MtDNA profile of West Africa Guineans: towards a better understanding of the Senegambia region

The matrilineal genetic composition of 372 samples from the Republic of Guiné-Bissau (West African coast) was studied using RFLPs and partial sequencing of the mtDNA control and coding region. The majority of the mtDNA lineages of Guineans (94%) belong to West African specific sub-clusters of L0-L3 haplogroups. A new L3 sub-cluster (L3h) that is found in both eastern and western Africa is present at moderately low frequencies in Guinean populations. A non-random distribution of haplogroups U5 in the Fula group, the U6 among the "Brame" linguistic family and M1 in the Balanta-Djola group, suggests a correlation between the genetic and linguistic affiliation of Guinean populations. The presence of M1 in Balanta populations supports the earlier suggestion of their Sudanese origin. Haplogroups U5 and U6, on the other hand, were found to be restricted to populations that are thought to represent the descendants of a southern expansion of Berbers. Particular haplotypes, found almost exclusively in East-African populations, were found in some ethnic groups with an oral tradition claiming Sudanese origin.info:eu-repo/semantics/publishedVersio

Explaining the Imperfection of the Molecular Clock of Hominid Mitochondria

The molecular clock of mitochondrial DNA has been extensively used to date various genetic events. However, its substitution rate among humans appears to be higher than rates inferred from human-chimpanzee comparisons, limiting the potential of interspecies clock calibrations for intraspecific dating. It is not well understood how and why the substitution rate accelerates. We have analyzed a phylogenetic tree of 3057 publicly available human mitochondrial DNA coding region sequences for changes in the ratios of mutations belonging to different functional classes. The proportion of non-synonymous and RNA genes substitutions has reduced over hundreds of thousands of years. The highest mutation ratios corresponding to fast acceleration in the apparent substitution rate of the coding sequence have occurred after the end of the Last Ice Age. We recalibrate the molecular clock of human mtDNA as 7990 years per synonymous mutation over the mitochondrial genome. However, the distribution of substitutions at synonymous sites in human data significantly departs from a model assuming a single rate parameter and implies at least 3 different subclasses of sites. Neutral model with 3 synonymous substitution rates can explain most, if not all, of the apparent molecular clock difference between the intra- and interspecies levels. Our findings imply the sluggishness of purifying selection in removing the slightly deleterious mutations from the human as well as the Neandertal and chimpanzee populations. However, for humans, the weakness of purifying selection has been further exacerbated by the population expansions associated with the out-of Africa migration and the end of the Last Ice Age

Croatian genetic heritage: Y-chromosome story

The aim of this article is to offer a concise interpretation of the scientific data about the topic of Croatian genetic heritage that was obtained over the past 10 years. We made a short overview of previously published articles by our and other groups, based mostly on Y-chromosome results. The data demonstrate that Croatian human population, as almost any other European population, represents remarkable genetic mixture. More than 3/4 of the contemporary Croatian men are most probably the offspring of Old Europeans who came here before and after the Last Glacial Maximum. The rest of the population is the offspring of the people who were arriving in this part of Europe through the southeastern route in the last 10 000 years, mostly during the neolithization process. We believe that the latest discoveries made with the techniques for whole-genome typing using the array technology, will help us understand the structure of Croatian population in more detail, as well as the aspects of its demographic history

Y-chromosomal diversity in the population of Guinea-Bissau: a multiethnic perspective

<p>Abstract</p> <p>Background</p> <p>The geographic and ethnolinguistic differentiation of many African Y-chromosomal lineages provides an opportunity to evaluate human migration episodes and admixture processes, in a pan-continental context. The analysis of the paternal genetic structure of Equatorial West Africans carried out to date leaves their origins and relationships unclear, and raises questions about the existence of major demographic phenomena analogous to the large-scale Bantu expansions. To address this, we have analysed the variation of 31 binary and 11 microsatellite markers on the non-recombining portion of the Y chromosome in Guinea-Bissau samples of diverse ethnic affiliations, some not studied before.</p> <p>Results</p> <p>The Guinea-Bissau Y chromosome pool is characterized by low haplogroup diversity (D = 0.470, sd 0.033), with the predominant haplogroup E3a*-M2 shared among the ethnic clusters and reaching a maximum of 82.2% in the Mandenka people. The Felupe-Djola and Papel groups exhibit the highest diversity of lineages and harbor the deep-rooting haplogroups A-M91, E2-M75 and E3*-PN2, typical of Sahel's more central and eastern areas. Their genetic distinction from other groups is statistically significant (P = 0.01) though not attributable to linguistic, geographic or religious criteria. Non sub-Saharan influences were associated with the presence of haplogroup R1b-P25 and particular lineages of E3b1-M78.</p> <p>Conclusion</p> <p>The predominance and high diversity of haplogroup E3a*-M2 suggests a demographic expansion in the equatorial western fringe, possibly supported by a local agricultural center. The paternal pool of the Mandenka and Balanta displays evidence of a particularly marked population growth among the Guineans, possibly reflecting the demographic effects of the agriculturalist lifestyle and their putative relationship to the people that introduced early cultivation practices into West Africa. The paternal background of the Felupe-Djola and Papel ethnic groups suggests a better conserved ancestral pool deriving from East Africa, from where they have supposedly migrated in recent times. Despite the overall homogeneity in a multiethnic sample, which contrasts with their social structure, minor clusters suggest the imprints of multiple peoples at different timescales: traces of ancestral inhabitants in haplogroups A-M91 and B-M60, today typical of hunter-gatherers; North African influence in E3b1-M78 Y chromosomes, probably due to trans-Saharan contacts; and R1b-P25 lineages reflecting European admixture via the North Atlantic slave trade.</p

Y-chromosome lineages in Cabo Verde Islands witness the diverse geographic origin of its first male settlers

The Y-chromosome haplogroup composition of the population of the Cabo Verde Archipelago was profiled by using 32 single-nucleotide polymorphism markers and compared with potential source populations from Iberia, west Africa, and the Middle East. According to the traditional view, the major proportion of the founding population of Cabo Verde was of west African ancestry with the addition of a minor fraction of male colonizers from Europe. Unexpectedly, more than half of the paternal lineages (53.5%) of Cabo Verdeans clustered in haplogroups I, J, K, and R1, which are characteristic of populations of Europe and the Middle East, while being absent in the probable west African source population of Guiné-Bissau. Moreover, a high frequency of J* lineages in Cabo Verdeans relates them more closely to populations of the Middle East and probably provides the first genetic evidence of the legacy of the Jews. In addition, the considerable proportion (20.5%) of E3b(xM81) lineages indicates a possible gene flow from the Middle East or northeast Africa, which, at least partly, could be ascribed to the Sephardic Jews. In contrast to the predominance of west African mitochondrial DNA haplotypes in their maternal gene pool, the major west African Y-chromosome lineage E3a was observed only at a frequency of 15.9%. Overall, these results indicate that gene flow from multiple sources and various sex-specific patterns have been important in the formation of the genomic diversity in the Cabo Verde islands.info:eu-repo/semantics/publishedVersio

Mitochondrial DNA Heritage of Cres Islanders – Example of Croatian Genetic Outliers

Diversity of mitochondrial DNA (mtDNA) lineages of the Island of Cres was determined by high-resolution phylogenetic analysis on a sample of 119 adult unrelated individuals from eight settlements. The composition of mtDNA pool of this Island population is in contrast with other Croatian and European populations. The analysis revealed the highest frequency of haplogroup U (29.4%) with the predominance of one single lineage of subhaplogroup U2e (20.2%). Haplogroup H is the second most prevalent one with only 27.7%. Other very interesting features of contemporary Island population are extremely low frequency of haplogroup J (only 0.84%), and much higher frequency of haplogroup W (12.6%) comparing to other Croatian and European populations. Especially interesting finding is a strikingly higher frequency of haplogroup N1a (9.24%) presented with African/south Asian branch almost absent in Europeans, while its European sister-branch, proved to be highly prevalent among Neolithic farmers, is present in contemporary Europeans with only 0.2%. Haplotype analysis revealed that only five mtDNA lineages account for almost 50% of maternal genetic heritage of this island and they present supposed founder lineages. All presented findings confirm that genetic drift, especially founder effect, has played significant role in shaping genetic composition of the isolated population of the Island of Cres. Due to presented data contemporary population of Cres Island can be considered as genetic »outlier« among Croatian populations

Maternal Genetic Legacy of the Eastern Adriatic Island of Krk – an Interplay of Evolutionary Forces and Island’s Historical Events in Shaping the Genetic Structure of Contemporary Island Population

This study presents genetic diversity and structure of contemporary Krk islanders revealed by high-resolution mitochondrial DNA analysis on a sample of 132 unrelated autochthonous adults from seven different settlements and regions of the island. Relatively high level of haplogroup and haplotype diversity in the overall island sample is an indicator of numerous migrations and gene flows throughout the history. Expectedly, the results show the highest frequency of haplogroup H (33.3%), yet this value is much lower compared to different Croatian and other European mainland populations. An interesting finding refers to highly elevated frequencies of some haplogroups, otherwise rare in Croatia and most of the Europe, such as I (11.3%) and W (7.6%) in Krk population, especially pronounced in some settlements. At the level of settlements, many of the major European haplogroups were found to be absent from their mtDNA gene pools, whereas several others show a pronounced deviation from an average. Overall, our results suggest a tangled interplay of different evolutionary forces, such as founder effects and a few strong bottlenecks, presumably due to epidemics, which have occurred in various periods of the island’s history. Cultural customs, such as frequent endogamy in some regions of the island during past centuries, have additionally shaped its genetic structure into the observed present-day diversity patterns

Maternal Genetic Legacy of the Eastern Adriatic Island of Krk – an Interplay of Evolutionary Forces and Island’s Historical Events in Shaping the Genetic Structure of Contemporary Island Population

This study presents genetic diversity and structure of contemporary Krk islanders revealed by high-resolution mitochondrial DNA analysis on a sample of 132 unrelated autochthonous adults from seven different settlements and regions of the island. Relatively high level of haplogroup and haplotype diversity in the overall island sample is an indicator of numerous migrations and gene flows throughout the history. Expectedly, the results show the highest frequency of haplogroup H (33.3%), yet this value is much lower compared to different Croatian and other European mainland populations. An interesting finding refers to highly elevated frequencies of some haplogroups, otherwise rare in Croatia and most of the Europe, such as I (11.3%) and W (7.6%) in Krk population, especially pronounced in some settlements. At the level of settlements, many of the major European haplogroups were found to be absent from their mtDNA gene pools, whereas several others show a pronounced deviation from an average. Overall, our results suggest a tangled interplay of different evolutionary forces, such as founder effects and a few strong bottlenecks, presumably due to epidemics, which have occurred in various periods of the island’s history. Cultural customs, such as frequent endogamy in some regions of the island during past centuries, have additionally shaped its genetic structure into the observed present-day diversity patterns

The genetic structure of south Asian populations as revealed by 650 000 SNPs

The analyses of dense marker sets covering the whole genome has revolutionised the field of (human) population genetics. Driven largely by the needs of biomedical research, these new data are helping to unveil our demographic past, exemplified by the study of mtDNA and Y-chromosome variation during the past &#8764;20 years. We have analysed (Illumina 650K SNPs) over 320 new samples from South and Central Asia and the Caucasus, together with the publicly available databases (HGDP panel and our published data set of &#8764;600 Eurasian samples) and illustrated the power of full genome analyses by addressing two specific questions. (i) What is the nature of genetic continuity and discontinuity between South Asia, Middle East and Central Asia? (ii) What are the genetic origins of the Munda speakers of India? We use principal component and structure-like analyses to reveal the structure in the genome wide SNP data. The most striking feature of the genetic structure of South Asian populations is the clear separation of the Indus valley and southern India populations. The genetic component prevalent in the latter region is marginal in the former and absent outside South Asia. By contrast, the component ubiquitous to Indus valley is also present (&#8764;30-40 %) among Indo-European speakers from Ganges valley and Dravidic speakers in southern India. Furthermore, this component can also be found in Central Asia and the Caucasus as well as in Middle East. We explored possibilities to identify the source region for this genetic component. Alternative models put the origins of Munda languages speakers either in South Asia (the Munda speakers sport exclusively autochthonous South Asian mtDNA variants) or in Southeast Asia, where the other Austro Asiatic languages have spread. Y-chromosome variation supports the latter model through sharing of hg O2a in both regions. We show that in addition to the dominant ancestry component being shared between the Indian Dravidic and Munda speakers, up to 30% of Munda speakers retain an ancestry component otherwise prevalent in East Asia. There is no widespread sign of South Asian ancestry component in Southeast Asia. This provides genomic support to the model by which Indian Austro-Asiatic populations derive from dispersal from Southeast/East Asia, followed by an extensive admixture with local Indian populations