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



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.


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.


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.


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.


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.


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.


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.


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.


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.


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Articles from Genome Biology are provided here courtesy of BioMed Central


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

Here is what I learned about my ancient ancestry:


Neanderthal Man



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.


  • 79% Western Africa

  • 5% Northwestern Europe

  • 4% Eastern Africa

  • 4% West Mediterranean

  • 3% Northeastern Europe

  • 3% Eastern Europe



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 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?

YFull Tree DNA SNP Search for your Haplogroup

YFull Tree – Y-SNP Search for Your Haplogroup

The various DNA testing companies often use different versions of the Y-chromosome tree. Even though you have tested onto the same branch at multiple companies, that branch may be named differently at each. This can make it hard to Google for resources about your haplogroup.

YFull maintains one of the three versions of the paternal, Y-chromosome, tree of human kind. The names used for haplogroups, tree branches, on their tree are usually in common use in the genetic genealogy community. Therefore, when looking for resources for your haplogroup, it is useful to be able to change to the haplogroup used by Yfull. This tutorial shows how to find your current haplogroup on the YFull tree.


Binary Polymorphism – A genetic change with two possible states. That is positive or negative — derived or ancestral. Most binary polymorphisms on the 2017 tree are Y-SNPs. For simplicity, I usually refer to all types of binary polymorphisms as variants.
Haplogroup – A branch on the Y-chromosome Tree defined by one or more binary polymorphism.
Y-chromosome – The human male sex chromosome. It is passed from a father to his sons each generation with only small random changes.
Y-DNA – The DNA contained on the Y-chromosome.
Y-SNP – This is a genetic change of exactly one base pair to another value, A changes to C. This is a type of binary polymorphism.
– A 3rd party site for Y-DNA results.

How To

Before you start, you should have your haplogroup from one of the Y-DNA testing companies.

Step 1

Go to the YFull tree page,

Step 2

On the top right of the page, click on the Search button.

Step 3

Put the Y-SNP from your haplogroup in the SNP name field. Then click the Search button. In the example, I am searching for the I-P109 haplogroup. The name of the Y-SNP is the information to the right of the dash, so in this case it is P109.

Step 4

In the search results, look for the name of the haplogroup in green on the right. That is the name for your haplogroup on the YFull tree. In the example, the YFull tree haplogroup is I-P109.

Step 5

Click on the haplogroup name to open the YFull tree to it.

What are your thoughts? Join the conversation.
Y-DNA – Applied Genealogy & Paternal Origins

Y DNA Tree of Mankind Paternal Lineages


The benefits of using the Y chromosome in genetic genealogy are often not well understood. Please consider that with Big Y and Y111 and in the future, Y500, this has all changed. Y DNA is a powerful, reliable family lineage tracker, from genealogy to the ancient. Since every woman has a father the Y can track up to half of all lineages. It also has a nice affinity to surnames, land and other legal records.
Y DNA is extremely high resolution and useful in the genealogical timeframe. At the same time it does not wash out like autosomal DNA so Y DNA can break through genealogical brick walls.|
PDF is at

Resource: Mike Wadna Y DNA access 1/10/2018



African Royal DNA Project

How to Check for African Royal DNA Project Matches

October 11, 2017

Note: Any problems understanding to procedures or questions please directed to me or

*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.  



  • Register at this link 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 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 . 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 

Strictly Roots!! 

DNA Test Options, Indigenous African Results and More

DNA Test Options, Indigenous African Results and More for further information. is not a testing company and does not suggest any of the companies listed in this article. We offer a connection to purchase DNA kits, but it is your decision based on what you want to test for ancestry. The top three testing companies based on company reputation, services offered, testing methods, software grade, research and scientific evidence, CLIA and FDA compliance (US based) customer reviews, price, customer service and return policy.

#1. CRI Genetics (Cellular Research Institute)

#2. Family Tree DNA

#3 Living DNA Your Ancestry

for further reading go to


DNA Test can be done at 12, 25, 37, 67 or 111 markers. I recommend the 67-marker test, it gives you the best results for your money.

For more information or questions contact: or

August 28, 2017

African Greetings Family!

   We hope you are all doing well.  Let’s start with a video of brother Saad Tafida.  He is an Indigenous African that tested to learn about his ancestry and to find his family in the Diaspora.  He is Fulani.  (He will tell you more about that on the video so we don’t want to spoil it).

   As it turns out, he is my eldest daughter’s DNA match.  She is able to watch these videos and learn more about a line of her culture and for that, we thank Saad tremendously!  We need more like him to share and explore with us.

Here are his results

He then downloaded his DNA raw data from the website that he tested with.  Then he uploaded to He speaks about that in his video.  He found more relatives that NEVER knew their ancestry.

 He uploaded the DNA Raw data to a few websites to find more family.  Click here to see how to do it.

BE ENCOURAGED!!  More Indigenous Africans are testing and are looking for us as well too!!  

Now, here is some info on the current sale prices for a few major DNA testing companies.  You can click on each image to go to the website.  So now, let’s talk about the tests.

My Heritage DNA Test Kit $69.00






Everyone has asked, how do I get started on my DNA testing journey. This is a great place to start. Save this note because it is very useful to return to in the future.. Please read below.

We are NOT a DNA testing company. We do NOT sell DNA tests or profit from the sales of any tests. You must purchase the DNA test on your own. We simply explain what is available for YOU to research and determine what works for you. The information is provided by those of us that have DNA tested with EACH of the companies listed below.

We are a community of Volunteers focused on the ACRO concept. ACRO means African Culture and Reconciliation Organization. We coordinate cultural reception and integration via language classes, naming ceremonies and other enriching events after you have received your results.

We facilitate reconciliation of the DNA Tested African Diaspora and their African ethnic groups of ancestry. We provide you with 3rd party tools for YOU to research so you can determine which DNA Testing company and /or 3rd party tools for family tree building are most useful to you. We provide helpful templates for initial communications with your DNA matches as well as methods on how to get the most out of your test results.


Here is a good starting point to Research your AtDNA, MtDNA and the male YDNA. Please see the chart below.

Green is the autosomal DNA that can be tested by Ancestry, FTDNA Myheritage, and 23andme (they also provide DNA matches)

Blue is the YDNA that can be tested by FTDNA’s YDNA test (they provide DNA matches) and African Ancestry (they do NOT provide DNA matches)

Red is the MtDNA that can be tested by FTDNA’s Mt DNA test (they provide DNA matches) and African Ancestry (they do NOT provide DNA matches)

23andMe DBA Test Kit

“The information … meant to provide a very simple explanation of your Y-DNA and MtDNA Ancestry used for genealogical purposes. Scientists estimate that the total amount of Y-DNA of a man is less than 1% and the total amount of MtDNA in either a man or a woman is less than 1%. It is important to understand that after taking a Y-DNA and an MtDNA test, the majority of everyone’s DNA remains untested and it is called Autosomal DNA, with another 5% of a female’s DNA or 2 1/2% of a male’s DNA being x-chromosomal DNA. In a man this would mean roughly 95.5% of his DNA is Autosomal and in a woman that figure would be roughly 94%. “

Click here or copy and paste ~~ >… ~~


UPDATE: We have been advised that African Ancestry does not do the Admix test anymore. Please check with their website to confirm.

Subscribe at

1. $79 Autosomal test ( saliva ) that analyses DNA from all of the contributors of your DNA. Both males and females can take this test. They test 700,000 markers !! Your DNA is tested 40 times and they provide you with percentages of your ancestry and a list of DNA matches that you can contact. You can research with those DNA matches to determine if they match on your mother’s side or your father’s side of the family. The DNA kit is mailed to you, you provide a small sample of saliva and follow the instructions to activate the kit. It takes about 6 to 8 weeks to receive a email from ancestry notifying you that your results are in. Sign into your ancestry account and explore your results.

You can download your DNA raw data from ancestry and upload it to ( ) for FREE to find more DNA matches. This is a website that allows us that have tested at,,, and , to upload there to find more family. And yes! It is FREE.

You can also upload your DNA raw data to for FREE.

Limitations of Ancestry: This test will not tell you the African ethnic groups that you share ancestry with. However, you may find African DNA matches that can tell you their ethnic group(s) and where they come from. Also when you upload to Gedmatch, you may find African matches that have also uploaded there. Results of an African American




2. $99 Autosomal test ( saliva ) that analyses DNA from all of the contributors of your DNA. Both males and females can take this test. They provide you with percentages of your ancestry and a list of DNA matches that you can contact. You can research with those DNA matches to determine if they match on your mother’s side or your father’s side of the family. The DNA kit is mailed to you, you provide a small sample of saliva and follow the instructions to activate the kit. Check with 23andme to determine the current wait time for their test results. Once you receive the email that your results are in, sign into your 23andme account and explore your results.

Advantage:  Over 4 million people around the world have DNA tested.  If you match them, you will see them in your DNA match list when you sign into your account.  You can download your DNA raw data from 23andme and upload it to ( ) for FREE to find more DNA matches. This is a website that allows us that have tested at,,, and , to upload there to find more family. And yes! It is FREE.

You can also upload your DNA raw data to for FREE.

Limitations of 23andme: This test will not tell you the African ethnic groups that you share ancestry with. However, you may find African DNA matches that can tell you their ethnic group(s) and where they come from. Also when you upload to Gedmatch, you may find African matches that have also uploaded there.

YOU research, YOU decide Results



3. Starting at $79 for the family finder test.   ( cheek swab ) **If you already DNA tested at or , please go to FTDNA and upload your DNA raw data from those sites to this one for FREE. It will SAVE you the cost of $99. FTDNA’s Autosomal DNA test is $99. (Keep in mine that your autosomal DNA is 50 % from your father and 50% from your mother) 

They also have Mtdna tests for your Direct maternal line and YDNA tests for your direct paternal line. Only males can take the YDNA test. See the website for prices on their MtDNA and YDNA tests.

Regarding their Autosomal DNA test, they provide you with percentages of your ancestry and a list of DNA matches that you can contact. You can research with those DNA matches to determine if they match on your mother’s side or your father’s side of the family. The DNA kit is mailed to you, you provide a small sample of saliva and follow the instructions to activate the kit. Check with FTDNA to determine the current wait time for their test results. Once you receive the email that your results are in, sign into your FTDNA account and explore your results. You can download your DNA raw data from FTDNA and upload it to ( ) for FREE to find more DNA matches. You can download your DNA raw data from FTDNA and upload it to ( ) for FREE to find more DNA matches. This is a website that allows us that have tested at, ,,, and , to upload there to find more family. And yes! It is FREE.

Limitations for FTDNA: Their African database is LOW so you may not have very many matches. If you have a higher percentage of NON- African DNA, you may have a lot of DNA matches. Results


4.  Visit to see if their company is for you. Starting at $89 (often times on sale  for around $69) . Their AtDNA (autosomal) is a (cheek swab) test.  The Autosomal DNA test, provides you with percentages of your ancestry and a list of DNA matches (actual relatives)  that you can contact. You can research with those DNA matches to determine if they match on your mother’s side or your father’s side of the family. The DNA kit is mailed to you, you provide a small sample of saliva and follow the instructions to activate the kit. (Keep in mine that your autosomal DNA is 50 % from your father and 50% from your mother) 

Advantage:  This website accepts DNA raw data from , and  So if you already tested with these other companies, you only need to upload the data.  If you test with this company, you can download your DNA raw data from MyHeritage and upload it to ( ) for FREE to find more DNA matches. This is a website that allows us that have tested at, ,,, and , to upload there to find more family. And yes! It is FREE.

Limitations:  The DNA match database is still growing so you may not have a lot of matches  (cousins) on Myheritage.  However, uploading the DNA raw data to will surely give you more DNA matches. Results


5. Visit to see if their company is for you. Starting at $200. Their MtDNA test about 8 markers of the HVR1 region. I would not recommend this company as a first choice at this point but it may be good after you have found that you have an African haplogroup with another company like FTDNA. This is a cheek swab test 

Advantage: If you took the YDNA test or MTDNA test with FTDNA and found that you have an African haplogroup, you may consider contacting them and paying around $200 to receive a certificate stating what African ethnic group(s) you share ancestry with. Their MtDNA and YDNA test starts at $285. ** About 35% of African Americans do NOT have African Mtdna line or YDNA line. See their website for details. Make an INFORMED decision.

Limitations of African Ancestry: They are the most costly DNA testing company for their YDNA, MtDNA test, and Autosomal. They do not test as many DNA markers as the other companies. The DNA raw data cannot be uploaded to any other website. They do not provide any DNA matches. If your test reveals your MtDNA line or your YDNA line is not African, you will not be able to find African relatives or African ethnic groups through them. You will need to test with one of the above companies. Source:… and… .

This test will not tell you that you are 100% of anything. It will not provide ANY percentages of your ethnicity. The percentages that they provide is a sequence similarity score. They test LESS than 1% of your DNA. The Cofounder can explain this to you. Certificate Example



Make an INFORMED decision.

Please visit the website for each DNA test, research it and determine which company works for YOU!!

Note: All images belong to their perspective companies. This is for educational purposes to encourage research in order to make an informed decision about DNA testing.

Originally posted :


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:

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


DNA Triangulation, What?

Triangulation is a term derived from surveying to describe a method of determining the Y-STR or mitochondrial DNA ancestral haplotype using two or more known data points. The term “Genetic Triangulation” was coined by genetic genealogist Bill Hurst in 2004 Triangulate

Here is a 3-step process for Triangulation: Collect, Arrange, Compare/Group.

  1. Collect all the Match-segments you can. I recommend testing at all three companies (23andMe, FTDNA, and AncestryDNA), and using GEDmatch. But, wherever you test, get all of your segments into a spreadsheet. If you are using more than one company, you need to download, and then arrange, the data in the same format as your spreadsheet. Downloading/arranging is best when starting a new spreadsheet. Downloading avoids typing errors, but direct typing is sometimes easier for updates. I recommend deleting all segments under 7cM – most of them will be IBC/IBS (false segments) anyway, and even the ones which may be IBD are very difficult to confirm as such. You are much better off doing as much Triangulation as you can with segments over 7cM (or use a 10cM threshold if you wish), and then adding smaller segments back in later, if you want to analyze them. NB: Some of your closer Matches will share multiple segments with you – each segment must be entered as a separate row in your spreadsheet. The minimum requirement for a Triangulation with a spreadsheet includes columns for MatchName, Chromosome, SegmentStartLocation, SengmentEndLocation, cMs and TG. Most of us also have columns for SNPs, company, testee, TG, and any other information of interest to you. Perhaps I need a separate blog post about spreadsheets… ;>j
  1. Arrange the segments by sorting the entire spreadsheet (Cntr-A) by Chromosome and Segment StartLocation. This is one sort with two levels – the Chromosome column is the first level. This puts all of your segments in order – from the first one on Chromosome 1 to the last one on Chromosome 23 (for sorting purposes I recommend changing Chromosome X to 23 or 23X so it will sort after 22). This serves the purpose of putting overlapping segments close to each other in the spreadsheet where they are easy to compare.
  1. Compare/Group overlapping segments. All of these segments are shared segments with you. So with segments that overlap each other, you want to know if they match each other at this location. If so this is Triangulation. This comparison is done a little differently at each company, but the goal is the same: two segments either match each other, or they don’t (or there isn’t enough overlapping segment information to determine a match). All the Matches who match each other will form a Triangulated Group, on one chromosome – call this TG A (or any other name you want). Go through the same process with the segments who didn’t match TG A. They will often match each other and will form a second, overlapping TG, on the other chromosome – call this TG B. [Remember you have two of each numbered chromosome.] So to review, and put it all a different way: All of your segments (every row of your spreadsheet) will go into one of 4 categories:
  • – TG A [the first one with segments which match each other]
  • – TG B [the other, overlapping, one with segments which match each other]
  • – IBC/IBS [the segments don’t match either TG A or TG B]
  • – Undetermined [there are not enough segments to form both TG A and TG B                            and/or there isn’t enough overlapping data to determine a match.]
  • NB: None of the segments in TG A should match any of the segments in TG B.
  1. At GEDmatch – the comparisons are easy. Just compare two kit numbers using the one-to-one utility to see if they match each other on the appropriate segment. The ones that do are Triangulated. You may also use the Tier1 Triangulation utility or the Segment utility. I prefer using the one-to-one utility and Chrome.
  1. At 23andMe you have several different utilities:
  • – Family Inheritance: Advanced lets you compare up to 5 Matches at a time. You may also request a spreadsheet of all your shared segments; sort that by chromosome and SegmentStart, and check to see if two of your Matches match each other. The ones that do are Triangulated.
  • – Countries of Ancestry: Sort a Match’s spreadsheet by chromosome and SegmentStart, search for your own name, and highlight the overlapping segments. The Matches on this highlighted list who are also on overlapping segments in your spreadsheet are Triangulated (the CoA spreadsheet confirms the match between two of your Matches)
  1. At FTDNA it’s a little trickier, because they don’t have a utility to compare two of your Matches. So the most positive method is to contact the Matches and ask them to confirm if they match your overlapping Matches, or not. The ones that do are Triangulated. An almost-as-good alternative is to use the InCommonWith utility. Look for the 2-squigley-arrows icon next to a Match’s name, click that, and select In Common With to get a list of your Matches who also match the Match you started with. Compare that list of Matches with the list of list of Matches with overlapping segments in your spreadsheet. Matches on both lists are considered to be Triangulated. Although this is not a foolproof method, it works most of the time. And if you find three or four ICW Matches in the same TG, the odds are much closer to 100%. Remember, every segment in your spreadsheet must go in one TG or the other, or be IBC/IBS, or be undetermined. If a particular Match, in one TG, is critical to your analysis, then try hard to confirm the Triangulation by contacting the Matches.
  1. AncestryDNA has no DNA analysis utilities. You need to convince your Matches to upload their raw data to GEDmatch (for free) or FTDNA (for a fee), and see the paragraphs above.

Comments to improve this blog post are welcomed.

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