High-resolution analysis of human Y-chromosome variation shows a sharp discontinuity and limited gene flow between northwestern Africa and the Iberian Peninsula

In the present study we have analyzed 44 Y-chromosome biallelic polymorphisms in population samples from northwestern (NW) Africa and the Iberian Peninsula, which allowed us to place each chromosome unequivocally in a phylogenetic tree based on >150 polymorphisms. The most striking results are that contemporary NW African and Iberian populations were found to have originated from distinctly different patrilineages and that the Strait of Gibraltar seems to have acted as a strong (although not complete) barrier to gene flow. In NW African populations, an Upper Paleolithic colonization that probably had its origin in eastern Africa contributed 75% of the current gene pool. In comparison, approximately 78% of contemporary Iberian Y chromosomes originated in an Upper Paleolithic expansion from western Asia, along the northern rim of the Mediterranean basin. Smaller contributions to these gene pools (constituting 13% of Y chromosomes in NW Africa and 10% of Y chromosomes in Iberia) came from the Middle East during the Neolithic and, during subsequent gene flow, from Sub-Saharan to NW Africa. Finally, bidirectional gene flow across the Strait of Gibraltar has been detected: the genetic contribution of European Y chromosomes to the NW African gene pool is estimated at 4%, and NW African populations may have contributed 7% of Iberian Y chromosomes. The Islamic rule of Spain, which began in a.d. 711 and lasted almost 8 centuries, left only a minor contribution to the current Iberian Y-chromosome pool. The high-resolution analysis of the Y chromosome allows us to separate successive migratory components and to precisely quantify each historical layer.     

Molecular variation at functional genes and the history of human populations--data on candidate genes for cardiovascular risk in the Mediterranean

A screening of 22 DNA polymorphisms has been performed in western Mediterranean populations (Iberian Peninsula, Morocco, and Central Mediterranean Islands). The analyzed markers correspond to polymorphic sites in several candidate genes for cardiovascular disease including apolipopoteins and their receptors (APOA1, APOB, APOE, APOC1, APOC2, LPA, and LDLR), genes implied in the hemostasis regulation (Factor VII, alpha and beta-fibrinogen, alpha and beta platelet-integrin, tissue plasminogen activator, and plasminogen activator inhibitor-1), and the angiotensin converting enzyme gene. The results are presented of a partial analysis carried out in following population samples: 6 from the Iberian Peninsula, 2 from Morocco, and 3 from Central Islands. The degree of inter-population diversity was significant and consistent with data from other kind of genetic polymorphisms. The apportionment of the allele frequency variance supported a geographic structure into three main regions: Central Mediterranean Islands, the Iberia Peninsula and North Africa. The genetic distance pattern is compatible with a south-to-north North African influence in the Iberian Peninsula and a remarkable gene flow from sub-Saharan Africa into Morocco. Epidemiologically, North Africa is characterized by high frequencies of LPA PNR alleles with high number of repeats (protective for cardiovascular risk) and high frequencies of the APOE*E4 allele (risk factor) as compared with European populations.     

Genomic ancestry of North Africans supports back-to-Africa migrations

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

The trans-Saharan slave trade - clues from interpolation analyses and high-resolution characterization of mitochondrial DNA lineages

Background  

A proportion of 1/4 to 1/2 of North African female pool is made of typical sub-Saharan lineages, in higher frequencies as geographic proximity to sub-Saharan Africa increases. The Sahara was a strong geographical barrier against gene flow, at least since 5,000 years ago, when desertification affected a larger region, but the Arab trans-Saharan slave trade could have facilitate enormously this migration of lineages. Till now, the genetic consequences of these forced trans-Saharan movements of people have not been ascertained.     

Ancient local evolution of African mtDNA haplogroups in Tunisian Berber populations

Our objective is to highlight the age of sub-Saharan gene flows in North Africa and particularly in Tunisia. Therefore we analyzed in a broad phylogeographic context sub-Saharan mtDNA haplogroups of Tunisian Berber populations considered representative of ancient settlement. More than 2,000 sequences were collected from the literature, and networks were constructed. The results show that the most ancient haplogroup is L3*, which would have been introduced to North Africa from eastern sub-Saharan populations around 20,000 years ago. Our results also point to a less ancient western sub-Saharan gene flow to Tunisia, including haplogroups L2a and L3b. This conclusion points to an ancient African gene flow to Tunisia before 20,000 BP. These findings parallel the more recent findings of both archaeology and linguistics on the prehistory of Africa. The present work suggests that sub-Saharan contributions to North Africa have experienced several complex population processes after the occupation of the region by anatomically modern humans. Our results reveal that Berber speakers have a foundational biogeographic root in Africa and that deep African lineages have continued to evolve in supra-Saharan Africa.     

Genetic Heterogeneity in Algerian Human Populations

The demographic history of human populations in North Africa has been characterized by complex processes of admixture and isolation that have modeled its current gene pool. Diverse genetic ancestral components with different origins (autochthonous, European, Middle Eastern, and sub-Saharan) and genetic heterogeneity in the region have been described. In this complex genetic landscape, Algeria, the largest country in Africa, has been poorly covered, with most of the studies using a single Algerian sample. In order to evaluate the genetic heterogeneity of Algeria, Y-chromosome, mtDNA and autosomal genome-wide makers have been analyzed in several Berber- and Arab-speaking groups. Our results show that the genetic heterogeneity found in Algeria is not correlated with geography or linguistics, challenging the idea of Berber groups being genetically isolated and Arab groups open to gene flow. In addition, we have found that external sources of gene flow into North Africa have been carried more often by females than males, while the North African autochthonous component is more frequent in paternally transmitted genome regions. Our results highlight the different demographic history revealed by different markers and urge to be cautious when deriving general conclusions from partial genomic information or from single samples as representatives of the total population of a region.     

Complex biogeographical distribution of genetic variation within Podarcis wall lizards across the Strait of Gibraltar

Abstract Aim To examine the effect of a known geological barrier on genetic variation within a wall lizard species complex. Location The Iberian Peninsula and North Africa. Methods Sequencing of partial 12S rRNA and cytochrome b mtDNA. Results The current distribution of genetic variability is not related to the opening of the Strait of Gibraltar. Conclusions Podarcis hispanica in North Africa is probably a species complex. The Strait of Gibraltar should not be used as a known barrier to gene flow in other land based organisms without careful sampling to test for multiple crossings since its formation.     

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.     

Biogeographical connections between the Maghreb and the Mediterranean peninsulas of southern Europe

The glacial–interglacial cycles have caused severe range modifications of species' distributions. In Europe, thermophilic species had to retreat into geographically distinct southern refugia during glaciations. This process produced strong genetic imprints, which are still detectable by the present pattern of genetic differentiation and the distribution of regional diversity. To reveal the biogeographical imprints in the western Mediterranean, we analysed 26 populations of the butterfly Maniola jurtina spread over large areas of its European and North African distribution range. The samples were analysed using allozyme electrophoresis. We detected three genetic groups, divided into Western Europe, Central/Eastern Europe, and Italy with the Maghreb. The North African samples randomly cluster within the Italian samples. Even the population sampled in Morocco is genetically closely related to these samples and not to the geographically neighbouring Iberian ones. Parameters of genetic diversity showed similar values over the whole study area. The observed genetic pattern reflects possible glacial refugia in Europe located in the Iberian Peninsula and the Balkans. For North Africa and Italy, our data reveal a colonization of Africa originating from Italy.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 98 , 693–703.     

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.     

Palatine torus in the pre-conquest inhabitants of the Canary Islands.

An unusually high frequency of palatine torus in prehistoric Canary Islands skeletal remains is investigated in terms of population origins, evolutionary forces (gene flow and genetic drift) and environmental effects. Palatine torus frequencies (percent presence) are compared between the Canary Islands sample and skeletal samples from proposed ancestral regions, including northwest Africa, northeast Africa, sub-Saharan Africa, southern Europe, northern Europe and western Asia. The frequency of palatine torus is much higher in the Canary Islands sample (23.8%) than in samples from Northern and sub-Saharan Africa (1.8-6.1%), southern Europe (7.5%) and western Asia (2.1%), but is much lower than in the sample from northern Europe (57.4%). Because biological and archaeological evidence provide strong support for a northwest African origin for indigenous Canary Islands populations, the relatively high occurrence of palatine torus in the Canary Islands populace cannot be explained by an alternative ancestry; rather, it may be best explained by either evolutionary forces such as genetic drift or gene flow, or by environmental forces, such as hard chewing or a heavy dependence on marine foods. Genetic drift and gene flow seem less likely, since frequencies of other dental traits known to be under strong genetic control do not differ greatly between the prehistoric Canary Islands and northwest African samples. Environmental factors such as diet seem the most likely explanation and may include heavy consumption of marine foods, which has been implicated in torus formation.     

Twenty nuclear DNA polymorphisms in a Moroccan population: a comparison with seven other human populations

A south central Moroccan sample was analyzed for 20 nuclear DNA polymorphisms (restriction fragment length polymorphisms). The population was chosen on the basis of available information on its history, making it suitable for comparisons with data from other European populations. The markers analyzed have been studied previously in several human groups from different continents, and data on African and European samples have been compared to evaluate the genetic affinity of the studied sample with other populations, especially with two Spanish groups: Basques and Andalusians. Heterozygosity levels showed intermediate values between the African and European groups and higher than those found so far in an African group for the studied markers. Genetic distances closely matched geographical relationships through neighbor-joining tree and correspondence analysis, the Moroccans being closer to the European groups than the sub-Saharan Africans included in the analysis. Allele distributions revealed specific population associations with large weight of several alleles in the differentiation of some groups. Gene flow from sub-Saharan Africa appears to be relevant in understanding the differentiation of present Moroccan populations.     

Polymorphic Alu insertions and genetic diversity among African populations

Thorough assessment of modern genetic diversity and interpopulation affinities within the African continent is essential for understanding the processes that have been at work during the course of worldwide human evolution. Regardless of whether autosomal, Y-chromosome, or mtDNA markers are used, allele- or haplotype-frequency data from African populations are necessary in setting the framework for the construction of global population phylogenies. In the present study we analyze genetic differentiation and population structure in a data set of nine African populations using 12 polymorphic Alu insertions (PAls). Furthermore, to place our findings within a global context, we also examined an equal number of non-African groups. Frequency data from 456 individuals presented for the first time in this work plus additional data obtained from the literature indicate an overall pattern of higher intrapopulation diversity in sub-Saharan populations than in northern Africa, a prominent differentiation between these two locations, an appreciably high degree of transcontinental admixture in Egypt, and significant discontinuity between Morocco and the Iberian peninsula. Moreover, the topologies of our phylogenetic analyses suggest that out of the studied sub-Saharan groups, the southern Bantu population of Sotho/ Tswana presents the highest level of antiquity, perhaps as a result of ancestral or acquired Khoisan genetic signals. Close affinities of eastern sub-Saharan populations with Egypt in the phylogenetic trees may indicate the existence of gene flow along the Nile River.     

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.     

Sex-biased initial eggs favours sons in the slightly size-dimorphic Scops owl (Otus scops)

There is considerable controversy concerning the origin of Iberian populations of the Mediterranean chameleon, Chamaeleo chamaeleon . Current opinion dictates that Spanish populations result from introductions during the 18^th and 19^th centuries, with subsequent translocations from the original populations to other parts of Spain. The Portugese population in the Algarve is believed to have been introduced from Africa or Spain during the 1920s. However, Holocene remains of chameleons suggest that the Malaga population at least could have a much older origin. Analysis of sequences from the mitochondrial 16S ribosomal RNA gene of samples from the Iberian Peninsula and North Africa revealed a double origin for the Iberian population. The Mediterranean Iberian (Malaga) population is closely related to Mediterranean North African populations, with Atlantic Iberian populations more closely related to populations of the Atlantic coast of North Africa. The overall genetic differentiation and diversity observed was very low, preventing precise dating of the colonization events. However this low level of differentiation is not consistent with Plio-Pleistocene colonization, the assumed timing for a natural colonization event and suggests that chameleons were probably introduced twice by man in the recent past. © 2002 The Linnean Society of London, Biological Journal of the Linnean Society , 2002, 75 , 1–7.     

Genetic position of Andalusians from Huelva in relation to other European and North African populations: a study based on GM and KM allotypes

An understanding of population relationships in the Mediterranean region is crucial to the reconstruction of recent human evolution. Andalusia, the most southern region of Spain, has been continuously and densely occupied since ancient times and has a rich history of contacts with many different Mediterranean populations. Thus, to understand the Mediterranean peopling process, investigators should analyze the population relationships between the Iberian peninsula and northern Africa based on an assessment of genetic diversity that takes Andalusia into consideration. The aim of this study was to address the extent of genetic variation in the Iberian peninsula between its geographic extremes (Huelva and the Basque area) and to explain the intensity of the phylogenetic relationships between Andalusians and other neighboring populations, such as those from North Africa. We present, for the first time, results on allotype markers (GM and KM) of human immunoglobulins in the Andalusian population from Huelva. The most frequent GM haplotypes in Andalusia correspond to those that are also the most common in Europe. A sub-Saharan haplotype was found at a relatively high frequency compared to other Iberian samples, and a North Asian marker did not reach polymorphic frequencies in the study sample. A hierarchical cluster analysis based on the first two principal components (94.1% of the total genetic variance) revealed an interesting geographic structure for the 49 populations selected from the literature. The Huelva sample showed a central position in the multivariate space--despite being geographically located at one of the extremes of the Mediterranean basin--and clustered with most Western European populations. Western Europe and Eastern Europe (the latter group paradoxically including Italy and the major islands of the western Mediterranean) were differentiated. North African populations were grouped in two clusters that did not separate either Arabs and Berbers or their present-day countries. Analysis of immunoglobulin allotype markers shows that gene flow among human populations should generally be interpreted in terms of complex patterns, with the observed frequencies being the consequence of the entire genetic and demographic history of the population. Single historical events rarely determine gene frequencies in large human populations. Analysis of the GM system has shown that the Andalusian population from Huelva, as a result of its complex history, is not simply an outstanding part of the Mediterranean world but rather the genetic center of gravity of that world.     

The history of African gene flow into Southern Europeans, Levantines, and Jews

Previous genetic studies have suggested a history of sub-Saharan African gene flow into some West Eurasian populations after the initial dispersal out of Africa that occurred at least 45,000 years ago. However, there has been no accurate characterization of the proportion of mixture, or of its date. We analyze genome-wide polymorphism data from about 40 West Eurasian groups to show that almost all Southern Europeans have inherited 1%-3% African ancestry with an average mixture date of around 55 generations ago, consistent with North African gene flow at the end of the Roman Empire and subsequent Arab migrations. Levantine groups harbor 4%-15% African ancestry with an average mixture date of about 32 generations ago, consistent with close political, economic, and cultural links with Egypt in the late middle ages. We also detect 3%-5% sub-Saharan African ancestry in all eight of the diverse Jewish populations that we analyzed. For the Jewish admixture, we obtain an average estimated date of about 72 generations. This may reflect descent of these groups from a common ancestral population that already had some African ancestry prior to the Jewish Diasporas.     

Regional differences in the distribution of the sub-Saharan, West Eurasian, and South Asian mtDNA lineages in Yemen

Despite its key location for population movements out of and back into Africa, Yemen has not yet been sampled on a regional level for an investigation of sub-Saharan, West Eurasian, and South Asian genetic contributions. In this study, we present mitochondrial DNA (mtDNA) data for regionally distinct Yemeni populations that reveal different distributions of mtDNA lineages. An extensive database of mtDNA sequences from North and East African, Middle Eastern and Indian populations was analyzed to provide a context for the regional Yemeni mtDNA datasets. The groups of western Yemen appear to be most closely related to Middle Eastern and North African populations, while the eastern Yemeni population from Hadramawt is most closely related to East Africa. Furthermore, haplotype matches with Africa are almost exclusively confined to West Eurasian R0a haplogroup in southwestern Yemen, although more sub-Saharan L-type matches appear in more northern Yemeni populations. In fact, Yemeni populations have the highest frequency of R0a haplotypes detected to date, thus Yemen or southern Arabia may be the site of the initial expansion of this haplogroup. Whereas two variants of the sub-Saharan haplogroup M1 were detected only in southwestern Yemen close to the Bab el-Mandeb Strait, different non-African M haplotypes were detected at low frequencies (approximately 2%) in western parts of the country and at a higher frequency (7.5%) in the Hadramawt. We conclude that the Yemeni gene pool is highly stratified both regionally and temporally and that it has received West Eurasian, Northeast African, and South Asian gene flow.     

Phylogeography of the lacertid lizard, Psammodromus algirus, in Iberia and across the Strait of Gibraltar

Aim  To determine genetic substructuring within the lacertid lizard Psammodromus algirus . To compare levels of variation across a geological barrier, the Strait of Gibraltar, and to compare this against the known age of the barrier using a molecular clock hypothesis. To compare the effect of the barrier within this species with previously published data from other organisms.
Location  The Iberian Peninsula and North Africa.
Methods  Partial sequences from the mitochondrial cytochrome b , 12S rRNA and 16S rRNA genes were obtained from 101 specimens belonging to the subfamily Gallotiinae and used in this study. The data set was aligned using C lustal X and phylogenetic trees produced using both maximum-parsimony and maximum-likelihood methods. Maximum likelihood estimates of divergence times for the combined data set (12S + 16S + cytochrome b ) were obtained after discovery of lineage rate constancy across the tree using a likelihood ratio test.
Results  Psammodromus algirus contains divergent eastern and western mtDNA clades within the Iberian Peninsula. The western clade has northern and southern lineages in Iberia and one in North Africa. This phylogeographical pattern indicates that the lizard invaded North Africa after the opening of the Strait, presumably by natural rafting.
Main conclusions  As in several other species, current patterns of genetic diversity within P. algirus are not directly related to the opening of the Strait of Gibraltar. Widespread sampling on both sides of the barrier is necessary to determine its effect on species in this area accurately.     

Genetic evidence for larger African population size during recent human evolution

Genetic evidence suggests that the long-term average effective size of sub-Saharan Africa is larger than other geographic regions. A method is described that allows estimation of relative long-term regional population sizes. This method is applied to 60 microsatellite DNA loci from a sample of 72 sub-Saharan Africans, 63 East Asians, and 120 Europeans. Average heterozygosity is significantly higher in the sub-Saharan African sample. Expected heterozygosity was computed for each region and locus using a population genetic model based on the null hypothesis of equal long-term population sizes. Average residual heterozygosity is significantly higher in the sub-Saharan African sample, indicating that African population size was larger than other regions during recent human evolution. The best fit of the model is with relative population weights of 0.73 for sub-Saharan Africa, 0.09 for East Asia, and 0.18 for Europe. These results are similar to those obtained using craniometric variation for these three geographic regions. These results, combined with inferences from other genetic studies, support a major role of Africa in the origin of modern humans. It is less clear, however, whether complete African replacement is the most appropriate model. An alternative is an African origin with non-African gene flow. While Africa is an important region in recent human evolution, it is not clear whether the gene pool of our species is completely out of Africa or predominately out of Africa.