New Canary Islands Roman mediated settlement hypothesis deduced from coalescence ages of curated maternal indigenous lineages

Numerous genetic studies have contributed to reconstructing the human history of the Canary Islands population. The recent use of new ancient DNA targeted enrichment and next-generation sequencing techniques on new Canary Islands samples have greatly improved these molecular results. However, the bulk of the available data is still provided by the classic mitochondrial DNA phylogenetic and phylogeographic studies carried out on the indigenous, historical, and extant human populations of the Canary Islands. In the present study, making use of all the accumulated mitochondrial information, the existence of DNA contamination and archaeological sample misidentification in those samples is evidenced. Following a thorough review of these cases, the new phylogeographic analysis revealed the existence of a heterogeneous indigenous Canarian population, asymmetrically distributed across the various islands, which most likely descended from a unique mainland settlement. These new results and new proposed coalescent ages are compatible with a Roman-mediated arrival driven by the exploitation of the purple dye manufacture in the Canary Islands.

Digging into the admixture strata of current-day Canary Islanders based on mitogenomes

The conquest of the Canary Islands by Europeans began at the beginning of the 15th century and culminated in 1496 with the surrender of the aborigines. The collapse of the aboriginal population during the conquest and the arrival of settlers caused a drastic change in the demographic composition of the archipelago. To shed light on this historical process, we analyzed 896 mitogenomes of current inhabitants from the seven main islands. Our findings confirm the continuity of aboriginal maternal contributions and the persistence of their genetic footprints in the current population, even at higher levels (>60% on average) than previously evidenced. Moreover, the age estimates for most autochthonous founder lineages support a first aboriginal arrival to the islands at the beginning of the first millennium. We also revealed for the first time that the main recognizable genetic influences from Europe are from Portuguese and Galicians.

Human molecular evolutionary rate, time dependency and transient polymorphism effects viewed through ancient and modern mitochondrial DNA genomes

Human evolutionary genetics gives a chronological framework to interpret the human history. It is based on the molecular clock hypothesis that suppose a straightforward relationship between the mutation rate and the substitution rate with independence of other factors as demography dynamics. Analyzing ancient and modern human complete mitochondrial genomes we show here that, along the time, the substitution rate can be significantly slower or faster than the average germline mutation rate confirming a time dependence effect mainly attributable to changes in the effective population size of the human populations, with an exponential growth in recent times. We also detect that transient polymorphisms play a slowdown role in the evolutionary rate deduced from haplogroup intraspecific trees. Finally, we propose the use of the most divergent lineages within haplogroups as a practical approach to correct these molecular clock mismatches.

Counterbalancing the time-dependent effect on the human mitochondrial DNA molecular clock

BACKGROUND

The molecular clock is an important genetic tool for estimating evolutionary timescales. However, the detection of a time-dependent effect on substitution rate estimates complicates its application. It has been suggested that demographic processes could be the main cause of this confounding effect. In the present study, I propose a new algorithm for estimating the coalescent age of phylogenetically related sequences, taking into account the observed time-dependent effect on the molecular rate detected by others.

RESULTS

By applying this method to real human mitochondrial DNA trees with shallow and deep topologies, I obtained significantly older molecular ages for the main events of human evolution than were previously estimated. These ages are in close agreement with the most recent archaeological and paleontological records favoring the emergence of early anatomically modern humans in Africa 315 ± 34 thousand years ago (kya) and the presence of recent modern humans outside of Africa as early as 174 ± 48 thousand years ago. Furthermore, during the implementation process, I demonstrated that in a population with fluctuating sizes, the probability of fixation of a new neutral mutant depends on the effective population size, which is in better accordance with the fact that under the neutral theory of molecular evolution, the fate of a molecular mutation is mainly determined by random drift.

CONCLUSIONS

I suggest that the demographic history of populations has a more decisive effect than purifying selection and/or mutational saturation on the time-dependent effect observed for the substitution rate, and I propose a new method that corrects for this effect.

Mitogenomes illuminate the origin and migration patterns of the indigenous people of the Canary Islands

The Canary Islands’ indigenous people have been the subject of substantial archaeological, anthropological, linguistic and genetic research pointing to a most probable North African Berber source. However, neither agreement about the exact point of origin nor a model for the indigenous colonization of the islands has been established. To shed light on these questions, we analyzed 48 ancient mitogenomes from 25 archaeological sites from the seven main islands. Most lineages observed in the ancient samples have a Mediterranean distribution, and belong to lineages associated with the Neolithic expansion in the Near East and Europe (T2c, J2a, X3a…). This phylogeographic analysis of Canarian ancient mitogenomes, the first of its kind, shows that some lineages are restricted to Central North Africa (H1cf, J2a2d and T2c1d3), while others have a wider distribution, including both West and Central North Africa, and, in some cases, Europe and the Near East (U6a1a1, U6a7a1, U6b, X3a, U6c1). In addition, we identify four new Canarian-specific lineages (H1e1a9, H4a1e, J2a2d1a and L3b1a12) whose coalescence dates correlate with the estimated time for the colonization of the islands (1^st millennia CE). Additionally, we observe an asymmetrical distribution of mtDNA haplogroups in the ancient population, with certain haplogroups appearing more frequently in the islands closer to the continent. This reinforces results based on modern mtDNA and Y-chromosome data, and archaeological evidence suggesting the existence of two distinct migrations. Comparisons between insular populations show that some populations had high genetic diversity, while others were probably affected by genetic drift and/or bottlenecks. In spite of observing interinsular differences in the survival of indigenous lineages, modern populations, with the sole exception of La Gomera, are homogenous across the islands, supporting the theory of extensive human mobility after the European conquest.

Carriers of mitochondrial DNA macrohaplogroup L3 basal lineages migrated back to Africa from Asia around 70,000 years ago

Background

The main unequivocal conclusion after three decades of phylogeographic mtDNA studies is the African origin of all extant modern humans. In addition, a southern coastal route has been argued for to explain the Eurasian colonization of these African pioneers. Based on the age of macrohaplogroup L3, from which all maternal Eurasian and the majority of African lineages originated, the out-of-Africa event has been dated around 60-70 kya. On the opposite side, we have proposed a northern route through Central Asia across the Levant for that expansion and, consistent with the fossil record, we have dated it around 125 kya. To help bridge differences between the molecular and fossil record ages, in this article we assess the possibility that mtDNA macrohaplogroup L3 matured in Eurasia and returned to Africa as basal L3 lineages around 70 kya.

Results

The coalescence ages of all Eurasian (M,N) and African (L3 ) lineages, both around 71 kya, are not significantly different. The oldest M and N Eurasian clades are found in southeastern Asia instead near of Africa as expected by the southern route hypothesis. The split of the Y-chromosome composite DE haplogroup is very similar to the age of mtDNA L3. An Eurasian origin and back migration to Africa has been proposed for the African Y-chromosome haplogroup E. Inside Africa, frequency distributions of maternal L3 and paternal E lineages are positively correlated. This correlation is not fully explained by geographic or ethnic affinities. This correlation rather seems to be the result of a joint and global replacement of the old autochthonous male and female African lineages by the new Eurasian incomers.

Conclusions

These results are congruent with a model proposing an out-of-Africa migration into Asia, following a northern route, of early anatomically modern humans carrying pre-L3 mtDNA lineages around 125 kya, subsequent diversification of pre-L3 into the basal lineages of L3, a return to Africa of Eurasian fully modern humans around 70 kya carrying the basal L3 lineages and the subsequent diversification of Eurasian-remaining L3 lineages into the M and N lineages in the outside-of-Africa context, and a second Eurasian global expansion by 60 kya, most probably, out of southeast Asia. Climatic conditions and the presence of Neanderthals and other hominins might have played significant roles in these human movements. Moreover, recent studies based on ancient DNA and whole-genome sequencing are also compatible with this hypothesis.

Electronic supplementary material

The online version of this article (10.1186/s12862-018-1211-4) contains supplementary material, which is available to authorized users.

Carriers of mitochondrial DNA macrohaplogroup R colonized Eurasia and Australasia from a southeast Asia core area

BACKGROUND

The colonization of Eurasia and Australasia by African modern humans has been explained, nearly unanimously, as the result of a quick southern coastal dispersal route through the Arabian Peninsula, the Indian subcontinent, and the Indochinese Peninsula, to reach Australia around 50 kya. The phylogeny and phylogeography of the major mitochondrial DNA Eurasian haplogroups M and N have played the main role in giving molecular genetics support to that scenario. However, using the same molecular tools, a northern route across central Asia has been invoked as an alternative that is more conciliatory with the fossil record of East Asia. Here, we assess as the Eurasian macrohaplogroup R fits in the northern path.

RESULTS

Haplogroup U, with a founder age around 50 kya, is one of the oldest clades of macrohaplogroup R in western Asia. The main branches of U expanded in successive waves across West, Central and South Asia before the Last Glacial Maximum. All these dispersions had rather overlapping ranges. Some of them, as those of U6 and U3, reached North Africa. At the other end of Asia, in Wallacea, another branch of macrohaplogroup R, haplogroup P, also independently expanded in the area around 52 kya, in this case as isolated bursts geographically well structured, with autochthonous branches in Australia, New Guinea, and the Philippines.

CONCLUSIONS

Coeval independently dispersals around 50 kya of the West Asia haplogroup U and the Wallacea haplogroup P, points to a halfway core area in southeast Asia as the most probable centre of expansion of macrohaplogroup R, what fits in the phylogeographic pattern of its ancestor, macrohaplogroup N, for which a northern route and a southeast Asian origin has been already proposed.

Carriers of human mitochondrial DNA macrohaplogroup M colonized India from southeastern Asia

Background

From a mtDNA dominant perspective, the exit from Africa of modern humans to colonize Eurasia occurred once, around 60 kya, following a southern coastal route across Arabia and India to reach Australia short after. These pioneers carried with them the currently dominant Eurasian lineages M and N. Based also on mtDNA phylogenetic and phylogeographic grounds, some authors have proposed the coeval existence of a northern route across the Levant that brought mtDNA macrohaplogroup N to Australia. To contrast both hypothesis, here we reanalyzed the phylogeography and respective ages of mtDNA haplogroups belonging to macrohaplogroup M in different regions of Eurasia and Australasia.

Results

The macrohaplogroup M has a historical implantation in West Eurasia, including the Arabian Peninsula. Founder ages of M lineages in India are significantly younger than those in East Asia, Southeast Asia and Near Oceania. Moreover, there is a significant positive correlation between the age of the M haplogroups and its longitudinal geographical distribution. These results point to a colonization of the Indian subcontinent by modern humans carrying M lineages from the east instead the west side.

Conclusions

The existence of a northern route, previously proposed for the mtDNA macrohaplogroup N, is confirmed here for the macrohaplogroup M. Both mtDNA macrolineages seem to have differentiated in South East Asia from ancestral L3 lineages. Taking this genetic evidence and those reported by other disciplines we have constructed a new and more conciliatory model to explain the history of modern humans out of Africa.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-016-0816-8) contains supplementary material, which is available to authorized users.

Mitochondrial DNA haplogroup phylogeny of the dog: Proposal for a cladistic nomenclature

Canis lupus familiaris mitochondrial DNA analysis has increased in recent years, not only for the purpose of deciphering dog domestication but also for forensic genetic studies or breed characterization. The resultant accumulation of data has increased the need for a normalized and phylogenetic-based nomenclature like those provided for human maternal lineages. Although a standardized classification has been proposed, haplotype names within clades have been assigned gradually without considering the evolutionary history of dog mtDNA. Moreover, this classification is based only on the D-loop region, proven to be insufficient for phylogenetic purposes due to its high number of recurrent mutations and the lack of relevant information present in the coding region. In this study, we design 1) a refined mtDNA cladistic nomenclature from a phylogenetic tree based on complete sequences, classifying dog maternal lineages into haplogroups defined by specific diagnostic mutations, and 2) a coding region SNP analysis that allows a more accurate classification into haplogroups when combined with D-loop sequencing, thus improving the phylogenetic information obtained in dog mitochondrial DNA studies.

Isolation and prominent aboriginal maternal legacy in the present-day population of La Gomera (Canary Islands)

The present-day population structure of La Gomera is outstanding in its high aboriginal heritage, the greatest in the Canary Islands. This was earlier confirmed by both mitochondrial DNA and autosomal analyses, although genetic drift due to the fifteenth century European colonization could not be excluded as the main factor responsible. The present mtDNA study of aboriginal remains and extant samples from the six municipal districts of the island indeed demonstrates that the pre-Hispanic colonization of La Gomera by North African people involved a strong founder event, shown by the high frequency of the indigenous Canarian U6b1a lineage in the aboriginal samples (65%). This value is even greater than that observed in the extant population (44%), which in turn is the highest of all the seven Canary Islands. In contrast to previous results obtained for the aboriginal populations of Tenerife and La Palma, haplogroups related to secondary waves of migration were not detected in La Gomera aborigines, indicating that isolation also had an important role in shaping the current population. The rugged relief of La Gomera divided into several distinct valleys probably promoted subsequent aboriginal intra-insular differentiation that has continued after the European colonization, as seen in the present-day population structure observed on the island.

The history of the North African mitochondrial DNA haplogroup U6 gene flow into the African, Eurasian and American continents

Background

Complete mitochondrial DNA (mtDNA) genome analyses have greatly improved the phylogeny and phylogeography of human mtDNA. Human mitochondrial DNA haplogroup U6 has been considered as a molecular signal of a Paleolithic return to North Africa of modern humans from southwestern Asia.

Results

Using 230 complete sequences we have refined the U6 phylogeny, and improved the phylogeographic information by the analysis of 761 partial sequences. This approach provides chronological limits for its arrival to Africa, followed by its spreads there according to climatic fluctuations, and its secondary prehistoric and historic migrations out of Africa colonizing Europe, the Canary Islands and the American Continent.

Conclusions

The U6 expansions and contractions inside Africa faithfully reflect the climatic fluctuations that occurred in this Continent affecting also the Canary Islands. Mediterranean contacts drove these lineages to Europe, at least since the Neolithic. In turn, the European colonization brought different U6 lineages throughout the American Continent leaving the specific sign of the colonizers origin.

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.

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.

Genetics, environment, and diabetes-related end-stage renal disease in the Canary Islands

AIMS

Type 1 and type 2 diabetes, complicated with renal disease, have a significantly higher incidence in the Canary Islands than in mainland Spain and other European countries. Present-day Canarian inhabitants consist of a mixed population with North African indigenous and European colonizer ancestors who have rapidly evolved from a rural to an urban life style. The aim of this work was to assess the possible role of genetic and environmental factors on diabetes-related end-stage renal disease incidence in the Canary Islands.

RESULTS

For both types of diabetes there is an ethnic susceptibility increased by diabetes family history. Whereas the Y-chromosome does not play a significant role, mitochondrial DNA (mtDNA) haplogroup differences point to a maternal origin for this ethnic predisposition, confirming susceptible and protective effects for haplogroups J and T, respectively. In addition, urban life style seems to be an additional risk factor for type 1 diabetes.

CONCLUSIONS

The maternal ethnic predisposition to diabetes complicated with kidney disease detected in the Canary Islands signals mtDNA and X-chromosome markers as the best candidates to uncover the genetic predisposition to this disease.

Susceptibility to primary angle closure glaucoma in Saudi Arabia: the possible role of mitochondrial DNA ancestry informative haplogroups

PURPOSE

In a previous preliminary analysis we reported that mitochondrial DNA (mtDNA) haplogroup R0a was significantly more frequent in primary angle closure glaucoma (PACG) Saudi patients than in healthy Saudi controls. This result prompted us to extend our work using a significant larger Saudi PACG cohort and more healthy controls.

METHODS

We sequenced the mtDNA regulatory hypervariable region-I (HVS-I) and coding regions, comprising haplogroup diagnostic polymorphisms, in 227 PACG Saudi patients and compared their haplogroup frequencies with those obtained from 186 matched healthy controls (free of PACG by examination) and from a large sample of 810 healthy Saudi Arabs representing the general Saudi population.

RESULTS

MtDNA Haplogroups R0a and J, the most abundant lineages in Saudi Arabia, were in significant higher frequencies in the PACG patients than in controls, while the widespread western Eurasian haplogroup U was associated with reduced risk to developing PACG.

CONCLUSIONS

Haplogroups R0a and J could be ancestry informative markers for PACG in the Saudi Arabian population. In addition, the western Eurasian haplogroup U may play a mild protective effect to this illness.

Mitochondrial DNA lineages of African origin confer susceptibility to primary open-angle glaucoma in Saudi patients

PURPOSE

We previously reported that certain mitochondrial DNA (mtDNA) polymorphisms in the coding region may be involved in the pathogenesis for primary open-angle-glaucoma (POAG). This encouraged us to extend our work and assess whether mtDNA diagnostic polymorphisms, defining geographically structured haplogroups, could be associated with the development of POAG.

METHODS

We sequenced the mtDNA regulatory hypervariable region-I (HVS-I) region and coding regions, comprising haplogroup diagnostic polymorphisms, in 176 POAG patients and 186 matched healthy controls (free of glaucoma by examination) of Saudi Arabia ascendancy. A large sample of 810 healthy Saudi Arabs representing the general Saudi population has also been included in the analysis. Assigning individuals into various mitochondrial haplogroups was performed using the nomenclature previously described for African and for Eurasian sequences.

RESULTS

African mtDNA haplotypes belonging to L haplogroups, excluding L2, confer susceptibility to POAG whereas the Eurasian haplogroup N1 was associated with reduced risk of developing POAG in Saudi Arabian population.

CONCLUSIONS

Saudi individuals with mtDNA of African origin are at higher risk of developing POAG. In addition, the mtDNA Eurasian haplogroup N1 may play a mild protective effect to this illness.

Eurasian and Sub-Saharan African mitochondrial DNA haplogroup influences pseudoexfoliation glaucoma development in Saudi patients

PURPOSE

To investigate whether different mitochondrial DNA (mtDNA) haplogroups have a role on the development of pseudoexfoliation glaucoma (PEG) in the Saudi Arab population.

METHODS

The mtDNA regulatory region and coding regions comprising mtDNA haplogroup diagnostic polymorphisms were sequenced in patients with PEG (n=94), healthy matched controls (free of PEG; n=112) and a healthy Saudi Arab population group (n=810).

RESULTS

The Eurasian haplogroup T and the Sub-Saharan African Haplogroup L2 confer susceptibility to PEG, whereas the Eurasian haplogroup N1 was associated with reduced risk to develop PEG in the Saudi Arab population.

CONCLUSIONS

Mitochondrial haplogroups T and L2 may play a role in the development of PEG in the Saudi Arabian population.

Improved ethanol precipitation of DNA

In this Short Communication, a shorter version of the standard DNA ethanol precipitation and purification protocol is described. It uses a mixture of 70% ethanol, 75 mM ammonium acetate and different concentrations of different carriers to perform DNA precipitation and washing in only one step.

Saudi Arabian Y-Chromosome diversity and its relationship with nearby regions

Background

Human origins and migration models proposing the Horn of Africa as a prehistoric exit route to Asia have stimulated molecular genetic studies in the region using uniparental loci. However, from a Y-chromosome perspective, Saudi Arabia, the largest country of the region, has not yet been surveyed. To address this gap, a sample of 157 Saudi males was analyzed at high resolution using 67 Y-chromosome binary markers. In addition, haplotypic diversity for its most prominent J1-M267 lineage was estimated using a set of 17 Y-specific STR loci.

Results

Saudi Arabia differentiates from other Arabian Peninsula countries by a higher presence of J2-M172 lineages. It is significantly different from Yemen mainly due to a comparative reduction of sub-Saharan Africa E1-M123 and Levantine J1-M267 male lineages. Around 14% of the Saudi Arabia Y-chromosome pool is typical of African biogeographic ancestry, 17% arrived to the area from the East across Iran, while the remainder 69% could be considered of direct or indirect Levantine ascription. Interestingly, basal E-M96* (n = 2) and J-M304* (n = 3) lineages have been detected, for the first time, in the Arabian Peninsula. Coalescence time for the most prominent J1-M267 haplogroup in Saudi Arabia (11.6 ± 1.9 ky) is similar to that obtained previously for Yemen (11.3 ± 2) but significantly older that those estimated for Qatar (7.3 ± 1.8) and UAE (6.8 ± 1.5).

Conclusion

The Y-chromosome genetic structure of the Arabian Peninsula seems to be mainly modulated by geography. The data confirm that this area has mainly been a recipient of gene flow from its African and Asian surrounding areas, probably mainly since the last Glacial maximum onwards. Although rare deep rooting lineages for Y-chromosome haplogroups E and J have been detected, the presence of more basal clades supportive of the southern exit route of modern humans to Eurasian, were not found.

Extraction of high-quality host DNA from feces and regurgitated seeds: a useful tool for vertebrate ecological studies

DNA extraction methods for genotyping non-invasive samples have led to great advances in molecular research for ecological studies, and have been particularly useful for analyzing threatened species. However, scarce amounts of fragmented DNA and the presence of Taq polymerase inhibitors in non-invasive samples are potential problems for subsequent PCR amplifications. In this study we describe a novel technique for extracting DNA from alimentary tract cells found on external surfaces of feces and regurgitated seeds. The presence of contaminants and inhibitors is minimized and samples are preserved intact for use in other ecological research (e.g. trophic studies). The amplification efficiency and purity of the extracted DNA from feces were significantly higher than in commonly used extraction procedures. Moreover, DNA of two bird species was identified from seeds expelled by regurgitation. Therefore, this method may be suitable for future ecological studies of birds, and other vertebrate groups.

Demographic history of Canary Islands male gene-pool: replacement of native lineages by European

BACKGROUND

The origin and prevalence of the prehispanic settlers of the Canary Islands has attracted great multidisciplinary interest. However, direct ancient DNA genetic studies on indigenous and historical 17th-18th century remains, using mitochondrial DNA as a female marker, have only recently been possible. In the present work, the analysis of Y-chromosome polymorphisms in the same samples, has shed light on the way the European colonization affected male and female Canary Island indigenous genetic pools, from the conquest to present-day times.

RESULTS

Autochthonous (E-M81) and prominent (E-M78 and J-M267) Berber Y-chromosome lineages were detected in the indigenous remains, confirming a North West African origin for their ancestors which confirms previous mitochondrial DNA results. However, in contrast with their female lineages, which have survived in the present-day population since the conquest with only a moderate decline, the male indigenous lineages have dropped constantly being substituted by European lineages. Male and female sub-Saharan African genetic inputs were also detected in the Canary population, but their frequencies were higher during the 17th-18th centuries than today.

CONCLUSION

The European colonization of the Canary Islands introduced a strong sex-biased change in the indigenous population in such a way that indigenous female lineages survived in the extant population in a significantly higher proportion than their male counterparts.

The maternal aborigine colonization of La Palma (Canary Islands)

Teeth from 38 aboriginal remains of La Palma (Canary Islands) were analyzed for external and endogenous mitochondrial DNA control region sequences and for diagnostic coding positions. Informative sequences were obtained from 30 individuals (78.9%). The majority of lineages (93%) were from West Eurasian origin, being the rest (7%) from sub-Saharan African ascription. The bulk of the aboriginal haplotypes had exact matches in North Africa (70%). However, the indigenous Canarian sub-type U6b1, also detected in La Palma, has not yet been found in North Africa, the cradle of the U6 expansion. The most abundant H1 clade in La Palma, defined by transition 16260, is also very rare in North Africa. This means that the exact region from which the ancestors of the Canarian aborigines came has not yet been sampled or that they have been replaced by later human migrations. The high gene diversity found in La Palma (95.2+/-2.3), which is one of the farthest islands from the African continent, is of the same level than the previously found in the central island of Tenerife (92.4+/-2.8). This is against the supposition that the islands were colonized from the continent by island hopping and posterior isolation. On the other hand, the great similarity found between the aboriginal populations of La Palma and Tenerife is against the idea of an island-by-island independent maritime colonization without secondary contacts. Our data better fit to an island model with frequent migrations between islands.

Mitochondrial DNA haplogroup H structure in North Africa

BACKGROUND

The Strait of Gibraltar separating the Iberian Peninsula from North Africa is thought to be a stronger barrier to gene flow for male than for female lineages. However, the recent subdivision of the haplogroup H at mitochondrial DNA (mtDNA) level has revealed greater genetic differentiation among geographic regions than previously detected. The dissection of the mtDNA haplogroup H in North Africa, and its comparison with the Iberian Peninsula and Near-East profiles would help clarify the relative affinities among these regions.

RESULTS

Like the Iberian Peninsula, the dominant mtDNA haplogroup H subgroups in North Africa are H1 (42%) and H3 (13%). The similarity between these regions is stronger in the North-West edge affecting mainly Moroccan Arabs, West Saharans and Mauritanians, and decreases eastwards probably due to gene flow from Near East as attested for the higher frequencies of H4, H5, H7, H8 and H11 subgroups. Moroccan Berbers show stronger affinities with Tunisian and Tunisian Berbers than with Moroccan Arabs. Coalescence ages for H1 (11 +/- 2 ky) and H3 (11 +/- 4 ky) in North Africa point to the possibility of a late Palaeolithic settlement for these lineages similar to those found for other mtDNA haplogroups. Total and partial mtDNA genomic sequencing unveiled stronger mtDNA differentiation among regions than previously found using HVSI mtDNA based analysis.

CONCLUSION

The subdivision of the mtDNA haplogroup H in North Africa has confirmed that the genetic differentiation found among Western and Eastern populations is mainly due to geographical rather than cultural barriers. It also shows that the historical Arabian role on the region had more a cultural than a demic effect. Whole mtDNA sequencing of identical H haplotypes based on HVSI and RFLP information has unveiled additional mtDNA differences between North African and Iberian Peninsula lineages, pointing to an older mtDNA genetic flow between regions than previously thought. Based on this new information, it seems that the Strait of Gibraltar barrier affected both male and female gene flow in a similar fashion.

Mitochondrial DNA variation in Jordanians and their genetic relationship to other Middle East populations

BACKGROUND

The Levant is a crucial region in understanding human migrations between Africa and Eurasia. Although some mitochondrial DNA (mtDNA) studies have been carried out in this region, they have not included the Jordan area. This paper deals with the mtDNA composition of two Jordan populations.

AIM

The main objectives of this article are: first, to report mtDNA sequences of an urban and an isolate sample from Jordan and, second, to compare them with each other and with other nearby populations.

SUBJECTS AND METHODS

The analyses are based on HVSI and HVSII mtDNA sequences and diagnostic RFLPs to unequivocally classify into haplogroups 101 Amman and 44 Dead Sea unrelated individuals from Jordan.

RESULTS

Statistical analysis revealed that, whereas the sample from Amman did not significantly differ from their Levantine neighbours, the Dead Sea sample clearly behaved as a genetic outlier in the region. Its outstanding Eurasian haplogroup U3 frequency (39%) and its south-Saharan Africa lineages (19%) are the highest in the Middle East. On the contrary, the lack ((preHV)1) or comparatively low frequency (J and T) of Neolithic lineages is also striking. Although strong drift by geographic isolation could explain the anomalous mtDNA pool of the Dead Sea sample, the fact that its mtDNA lineage composition mirrors, in geographic origin and haplogroup frequencies, its Y-chromosome pool, points to founder effect as the main cause. Ancestral M1 lineages detected in Jordan that have affinities with those recently found in Northwest but not East Africa question the African origin of the M1 haplogroup.

CONCLUSION

Results are in agreement with an old human settlement in the Jordan region. However, in spite of the attested migratory spreads, genetically divergent populations, such as that of the Dead Sea, still exist in the area.

The role of mitochondrial haplogroups in glaucoma: a study in an Arab population

PURPOSE

Glaucoma prevalence can vary geographically and ethnically, which suggests that a genetic element could play a significant role. Studies investigating the role of various mitochondrial haplogroups in the pathogenesis of glaucoma are scarce.

METHODS

We compared the prevalence of different mitochondrial haplogroups in 107 glaucoma patients (49 primary open-angle glaucoma, POAG; 29 primary angle-closure glaucoma, PACG; and 29 pseudoexfoliation glaucoma, PEG) and 552 maternally unrelated normal controls. All patients and controls were Saudi Arabs.

RESULTS

There was no statistically significant difference between patients and controls for all mitochondrial haplogroups tested except for PACG patients with mitochondrial haplogroup preHV1 (odds ratio=4.9; 95% CI 2.3 - 10.5; p=0.00002).

CONCLUSIONS

Patients with preHV1 mitochondrial haplogroups are at higher risk of developing PACG. However, our study group is relatively small and further studies with more patients in other populations are needed to confirm this interesting finding.

Mitochondrial lineage M1 traces an early human backflow to Africa

Background

The out of Africa hypothesis has gained generalized consensus. However, many specific questions remain unsettled. To know whether the two M and N macrohaplogroups that colonized Eurasia were already present in Africa before the exit is puzzling. It has been proposed that the east African clade M1 supports a single origin of haplogroup M in Africa. To test the validity of that hypothesis, the phylogeographic analysis of 13 complete mitochondrial DNA (mtDNA) sequences and 261 partial sequences belonging to haplogroup M1 was carried out.

Results

The coalescence age of the African haplogroup M1 is younger than those for other M Asiatic clades. In contradiction to the hypothesis of an eastern Africa origin for modern human expansions out of Africa, the most ancestral M1 lineages have been found in Northwest Africa and in the Near East, instead of in East Africa. The M1 geographic distribution and the relative ages of its different subclades clearly correlate with those of haplogroup U6, for which an Eurasian ancestor has been demonstrated.

Conclusion

This study provides evidence that M1, or its ancestor, had an Asiatic origin. The earliest M1 expansion into Africa occurred in northwestern instead of eastern areas; this early spread reached the Iberian Peninsula even affecting the Basques. The majority of the M1a lineages found outside and inside Africa had a more recent eastern Africa origin. Both western and eastern M1 lineages participated in the Neolithic colonization of the Sahara. The striking parallelism between subclade ages and geographic distribution of M1 and its North African U6 counterpart strongly reinforces this scenario. Finally, a relevant fraction of M1a lineages present today in the European Continent and nearby islands possibly had a Jewish instead of the commonly proposed Arab/Berber maternal ascendance.

Eurasian and African mitochondrial DNA influences in the Saudi Arabian population

Background

Genetic studies of the Arabian Peninsula are scarce even though the region was the center of ancient trade routes and empires and may have been the southern corridor for the earliest human migration from Africa to Asia. A total of 120 mtDNA Saudi Arab lineages were analyzed for HVSI/II sequences and for haplogroup confirmatory coding diagnostic positions. A phylogeny of the most abundant haplogroup (preHV)1 (R0a) was constructed based on 13 whole mtDNA genomes.

Results

The Saudi Arabian group showed greatest similarity to other Arabian Peninsula populations (Bedouin from the Negev desert and Yemeni) and to Levantine populations. Nearly all the main western Asia haplogroups were detected in the Saudi sample, including the rare U9 clade. Saudi Arabs had only a minority sub-Saharan Africa component (7%), similar to the specific North-African contribution (5%). In addition, a small Indian influence (3%) was also detected.

Conclusion

The majority of the Saudi-Arab mitochondrial DNA lineages (85%) have a western Asia provenance. Although the still large confidence intervals, the coalescence and phylogeography of (preHV)1 haplogroup (accounting for 18 % of Saudi Arabian lineages) matches a Neolithic expansion in Saudi Arabia.

Mitochondrial DNA variation in Mauritania and Mali and their genetic relationship to other Western Africa populations

Mitochondrial DNA (mtDNA) variation was analyzed in Mauritania and Mali, and compared to other West African samples covering the considerable geographic, ethnic and linguistic diversity of this region. The Mauritanian mtDNA profile shows that 55% of their lineages have a west Eurasian provenance, with the U6 cluster (17%) being the best represented. Only 6% of the sub-Saharan sequences belong to the L3A haplogroup a frequency similar to other Berber speaking groups but significantly different to the Arabic speaking North Africans. The historic Arab slave trade may be the main cause of this difference. Only one HV west Eurasian lineage has been detected in Mali but 40% of the sub-Saharan sequences belong to cluster L3A. The presence of L0a representatives demonstrates gene flow from eastern regions. Although both groups speak related dialects of the Mande branch, significant genetic differences exist between the Bambara and Malinke groups. The West African genetic variation is well structured by geography and language, but more detailed ethnolinguistic clustering suggest that geography is the main factor responsible for this differentiation.

The mitochondrial lineage U8a reveals a Paleolithic settlement in the Basque country

BACKGROUND

It is customary, in population genetics studies, to consider Basques as the direct descendants of the Paleolithic Europeans. However, until now there has been no irrefutable genetic proof to support this supposition. Even studies based on mitochondrial DNA (mtDNA), an ideal molecule for constructing datable maternal genealogies, have failed to achieve this. It could be that incoming gene flow has replaced the Basque ancient lineages but it could also be that these lineages have not been detected due to a lack of resolution of the Basque mtDNA genealogies. To assess this possibility we analyzed here the mtDNA of a large sample of autochthonous Basques using mtDNA genomic sequencing for those lineages that could not be unequivocally classified by diagnostic RFLP analysis and control region (HVSI and HVSII) sequencing.

RESULTS

We show that Basques have the most ancestral phylogeny in Europe for the rare mitochondrial subhaplogroup U8a. Divergence times situate the Basque origin of this lineage in the Upper Palaeolithic. Most probably, their primitive founders came from West Asia. The lack of U8a lineages in Africa points to an European and not a North African route of entrance. Phylogeographic analysis suggest that U8a had two expansion periods in Europe, the first, from a south-western area including the Iberian peninsula and Mediterranean France before 30,000 years ago, and the second, from Central Europe around 15,000-10,000 years ago.

CONCLUSION

It has been demonstrated, for the first time, that Basques show the oldest lineages in Europe for subhaplogroup U8a. Coalescence times for these lineages suggest their presence in the Basque country since the Upper Paleolithic. The European U8 phylogeography is congruent with the supposition that Basques could have participated in demographic re-expansions to repopulate central Europe in the last interglacial periods.

Mitochondrial DNA diversity in 17th-18th century remains from Tenerife (Canary Islands)

Mitochondrial DNA sequences and restriction fragment length polymorphisms were retrieved (with >80% efficiency) from a 17th-18th century sample of 213 teeth from Tenerife. The genetic composition of this population reveals an important ethnic heterogeneity. Although the majority of detected haplotypes are of European origin, the high frequency of sub-Saharan African haplotypes (15.63%), compared to that of the present-day population (6.6%), confirms the importance of the Canary Islands in the black slave trade of that epoch. The aboriginal substrate, inferred from the U6b1 haplotypes (8.59%), has also decreased due to European input. Finally, the presence of Amerindian lineages (1.5%) reveals that the Canary Islands have also received genetic flow from America.

Isolates in a corridor of migrations: a high-resolution analysis of Y-chromosome variation in Jordan

A high-resolution, Y-chromosome analysis using 46 binary markers has been carried out in two Jordan populations, one from the metropolitan area of Amman and the other from the Dead Sea, an area geographically isolated. Comparisons with neighboring populations showed that whereas the sample from Amman did not significantly differ from their Levantine neighbors, the Dead Sea sample clearly behaved as a genetic outlier in the region. Its high R1*-M173 frequency (40%) has until now only been found in northern Cameroonian samples. This contrasts with the comparatively low presence of J representatives (9%), which is the modal clade in Middle Eastern populations, including Amman. The Dead Sea sample also showed a high presence of E3b3a-M34 lineages (31%), which is only comparable to that found in Ethiopians. Although ancient and recent ties with sub-Saharan and eastern Africans cannot be discarded, it seems that isolation, strong drift, and/or founder effects are responsible for the anomalous Y-chromosome pool of this population. These results demonstrate that, at a fine scale, the smooth, continental clines detected for several Y-chromosome markers are often disrupted by genetically divergent populations.

Mitochondrial genome variation in eastern Asia and the peopling of Japan

To construct an East Asia mitochondrial DNA (mtDNA) phylogeny, we sequenced the complete mitochondrial genomes of 672 Japanese individuals (http://www.giib.or.jp/mtsnp/index_e.html). This allowed us to perform a phylogenetic analysis with a pool of 942 Asiatic sequences. New clades and subclades emerged from the Japanese data. On the basis of this unequivocal phylogeny, we classified 4713 Asian partial mitochondrial sequences, with <10% ambiguity. Applying population and phylogeographic methods, we used these sequences to shed light on the controversial issue of the peopling of Japan. Population-based comparisons confirmed that present-day Japanese have their closest genetic affinity to northern Asian populations, especially to Koreans, which finding is congruent with the proposed Continental gene flow to Japan after the Yayoi period. This phylogeographic approach unraveled a high degree of differentiation in Paleolithic Japanese. Ancient southern and northern migrations were detected based on the existence of basic M and N lineages in Ryukyuans and Ainu. Direct connections with Tibet, parallel to those found for the Y-chromosome, were also apparent. Furthermore, the highest diversity found in Japan for some derived clades suggests that Japan could be included in an area of migratory expansion to Continental Asia. All the theories that have been proposed up to now to explain the peopling of Japan seem insufficient to accommodate fully this complex picture.

Ancient mtDNA analysis and the origin of the Guanches

The prehistoric colonisation of the Canary Islands by the Guanches (native Canarians) woke up great expectation about their origin, since the Europeans conquest of the Archipelago. Here, we report mitochondrial DNA analysis (HVRI sequences and RFLPs) of aborigine remains around 1000 years old. The sequences retrieved show that the Guanches possessed U6b1 lineages that are in the present day Canarian population, but not in Africans. In turn, U6b, the phylogenetically closest ancestor found in Africa, is not present in the Canary Islands. Comparisons with other populations relate the Guanches with the actual inhabitants of the Archipelago and with Moroccan Berbers. This shows that, despite the continuous changes suffered by the population (Spanish colonisation, slave trade), aboriginal mtDNA lineages constitute a considerable proportion of the Canarian gene pool. Although the Berbers are the most probable ancestors of the Guanches, it is deduced that important human movements have reshaped Northwest Africa after the migratory wave to the Canary Islands.

Mitochondrial DNA transit between West Asia and North Africa inferred from U6 phylogeography

BACKGROUND

World-wide phylogeographic distribution of human complete mitochondrial DNA sequences suggested a West Asian origin for the autochthonous North African lineage U6. We report here a more detailed analysis of this lineage, unraveling successive expansions that affected not only Africa but neighboring regions such as the Near East, the Iberian Peninsula and the Canary Islands.

RESULTS

Divergence times, geographic origin and expansions of the U6 mitochondrial DNA clade, have been deduced from the analysis of 14 complete U6 sequences, and 56 different haplotypes, characterized by hypervariable segment sequences and RFLPs.

CONCLUSIONS

The most probable origin of the proto-U6 lineage was the Near East. Around 30,000 years ago it spread to North Africa where it represents a signature of regional continuity. Subgroup U6a reflects the first African expansion from the Maghrib returning to the east in Paleolithic times. Derivative clade U6a1 signals a posterior movement from East Africa back to the Maghrib and the Near East. This migration coincides with the probable Afroasiatic linguistic expansion. U6b and U6c clades, restricted to West Africa, had more localized expansions. U6b probably reached the Iberian Peninsula during the Capsian diffusion in North Africa. Two autochthonous derivatives of these clades (U6b1 and U6c1) indicate the arrival of North African settlers to the Canarian Archipelago in prehistoric times, most probably due to the Saharan desiccation. The absence of these Canarian lineages nowadays in Africa suggests important demographic movements in the western area of this Continent.

Mitochondrial DNA affinities at the Atlantic fringe of Europe

Mitochondrial DNA analysis of Atlantic European samples has detected significant latitudinal clines for several clusters with Paleolithic (H) and Neolithic (J, U4, U5a1, and U5a1a) coalescence ages in Europe. These gradients may be explained as the result of Neolithic influence on a rather homogeneous Paleolithic background. There is also evidence that some Neolithic clusters reached this border by a continental route (J, J1, J1a, U5a1, and U5a1a), whereas others (J2) did so through the Mediterranean coast. An important gene flow from Africa was detected in the Atlantic Iberia. Specific sub-Saharan lineages appeared mainly restricted to southern Portugal, and could be attributed to historic Black slave trade in the area and to a probable Saharan Neolithic influence. In fact, U6 haplotypes of specific North African origin have only been detected in the Iberian peninsula northwards from central Portugal. Based on this peculiar distribution and the high diversity pi value (0.014 +/- 0.001) in this area compared to North Africa (0.006 +/- 0.001), we reject the proposal that only historic events such as the Moslem occupation are the main cause of this gene flow, and instead propose a pre-Neolithic origin for it.

A predominant European ancestry of paternal lineages from Canary Islanders

We genotyped 24 biallelic sites and 5 microsatellites from the non-recombining portion of the Y chromosome in 652 males from the Canary Islands. The results indicate that, contrary to mtDNA data, paternal lineages of the current population are overwhelmingly (>90%) of European origin, arguing for a highly asymmetric pattern of mating after European occupation. However, the presence of lineages of indisputable African assignation demonstrates that an aboriginal background still persists (<10%). On the basis of distribution and dating of some of these lineages we derived a genetic perspective of settlement processes of the archipelago in two stages, congruent with anthropological, archaeological and linguistic findings.

Structure and evolution of the mitochondrial DNA complete control region in the Drosophila subobscura subgroup

The complete A + T-rich region of mitochondrial DNA (mtDNA) has been cloned and sequenced in the species of the Drosophila subobscura subgroup D. subobscura, D. madeirensis and D. guanche. Comparative analysis of these sequences with others already published has identified new sequence motifs that are conserved in Drosophila and other insects. A putative bi-directional promoter and a stop signal are proposed to be involved in the primary mtDNA strand replication of Drosophila. This region strongly resolves relationships of the species included in a phylogenetic analysis, both for closely related species and also at deeper phylogenetic levels when only the left and central domains are taken into account.

The peopling of the Canary Islands: a CD4/Alu microsatellite haplotype perspective

A new CD4 microsatellite allele with three TTTTC complete repetitions, previously described only in hominoids, has been found in this screening. The number of haplotypes and heterozygosities in the Canary Islands (15 and 0.746+/-0.007) is more similar to Iberian (14 and 0.748+/-0.015) than to North African (18 and 0.827+/-0.009) values. However, in some islands, with less European migratory impact, haplotypes with major African assignation (90[+] and 130[+]) reach frequencies similar to African populations. There is a significant negative correlation between geographic distances to Africa and insular heterozygosity values, which suggests a main aborigine colonization from East to West still detectable today.

Major genomic mitochondrial lineages delineate early human expansions

BACKGROUND

The phylogeographic distribution of human mitochondrial DNA variations allows a genetic approach to the study of modern Homo sapiens dispersals throughout the world from a female perspective. As a new contribution to this study we have phylogenetically analysed complete mitochondrial DNA(mtDNA) sequences from 42 human lineages, representing major clades with known geographic assignation.

RESULTS

We show the relative relationships among the 42 lineages and present more accurate temporal calibrations than have been previously possible to give new perspectives as how modern humans spread in the Old World.

CONCLUSIONS

The first detectable expansion occurred around 59,000-69,000 years ago from Africa, independently colonizing western Asia and India and, following this southern route, swiftly reaching east Asia. Within Africa, this expansion did not replace but mixed with older lineages detectable today only in Africa. Around 39,000-52,000 years ago, the western Asian branch spread radially, bringing Caucasians to North Africa and Europe, also reaching India, and expanding to north and east Asia. More recent migrations have entangled but not completely erased these primitive footprints of modern human expansions.

Y-chromosome differentiation in Northwest Africa

Variation of seven Y-chromosomal DNA polymorphisms, one microsatellite (DYS19), and six biallelic markers (DYS287, DYS271, SRY-2627, SRY-1532, 92R7, and M9), were studied in males from Northwest Africa. To evaluate the degree of differentiation in this region, males from neighboring areas such as the Iberian Peninsula and sub-Saharan Africa were also typed. The results show a large number of paternal lineages of Northwest African origin (over 75%), supporting a long-term population continuity in the area. When the analysis of molecular variance (AMOVA) was performed both on the microsatellite and biallelic marker combinations or haplogroups, a large degree of differentiation among areas was revealed. In spite of these geographic differences, some gene flow between areas was detected by the presence of haplogroups with other geographical origins.

Northwest African distribution of the CD4/Alu microsatellite haplotypes

We have analysed a linked microsatellite/Alu polymorphism at the CD4 locus (CD4/Alu) in 666 chromosomes from samples of the Iberian Peninsula, Northwest Africa, and West sub-Saharan Africa. The Iberian Peninsula differs from other European populations by its higher levels of haplotype diversity (0.75), and weaker association between the microsatellite allele 90 and Alu(-) chromosomes. These results are explainable by a substantial gene flow from Northwest Africa. Significant geographic clines for the five major haplotypes suggest a south to north migration from sub-Saharan Africa into Northwest Africa. In spite of this, the consistent presence of haplotype 110(-) in this area is congruent with an ancient and autochthonous human presence in Northwest Africa.

Phylogeographic patterns of mtDNA reflecting the colonization of the Canary Islands

Although the Canary Islands were settled by humans, possibly of Berber origin, as late as 2500 years ago, the precise course and numbers of early migrations to the archipelago remain controversial. We have therefore analysed mtDNA variation (HVS-I as well as selected RFLP sites) in 300 individuals from the seven Canary Islands. The distribution and variation across the islands in a specific mtDNA clade of Northwest African ancestry suggest that there was one dominant initial settlement process that affected all the islands, from east to west. This indicates that a certain genetic affinity of present-day Canary Islanders to Northwest African Berbers mainly stems from the autochthonous population rather than slaves captured on the neighbouring African coast. The slave trade after the European conquest left measurable, though minor, traces in the mtDNA pool of the Canary Islands, which in its majority testifies to the European immigration.

Mitochondrial DNA analysis of northwest African populations reveals genetic exchanges with European, near-eastern, and sub-Saharan populations

Genetic studies have emphasized the contrast between North African and sub-Saharan populations, but the particular affinities of the North African mtDNA pool to that of Europe, the Near East, and sub-Saharan Africa have not previously been investigated. We have analysed 268 mtDNA control-region sequences from various Northwest African populations including several Senegalese groups and compared these with the mtDNA database. We have identified a few mitochondrial motifs that are geographically specific and likely predate the distribution and diversification of modern language families in North and West Africa. A certain mtDNA motif (16172C, 16219G), previously found in Algerian Berbers at high frequency, is apparently omnipresent in Northwest Africa and may reflect regional continuity of more than 20,000 years. The majority of the maternal ancestors of the Berbers must have come from Europe and the Near East since the Neolithic. The Mauritanians and West-Saharans, in contrast, bear substantial though not dominant mtDNA affinity with sub-Saharans.

Molecular diagnosis of alkaptonuria mutation by analysis of homogentisate 1,2 dioxygenase mRNA from urine and blood

Alkaptonuria (AKU) is caused by lack of homogentisate 1, 2 dioxygenase (HGO) activity. From the complete sequence of a human HGO cDNA, primers were designed in order to obtain reverse transcription-polymerase chain reaction products from tissues with ectopic transcription amenable to diagnostic analysis. A search for mutations in HGO cDNA was performed in an AKU family using urine and blood samples. The results show complete cosegregation (Z = 6.32; theta = 0) between a C-->T transition at position 817 of the human HGO cDNA and AKU. This mutation predicts a Pro-->Ser replacement at amino acid 230, and generates an EcoRV site.

Expression of carbamoyl-phosphate synthetase III mRNA during the early stages of development and in muscle of adult rainbow trout (Oncorhynchus mykiss)

It has been reported that the activities of the urea cycle-related enzymes ornithine carbamoyltransferase and carbamoyl-phosphate synthetase III (CPSase III) are induced during early life stages of ammonotelic rainbow trout (Oncorhynchus mykiss), suggesting that the urea cycle may play a physiological role in early development in teleost fish (Wright, P. A., Felskie, A., and Anderson, P. M. (1995) J. Exp. Biol. 198, 127-135). CPSase III cDNA prepared from embryo mRNA was sequenced, confirming the existence of the CPSase III gene in trout and its expression. The deduced amino acid sequence of the CPSase III is homologous to other CPSases. Supporting evidence for the expression of CPSase III activity in trout embryos was obtained by demonstrating expression of CPSase III mRNA as early as day 3 post-fertilization, reaching a maximum at 10-14 days, declining to a minimum at day 70, and then increasing to a relatively constant level from days 90 to 110 (relative to total RNA). Unexpectedly, in tissues of adult and fingerling trout, CPSase III mRNA was found to be present in muscle but not in other tissues, including liver. This finding was confirmed by assay of extracts, which showed CPSase III and ornithine carbamoyltransferase activity in muscle but not in other tissues. The pyrimidine nucleotide pathway-related CPSase II mRNA was expressed in all tissues.