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Map of sub-Sahara Africa indicating geographical location and linguistic groups. Geometric figures represent linguistic affiliations and geographic locations.
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Here, we present 12 loci paternal haplotypes (Y-STR profiles) against
the backdrop of the Y-SNP marker system of Bantu males from the
Maputo Province of Southeast Africa, a region believed to represent
the southeastern fringe of the Bantu expansion. Our Maputo Bantu
group was analyzed within the context of 27 geographically relevant
reference popul...
Contexts in source publication
Context 1
... 27 reference populations were typed for the same 12 Y-STR loci and binary Y-SNP markers genotyped for the MAP population in this study. A list of populations, abbreviations, sample number, geographical regions, language affiliations and references is provided in Table 1. A map of Africa indicating the locations of the populations is included in Fig. ...Context 2
... relationships among the MAP and the reference populations were assessed using MDS analysis based on Rst distances derived from the Y-STR data (Fig. 2) and confirmed by a MDS utilizing the Jaccard similarity indices (Supplementary Fig. 1). The 12-loci MDS plot (Fig. 2) displays a loose aggregation of populations mainly on the right side of the plot encompassing all of the Bantu groups including those from both East (RWA, SUK and TUR) as well as West (AKE, BEN, DUM, ESH, EVI, FAN, GAL, KOT, MAK, NDU, NGU, NZE, OBA, ORU, PUN, SHA, TEK and TSO) Africa. ...Context 3
... total of 27 geographically relevant reference populations were selected for genetic comparison including West African and East African Bantus as well as six non-Bantu groups (Pygmy populations from Gabon and Cameroon, and the Burunge, Datog, Hadza and Sandawe from Tanzania). The 27 reference populations were typed for the same 12 Y-STR loci and binary Y-SNP markers genotyped for the MAP population in this study. A list of populations, abbreviations, sample number, geographical regions, language affiliations and references is provided in Table 1. A map of Africa indicating the locations of the populations is included in Fig. ...Context 4
... relationships among the MAP and the reference populations were assessed using MDS analysis based on Rst distances derived from the Y-STR data (Fig. 2) and confirmed by a MDS utilizing the Jaccard similarity indices (Supplementary Fig. 1). The 12-loci MDS plot (Fig. 2) displays a loose aggregation of populations mainly on the right side of the plot encompassing all of the Bantu groups including those from both East (RWA, SUK and TUR) as well as West (AKE, BEN, DUM, ESH, EVI, FAN, GAL, KOT, MAK, NDU, NGU, NZE, OBA, ORU, PUN, SHA, TEK and TSO) Africa. Although the MAP is immediately surrounded by Bantu tribes (SUK and TUR from Tanzania and ESH and MAK from Gabon), it is positioned near the upper perimeter of the Bantu cluster and close to two non-Bantu populations from Tanzania, DAT (Nilo-Saharan) and SAN ...Similar publications
China is a multinational country composed of 56 ethnic groups of which the Han Chinese accounts for 91.60%. Qinghai Province is located in the northeastern part of the Qinghai–Tibet Plateau, has an area of 72.12 km², and is the fourth largest province in China. In the present study, we investigated the genetic polymorphisms of 20 short tandem repea...
Short tandem repeats (STRs) are attractive to genetic applications like forensic, anthropological and population genetics studies. The Huaxia Platinum System was specifically developed to allow co-amplification and detection of all markers in the expanded CODIS core loci and the Chinese National Database. In this study, in continuation to our previ...
Citations
... which includes samples from haplogroup A. Haplogroup A is virtually restricted to the African continent, reaching the highest frequencies in Khoisan-speaking populations. It is also frequent in the Nilotic groups from east and northeast Africa 23,36-38 , and it was sporadically observed in the southeast and southwest populations 39,40 . Some lineages inside clade A have geographic specificity. ...
... Nevertheless, recent studies showed that haplogroup B2a was already present in Khoisan groups before their contact with Bantu-speaking populations 43,45 . We identified three samples belonging to B2a-M150* in Palenque (5.17% of the African lineages), all lacking the M109-derived allele usually present in southwest, southeast and south African Bantu populations 40,46,47 . Subclade B2a is widely dispersed throughout sub-Saharan Africa 44,45 . ...
... The haplogroup E1b1a-M2 (and its sub-lineages) is widely spread in Africa and highly prevalent in all Bantu sub-Saharan populations, with frequencies above 80% in most populations 39,40,46,47 . In Palenque, 45.26% of the samples (74.14% of the African samples) belong to the haplogroup E1b1a-M2*(xM154,M191) and to its sub-clade E1b1a-M191. ...
San Basilio de Palenque is an Afro-descendant community near Cartagena, Colombia, founded in the sixteenth century. The recognition of the historical and cultural importance of Palenque has promoted several studies, namely concerning the African roots of its first inhabitants. To deepen the knowledge of the origin and diversity of the Palenque parental lineages, we analysed a sample of 81 individuals for the entire mtDNA Control Region as well as 92 individuals for 27 Y-STRs and 95 for 51 Y-SNPs. The results confirmed the strong isolation of the Palenque, with some degree of influx of Native American maternal lineages, and a European admixture exclusively mediated by men. Due to the high genetic drift observed, a pairwise FST analysis with available data on African populations proved to be inadequate for determining population affinities. In contrast, when a phylogenetic approach was used, it was possible to infer the phylogeographic origin of some lineages in Palenque. Contradicting previous studies indicating a single African origin, our results evidence parental genetic contributions from widely different African regions.
... The molecular genetic footprints of African slavery in both North America and Southwest Asia (the Arab Mashriq), indicated by a preponderance of European Y-chromosomal haplogroups coupled with a preponderance of sub-Saharan African mtDNA haplogroups in modern African American populations(Lind et al., 2007) and by a preponderance of Southwest Asian (Mashriqi Arab) Y-chromosomal haplogroups coupled with a substantial proportion of sub-Saharan African mtDNA haplogroups in modern Mashriqi Arab populations(Richards et al., 2003); 2. The molecular genetic footprint of the Neolithic Bantu expansion from West Africa, indicated by a preponderance of West African Y-chromosomal haplogroups coupled with a preponderance of aboriginal mtDNA haplogroups in sub-Saharan Africa(Berniell-Lee et al., 2009;Gignoux et al. 2011;Li et al., 2014;Rowold et al., 2014;Wood et al., 2005); 3. The molecular genetic footprint of the Islamic imperial Arab expansion into the North African Maghreb, indicated by a preponderance of Arabian Peninsula Y-chromosomal haplogroups coupled with a preponderance of aboriginal mtDNA haplogroups in the North African Maghreb(Chiaroni et al., 2010;Regueiro et al., 2015;Triki-Fendri & Rebai, 2014); 4. The molecular genetic footprint of the Southwest Asian Neolithic expansion into Europe, indicated by a preponderance of Southwest Asian Y-chromosomal haplogroups coupled with a preponderance of aboriginal (Paleolithic European) mtDNA haplogroups in Europe(Balaresque et al., 2010;Chikhi et al., 2002; Fernández et al., 2014;Francalacci et al., 2010;Lacan et al., 2011;Richards et al., 2000;Semino et al., 2000; Sjödin & François, 2011;Torroni et al., 2001); 5. The molecular genetic footprint of the Anglo-Saxon invasion and migration into Britain, indicated by a preponderance of Anglo-Saxon Y-chromosomal haplogroups coupled with a preponderance of aboriginal (native British) mtDNA haplogroups in Britain(Weale et al., 2002); 6. ...
This article presents a discussion of neurocognitive hacking and its potential for use at the strategic, operational, and tactical levels of cyber conflict. Neurocognitive hacking refers to the ability to activate specific neural areas of the brain, via subliminal or supraliminal stimuli, to shape the behavioral outcomes of an adversary. Research suggests that awareness of mortality-related stimuli has neural correlates in the right amygdala and left anterior cingulate cortex and mediates negative behavior toward out-group members, including unconscious discriminatory behavior. Given its in-group/out-group dynamic, the phenomenon could be exploited for use in information operations toward target populations, specifically ones that are multiethnic, multicultural, or multireligious. Although development of the theoretical framework behind neurocognitive hacking is ongoing, mortality-related stimuli are proposed to activate one’s unconscious vigilance system to further evaluate the locus and viability of the suspect stimuli. Research suggests that the subsequent discriminatory affective reactions directed toward out-group members are representative of automatic heuristics evolved to protect the organism in the event a stimulus represents a more serious threat to survival. Therefore, presenting mortality-related stimuli over computer networks to targeted audiences may facilitate the ingestion of tailored propaganda or shaping of specific behavioral outcomes within a population, including sowing division in a target community or weakening support for a specific political regime.
... ; 2. The molecular genetic footprint of the Neolithic Bantu expansion from West Africa, indicated by a preponderance of West African Y-chromosomal haplogroups coupled with a preponderance of aboriginal mtDNA haplogroups in sub-Saharan Africa(Berniell-Lee et al., 2009;Gignoux et al. 2011;Li et al., 2014;Rowold et al., 2014;Wood et al., 2005); 3. The molecular genetic footprint of the Islamic imperial Arab expansion into the North African Maghreb, indicated by a preponderance of Arabian Peninsula Y-chromosomal haplogroups coupled with a preponderance of aboriginal mtDNA haplogroups in the North African Maghreb (Chiaroni et al., 2010; Regueiro et al., 2015; Triki-Fendri & Rebai, 2014); 4. The molecular genetic footprint of the Southwest Asian Neolithic expansion into Europe, indicated by a preponderance of Southwest Asian Y-chromosomal haplogroups coupled with a preponderance of aboriginal (Paleolithic European) mtDNA haplogroups in Europe (Balaresque et al., 2010; Chikhi et al., 2002; Fernández et al., 2014; Francalacci et al., 2010; Lacan et al., 2011; Richards et al., 2000; Semino et al., 2000; Sjödin & François, 2011; Torroni et al., 2001); 5. The molecular genetic footprint of the Anglo-Saxon invasion and migration into Britain, indicated by a preponderance of Anglo-Saxon Y-chromosomal haplogroups coupled with a preponderance of aboriginal (native British) mtDNA haplogroups in Britain (Weale et al., 2002); 6. ...
Knowledge of evolutionary influences on patterns of human mating, social interactions, and differential health is increasing, yet these insights have rarely been applied to historical analyses of human population dynamics. The genetic and evolutionary forces behind biases in interethnic mating and in the health of individuals of different ethnic groups in Latin America and the Caribbean since the European colonization of America are still largely ignored. We discuss how historical and contemporary sociocultural interactions and practices are strongly influenced by population-level evolutionary forces. Specifically, we discuss the historical implications of functional (de facto) polygyny, sex-biased admixture, and assortative mating in Latin America. We propose that these three evolutionary mechanisms influenced mating patterns, shaping the genetic and cultural landscape across Latin America and the Caribbean. Further, we discuss how genetic differences between the original populations that migrated at different times into Latin America contributed to their accommodation to and survival in the different local ecologies and interethnic interactions. Relevant medical and social implications follow from the genetic and cultural changes reviewed.
... Supplementary Table 1 provides the population designations and number of individuals in each of the three genotyped groups. Isolation of the genomic DNA was performed as previously described (Rowold et al., 2014;Chennakrishnaiah et al., 2013). ...
... Especially interesting is the observation that although there appears to be an asymmetrical longitudinal partitioning of E1b1b1-M35 and R1b1-P25 in the eastern versus western regions of the continent, respectively, as reported in previous investigations (Luis et al., 2004;Rowold et al., 2014), both of these polymorphisms are present in the Maputo and Central Mozambique collections. The absence of E1b1b1-M35 and R1b1-P25 in North Mozambique may be due to detection failure considering the small sample size (N = 10). ...
... These studies have detected a substantial fraction of Pygmy mtDNA lineages within the Bantu speakers, but rarely the opposite [17,18]. For example, traces (around 1%) of RHG Y chromosomes have been found in Bantu-speaking groups from Gabon and Cameroon [12] and signals of hunter-gatherer Khoisan Y chromosomes in Bantu-speaking groups from Mozambique [21]. ...
Background
Bioko is one of the few islands that exist around Africa, the most genetically diverse continent on the planet. The native Bantu-speaking inhabitants of Bioko, the Bubi, are believed to have colonized the island about 2000 years ago. Here, we sequenced the genome of thirteen Bubi individuals at high coverage and analysed their sequences in comparison to mainland populations from the Gulf of Guinea.
Results
We found that, genetically, the closest mainland population to the Bubi are Bantu-speaking groups from Angola instead the geographically closer groups from Cameroon. The Bubi possess a lower proportion of rainforest hunter-gatherer (RHG) ancestry than most other Bantu-speaking groups. However, their RHG component most likely came from the same source and could have reached them by gene flow from the mainland after island settlement. By studying identity by descent (IBD) genomic blocks and runs of homozygosity (ROHs), we found evidence for a significant level of genetic isolation among the Bubi, isolation that can be attributed to the island effect. Additionally, as this population is known to have one of the highest malaria incidence rates in the world we analysed their genome for malaria-resistant alleles. However, we were unable to detect any specific selective sweeps related to this disease.
Conclusions
By describing their dispersal to the Atlantic islands, the genomic characterization of the Bubi contributes to the understanding of the margins of the massive Bantu migration that shaped all Sub-Saharan African populations.
Electronic supplementary material
The online version of this article (10.1186/s12864-019-5529-0) contains supplementary material, which is available to authorized users.
... The STM1 individual bore the M343 mutation characteristic of haplogroup R1b, consistent with the back-to-Africa R1b1c-V88 haplogroup reported in [24]; however, we did not observe any of the SNPs specific to the V88 branch. Whereas for STM2, we identified a common and widespread African haplogroup characteristic of the Bantu expansion [42], E1b1a1a1-M80, consistent with the results from the analyses of the autosomal chromosomes [24]. For the remaining individuals, we could not resolve haplogroups due to the reduced complexity and endogenous content of the libraries. ...
Abstract Background As most ancient biological samples have low levels of endogenous DNA, it is advantageous to enrich for specific genomic regions prior to sequencing. One approach—in-solution capture-enrichment—retrieves sequences of interest and reduces the fraction of microbial DNA. In this work, we implement a capture-enrichment approach targeting informative regions of the Y chromosome in six human archaeological remains excavated in the Caribbean and dated between 200 and 3000 years BP. We compare the recovery rate of Y-chromosome capture (YCC) alone, whole-genome capture followed by YCC (WGC + YCC) versus non-enriched (pre-capture) libraries. Results The six samples show different levels of initial endogenous content, with very low (
... doi: bioRxiv preprint however, we did not observe any of the SNPs specific to the V88 branch. Whereas for STM2, we identified a common and widespread African haplogroup characteristic of the Bantu expansion [40], E1b1a1a1-M80, consistent with the results from the analyses of the autosomal chromosomes [22]. For the remaining individuals, we could not resolve haplogroups due to the low depth at which they were sequenced due to limited budget, although our results might be impacted by the paucity of Y-SNPs that define the tips of the Native American haplogroups versus haplogroups from other well-characterized populations in the database employed. ...
Background
As most ancient biological samples have low levels of endogenous DNA, it is advantageous to enrich for specific genomic regions prior to sequencing. One approach – in-solution capture-enrichment – retrieves sequences of interest and reduces the fraction of microbial DNA. In this work, we implement a capture-enrichment approach targeting informative regions of the Y chromosome in six human archaeological remains excavated in the Caribbean and dated between 200 and 3,000 years BP. We compare the recovery rate of Y-chromosome capture (YCC) alone, whole-genome capture followed by YCC (WGC+Y) versus non-enriched (pre-capture) libraries.
Results
We recovered 17–4,152 times more targeted unique Y-chromosome sequences after capture, where 0.01-6.2% (WGC+Y) and 0.01-23.5% (YCC) of the sequence reads were on-target, compared to 0.0002-0.004% pre-capture. In samples with endogenous DNA content greater than 0.1%, we found that WGC followed by YCC (WGC+Y) yields lower enrichment due to the loss of complexity in consecutive capture experiments, whereas in samples with lower endogenous content, WGC+Y yielded greater enrichment than YCC alone. Finally, increasing recovery of informative sites enabled us to assign Y-chromosome haplogroups to some of the archeological remains and gain insights about their paternal lineages and origins.
Conclusions
We present to our knowledge the first in-solution capture-enrichment method targeting the human Y-chromosome in aDNA sequencing libraries. YCC and WGC+Y enrichments lead to an increase in the amount of Y-DNA sequences, as compared to libraries not enriched for the Y-chromosome. Our probe design effectively recovers regions of the Y-chromosome bearing phylogenetically informative sites, allowing us to identify paternal lineages with less sequencing than needed for pre-capture libraries. Finally we recommend considering the endogenous content in the experimental design and avoiding consecutive rounds of capture for low-complexity libraries, as clonality increases considerably with each round.
... Supplementary Table 1 provides the population designations and number of individuals in each of the three genotyped groups. Isolation of the genomic DNA was performed as previously described (Rowold et al., 2014;Chennakrishnaiah et al., 2013). ...
... Especially interesting is the observation that although there appears to be an asymmetrical longitudinal partitioning of E1b1b1-M35 and R1b1-P25 in the eastern versus western regions of the continent, respectively, as reported in previous investigations (Luis et al., 2004;Rowold et al., 2014), both of these polymorphisms are present in the Maputo and Central Mozambique collections. The absence of E1b1b1-M35 and R1b1-P25 in North Mozambique may be due to detection failure considering the small sample size (N = 10). ...
Here we report the results of fine resolution Y chromosomal analyses (Y-SNP and Y-STR) of 267 Bantu-speaking males from three populations located in the southeast region of Africa. In an effort to determine the relative Y chromosomal affinities of these three genotyped populations, the findings are interpreted in the context of 74 geographically and ethnically targeted African reference populations representing four major ethno-linguistic groups (Afro-Asiatic, Niger Kordofanin, Khoisan and Pygmoid). In this investigation, we detected a general similarity in the Y chromosome lineages among the geographically dispersed Bantu-speaking populations suggesting a shared heritage and the shallow time depth of the Bantu Expansion. Also, micro-variations in the Bantu Y chromosomal composition across the continent highlight location-specific gene flow patterns with non-Bantu-speaking populations (Khoisan, Pygmy, Afro-Asiatic). Our Y chromosomal results also indicate that the three Bantu-speaking Southeast populations genotyped exhibit unique gene flow patterns involving Eurasian populations but fail to reveal a prevailing genetic affinity to East or Central African Bantu-speaking groups. In addition, the Y-SNP data underscores a longitudinal partitioning in sub-Sahara Africa of two R1b1 subgroups, R1b1-P25* (west) and R1b1a2-M269 (east). No evidence was observed linking the B2a haplogroup detected in the genotyped Southeast African Bantu-speaking populations to gene flow from contemporary Khoisan groups.
... The available genetic data on sub-Saharan African populations including mtDNA and Y-specific markers [7][8][9][10] indicate various degrees of admixture between the invading Bantus and the autochthonous populations of sub-Saharan Africa, depending on the indigenous tribes involved, location and marker system employed. But, for the most part, Bantu DNA is overwhelmingly present in most sub-Equatorial African populations, including the Southeast African Bantus [11]. ...
... The simplest possible projections were obtained by subjecting the resulting MJ networks to post processing using maximum parsimony parameters. Y-specific haplogroup data for the Maputo individuals was obtained from the literature [11]. ...
The aim of this investigation is to determine the capacity of the newly available Y-STR multiplex system, PowerPlex ® Y23, to discriminate between populations of similar ancestry, specifically of African descent. Using network analysis, the parti - tioning of the 23-loci haplotypes was assessed in relation to Y-specific haplogroups. In the network projection, a number of Bantu haplogroups including E1b1a1a1a-M58, B2a1a-M109 and E2b-M98 as well as non-Bantu African haplogroups such as B2b2-M115 and A1b1b2b1-M118 segregate differentially based on Y-STR haplotypes. Further, we contrast population genetics parameters of the Bantu Southeast African and African American populations. Also, the genetic distance values il- lustrate the robust capacity of the PowerPlex ® Y23 system to discriminate among populations. Noteworthy, we demonstrate that the two populations of African ancestry are as genetically different from each other as the African American population is from the Caucasian, Hispanic and Native American groups. For the first time, allelic and genotypic frequencies for the 23 Y-STR loci included in the PowerPlex ® Y23 forensic system are provided for a continental Southeast African population, the Bantu from the Maputo Province.
