regard, the region of Asturias has not been extensively studied, despite its convoluted history with prolonged periods of isolation. As mitochondrial DNA is a kind of data that has been commonly used in human population genetics, we conducted a thorough regional study in which we collected buccal swabs from 429 individuals with confirmed Asturian ancestry. The joint analysis of these sequences with a large continent-wide database and previously published diversity patterns allowed us to discuss a new explanation for the population dynamics inside the Franco-Cantabrian area, based on range expansion theory. This approximation to previously contradictory findings has made them compatible with most proposals about the postglacial resettlement of Western Europe.

Ancient DNA from hunter-gatherer and farmer groups from Northern Spain supports a random dispersion model for the Neolithic expansion into Europe

Background/Principal Findings

The phenomenon of Neolithisation refers to the transition of prehistoric populations from a hunter-gatherer to an agro-pastoralist lifestyle. Traditionally, the spread of an agro-pastoralist economy into Europe has been framed within a dichotomy based either on an acculturation phenomenon or on a demic diffusion. However, the nature and speed of this transition is a matter of continuing scientific debate in archaeology, anthropology, and human population genetics. In the present study, we have analyzed the mitochondrial DNA diversity in hunter-gatherers and first farmers from Northern Spain, in relation to the debate surrounding the phenomenon of Neolithisation in Europe.

Methodology/Significance

Analysis of mitochondrial DNA was carried out on 54 individuals from Upper Paleolithic and Early Neolithic, which were recovered from nine archaeological sites from Northern Spain (Basque Country, Navarre and Cantabria). In addition, to take all necessary precautions to avoid contamination, different authentication criteria were applied in this study, including: DNA quantification, cloning, duplication (51% of the samples) and replication of the results (43% of the samples) by two independent laboratories. Statistical and multivariate analyses of the mitochondrial variability suggest that the genetic influence of Neolithisation did not spread uniformly throughout Europe, producing heterogeneous genetic consequences in different geographical regions, rejecting the traditional models that explain the Neolithisation in Europe.

Conclusion

The differences detected in the mitochondrial DNA lineages of Neolithic groups studied so far (including these ones of this study) suggest different genetic impact of Neolithic in Central Europe, Mediterranean Europe and the Cantabrian fringe. The genetic data obtained in this study provide support for a random dispersion model for Neolithic farmers. This random dispersion had a different impact on the various geographic regions, and thus contradicts the more simplistic total acculturation and replacement models proposed so far to explain Neolithisation.

Genetic continuity in the Franco-Cantabrian region: new clues from autochthonous mitogenomes

Background

The Late Glacial Maximum (LGM), ∼20 thousand years ago (kya), is thought to have forced the people inhabiting vast areas of northern and central Europe to retreat to southern regions characterized by milder climatic conditions. Archaeological records indicate that Franco-Cantabria might have been the major source for the re-peopling of Europe at the beginning of the Holocene (11.5 kya). However, genetic evidence is still scarce and has been the focus of an intense debate.

Methods/Principal Findings

Based on a survey of more than 345,000 partial control region sequences and the analysis of 53 mitochondrial DNA (mtDNA) genomes, we identified an mtDNA lineage, HV4a1a, which most likely arose in the Franco-Cantabrian area about 5.4 kya and remained confined to northern Iberia.

Conclusions/Significance

The HV4a1a lineage and several of its younger branches reveal for the first time genetic continuity in this region and long-term episodes of isolation. This, in turn, could at least in part explain the unique linguistic and cultural features of the Basque region.

Evidence of pre-Roman tribal genetic structure in Basques from uniparentally inherited markers

Basque people have received considerable attention from anthropologists, geneticists, and linguists during the last century due to the singularity of their language and to other cultural and biological characteristics. Despite the multidisciplinary efforts performed to address the questions of the origin, uniqueness, and heterogeneity of Basques, the genetic studies performed up to now have suffered from a weak study design where populations are not analyzed in an adequate geographic and population context. To address the former questions and to overcome these design limitations, we have analyzed the uniparentally inherited markers (Y chromosome and mitochondrial DNA) of ~900 individuals from 18 populations, including those where Basque is currently spoken and populations from adjacent regions where Basque might have been spoken in historical times. Our results indicate that Basque-speaking populations fall within the genetic Western European gene pool, that they are similar to geographically surrounding non-Basque populations, and also that their genetic uniqueness is based on a lower amount of external influences compared with other Iberians and French populations. Our data suggest that the genetic heterogeneity and structure observed in the Basque region result from pre-Roman tribal structure related to geography and might be linked to the increased complexity of emerging societies during the Bronze Age. The rough overlap of the pre-Roman tribe location and the current dialect limits support the notion that the environmental diversity in the region has played a recurrent role in cultural differentiation and ethnogenesis at different time periods.

The Basque paradigm: genetic evidence of a maternal continuity in the Franco-Cantabrian region since pre-Neolithic times

Different lines of evidence point to the resettlement of much of western and central Europe by populations from the Franco-Cantabrian region during the Late Glacial and Postglacial periods. In this context, the study of the genetic diversity of contemporary Basques, a population located at the epicenter of the Franco-Cantabrian region, is particularly useful because they speak a non-Indo-European language that is considered to be a linguistic isolate. In contrast with genome-wide analysis and Y chromosome data, where the problem of poor time estimates remains, a new timescale has been established for the human mtDNA and makes this genome the most informative marker for studying European prehistory. Here, we aim to increase knowledge of the origins of the Basque people and, more generally, of the role of the Franco-Cantabrian refuge in the postglacial repopulation of Europe. We thus characterize the maternal ancestry of 908 Basque and non-Basque individuals from the Basque Country and immediate adjacent regions and, by sequencing 420 complete mtDNA genomes, we focused on haplogroup H. We identified six mtDNA haplogroups, H1j1, H1t1, H2a5a1, H1av1, H3c2a, and H1e1a1, which are autochthonous to the Franco-Cantabrian region and, more specifically, to Basque-speaking populations. We detected signals of the expansion of these haplogroups at ∼4,000 years before present (YBP) and estimated their separation from the pan-European gene pool at ∼8,000 YBP, antedating the Indo-European arrival to the region. Our results clearly support the hypothesis of a partial genetic continuity of contemporary Basques with the preceding Paleolithic/Mesolithic settlers of their homeland.

Influence of evolutionary forces and demographic processes on the genetic structure of three Croatian populations: a maternal perspective

BACKGROUND

Many Croatian islands are examples of genetic isolates, with low level of heterozygosity and high level of inbreeding, due to practice of endogamy.

AIM

The aim was to study the genetic structure of two insular and one mainland population through high-resolution phylogenetic analysis of mitochondrial DNA (mtDNA).

SUBJECTS AND METHODS

MtDNA polymorphisms were explored in 300 unrelated individuals from Mljet, Lastovo and the coastal city of Dubrovnik, based on SNP polymorphisms.

RESULTS

All mtDNA haplogroups found in the sample were of typical European origin. However, the frequency distribution of their subclades differed significantly from other Croatian and European populations. MtDNA haplotype analysis revealed only two possible founder lineages on Mljet and six on Lastovo, accounting for almost half of the sample on both islands. The island of Mljet also has the lowest reported haplotype and nucleotide diversity among Croatian isolates and the island of Lastovo, a new sublineage of a usually quite rare U1b clade.

CONCLUSION

The results can be explained by the effect evolutionary forces have on genetic structure, which is in line with the specific demographic histories of the islands. An additional research value of these two island isolates is the appearance of certain Mendelian disorders, highlighting their importance in epidemiological studies.

Paternal genetic history of the Basque population of Spain

This study examines the genetic variation in Basque Y chromosome lineages using data on 12 Y-short tandem repeat (STR) loci in a sample of 158 males from four Basque provinces of Spain (Alava, Vizcaya, Guipuzcoa, and Navarre). As reported in previous studies, the Basques are characterized by high frequencies of haplogroup R1b (83%). AMOVA analysis demonstrates genetic homogeneity, with a small but significant amount of genetic structure between provinces (Y-short tandem repeat loci STRs: 1.71%, p = 0.0369). Gene and haplotype diversity levels in the Basque population are on the low end of the European distribution (gene diversity: 0.4268; haplotype diversity: 0.9421). Post-Neolithic contribution to the paternal Basque gene pool was estimated by measuring the proportion of those haplogroups with a Time to Most Recent Common Ancestor (TMRCA) previously dated either prior (R1b, I2a2) or subsequent to (E1b1b, G2a, J2a) the Neolithic. Based on these estimates, the Basque provinces show varying degrees of post-Neolithic contribution in the paternal lineages (10.9% in the combined sample).

Ancient DNA from an Early Neolithic Iberian population supports a pioneer colonization by first farmers

The Neolithic transition has been widely debated particularly regarding the extent to which this revolution implied a demographic expansion from the Near East. We attempted to shed some light on this process in northeastern Iberia by combining ancient DNA (aDNA) data from Early Neolithic settlers and published DNA data from Middle Neolithic and modern samples from the same region. We successfully extracted and amplified mitochondrial DNA from 13 human specimens, found at three archaeological sites dated back to the Cardial culture in the Early Neolithic (Can Sadurní and Chaves) and to the Late Early Neolithic (Sant Pau del Camp). We found that haplogroups with a low frequency in modern populations-N* and X1-are found at higher frequencies in our Early Neolithic population (∼31%). Genetic differentiation between Early and Middle Neolithic populations was significant (F(ST) ∼0.13, P<10(-5)), suggesting that genetic drift played an important role at this time. To improve our understanding of the Neolithic demographic processes, we used a Bayesian coalescence-based simulation approach to identify the most likely of three demographic scenarios that might explain the genetic data. The three scenarios were chosen to reflect archaeological knowledge and previous genetic studies using similar inferential approaches. We found that models that ignore population structure, as previously used in aDNA studies, are unlikely to explain the data. Our results are compatible with a pioneer colonization of northeastern Iberia at the Early Neolithic characterized by the arrival of small genetically distinctive groups, showing cultural and genetic connections with the Near East.

Sephardic signature in haplogroup T mitochondrial DNA

A rare combination of mutations within mitochondrial DNA subhaplogroup T2e is identified as affiliated with Sephardic Jews, a group that has received relatively little attention. Four investigations were pursued: Search of the motif in 250 000 control region records across 8 databases, comparison of frequencies of T subhaplogroups (T1, T2b, T2c, T2e, T4, T(*)) across 11 diverse populations, creation of a phylogenic median-joining network from public T2e control region entries, and analysis of one Sephardic mitochondrial full genomic sequence with the motif. It was found that the rare motif belonged only to Sephardic descendents (Turkey, Bulgaria), to inhabitants of North American regions known for secret Spanish-Jewish colonization, or were consistent with Sephardic ancestry. The incidence of subhaplogroup T2e decreased from the Western Arabian Peninsula to Italy to Spain and into Western Europe. The ratio of sister subhaplogroups T2e to T2b was found to vary 40-fold across populations from a low in the British Isles to a high in Saudi Arabia with the ratio in Sephardim more similar to Saudi Arabia, Egypt, and Italy than to hosts Spain and Portugal. Coding region mutations of 2308G and 14499T may locate the Sephardic signature within T2e, but additional samples and reworking of current T2e phylogenetic branch structure is needed. The Sephardic Turkish community has a less pronounced founder effect than some Ashkenazi groups considered singly (eg, Polish), but other comparisons of interest await comparable averaging. Registries of signatures will benefit the study of populations with a large number of smaller-size founders.

The evolutionary history of TLR4 polymorphisms in Europe

Infections exert important evolutionary pressures shaping the human genome, especially on genes involved in host defense. A crucial step for host defense is recognition of pathogens by pattern recognition receptors on innate immune cells, among which Toll-like receptor 4 (TLR4) is one of the best known. Genetic variation in TLR4 (Asp299Gly, Thr399Ile) has been recently described. Haplotype frequencies of these polymorphisms differ among African, Asian and European populations, suggesting evolutionary pressures exerted by local infections. The TLR4 299Gly/399Ile haplotype, characteristic mainly of European populations, has relatively high frequency in the Iberian peninsula. This region is also described as refuge area during the last glacial maximum 20,000 years ago, from which repopulation of Europe took place. We speculate that a genetic bottleneck in the Iberian peninsula could have promoted the increased frequency of this haplotype by genetic drift. This hypothesis is supported by three arguments: (1) the West-East gradient of prevalence in the haplotype among European populations; (2) ancient DNA from Neolithic burials in the Iberian peninsula, dated 6,600-4,500 years before present, confirmed the relatively high frequency of this haplotype in the region, and (3) no functional differences between this haplotype and wild-type TLR4 have been found. In contrast, the disappearance of the 299Gly/399Thr haplotype in Europe is most likely due to negative selection due to sepsis. In conclusion, differences in distribution of TLR4 polymorphisms Asp299Gly and Thr399Ile in European populations are most likely due to a combination of population migration events combined with selection due to sepsis.

The maternal legacy of Basques in northern navarre: New insights into the mitochondrial DNA diversity of the Franco-Cantabrian area

Autochthonous Basques are thought to be a trace from the human population contraction that occurred during the Last Glacial Maximum, based mainly on the salient frequencies and coalescence ages registered for haplogroups V, H1, and H3 of mitochondrial DNA in current Basque populations. However, variability of the maternal lineages still remains relatively unexplored in an important fraction of the Iberian Basque community. In this study, mitochondrial DNA diversity in Navarre (North Spain) was addressed for the first time. To that end, HVS-I and HVS-II sequences from 110 individuals were examined to identify the most relevant lineages, including analysis of coding region SNPs for the refinement of haplogroup assignment. We found a prominent frequency of subhaplogroup J1c (11.8%) in Navarre, coinciding with previous studies on Basques. Subhaplogroup H2a5, a putative autochthonous Basque lineage, was also observed in Navarre, pointing to a common origin of current Basque geographical groups. In contrast to other Basque subpopulations, comparative analyses at Iberian and European scales revealed a relevant frequency of subhaplogroup H3 (10.9%) and a frequency peak for U5b (15.5%) in Navarre. Furthermore, we observed low frequencies for maternal lineages HV0 and H1 in Navarre relative to other northern Iberian populations. All these findings might be indicative of intense genetic drift episodes generated by population fragmentation in the area of the Franco-Cantabrian refuge until recent times, which could have promoted genetic microdifferentiation between the different Basque subpopulations.

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

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.