Spatial genetic patterns of Octopus vulgaris Mediterranean populations support the hypothesis of a transitional zone across the Siculo-Tunisian Strait

AbstractRecent research hypothesised that the Siculo-Tunisian Strait might fit, at least for some species, the picture of a genetic transitional zone instead of a sharp genetic break between the Western and Eastern Mediterranean basins. The present study aimed at using the common Octopus, Octopus vulgaris as an empirical test-case to evaluate this hypothesis. To accomplish this goal, 458 new sequences of the mitochondrial gene cytochrome c oxidase subunit I were used. Combining the new sequences with those available on public databases, we assembled a dataset containing 920 sequences to investigate the spatial genetic patterns across 34 Mediterranean populations of O. vulgaris. The genetic structure of this species was assessed combining analysis of molecular variance and Median-Joining networks. Results supported the hypothesis of a complex spatial genetic pattern across the Sicilian channel. Contemporary factors, such as marine currents, likely affect the species' genetic structuring across this area. Overall, our results highlighted that focusing the attention on the whole transitional area rather than on a unique genetic break might help to detect similar patterns across different species. Finally, acknowledging the occurrence of complex spatial genetic patterns across transitional zones may improve stock identification and management practices for commercially valuable species

Genome-Wide and Paternal Diversity Reveal a Recent Origin of Human Populations in North Africa.

The geostrategic location of North Africa as a crossroad between three continents and as a stepping-stone outside Africa has evoked anthropological and genetic interest in this region. Numerous studies have described the genetic landscape of the human population in North Africa employing paternal, maternal, and biparental molecular markers. However, information from these markers which have different inheritance patterns has been mostly assessed independently, resulting in an incomplete description of the region. In this study, we analyze uniparental and genome-wide markers examining similarities or contrasts in the results and consequently provide a comprehensive description of the evolutionary history of North Africa populations. Our results show that both males and females in North Africa underwent a similar admixture history with slight differences in the proportions of admixture components. Consequently, genome-wide diversity show similar patterns with admixture tests suggesting North Africans are a mixture of ancestral populations related to current Africans and Eurasians with more affinity towards the out-of-Africa populations than to sub-Saharan Africans. We estimate from the paternal lineages that most North Africans emerged ~15,000 years ago during the last glacial warming and that population splits started after the desiccation of the Sahara. Although most North Africans share a common admixture history, the Tunisian Berbers show long periods of genetic isolation and appear to have diverged from surrounding populations without subsequent mixture. On the other hand, continuous gene flow from the Middle East made Egyptians genetically closer to Eurasians than to other North Africans. We show that genetic diversity of today's North Africans mostly captures patterns from migrations post Last Glacial Maximum and therefore may be insufficient to inform on the initial population of the region during the Middle Paleolithic period.This study was supported in parts by Spanish Government MCINN grant CGL2010-14944/BOS and Programa de Cooperación Interuniversitaria e Investigación Científica, Spanish Ministry of Foreign Affairs and Cooperation grants A75180/06, A/8394/07, B/018514/08, A1/040218/11.Peer Reviewe

Study of the human African genome landscape through the analysis of complete genomes

Trabajo presentado en la Annual Meeting of the Society for Molecular Biology and Evolution (SMBE 2015), celebrada en Viena del 12 al 16 de julio de 2015.Understanding the genetic diversity in humans within the African continent is pivotal to have a full picture of the demographic history of the human species. Here, we study complete genome sequeces of a diverse panel of African individuals in terms of geographical location, linguistic context and lifestyle. Most African diversity studies have mainly focused on uniparental markers or selected autosomal markers, which introduce an ascertainment bias in the analysis. The analysis of complete genomes has been poorly developed in the study of African human genomics and internal population diversity. The main goals of this study are: 1. Characterisation of the internal human diversity in Africa overcoming ascertainment bias-related problems by using complete genomes. 2. Characterization of the deepest splits in the human lineage and the processes (such as migrations and admixtures) that have shaped the current genetic map.Funded by: MINECO CGL 2013-44351-P.N

Demographic inferences from a diverse panel of African human genomes

Trabajo presentado en la Annual Meeting of the Society for Molecular Biology and Evolution (SMBE 2015), celebrada en Viena del 12 al 16 de julio de 2015.Understanding genetic variation across ethnically and geographically diverse extant African populations is of great importance for reconstructing human complex demographic history. Here, we study the recent history and relationships among 15 different African populations, by analyzing the whole-genome sequence data of 21 individuals sequenced at deep coverage covering all major contine ntal linguistic groups, ecosystems and life-styles within Africa. We detected 12 million single nucleotide substitutions, providing a rich picture of the genome diversity and population history in Africa. We observe a remarkable correlation among genetic diversity and geographic origins and recent demographic history of the individuals studied. While different hunter-gatherer groups show more differentiation compared with the rest of samples, Bantu individuals are genetically more homogeneous and present evidence of admixture with neighboring hunter-gatherer groups, depending on the geographic area. Northern African individuals are closely related to non-African populations, in agreement with a recent split of both groups and continuous gene flow. To gain in sight into the deepest split of our species, we explore if recent admixture of Pygmies and Khoesan with other populations may cover up their real diversity, becoming the human most diverse groups.N

Whole-genome sequence analysis of a Pan African set of samples reveals archaic gene flow from an extinct basal population of modern humans into sub-Saharan populations

BackgroundPopulation demography and gene flow among African groups, as well as the putative archaic introgression of ancient hominins, have been poorly explored at the genome level.ResultsHere, we examine 15 African populations covering all major continental linguistic groups, ecosystems, and lifestyles within Africa through analysis of whole-genome sequence data of 21 individuals sequenced at deep coverage. We observe a remarkable correlation among genetic diversity and geographic distance, with the hunter-gatherer groups being more genetically differentiated and having larger effective population sizes throughout most modern-human history. Admixture signals are found between neighbor populations from both hunter-gatherer and agriculturalists groups, whereas North African individuals are closely related to Eurasian populations. Regarding archaic gene flow, we test six complex demographic models that consider recent admixture as well as archaic introgression. We identify the fingerprint of an archaic introgression event in the sub-Saharan populations included in the models (similar to 4.0% in Khoisan, similar to 4.3% in Mbuti Pygmies, and similar to 5.8% in Mandenka) from an early divergent and currently extinct ghost modern human lineage.ConclusionThe present study represents an in-depth genomic analysis of a Pan African set of individuals, which emphasizes their complex relationships and demographic history at population level.Peer reviewe

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 genomic analysis of current-day North African populations reveals the existence of trans-Saharan migrations with different origins and dates

Data de publicació electrònica: 28-11-2022The Sahara Desert has acted as a barrier to human gene-flow between the northern and central parts of Africa since its aridification. Nonetheless, some contacts between both sides of the desert have occurred throughout history, mainly driven by commercial activity. Part of this was the infamous trans-Saharan slave trade, which forcedly brought peoples from south of the Sahara to North Africa from Roman times until the nineteenth century. Although historical records exist, the genetic aspects of these trans-Saharan migrations have not been deeply studied. In the present study, we assess the genetic influence of trans-Saharan migrations in current-day North Africa and characterize its amount, geographical origin, and dates. We confirm the heterogeneous and generally low-frequency presence of genomic segments of sub-Saharan origin in present-day North Africans acquired in recent historical times, and we show evidence of at least two admixture events: one dated around the thirteenth-fourteenth centuries CE between North Africans and a Western-sub-Saharan-like source similar to current-day Senegambian populations, and another one dated around the seventeenth century CE involving Tunisians and an Eastern-sub-Saharan-like source related to current-day south-Sudan and Kenyan populations. Time and location coincide with the peak of trans-Saharan slave-trade activity between Western African empires and North African powers, and are also concordant with the possibility of continuous recent south-to-north gene-flow. These findings confirm the trans-Saharan human genetic contacts, providing new and precise evidence about its possible dates and geographical origins, which are pivotal to understanding the genomic composition of an underrepresented region such as North Africa.Open Access funding provided thanks to the CRUE-CSIC agreement with Springer Nature. This work was supported by the Spanish Ministry of Science, Innovation and Universities (MCIU) and the Agencia Estatal de Investigación (AEI) [PID2019-106485 GB-I00/AEI/1.0.13039/501100011033]; and “Unidad de Excelencia María de Maeztu” [AEI, CEX2018-000792-M]. ML-S was supported by an FPI-MINECO PRE2018-084178 fellowship

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. Pay-Per-View Download To access this article as a PDF pay-per-view download via BioOne, please click here

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

Versión final disponible en www3.interscience.wiley.comHuman 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.Peer reviewe

Substructure of a Tunisian Berber Population as Inferred from 15 Autosomal Short Tandem Repeat Loci

Currently, language and cultural practices are the only criteria to distinguish between Berber autochthonous Tunisian populations. To evaluate these populations’ possible genetic structure and differentiation, we have analyzed 15 autosomal short tandem repeat loci (CSF1PO, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D21S11, FGA, TH01, TPOX, VWA, D2S1338, and D19S433) in three southern Tunisian Berber groups: Sened, Matmata, and Chenini-Douiret. The exact test of population differentiation based on allele frequencies at the 15 loci shows significant P values at 7 loci between Chenini-Douiret and both Sened and Matmata, whereas just 5 loci show significant P values between Sened and Matmata. Comparative analyses between the three Berber groups based on genetic distances show that P values for FST distances are significant between the three Berber groups. Population analysis performed using Structure shows a clear differentiation between these Berber groups, with strong genetic isolation of Chenini-Douiret. These results confirm at the autosomal level the high degree of heterogeneity of Tunisian Berber populations that had been previously reported for uniparental markers