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Characterizing the Admixed African Ancestry of African Americans

This article is relevant today as African American seek out their connections and ancestry with people of Africa. This questions the use and reliance on DNA testing with companies in the US.

. 2009; 10(12): R141.
Published online 2009 Dec 22. doi:  10.1186/gb-2009-10-12-r141
PMCID: PMC2812948
PMID: 20025784

Characterizing the admixed African ancestry of African Americans

Abstract

Background

Accurate, high-throughput genotyping allows the fine characterization of genetic ancestry. Here we applied recently developed statistical and computational techniques to the question of African ancestry in African Americans by using data on more than 450,000 single-nucleotide polymorphisms (SNPs) genotyped in 94 Africans of diverse geographic origins included in the HGDP, as well as 136 African Americans and 38 European Americans participating in the Atherosclerotic Disease Vascular Function and Genetic Epidemiology (ADVANCE) study. To focus on African ancestry, we reduced the data to include only those genotypes in each African American determined statistically to be African in origin.

Results

From cluster analysis, we found that all the African Americans are admixed in their African components of ancestry, with the majority contributions being from West and West-Central Africa, and only modest variation in these African-ancestry proportions among individuals. Furthermore, by principal components analysis, we found little evidence of genetic structure within the African component of ancestry in African Americans.

Conclusions

These results are consistent with historic mating patterns among African Americans that are largely uncorrelated to African ancestral origins, and they cast doubt on the general utility of mtDNA or Y-chromosome markers alone to delineate the full African ancestry of African Americans. Our results also indicate that the genetic architecture of African Americans is distinct from that of Africans, and that the greatest source of potential genetic stratification bias in case-control studies of African Americans derives from the proportion of European ancestry.

Background

Numerous studies have estimated the rate of European admixture in African Americans; these studies have documented average admixture rates in the range of 10% to 20%, with some regional variation, but also with substantial variation among individuals []. For example, the largest study of African Americans to date, based on autosomal short tandem repeat (STR) markers, found an average of 14% European ancestry with a standard deviation of approximately 10%, and a range of near 0 to 65% [], whereas another study based on ancestry informative markers (AIMs) found an average of 17.7% European ancestry with a standard deviation of 15.0% []. By using nine AIMs, Parra and colleagues [] found substantial variation of European ancestry proportions in African-American populations across the United States, ranging from just over 10% in a Philadelphia group to more than 20% in a New Orleans population. Similar levels (11% to 15%) of European ancestry also were reported by Tishkoff and co-workers [], based on more than 1,000 nuclear microsatellite and insertion/deletion markers.

Although much attention has been paid in the genetics literature to the continental admixture underlying the genetic makeup of African Americans, less attention has been paid to the within-continental contribution to African Americans, in particular from the continent of Africa. Studies have focused primarily on the matrilineally inherited mitochondrial DNA (mtDNA) and patrilineally inherited Y chromosome []. These two DNA sources have gained wide prominence owing, in part, to their use by ancestry-testing companies to identify the regional and ethnic origins of their subscribers. Yet these two sources provide a very narrow perspective in delineating only two of possibly thousands of ancestral lineages in an individual.

The majority of African Americans derive their African ancestry from the approximately 500,000 to 650,000 Africans that were forcibly brought to British North America as slaves during the Middle Passage [,]. These individuals were deported primarily from various geographic regions of Western Africa, ranging from Senegal to Nigeria to Angola. Thus, it has been estimated that the majority of African Americans derive ancestry from these geographic regions, although more central and eastern locations also have contributed []. Recent studies of African and African-American mtDNA haplotypes and autosomal microsatellite markers also confirmed a broad range of Western Africa as the likely roots of most African Americans [,].

The recent development of high-density single-nucleotide polymorphism (SNP) genotyping assays, used primarily in genome-wide association (GWA) studies, has also provided unprecedented opportunities to address questions related to the evolution and migration patterns of humans. Most of the GWA studies to date have focused on European or European-derived populations of U.S. Caucasians, but a few have included minorities. The latter studies provide unique opportunities to address questions of ancestral origins in admixed populations, such as African Americans and Latinos [].

Although the application of high-density genotyping to a broad range of worldwide indigenous populations has not yet been accomplished, an important first step has been achieved through the recent genotyping of the Human Genome Diversity Panel (HGDP). This effort resulted in nearly 1,000 subjects from 51 populations being genotyped at more than 500,000 polymorphic sites [,]. These data now provide a basis for finer-scale analysis of the ancestral origins of admixed groups, such as African Americans and Latinos, in addition to enabling the accurate characterization of genetic and evolutionary relationships among these populations.

In this study, we characterize the African origins of African Americans by making use of the high-density genotype data generated for 94 HGDP indigenous Africans from differing geographic and linguistic groups, including 21 Mandenka from West Africa, 21 Yoruba from West Central Africa, 15 Bantu speakers from Southwestern and Eastern Africa, 20 Biaka Pygmy and 12 Mbuti Pygmy from Central Africa, and five San from Southern Africa []. These subjects are used to represent the potential African ancestors of 136 African Americans recently genotyped in a GWA study of early-onset coronary artery disease (ADVANCE) []. In addition, we include 38 U.S. Caucasian subjects from ADVANCE to represent the European ancestors of the African Americans.

The use of high-density SNP data for ancestral reconstruction presents some unique statistical and computational challenges. To this end, we previously developed analytic techniques for estimating individual ancestry (IA) from multiple populations (frappe), as well as for the reconstruction of ancestry blocks in admixed individuals (saber) by using data from more than 450,000 SNP genotypes [,]. Here, we provide a unique application of saber to identify the ancestral origins of each of the more than 450,000 genotypes in African-American individuals, to reduce the analysis to those genotypes that are exclusively of African origin. We note that 58 of the ADVANCE African Americans were also participants of the CARDIA study and had previously been analyzed with 42 Ancestry Informative Markers []. We also used principal components analysis (PCA) to define the genetic structure, and in particular the African genetic structure, underlying African Americans. Another recent study used principal components analysis for the African populations of HGDP, but did not relate those results to African Americans []. To our knowledge, the analyses reported here represent the first effort to characterize the African origin of African Americans by isolating the African-derived genome in each African American individual.

Results

African and European ancestry in African Americans

Principal components analysis of more than 450,000 SNPs, including all populations (Africans, African Americans, and US Caucasians), revealed, as expected, a major separation between the African and U.S. Caucasian populations along the first principal component (PC1), whereas the second principal component (PC2) led to the separation of the various African groups (Figure (Figure1).1). The two pygmy populations (Biaka, Mbuti) and the San of South Africa are well separated from the other African groups, whereas a greater genetic affinity appears to exist between the Mandenka of West Africa, the Yoruba of Central West Africa, and the Bantu speakers, who derive from Kenya and Southwestern Africa. It is also clear in Figure Figure11 that the African Americans lie on a direct line between the European Americans and the West Africans, reflecting their varying levels of admixture between these two ancestral groups.

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Principal components analysis of Africans, U.S. Caucasians, and African Americans. Inset bar plot displays individual ancestry estimates for African Americans from a supervised structure analysis by using frappe with K = 7, fixing six African and one U.S. Caucasian populations. The color scheme of the bar plot matches that in the PCA plot.

These results were confirmed in the estimation of IA by using the program frappe (also in Figure Figure1).1). The amount of European ancestry shows considerable variation, with an average (± SD) of 21.9% ± 12.2%, and a range of 0 to 72% (Table (Table1).1). The largest African ancestral contribution comes from the Yoruba, with an average of 47.1% ± 8.7% (range, 18% to 64%), followed by the Bantu at 14.8% ± 5.0% (range, 3% to 28%) and Mandenka at 13.8% ± 4.5% (range, 3% to 29%). The contributions from the other three African groups were quite modest, with an average of 1.7% from the Biaka, 0.5% from the Mbuti, and 0.3% from the San. In the bar plot of frappe estimates, individuals (vertical bars) are arranged in order (left to right) corresponding to their value on the first PC coordinate. Clearly, this order correlates nearly perfectly with a decreasing proportion of European ancestry (Figure S1 in Additional file 1). Thus, the most important source of genetic structure in African Americans is based on the degree of European admixture.

Table 1

Estimates of European ancestry and proportional African ancestries in African Americans by US region of birth

U.S. region of birth Numbera European ancestry (%) Total African ancestry (%)b
Mandenka Yoruba Bantu Biaka Mbuti San

West 58 (58) 19.9 ± 8.5 18.9 ± 4.1 64.0 ± 5.3 13.7 ± 4.3 1.1 ± 0.8 0.2 ± 0.2 2.0 ± 0.5
South 12 (10) 24.0 ± 15.6 22.6 ± 5.7 60.0 ± 9.5 14.2 ± 5.4 1.1 ± 0.7 0.2 ± 0.4 1.9 ± 1.0
Midwest 4 (4) 19.4 ± 10.2 19.4 ± 2.0 64.0 ± 5.5 13.1 ± 5.5 0.9 ± 0.9 0.3 ± 0.3 2.2 ± 0.7
Southwest 2 (2) 17.0 ± 6.5 21.4 ± 0.7 65.1 ± 1.0 10.5 ± 0.3 1.1 ± 0.4 0.1 ± 0.0 1.7 ± 1.0
All 136 (128) 21.9 ± 12.2 19.2 ± 4.0 63.7 ± 4.9 13.8 ± 3.8 1.0 ± 0.8 0.2 ± 0.3 2.0 ± 0.6

aNumbers in parentheses are those used for estimation of African ancestries after removal of eight individuals with high values of European ancestry; birth-location information was missing for 60 individuals.

bBased on frappe analysis of African genotypes only (n = 128).

African components of ancestry in African Americans

We estimate that, on average, nearly 80% of the ancestry in our samples of African Americans is of African origin. A careful examination of the African component of ancestry in the African Americans is facilitated by restricting the analysis to those portions of their genomes that are exclusively of African origin. To do so, we used the program saber to infer European- versus African-derived alleles for each individual, and retained for analysis only those loci that had a high probability of harboring two African-derived alleles, while denoting the other genotypes as missing. For these and all subsequent analyses, we included the 128 African Americans whose estimated African ancestry exceeded 55%, based on the initial frappe analysis (see Methods).

As a validation of the accuracy of this partitioning procedure, we performed PCA on the combined set of U.S. Caucasians, Africans, and the African Americans with putative non-African-derived genotypes removed (that is, coded as missing). For comparison, we also examined the results of the same analysis, but including all of the genotype data of the African Americans. For these analyses, we included only the three African population groups that, based on the first analysis, contributed significantly to the African Americans (the Mandenka, Yoruba, and Bantu). As shown previously, when all genotypes are included, the African Americans lie intermediate between the Africans and European Americans, at varying distances based on their degree of admixture (Figure (Figure2a).2a). By contrast, when only the putative African-derived genotypes in the African Americans are included, the African Americans now cluster tightly with the Africans (Figure (Figure2b).2b). This result provides confidence that the application of saber has enabled us to partition accurately the genomes of the African Americans with regard to European versus African ancestry.

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Principal components analysis of Africans, U.S. Caucasians, and African Americans including (a) all genotypes, and (b) only the genotypes of African origin in the African Americans. Comparison of (a) and (b) demonstrates the effective elimination of the European ancestry component from African Americans by using saber.

We then characterized the African ancestry in African Americans by performing PCA and estimating IA with frappe by using the U.S. Caucasians, Africans, and African Americans, with non-African genotypes removed. To determine whether we could distinguish the African populations from one another, we first ran frappe including all the 94 African individuals (setting K = 6). This unsupervised analysis unambiguously separated the San and Pygmy populations from the West Africans and, to a lesser degree, the three West African populations (Yoruba, Mandenka, and Bantu). To be confident in the groupings of the West African population, we performed a series of leave-one-out frappe analyses that include 57 individuals from the three West African populations: in each frappe run, we fixed all individual within their respective populations except for one, whose ancestry was allowed to be admixed and estimated (see Methods). Results are given in Figure S2 in Additional file 1. The close genetic relationship of these three groups is evidenced by the imperfect ancestry allocation to an individual’s own population. However, in every case, frappe assigns the majority ancestry to an individual’s own population, and in most cases, the large majority. The Bantu appear to have closest ancestry to the Yoruba. This is consistent with the Nigerian origins of the Yoruba and the presumed origins of the Bantu from the southwestern modern boundary of Nigeria and Cameroon [], and the subsequent migration of the Bantu east and south [,].

Figure Figure33 displays the PCA results of the African Americans and the three closely related African populations (Yoruba, Mandenka, and Bantu). Several features are worth comment. First, despite their genetic similarity, PCA shows clear separation among the Yoruba, Mandenka, and Bantu populations, based on the first two PCs. Second, Figure Figure33 reveals that the African Americans are placed as a single cluster in the convex hull defined by the three African groups.

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Principal components analysis of three West and Central West African populations (Mandenka, Yoruba, and Bantu) and African Americans by using only African-origin genotypes in the African Americans.

Figure Figure44 presents the results of the frappe analysis of the 128 African Americans, in which the six HGDP African populations and Caucasians from ADVANCE were included in the analysis as fixed groups, and proportional ancestry estimated for the African Americans. Consistent with Figure Figure1,1, Figure Figure44 shows that all African Americans are estimated to have significant ancestry from each of the three West and Central West African groups (Mandenka, Yoruba, and Bantu), with only modest variation among individuals in their ancestral proportions from these three groups. As expected, little to no European ancestry is estimated in this frappe analysis.

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Individual ancestry estimates in African Americans by using only their African genotypes, from a supervised structure analysis with frappe, including all six African populations and U.S. Caucasians as fixed (K = 7). Color coding of populations is the same as that in Figure 1.

Table Table11 provides the averages and standard deviations of IA derived from the frappe analysis described earlier (Figure (Figure4)4) for the African components of African ancestry for the 128 African Americans. Overall, we estimate within-Africa contributions of 64%, 19%, and 14% from Yoruba, Mandenka, and Bantu, respectively. The variances for the various African IA components are much smaller than those for the European IA and are roughly similar across groups (SD ranging from 0.038 to 0.049). These observations are consistent with visual inspection of the bar chart in Figure Figure4,4, that African Americans generally derive substantial ancestry from all three West and Central West African population groups. We also note from Table Table11 that no significant differences exist among African-American subgroups defined by U.S. region of birth, in terms of IA estimates for any African ancestral component, nor are any significant differences in IA found, based on gender (data not shown).

Thus, the PC and frappe analyses of the 128 African Americans based only on their African-derived genotypes suggest a lack of genetic structure within the African component of their ancestry. To assess this question further, we performed an additional PC analysis on only the African Americans, including only the African-derived genotypes for each individual.

Figure Figure55 shows the PCA restricted to African-derived genotypes within the African Americans. In this case, each PC accounts for a very modest amount of variance, and no clear pattern is evident. The distribution of the proportion of variance explained by each PC revealed a continuous distribution with no outliers (data not shown).

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Principal components analysis of African Americans based on African-derived genotypes only. Little evidence for structure exists in the African component of ancestry.

To confirm that this lack of structure was not an artifact of removing genotype data, we performed a similar PC analysis on the original 94 Africans, but randomly deleting genotypes from these subjects at a rate comparable to the genotype removal rate in the African Americans (see Methods). Results are shown in Figure S3a (full genotype data) and Figure S3b (genotype data removed) in Additional file 1. As can be seen, the two figures appear nearly identical, each demonstrating the structure that exists among these African populations. Thus, the deletion of genotypes did little to diminish the display of population structure, and so the lack of structure that we observed within the African Americans (after removing non-African genotypes) is unlikely due to missing genotype data.

Another question relates to potential impact of missing genotypes on the frappe analysis of the African Americans. Individuals with high levels of European ancestry (who have more genotype data removed) provide less information regarding their African ancestral components, and thus the variance of the African components of IA increases with the amount of European ancestry, but not in a directional way.

Discussion

As expected, PCA on our entire sample revealed the greatest genetic differentiation between the US Caucasians and the Africans, with the African Americans intermediate between them, reflecting their recent admixture between ancestors from Europe and Africa. Our estimate of European individual admixture (IA) in the African Americans was also roughly consistent with prior studies [], with an average of 21.9%. We found considerable variation among individuals in terms of European IA, and a number of individuals with particularly high European IA values (eight individuals of 136, or 6% with values greater than 45%).

Prior studies focusing on mtDNA and Y chromosomes have found a greater African and lesser European representation of mtDNA haplotypes compared with Y chromosome haplotypes in African Americans, suggesting a greater contribution of African matrilineal descent compared with patrilineal descent [,]. For example, Kayser and colleagues [] estimated that 27.5% to 33.6% of Y chromosomes in African Americans are of European origin, compared with 9.0% to 15.4% of mtDNA haplotypes.

One study of nine short tandem repeat (STR) loci compared the Y chromosomes of African Americans with those of various African populations, including West Africans, West Central Africans (Cameroon), South Africans, Mbuti Pygmies, Mali, San, and Ethiopians []. In a multiple dimensional scaling analysis, these authors placed the African Americans in the middle of these African groups, suggesting origins from multiple African populations. However, they also found that they could not differentiate the Y-chromosome distributions of West African and West Central African groups, presumably a major source of ancestry for African Americans.

Another study of mtDNA haplotypes in African Americans and different African populations found that more than 50% of the African-American mtDNAs exactly matched common haplotypes shared among multiple African ethnic groups, whereas 40% matched no sequences in the African database they referenced []. Fewer than 10% of African-American mtDNA haplotypes matched exactly to a single African ethnic group. The haplotypes that did match were more often found in ethnic groups of West African or Central West African than of East or South African origin.

The most extensive examination of mtDNA haplotypes in Africans and African Americans [] used mtDNA data from a large number of African ethnic groups spread around the continent. These authors observed large similarities in mtDNA profiles among ethnic groups from West, Central West, and South West Africa, with a continuous geographic gradient. As observed previously [], these authors also found that many mtDNA haplotypes were widely distributed across Africa, making it impossible to trace African ancestry to a particular region or group, based on mtDNA data alone. These authors also estimated the proportionate ancestry within Africa based on African American mtDNA haplotypes as 60% from West Africa, 9% from Central West Africa, 30% from South West Africa, and minimal ancestry from North, East, Southeast, or South Africa.

These studies all suggest close genetic kinship among various West African, Central West African, and South West African ethnic groups. A prior analysis of genetic structure among the African populations included in the HGDP based on 377 autosomal STR loci was able to define distinct genetic clusters for the Biaka, Mbuti, and San; however, the study lacked the power to differentiate the Mandenka, Yoruba, and Bantu groups []. Similarly, another study examining two ethnic groups from Ghana (Akan and Gaa-Adangbe) and two from Nigeria (Yoruba, Igbo), based on 372 autosomal microsatellite markers in 493 individuals, did not differentiate these groups by genetic cluster analysis and found only modest genetic differences between them []. In contrast, greater resolution of African ethnic groups, particularly for the Mandenka and Yoruba, was possible in our analysis, based on more than 450,000 SNPs. We note that, in a recent study of malaria, PCA distinguished the HapMap YRI individuals from the Mandenka individuals in the Gambian sample on the basis of 100,715 SNPs; however, admixture analysis with a few selected markers did not reveal clear clusters that correspond to self-reported ancestry [].

It is of interest to compare our African admixture estimates to descriptions of proportional representation of various African groups to the Middle Passage and slave trade occurring in post-Columbian America. A highly detailed census based on historic records has been documented by several authors []. Africans were deported from numerous locations along the broad western coast of Africa, ranging from Senegal in the far west all the way down to Angola in the southwest. In addition, a smaller number of slaves were taken from the southeast of Africa. In terms of numbers, the largest group, approximately 50% to 60%, derived from Central and Southern West Africa and the Bight of Biafra; approximately 10% from Western Africa; 25% to 35% from the West Coast in between (Windward Coast, Gold Coast, and Bight of Benin), and the remaining 5% from Southeast Africa []. These estimates show considerable consistency with our results, which also indicated the largest ancestral component of African Americans to be from Central West Africa, followed by West Africa and Southwest Africa. However, because we did not have groups representative of Southeastern and other parts of Southern Africa, we may have underestimated their ancestral representation among African Americans.

It is important to note that considerable migration has occurred among African ethnic groups over the past three millennia or more. For example, the two Bantu groups included in our analysis originated from a more-central African location (Nigeria-Cameroon) several millennia ago, making precise geographic localization of African ancestry difficult []. This difficulty is also reflected in the close genetic relationships among the various West, West Central, and South West African groups, who also show considerable overlap in terms of mtDNA haplotypes.

Our results are based on examination of the entire autosomal genome and, therefore, provide a more-robust picture of the admixed African ancestry of individual African Americans compared with prior analyses, which focused on only a single locus (mtDNA or Y chromosome). We found all African Americans in our sample to be admixed, with representation from various geographic regions of Western Africa. The amount of variation in the African components of ancestry among the African Americans was quite modest, suggesting considerable similarity in African genetic profiles among African Americans. Thus, African ancestry testing based on a single locus, such as the mtDNA or Y chromosome, as is commonly done by ancestry-testing companies, provides only a very limited, and in many cases, misleading picture of an individual’s African ancestry [].

An important limitation in our analysis is the modest number of African subjects and groups represented. However, we were clearly able to exclude certain African ethnic groups as contributing substantially to African Americans, such as the two Pygmy and San groups. Furthermore, the close genetic similarity observed among West, Central West, and Southwest African ethnic groups (such as the Mandenka, Yoruba, and Bantu), found by us and others [], suggests that precise identification of ancestry for African Americans may be difficult, even with the inclusion of additional ethnic groups.

Very recently, the limited range of African groups included in population genetic studies of Africans was addressed in a landmark study of 113 geographically diverse African ethnic groups by Tishkoff and co-workers []. These authors included 848 microsatellite, 476 indel, and four SNP markers. to examine genetic structure among these groups, as well as among 98 African Americans from four U.S. recruitment sites. In a genetic cluster analysis, they found only modest differentiation among West Africans, similar to the findings from other studies of a subset of these groups, based on a comparable number of markers. They also estimated proportionate African ancestry among their African Americans in a structured analysis including African ethnic subgroups, allowing the African Americans to be admixed. Comparable to our results, within the African Americans, they also found the majority African ancestry to be West, Central West, and Southwest African, including Bantu and non-Bantu speakers, with somewhat greater representation of the Bantu speakers (about 50% of the African total component) than the Western non-Bantu speakers (for example, Mandenka, about 30% of the African total component). Larger collections of indigenous African populations, such as those described earlier [], when assayed with dense genotyping arrays, as done in this study (to allow finer genetic differentiation), will likely add further clarification of the African ancestral origins of African Americans.

The results of our analysis also strongly point to random mating among African Americans with respect to the African components of their ancestry. This is reflected both by the modest variances we observed in the African IA components, and also by the lack of structure in the PC analysis of African Americans with non-African genotypes removed. This conclusion is consistent with the idea that, for most African Americans, specific African origins are mixed or unknown or both and do not affect social characteristics that influence the choice of mate. It is also consistent with the notion that the African slaves brought to North America were mixed with regard to their geographic and ethnic ancestry and language []. By contrast, considerably greater variation in the proportion of European ancestry was found within the African Americans in our study. This high level of variation in European ancestry may reflect recent admixture or nonrandom mating (for example, as seen in Latino populations []), or both; these questions require additional study.

Conclusions

African Americans typically have African and European genetic ancestry. We sought to characterize the African ancestry of African Americans by using data on more than 450,000 SNPs genotyped in 94 Africans of diverse geographic origins, as well as 136 African Americans and 38 U.S. Caucasians. To focus on African ancestry, we reduced the data to include only those genotypes in each African American that are African in origin. We found that all the African Americans are admixed in the African component of their ancestry, with estimated contributions of 19% West (for example, Mandenka), 63% West Central (for example, Yoruba), and 14% South West Central or Eastern (for example, Bantu speakers), with little variation among individuals. Furthermore, we found little evidence of genetic structure within the African component of ancestry in African Americans, but significant structure related to the proportion of European ancestry. These results are consistent with mating patterns among African Americans that are unrelated to African ancestral origins, cast doubt on the general utility of mtDNA or Y-chromosome markers alone to delineate the full African ancestry of African Americans, and show that the proportion of European ancestry is the leading source of stratification bias in genetic case-control studies of African Americans.

Materials and methods

Selection of populations and individuals

Individuals included in analyses presented here come from two studies. A total of 102 indigenous African individuals and their genotype data were obtained from the Human Genome Diversity Project (HGDP) and comprised five San, 22 Biaka Pygmy, 13 Mbuti Pygmy, 22 Mandenka, 21 Yoruba, 11 Kenyan Bantu, and eight Southwest African Bantu (one Pedi, one Southern Sotho, two Tswana, one Zulu, two Herero, and one Ovambo). In total, eight individuals were removed from analyses for the following reasons: three Kenyan Bantu had significant Middle Eastern ancestry, based on previous analysis []; and three additional Kenyan Bantu and two Mandenka were removed because they were first cousins to other included subjects. This left a total of 94 indigenous Africans for analysis. The 136 self-described African-American individuals studied represent a subset of participants of the Atherosclerosis, Vascular Function and Genetic Epidemiology (ADVANCE) study [] selected for genotyping in the context of a GWA case-control study of early-onset coronary artery disease (CAD). From the ADVANCE study, we also randomly sampled 38 of 590 US Caucasians to anchor the European component of African-American ancestry. Thus, in total, 268 individuals are included in this study.

All ADVANCE subjects were recruited from the membership of Kaiser Permanente of Northern California. Among the 136 African Americans, 49 (36%) were affected with CAD (with first presentation at younger than 45 year for male and 55 years for female subjects), and 36 (26.4%) were male subjects. Of the 87 controls, frequency matched by age to the cases, 58 represented participants in the Coronary Artery Risk Development in Young Adults (CARDIA) study originally recruited at the Kaiser Oakland field center who attended the study’s Year 15 examination in 2000 to 2001 [,]. For 76 (55.9%) of these African-American individuals, we had information on state of birth, with 58 stating they were born in the West (California), 12 in the South (Alabama, Louisiana, Mississippi, Virginia), four in the Midwest (Indiana, Michigan, Missouri, Ohio), and two in the Southwest (Texas). The description of recruitment of these subjects can be found elsewhere [].

Genotyping and marker selection

Genotype data were derived from two different research projects. The HGDP individuals were genotyped on the Illumina 650 K Beadarray; experimental protocol and SNP quality-control analysis for the HGDP project and genotyping results were described previously [,]. In total, 938 individuals and 642,690 autosomal SNPs passed all quality-control criteria. Genotype data for U.S. African American and Caucasian individuals were obtained from the ADVANCE study, in which genotyping was performed on the Illumina 550 K Beadarray by the same group of investigators, followed by identical quality-control analysis. After removing markers that were absent from either the HGDP dataset or the ADVANCE dataset, the final combined genotype dataset for all analyses in this study consisted of 454,132 autosomal SNPs.

Population structure and ancestry estimation

We performed PCAs according to the algorithm described by []. Genome-wide European admixture proportions in African-American individuals were estimated by using the program frappe, which implements an Estimation-Maximization (EM) algorithm for simultaneously inferring each individual’s ancestry proportion and allele frequencies in the ancestral populations []. In this analysis, ancestry of the African Americans is allowed to have come from any of the K = 7 ancestral populations: San, Biaka Pygmy, Mbuti Pygmy, Mandenka, Yoruba, Bantu, or European. Ancestries of the indigenous African individuals and U.S. Caucasians were assumed to be homogeneous and fixed. However, to determine the robustness of these assignments for the closely related West and Central West African populations, we performed an additional frappe analysis on just these groups (Mandenka, Yoruba, Bantu; n = 57). We fixed all individuals in their respective population groups (Mandenka, Yoruba, or Bantu), except for one, who was allowed to be admixed, and the admixture was estimated. This procedure was repeated 57 times for each individual, so that each person’s potential admixture was estimated. In this way, we tested the robustness of the population definitions. If the populations are not distinct, then the individual admixture estimates should appear random; by contrast, if an individual’s ancestry is assigned primarily to his or her population of origin, population distinctiveness can be assumed. Furthermore, this analysis provides a closely matched contrast to the African Americans, whose proportionate individual ancestry is estimated in a similar fashion.

Defining African SNP genotypes

To focus exclusively on the African ancestral component, we removed genotypes containing European-derived alleles from the African-American individuals by using the program saber. This program allowed us to infer European versus African ancestry for each SNP genotype in an individual []. Saber implements a Markov-Hidden Markov Model, which infers locus-specific ancestry based on ancestral allele frequencies at each marker, as well as the ancestral haplotype frequencies between pairs of neighboring markers and assumes a block structure for ancestry along a chromosome. For this analysis, saber required the genome-wide average European ancestry for each admixed individual, which was estimated by using frappe, as described earlier (K = 7). We also supplied the estimated African and European ancestral allele frequencies for all SNPs to saber, which improved the estimation of the ancestral haplotype frequencies. Saber produces a posterior estimate of European ancestry at each SNP, which concentrates near 0, 0.5 and 1, corresponding to 0, 1, or 2 European-derived alleles. Although it is feasible to infer phase and ancestry jointly by using saber, we chose to remove SNP genotypes (as opposed to single alleles) in which at least one allele is European derived. Thus, for a given individual, we were left only with SNP genotypes that were highly likely to be homozygous in African origin. The proportion of genotypes removed for an individual is approximately 1 – α2, where α represents the genome-wide estimate of African ancestry for that individual. As a result, the amount of genotype data varied among individuals based on the degree of European versus African ancestry. To allow adequate information about the African component of their genome, we excluded eight individuals with estimated European ancestry of 45% or greater, leaving a total sample of 128 individuals with at least 30% of their genotype data retained. The proportion of genotypes retained ranged from 31% to 99%, with a median of 67% and mean of 66%. In terms of proportion of genotypes retained at individual loci, the mean is the same as stated earlier (66%), with a standard deviation of 0.05. Thus, assuming a normal distribution, 95% of the proportions of genotypes retained across loci lie between 56% and 77%. We note that even after removing genotypes, a large number of marker genotypes are retained for each individual, with a minimum of 143,025.

Genetic structure of the African-derived genome

This analysis focused on IA estimation and PCA based on African-origin SNP genotypes. For IA estimation, we used the program frappe with K = 7 (Yoruba, Mandenka, Bantu, Biaka Pygmy, Mbuti Pygmy, San, and U.S. Caucasians as ancestral individuals). U.S. Caucasians were included in the model to ensure that the European ancestral component had been properly removed from all individuals.

In performing PCA of the Africans and African Americans together, our goal was to understand the relationship between African Americans and Africans. We focused on the 57 West and Central West Africans in this analysis (Yoruba, Mandenka, and Bantu) because these were the only African populations contributing to African-American ancestry. In this case, a standard PCA would be influenced by the much larger sample size of African Americans compared with any of the African groups. Because we were interested in the projection of the African component of ancestry of the African Americans onto the African structure, we instead performed the PCA 128 times, each time including a different single African American whose non-African genotypes had been removed.

In PCAs involving U.S. Caucasian subjects, the same 38 ADVANCE Caucasians were used. All PCAs were performed by using the statistical package R.

To address the question of whether removal of a varying amount of genotype data among individuals would bias the PC analysis, we performed a genotype-reduction procedure on the 94 indigenous African populations, to mimic the reduction of genotype data among the African Americans. We then performed two PCAs, the first based on complete genotype information, and then another based on the reduced genotype data. Significant differences between the results of these analyses would indicate that some bias occurs simply because of the uneven data reduction; lack of differences would indicate the opposite.

Abbreviations

ADVANCE: Atherosclerotic Disease Vascular Function and Genetic Epidemiology; AIM: ancestry informative marker; CAD: coronary artery disease; CARDIA: Coronary Artery Risk Development in Young Adults; EM: estimation-maximization; GWA: genome-wide association; HGDP: Human Genome Diversity Panel; IA: individual ancestry; PC: principal component; PCA: principal component analysis; SNP: single nucleotide polymorphism; STR: short tandem repeat.

Authors’ contributions

FZ, HT, and NR conceived of the study, performed the statistical analyses, and drafted the manuscript. AB, DA, and BN contributed to the data analyses. TQ, TLA, JWK, CI, ASG, MAH, and SS are ADVANCE investigators and had the overall responsibility for study design and implementation, including subject recruitment and assessment. RRM, DA, JL, and AS generated high-density SNP genotype data on ADVANCE. All authors contributed to and approved of the manuscript.

Additional files

The following additional files for this article are available online:

Additional file 1 contains three supplementary figures. Figure S1 shows PC1 from PCA of African Americans based on all genotype data versus African IA from frappe analysis. The figure shows near-perfect correlation between PC1 and African IA. Figure S2 shows a Frappe analysis of 57 Yoruba, Mandenka, and Bantu speakers, based on estimating admixed ancestry one individual at a time, fixing all others in their defined population. Results show majority assignment to an individual’s own population group. Figure S3a shows a PCA of indigenous Africans (n = 94) based on all genotype data. Figure S3b shows a PCA of indigenous Africans (n = 94) based on variable removal of genotype data. Note that the figure shows nearly identical genetic structure to that in Figure Figure3a,3a, including the separation of Yoruba, Mandenka, and Bantu.

 

Supplementary Material

Additional data file 1:

Figure S1 shows PC1 from PCA of African Americans based on all genotype data versus African IA from frappe analysis. The figure shows near-perfect correlation between PC1 and African IA. Figure S2 shows a Frappe analysis of 57 Yoruba, Mandenka, and Bantu speakers, based on estimating admixed ancestry one individual at a time, fixing all others in their defined population. Results show majority assignment to an individual’s own population group. Figure S3a shows a PCA of indigenous Africans (n = 94) based on all genotype data. Figure S3b shows a PCA of indigenous Africans (n = 94) based on variable removal of genotype data. Note that the figure shows nearly identical genetic structure to that in Figure Figure3a,3a, including the separation of Yoruba, Mandenka, and Bantu.

Acknowledgements

We thank Dr. Sandra Beleza for helpful comments on the manuscript. This research was supported by the National Institutes of Health, including NIGMS grant GM073059 (to HT), and NHLBI grant HL087647 (to TQ). FZ was supported by a Stanford Graduate Fellowship. HT is supported by a Sloan Foundation Research Fellowship. The ADVANCE investigators thank the study participants and the staff who contributed to the ADVANCE study.

References

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The Ancient Origins of New Zealanders

Biological anthropologist Professor Lisa Matisoo-Smith is researching the genetic make-up of Kiwis.

Biological anthropologist Professor Lisa Matisoo-Smith is researching the genetic make-up of Kiwis.

Aotearoa was the final destination of a very long journey that began in Africa over 65,000 years ago.  Whether you’re a red-headed country music singer in Gore or a Filipino dairy worker in Dannevirke, your ancestral homeland is Africa.

When a small band of modern humans filtered out of Africa into Europe and Asia, they encountered other human types who had arrived there hundreds of thousands of years before.  Our new breed of taller, seemingly more savvy and better equipped men and women co-existed with Neanderthals for at least 10,000 years before they died out, whether through force or happenstance.

Our common ancestor was Homo erectus.  We were not yet so different from Neanderthals that we couldn’t interbreed.  The encounters were rare and rarely productive but nevertheless, everyone today who is NOT of pure African descent carries a small percentage of Neanderthal DNA, about 2 percent – slightly more in Asian populations who seem to have had additional, later encounters. Those Neanderthal jokes about our colleagues and former boyfriends have rebounded on us.

Skeleton of the Neanderthal boy recovered from the El Sidron cave, Spain.

PALEOANTHROPOLOGY GROUP MNCN-CSIC

Skeleton of the Neanderthal boy recovered from the El Sidron cave, Spain.

This genetic legacy has given us some good and bad traits, such as stronger hair and skin, a predisposition to type 2 diabetes and Crohn’s disease, and increased risk of nicotine addiction. Apparently, Neanderthals shared our on/off faculty for appreciating the defining note of pinot noir and violets, a compound called beta ionine.  A single nucleotide difference (a basic component of DNA) distinguishes the active and inactive version of the gene.

READ MORE:
Tracing where the first Kiwis came from
Gene analysis project goes way, way back

The first scientist to think of using differences in our DNA to trace our origins and relatedness grew up on a farm in Pukekohe.

Professor Lisa Matisoo-Smith hands out DNA test kits to 50 people in Nelson after introducing the audience to the Allan ...

Martin de Ruyter

Professor Lisa Matisoo-Smith hands out DNA test kits to 50 people in Nelson after introducing the audience to the Allan Wilson Centre project The Longest Journey from Africa to Aotearoa.

The late, great New Zealand scientist, Allan Wilson, who should be a household name here, spent his adult life in America, based at the University of California, Berkeley.  He died in 1991 from leukaemia, aged 56. Wilson deduced that chimpanzees and the first human species diverged from a common ancestor only 5-7 million years ago, not  about 30m as previously thought – a bit too close for comfort for some.

It caused a bitter controversy at the time, and not just among evolution deniers. Scientists are human too, and not always objectively ‘sapiens’. Reputations become nailed to old masts.

Wilson led a group of evolutionary biologists who realised that we could reconstruct human history by studying markers in our mitochondrial DNA (mtDNA), which is inherited lock, stock and barrel from mother, and not mixed up with father’s DNA when sperm meets egg.  Every so often, a spelling mistake, known as a mutation, is made when the DNA is being copied. Once a mutation occurs, it is then passed on to all future generations.

These mtDNA mutations rarely have any effect on the person.  Wilson and his team realised that if they looked at mtDNA from people around the world, they could compare the DNA and draw a family tree, identifying when and where these mutations occurred. The different mtDNA lineages could be used to trace the movement of populations across the globe.

They calculated that all humans alive today trace their origin back to one woman – so-called Mitochondrial Eve – who lived in Africa a mere 150,000 years ago.  This doesn’t mean that she was the only woman on Earth at the time, but that all other lines have since become dead ends, literally.

The different branches of the mitochondrial family tree are labelled by letters, with each branch defined by a particular mutation or combination of mutations.

The oldest lineages are the L branches, which are found only in African populations. About 65,000 years ago, a small group of humans carrying the L3 lineage left Africa, probably through what is now Egypt. This group soon split and the mutations occurred that define the two main non-African lineages, the M and N branches. Women carrying the N lineages gave rise to all European lineages, with the most common branches found in Western Europeans today being H, U, J, T, K, V, and X. These seven Western European maternal ancestors inspired the book The Seven Daughters of Eve by Bryan Sykes.  He named these clan mothers Helena, Ursula, Jasmine, Tara, Katrine, Velda and Xenia.

While Helena, Ursula, Jasmine and the girls went north, some of our ancestors headed east and moved very quickly through southern Asia, towards the Pacific. They could walk through what is now Island Southeast Asia when ice ages locked up massive volumes of water and sea levels fell.  Recent research suggests that they arrived in Australia and New Guinea, which were joined in a super-continent called Sahul, as early as 60-65,000 years ago.  Aboriginal Australians and Papuans have been geographically and genetically isolated for a very long time.

It was a one-way journey for them. These people carried mtDNA lineages belonging to the M branch, as well as some N lineages.

On those early forays into Asia, it seems we also interbred with another group of long-separate Homo erectus descendants called Denisovans, after the cave in Siberia where the relics of these people were miraculously discovered – part of the finger-bone of a small girl and a few teeth – amidst tonnes of rock and dirt.  These treasured remains were so well preserved that scientists were able to sequence the entire genome (the complete set of an organism’s DNA).  Those first modern humans who travelled through Asia clearly ran into Denisovans on the way. Their descendants today, including Aboriginal Australians and many Pacific people, carry up to 5 per cent Denisovan DNA.  Interestingly, this inheritance confers an ability to thrive at high altitudes and is present in the Sherpa people.

Allan Wilson’s work has inspired a generation of evolutionary biologists, including a group of outstanding researchers at the University Otago.  Leader of the allanwilson@otago research group is Professor Lisa Matisoo-Smith, a biological anthropologist who also uses DNA as her archaeological pick-axe. She is fine-tuning what we know about the populations of the Pacific, and Aotearoa in particular.  She recently randomly sampled the DNA of over 2000 New Zealanders to analyse our ancient maternal and paternal lines.

Lisa is currently writing up the results and the stories of some of her New Zealand subjects in a book she plans to publish in 2019, when we will be commemorating the first Maori and European landings here.  But she can tell you the punch line now. We are as diverse a population as you’ll find anywhere. Kiwis carry all of the major mitochondrial DNA diversity seen in the world – lineages A to Z.

The history of human evolution and migration is one of the fastest moving areas of science. New findings, such as fossils of the diminutive Homo floresiensis (the hobbit people), are coming thick and fast and adding intriguing sub-plots to the main storyline.

We have an insatiable desire to know about our past.  Genealogy is big business. But while DNA is hard evidence of our origins, relatedness, and some of the routes taken by our ancestors, it is only part of the story and actually reveals very little about who we are. New Zealanders are not defined by their DNA or bound in spirit by genetic similarity.

What we do share in common are the long journeys we and our forebears risked to come here, whether by waka, sailing ship or 777, to escape depression and social immobility in Britain, Pol Pot’s genocide, wars in Europe and the Middle East, or in search of adventure and a better life.

Our ancestors, all six thousand generations since Mitochondrial Eve, were survivors and we are their testament.

Next week:  Who were the first New Zealanders?  How many were there, and where did they come from?

Information and research provided by Professor Lisa Matisoo-Smith FRSNZ, University of Otago

 

CELL, ORGANELLES AND DNA RESOURCES

CELL, ORGANELLES, & DNA RESOURCES FOR TEACHERS, GENETIC GENEALOGIST AND YOU

Resource: Unlockinglifecode.org access 1/2018

1 | Cell
2 | Nucleus
3 | Golgi Body
4 | Mitochondrion
5 | Lysosome
6 | Centriole
7 | Ribosome
8 | Rough Endoplasmic Reticulum
9 | Smooth Endoplasmic Reticulum
10 | Cytoplasm
11 | Nucleopore
12 | Chromosome
13 | Gene
14 | DNA
15 | Base Pair
Read this! |

What I Learn About My Ancient Ancestry (Geno 2 Project)

Here is what I learned about my ancient ancestry:

I AM

Neanderthal Man

0.7%

NEANDERTHAL

Modern Man

As humans were first migrating out of Africa more than 60,000 years ago, Neanderthals were still living in Eurasia. It seems our ancestors hit it off, leaving a small trace of these ancient relatives in my DNA.

I AM

  • 79% Western Africa

  • 5% Northwestern Europe

  • 4% Eastern Africa

  • 4% West Mediterranean

  • 3% Northeastern Europe

  • 3% Eastern Europe

MY MAP

MY MATERNAL LINEAGE BEGAN ABOUT 150,000 YEARS AGO.

My maternal ancestors spread from east-central Africa to northwestern Africa at a time when the climate and landscape were more hospitable. They settled from the central-West African coast to North Africa. In the north, my cousins are now part of populations such as the Berber peoples. The Berbers are traditionally livestock herders. Toward west-central Africa, I have cousins among traditional farming groups.

My maternal branch is L2a1a2

Maternal Map

MY PATERNAL LINEAGE BEGAN AT LEAST 180,000 YEARS AGO.

My paternal ancestors spread from Central Africa to West Africa. My cousins include the Bantu-speaking people. The Bantu had an advanced farming culture, and were the first people in sub-Saharan Africa to work iron. Later expansions to the east and south introduced agriculture across Africa and spread the Bantu languages throughout the continent.

My paternal branch is E-U186

Paternal Map

That’s my story. What’s your story?

Who are your ancestors, Can you identify your relatives?

We are all over this world in many countries, with differences, shades of color, opinions, thoughts. Make no mistake we are one, our ancestors came out of Africa. It’s in your DNA. I have found relatives in Brazil, India, Iran, Syria, Australia, Mexico, Boro Bora, Korea, China, and Japan. Never stop your journey finding your past. Gedmatch is a good place to start.

DNA collection, testing, and results are different for people of color and the algorithms used are not geared towards our DNA but can be very useful.  It is Eurocentric, however, Helix, National Geo2, and 23andMe are moving towards a more inclusive model. Also, there are new projects in many countries to match DNA for people around the world.

 

 

 

African Royal DNA Project

How to Check Genesis.Gedmatch.com for African Royal DNA Project Matches

October 11, 2017

Note: Any problems understanding to procedures or questions please directed to me or RoyalDNA@DNATestedAfricans.org

*Great website with a ton of information, highly recommended.

 

AdaEze Naja Chinyere Njoku

Here’s a workable solution to help you check to see if you match any African Royal DNA Project Kits.  Because there are so many of you, we cannot compare your DNA for you all. This is the quickest way to check for yourself to see if you match any of the kits we manage. You MUST follow these steps prior to contacting us about the potential DNA match.  This also helps YOU to learn how too use the FREE tools.  

PLEASE REMEMBER THAT WE DO NOT POST GEDMATCH OR GENESIS KIT NUMBERS IN ANY SOCIAL MEDIA. SHARING THE GEDMATCH ON GENESIS NUMBERS IN ANY FORUM, WILL RESULTS IN PERMANENT REMOVAL FOR ALL GROUPS AND PROGRAMS.  PRIVACY AND SAFETY IS MOST IMPORTANT. THIS INCLUDES FTDNA KIT #S AND ANY KIT # THAT YOU RECEIVE REGARDING YOUR ANCESTRY AND DNA UPLOADS.  When sending emails to your Gedmatch and / or Genesis matches, send one email per person.  That is their rule.  No mass emails.  If you are caught, Gedmatch may delete your data and you lose access. 

 

  • Register at this link https://genesis.gedmatch.com/ if you have not done so. If you register and get a notice that the email you are using already exists, simply log into the link with your Gedmatch.com log in credentials. (Please read the website first before making a decision to upload your DNA Raw data)

  • Upload your DNA Raw Data. It may take a day or 2 for your matches to populate.

  • If any African Royal appears on your match list, you MUST complete the one to one comparison. The CMs must be at least 7 and the SNPs must be at least 700 to be a CONFIRMED match.  Click on your Genesis kit #. You will see a list of matches. You are almost there! 

  • If you do not see them on your list, you are not a match. Their names are distinctive and includes ethnic group(s) and they will include their ethnic groups(s).

  •  If you see any of the Royals’ names there, click on the letter “A” beside their name . This will allow you to do a one to one comparison.

 

The one to one comparison will show the chromosomes that you match on .

The above image shows 4 rows of matching for Chromosome 1.  The Centimorgans (CMs) on 1 row MUST be at least 7 and the the SNPs must be 700.  You cannot add up all of them to meet this requirement

The image below shows on row 1 that this match has 47.2 CMs and 6,993 SNPs.  That means they are a legitimate match.

 

  • If the above requirements are met, copy the chromosome details that you match on and draft an email to RoyaLDNA@DNATestedAfricans.org . Paste the info in the email .  

 

  • We will then provide you with contact Info for your DNA match if they provided it to us. 

See our DNA Tested African Descendants group guidelines http://goo.gl/forms/Om5AqGGahm 

Strictly Roots!! 

IRISH SLAVE TRADE LONG AGO BUT NOT FORFOTTEN (DNA)

I finally decided to post this article after some research and review of my DNA. I am a mixture of European ancestry. To be specific my ancestor DNA indicate Ireland and Wales as home to many of my ancestor.Forced to the Caribbean, South America, and the United States as slaves. Many who want to use the term indentured servant, not quite the case. There are many records of Virginia colonial townships and counties that sold white women who were slaves or indentured servants for having children with Africans without permission of their masters, along with their children by the courts to compensate the owners. Most of these slaves ended up in the Low Country of South Carolina on rice or indigo plantations.  See Westmoreland County Court Records in colonial times for examples.

The next time you see an Irish or person from Wales, you may be looking at a cousin. I think it will help to build bridges and bring understanding, not to divide us.

IRISH SLAVE TRADE – THE FORGOTTEN “WHITE” SLAVES

They came as slaves; vast human cargo transported on tall British ships bound for the Americas. They were shipped by the hundreds of thousands and included men, women, and even the youngest of children.

Whenever they rebelled or even disobeyed an order, they were punished in the harshest ways. Slave owners would hang their human property by their hands and set their hands or feet on fire as one form of punishment. They were burned alive and had their heads placed on pikes in the marketplace as a warning to other captives.

We don’t really need to go through all of the gory details, do we? We know all too well the atrocities of the African slave trade.

But, are we talking about African slavery? King James II and Charles I also led a continued effort to enslave the Irish. Britain’s famed Oliver Cromwell furthered this practice of dehumanizing one’s next door neighbor.

The Irish slave trade began when 30,000 Irish prisoners were sold as slaves to the New World. King James I Proclamation of 1625 required Irish political prisoners be sent overseas and sold to English settlers in the West Indies. By the mid-1600s, the Irish were the main slaves sold to Antigua and Montserrat. At that time, 70% of the total population of Montserrat were Irish slaves.

Ireland quickly became the biggest source of human livestock for English merchants. The majority of the early slaves to the New World were actually white.

From 1641 to 1652, over 500,000 Irish were killed by the English and another 300,000 were sold as slaves. Ireland’s population fell from about 1,500,000 to 600,000 in one single decade. Families were ripped apart as the British did not allow Irish dads to take their wives and children with them across the Atlantic. This led to a helpless population of homeless women and children. Britain’s solution was to auction them off as well.

During the 1650s, over 100,000 Irish children between the ages of 10 and 14 were taken from their parents and sold as slaves in the West Indies, Virginia, and New England. In this decade, 52,000 Irish (mostly women and children) were sold to Barbados and Virginia. Another 30,000 Irish men and women were also transported and sold to the highest bidder. In 1656, Cromwell ordered that 2000 Irish children be taken to Jamaica and sold as slaves to English settlers.

Many people today will avoid calling the Irish slaves what they truly were: Slaves. They’ll come up with terms like “Indentured Servants” to describe what occurred to the Irish. However, in most cases from the 17th and 18th centuries, Irish slaves were nothing more than human cattle.

As an example, the African slave trade was just beginning during this same period. It is well recorded that African slaves, not tainted with the stain of the hated Catholic theology and more expensive to purchase, were often treated far better than their Irish counterparts.

African slaves were very expensive during the late 1600s (50 Sterling). Irish slaves came cheap (no more than 5 Sterling). If a planter whipped or branded or beat an Irish slave to death, it was never a crime. A death was a monetary setback, but far cheaper than killing a more expensive African. The English masters quickly began breeding the Irish women for both their own personal pleasure and for greater profit. Children of slaves were themselves slaves, which increased the size of the master’s free workforce. Even if an Irish woman somehow obtained her freedom, her kids would remain slaves of her master. Thus, Irish moms, even with this new found emancipation, would seldom abandon their kids and would remain in servitude.

In time, the English thought of a better way to use these women (in many cases, girls as young as 12) to increase their market share: The settlers began to breed Irish women and girls with African men to produce slaves with a distinct complexion. These new “mulatto” slaves brought a higher price than Irish livestock and, likewise, enabled the settlers to save money rather than purchase new African slaves. This practice of interbreeding Irish females with African men went on for several decades and was so widespread that, in 1681, legislation was passed “forbidding the practice of mating Irish slave women to African slave men for the purpose of producing slaves for sale.” In short, it was stopped only because it interfered with the profits of a large slave transport company.

England continued to ship tens of thousands of Irish slaves for more than a century. Records state that, after the 1798 Irish Rebellion, thousands of Irish slaves were sold to both America and Australia. There were horrible abuses of both African and Irish captives. One British ship even dumped 1,302 slaves into the Atlantic Ocean so that the crew would have plenty of food to eat.

There is little question that the Irish experienced the horrors of slavery as much (if not more in the 17th Century) as the Africans did. There is, also, very little question that those brown, tanned faces you witness in your travels to the West Indies are very likely a combination of African and Irish ancestry. In 1839, Britain finally decided on its own to end its participation in Satan’s highway to hell and stopped transporting slaves. While their decision did not stop pirates from doing what they desired, the new law slowly concluded THIS chapter of nightmarish Irish misery.

But, if anyone, black or white, believes that slavery was only an African experience, then they’ve got it completely wrong.

Irish slavery is a subject worth remembering, not erasing from our memories.

But, where are our public (and PRIVATE) schools???? Where are the history books? Why is it so seldom discussed?

Do the memories of hundreds of thousands of Irish victims merit more than a mention from an unknown writer?

Or is their story to be one that their English pirates intended: To (unlike the African book) have the Irish story utterly and completely disappear as if it never happened.

None of the Irish victims ever made it back to their homeland to describe their ordeal. These are the lost slaves; the ones that time and biased history books conveniently forgot.


New GEDmatch Genesis Beta

 
 

 

GEDmatch Genesis

GEDmatch Genesis is a peek at things to come for GEDmatch. It provides two things:

    • Ability to accept uploads from testing companies with formats and SNP sets not compatible with the current main GEDmatch database.
  • A new comparison algorithm that we believe will provide better accuracy, and more flexibility. More info: The Genesis Algorithm

During this initial deployment, the GEDmatch Genesis database will be separate from the main GEDmatch database, and comparisons for one will not show entries made in the other. Eventually, the 2 databases will be merged, and results will include entries from both. Likewise, the benefits of the Genesis comparison algorithm will eventually become available to all GEDmatch users.

The initial offering of Genesis applications will be limited to autosomal DNA matches. That too will be expanded as we move forward in our effort to convert existing GEDmatch software to the new algorithm.

We hope you find this transition to GEDmatch Genesis useful.

 

 

 

The Genesis Algorithm

For several years, GEDmatch has provided genetic genealogists, both beginners and experts, the ability to search for matches among kits in their database without regard to vendor. Also, GEDmatch has provided a rich suite of analysis programs allowing users to dig deeply into the genetic details of their matches, enhance the reports from their vendors, and even pursue their own original research ideas. Our algorithms are evolving to extract the most trustworthy and meaningful matching information possible using the markers common to pairs of kits even though sometimes limited.

Unfortunately, all too often, kits appear to share a DNA segment purely by chance. To combat this confusing phenomenon, we recently have developed a reliability measure that allows users to assess the quality of a matching segment in an intuitively appealing fashion. We also use the measure to guide our matching algorithms as they wring the greatest amount of useful information possible from the markers common to pairs of kits.

If we could assume that marker characteristics were uniform in all regions within chromosomes, we could use a “one size fits all” requirement for matching segments as is sometimes done. Unfortunately, the relevant characteristics vary widely. Some long segments with few markers may be accidental matches. Some marker rich short segments are often discarded although they are profoundly non-random.

Using the characteristics of each and every marker in a segment, we compute the expected number of purely chance matches to it to be found in the database. That number is then used to classify the segment into one of several levels reflecting the likelihood that the random matches may overwhelm the real ones. When a user executes a one-to-many search or a one-to-one comparison specifying a minimum segment length, the display can then include an estimate of validity for each segment found.

One can assume those segments designated to be valid are the result of a DNA inheritance process rather than mere chance. Questions may still remain about how far back shared DNA originates, but a confounding factor has been removed.

sources:

https://genesis.gedmatch.com/select.php

https://genesis.gedmatch.com/Qblurb.html

 

Introducing The DNA Match Review Page 23&Me

 

 

 

If you’ve taken a MyHeritage DNA test or uploaded your DNA data to MyHeritage, then you will have received a list of your DNA Matches. The list shows people whose DNA matches yours, the percentage of DNA you share, and your possible relationship. DNA results can imply several possible relationships between you and a DNA Match, such as 3rd – 4th cousin, but now you’d like to understand how you are related to the match. Where do you go from here?

We’ve just released a new feature — the DNA Match Review page — to help you answer that question. The new page offers a plethora of detailed information about each of your DNA Matches. Your DNA Match details are now consolidated into one place with different sections that will help you discover how the match may be related to you. This can open the door to new connections and discoveries to advance your family history research.

Below we describe the Match Review page comprehensively. We recommend reading this in depth because it includes important information about exciting new features, some of which are available only on MyHeritage.

Accessing the Review Match Page

On the DNA Matches list, click the “Review match” button in the bottom right corner of any of your matches, as shown below.

Accessing the new DNA Match Review page (click to zoom)

If you need a reminder on how to take full advantage of the features of the DNA Matches list, such as the powerful filters, see our previous blog post.

The DNA Match Review page shows all relevant data about the match, combining information from DNA and family trees. It is displayed in an easy to use side-by-side comparison. Here’s how the page looks, and below this image, we’ll breakdown these sections for you.

DNA Match Review page (click to zoom)

The Match Review page includes the following sections:

Smart Matches

Smart Matching™ is a MyHeritage technology that matches people in your family tree with people in other family trees that users all over the world have created on MyHeritage.

The presence of Smart Matches increases the confidence of DNA Matches — If you share a percentage of DNA with someone, and your trees also have Smart Matches, it increases the likelihood that you are related and makes it easier for you to understand how you are related. You can contact the match and learn from each other about your shared common relatives.

Smart Matches™ section (click to zoom)

When a DNA Match is correct, i.e. is not a false positive, it means that you and the match have a common ancestor, from which both of you inherited some DNA. The DNA Match is found by MyHeritage if both of you inherited the same segments of DNA from that ancestor. If you have Smart Matches with the family tree of your DNA Match, they may include your common ancestor, or at the least help point you in the direction of that ancestor.

We’ve found that in many cases, when DNA brings two relatives together, neither of them knows about the other and it is rare for their family trees to overlap. That’s why in most of the DNA Matches you’ll review, there won’t be a Smart Matches section. When it does exist, you should rejoice as you will likely be able to find out exactly how you are related.

Ancestral Surnames

Ancestral surnames are the surnames of your direct ancestors (or the surnames of the direct ancestors of your DNA Match), which are retrieved from your family trees on MyHeritage. In DNA context, ancestral surnames are very important because every person is an aggregation of DNA segments from his or her ancestors. Therefore, the ancestral surnames indicate the families from which people have inherited their DNA, assuming their family trees are correct and faithfully depict their biological roots.

On MyHeritage, most DNA customers have family trees, which is very fortunate as it allows us to retrieve ancestral surnames and compare them for most DNA Matches.

If you and a DNA Match have shared ancestral surnames, this section will show the ancestral surnames you have in common – those surnames that appear in both your family trees, going back 10 generations.

Shared Ancestral Surnames section (click to zoom)

This section can be extremely useful in determining which common ancestor you and the match share, helping you identify a potential common ancestor. Be careful though if the ancestral surname is very common, like Miller or Smith, because that is very likely not the same family. However, if the ancestral surname that you and your match share is extremely rare, such as Dankworth or Culpepper, you’re certainly on the cusp of understanding how you are related.

Click on the button “View all ancestral surnames” in the bottom right corner of this section, to see a new window with an alphabetized list of all the ancestral surnames in both your family tree and your DNA Match’s family tree. In this new window, you will be able to scroll through all ancestral surnames, and the surnames you share will be highlighted in purple.

Viewing a list of all ancestral surnames (click to zoom)

Don’t have any shared ancestral surnames? Then we will still show you the ancestral surnames in both your family tree and the match’s family tree. This could be helpful if one of their surnames is similar to yours (though with a different spelling), or perhaps a surname will ring a bell and remind you of a relative not yet listed in your tree.

For example, you may have ancestors with the last name MacQuoid but you don’t know exactly where they connect in your tree, so you’ve never added them. After reviewing a DNA Match’s ancestral surnames, you might notice they have the surname MacQuoid in their tree, and you can begin putting together the puzzle of how you are related.

Next to each ancestral surname, we also list associated countries where vital events (birth, marriage, death, burial, etc.) occurred for the ancestors with that surname. This will be useful when trying to understand the possible relationship you might have with your DNA Match. For example, if you both share an ancestral surname from the same country, it can increase the strength of the match. You might not get excited about sharing the ancestral surname of Levine, but if both of you have Levine from Hungary, that could be more interesting. In addition, if you don’t have a shared surname, but you do share ancestors from the same countries, it could mean that you both share roots in the same region.

The list of ancestral surnames and their countries, even beyond the context of DNA, is very handy. We recommend for genealogists to copy the list of ancestral surnames and use it when they email other genealogists since the list serves as a convenient way of expressing one’s research interests. Some genealogists even use the ancestral surnames list as their email signature!

Shared DNA Matches

Shared DNA Matches are people who share DNA with both you and your DNA Match, meaning both of you have the same person in your list of DNA Matches. This is another way of increasing the confidence in your DNA Match and helps you learn which side of the family your DNA Match is on.

MyHeritage has a unique way of showing Shared DNA Matches. Unlike other testing services, we display – in one chart – how both you and your DNA Match are genetically related to the same person.

Shared DNA Matches section (click to zoom)

In this section, the name of each Shared DNA Match is clickable and allows you to go to the DNA Match Review page for that specific match.

If you and your DNA Match have many Shared DNA Matches, you can click on the button “Show more DNA Matches” in the bottom right corner of the section to review all of your Shared DNA Matches.

The Shared DNA Matches page helps you cluster our DNA Matches. Each cluster may indicate matches having the same common ancestor (sometimes there may be several different ancestors). You can collaborate with your matches to try to determine who that common ancestor is.

In time, you will learn to appreciate the power of the Shared DNA Matches page. For example, if you review a match and spot your paternal uncle in the list of shared matches, that is a good indication that the match is paternal for you. Testing more of your relatives will help you get more value from the Shared DNA Matches page, as it will help you determine the path to the common ancestor for many of your matches.

Pedigree Charts

Pedigree Charts show the main individual and their direct line of ancestors, i.e., parents, grandparents, great-grandparents, etc. These charts are especially helpful when looking for common ancestors and for identifying common names, which can provide an idea of how you are related.

The Pedigree Chart section shows your match’s direct ancestors in one tab and shows your own pedigree chart in an adjacent tab. Viewing the Pedigree Chart of your match’s family tree in this way makes it easy to check where your trees may overlap, and see if you spot anything familiar.

Pedigree Charts section (click to zoom)

The Pedigree Chart is condensed to show a lot of information in little space.
To view the full tree, click “View full tree” at the bottom right corner.

Women appear in the Pedigree Chart with their maiden names. To see more information about any person, hover the mouse over the card. A callout will open, as shown below, adding more information, such as birthplace and death place. It will also provide you with handy links to view the family tree around that person, visit the profile or research that person in MyHeritage’s huge collection of 8.1 billion historical records.

Person callout in Pedigree Chart (click to zoom)

If you are using MyHeritage DNA and still don’t have a family tree on MyHeritage, please build one now. It is very helpful for making sense of your DNA Matches and will also be helpful for other users whose DNA matches your own.

Whenever viewing the family tree of another person, living ancestors will be privatized.

Shared Ethnicities

For every DNA test taken on MyHeritage, or uploaded to MyHeritage, we calculate an Ethnicity Estimate, which finds ethnic origins. MyHeritage offers a breakdown of 42 different ethnic regions – more than any other major commercial DNA testing company.

The Shared Ethnicities section compares the Ethnicity Estimate of your DNA Match to your own to find similarities. This interesting section is visual and only displayed on MyHeritage this way. You will see the exact percentage break down of your ethnicities side-by-side with your DNA Match’s ethnicities, and those you share will be highlighted in purple.

Shared Ethnicities section (click to zoom)

The Shared Ethnicities section can be useful for indicating the regions where you and your DNA Match may have common ancestral origins. Be aware though that you might share an ethnicity with a DNA Match, but not because you inherited it from the common ancestor that you share. Each of you may have gotten that ethnicity from other ancestors that you do not share.

You can use a toggle on the top right corner to show only shared ethnicities or all ethnicities. Click any ethnicity for more information about it.

Next steps

We’re not done with the Review Match page yet! Additional features are on the way to make the Review Match page even more informative and useful, such as the commonly requested Chromosome Browser, so keep an eye out for them.

Cost

For MyHeritage DNA customers, some sections on the Review Match page require a family site subscription to view them in their entirety. Users with a Premium, Premium Plus, or Complete subscription will have full access to all sections on the Review Match page, while Basic users will have a partial view of some sections.

Note: Some features listed above may not be shown for each of your DNA Matches if not relevant for that match. For example, if you match with someone who doesn’t have a family tree, then for that match you will not see tree components such as the Pedigree Chart, ancestral surnames and Smart Matches.

Conclusion

Take advantage of our new DNA Match Review page and delve into your DNA Matches. Matches previously overlooked can now be explored for new possible family connections. Instead of piecing together the puzzle yourself from scratch, these new tools will help you better understand how you are related to your matches.

Not in on the DNA action yet? Order your MyHeritage DNA kit today or, if you’ve already had your DNA tested by another company, upload your DNA data to MyHeritage and receive a comprehensive DNA Ethnicity Analysis and DNA Matching for free.

Enjoy!

MyHeritage Team

Leave a comment

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  • Jason Lee

    August 22, 2017

    Where’s the chromosome browser?

    • Esther

      August 23, 2017

      Hi Jason,

      We hope to release a chromosome browser in the near future. Stay tuned!

      Best,
      Esther / MyHeritage Team

Centimorgans in Genetic Geealogy

Reprinted from the International Society of Genetic Genealogy August 2, 2017. No adjustment was made to this article and is the ISOGG position.

 

In genetic genealogy, a centiMorgan (cM) or map unit (m.u.) is a unit of recombinant frequency which is used to measure genetic distance. It is often used to imply distance along a chromosome, and takes into account how often recombination occurs in a region. A region with few cMs undergoes relatively less recombination. The number of base pairs to which it corresponds varies widely across the genome (different regions of a chromosome have different propensities towards crossover). One centiMorgan corresponds to about 1 million base pairs in humans on average. The centiMorgan is equal to a 1% chance that a marker at one genetic locus on a chromosome will be separated from a marker at a second locus due to crossing over in a single generation.

The genetic genealogy testing companies 23andMeAncestryDNAFamily Tree DNA and MyHeritage DNA use centiMorgans to denote the size of matching DNA segments in autosomal DNA tests. Segments which share a large number of centiMorgans in common are more likely to be of significance and to indicate a common ancestor within a genealogical timeframe.

The centiMorgan was named in honor of geneticist Thomas Hunt Morgan by his student Alfred Henry Sturtevant. Note that the parent unit of the centiMorgan, the Morgan, is rarely used today.

23andMe and Family Tree DNA both use HapMap to infer their centiMorgans.

centiMorgans vs megabases

CentiMorgans are interpolated numbers that take into consideration each area of a chromosome and its propensity to recombine. This means if two cousins share 40 cM on chromosome 1, and two different cousins share 40 cM on chromosome 5, they both can be predicted to share a certain degree of relationship statistically. Megabases vary slightly in different locations so that in the same scenario, if both sets shared 40 Mb pairs, it would be more difficult to ensure they are of a similar degree of relation without further accounting for location, chromosome and other factors.[1]

Ann Turner provides a useful explanation: “I think of the cM as being a unit of ‘effective’ distance. As an analogy, a mile is a fixed quantity (5280 feet), and so are megabases. But the probability that a person can walk a mile in 20 minutes is more fluid. If the terrain is very rough, the “effective” distance of a literal mile might be more like two miles if you’re trying to arrive at a certain time. We’re more interested in the probability that a segment will be passed on intact than the size of the segment in Mb”.[2]

As the cM is an empirical measure, based on recombination events in a particular dataset of parents and offspring, it can vary somewhat from study to study. This set of maps for each chromosome shows that the general shape of the centiMorgan vs megabase curve is similar for two datasets, but the absolute values are not quite the same:

http://web.archive.org/web/20070113005025/http://compgen.rutgers.edu/maps/compare.pdf

cm values per chromosome

The following table compares cM values per chromosome at Family Tree DNAGEDmatch, and 23andMeAncestryDNA uses 3475 as the total cM according to the help screen for confidence level in a DNA match. This presumably excludes the X chromosome.

CM chromosome FTDNA&GEDMatch&23andMe.jpg

Probability of crossover

The following chart shows the estimated probability that a segment will be affected by a crossover. The chart does not take into account some variables such as inversions and different recombination rates for males and females.

Crossover probability centiMorgans.png

Converting centiMorgans into percentages

In order to get an approximate percentage of shared DNA from a Family Tree DNA Family Finder test, take all of the segments above 5 cM, add them together and then divide by 68.

The way the calculation works is that your total genome in cMs with the Family Finder test is 6770 cM. A half-identical match (such as a parent/child) is 3385 cM. This number has to be doubled to represent both the maternal and paternal sides giving a total of 6770 cM. Matt Dexter explains: “The reason the number is not 6770 or 6800, but rather 68, is that it saves an additional step doing the math to convert an answer to percent. For example, 3385 / 6770 = .5 then as a second step, .5 times 100 = 50%. Using 68 to start with saves the added math step. So (3385 / 6800) * 100 is the same thing as 3385 / 68, which results in = 50%.”[3]

Human reference genome

The centiMorgan totals per chromosome are based on the Human Reference Genome. 23andMe and Ancestry DNA use Build 37. Family Tree DNA use Build 37 for matching but Build 36 for segment boundaries in the Chromosome Browser. Raw data files are provided in both formats. Build 37 filled in quite a few gaps, and the number of base pairs in each of the chromosomes was longer in Build 37 as compared to Build 36. Consequently the cM totals per chromosome are lower for Family Finder than they are for 23andMe. GedMatch use Build 36, and convert AncestryDNA and 23andMe data from Build 37 to Build 36 for backward compatibility.

The latest version of the Human Reference Genome, Build 38, was released in December 2013. However, none of the companies have as yet adopted Build 38 and there is a “gentleman’s agreement” in place to stick with Build 37 for the present time.

Further reading

Resources

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