Genetic study reveals surprising ancestry of many Americans By Lizzie WadeDec. 18, 2014
In the United States, almost no one can trace their ancestry back to just one place. And for many, the past may hold some surprises, according to a new study. Researchers have found that a significant percentage of African-Americans, European Americans, and Latinos carry ancestry from outside their self-identified ethnicity. The average African-American genome, for example, is nearly a quarter European, and almost 4% of European Americans carry African ancestry.
Until recently, “human population geneticists have tended to ignore the U.S.,” says Joanna Mountain, a geneticist and senior director of research at 23andMe, a company in Mountain View, California, that offers genetic testing. With its long history of migrations from around the world, she says, the country was “considered to be kind of messy in terms of genetics.” But Mountain and her colleagues thought they might have a fighting chance of deciphering Americans’ complex genetic ancestry. Their secret weapon? 23andMe’s huge database of genetic information.
When a person signs up for a 23andMe genetic analysis, they can choose whether to make their data (with any identifying information removed) available for research. At the time when Mountain’s team compiled the database for their study, 23andMe had 500,000 customers, and about 80% of them had given their permission for their information to be used in that way. (Today, the company has about 800,000 customers.) That makes the data set used for the study “an order of magnitude bigger” than those usually used to examine population mixing, says Katarzyna Bryc, a population geneticist at 23andMe and lead author of the new paper.
The team started by looking at the average genetic ancestry of the three largest groups in the United States: European Americans, African-Americans, and Latinos. Those categories are based on how 23andMe customers defined themselves. But as you might expect in a country where different groups of people have been meeting and mixing for hundreds of years, the genetic lines between the groups are quite blurred.
“You see all of those different ancestries in each of these groups,” Bryc explains. The average African-American genome, for example, is 73.2% African, 24% European, and 0.8% Native American, the team reports online today in The American Journal of Human Genetics. Latinos, meanwhile, carry an average of 18% Native American ancestry, 65.1% European ancestry (mostly from the Iberian Peninsula), and 6.2% African ancestry.
The new study adds an unprecedented level of detail to patterns that had been noticed in previous, more general studies. For example, the 23andMe data reveals that the proportion of different ancestries, even within one self-identified ethnic group, vary significantly by state. Latinos with the highest proportion of African ancestry (about 20%) are from Louisiana, followed by states such as Georgia, North Carolina, New York, and Pennsylvania. In Tennessee and Kentucky, Latinos tend to have high proportions of European ancestry. And in the Southwest, where states share a border with Mexico, Latinos tend to have higher proportions of Native American ancestry.
At least 3.5% of European Americans carry African ancestry, though the averages vary significantly by state. In South Carolina and Louisiana, about 12% of European Americans have at least 1% African ancestry. In Louisiana, too, about 8% of European Americans carry at least 1% Native American ancestry.
In many states, the history of the region is written in the genomes of its current residents. Louisiana, for example, was a trading hub where different populations met and mingled. But sometimes the stories are even more specific. Oklahoma is the state where the most African-Americans have significant Native American ancestry, Bryc notes. That contact can be traced back to the Trail of Tears, when thousands of Native Americans were forcibly relocated to Oklahoma, which was also home to a significant number of black slaves. “You can really see historical events and historical migrations in the genetics,” Bryc says. “We weren’t actually expecting to be able to see that as clearly as we do.”
Another way that history shows up in contemporary genomes is in what researchers call a sex bias. By looking at the kinds of DNA that are passed down only by mothers, they can calculate how many of a person’s ancestors from each population were male and female. In all three populations, they found the same signal: European ancestors tended to be male, while African and Native American ancestors tended to be female. That imbalance reflects the fact that for much of U.S. history, European men were the most aggressive colonizers, Mountain says. This mixing seems to have started almost immediately after the first European colonizers and African slaves arrived in North America. “It suggests that really early U.S. history may have been a time of a lot of mixture,” Bryc says.
The fact that so many people in the United States carry a mix of different ancestries could have important medical implications. Today, doctors often assume that certain genetic variants are associated only with particular populations—think about sickle cell anemia in African-Americans, for example. But a person’s self-identified ethnicity—or the ethnicity her doctor assumes she is—doesn’t “necessarily correspond to [her] underlying genetics,” Bryc says. In a mixed population like the United States, it’s perfectly possible that a European American could carry the sickle cell variant that’s more common in African-Americans. In order for personalized medicine to live up to its potential, she says, doctors need to “consider the person” and her or his ancestry in all its complexity, rather than just falling back on reductive census categories.
The new study is “a beautiful piece of work,” says Andrés Moreno-Estrada, a population geneticist at Stanford University in Palo Alto, California, who has studied genetic diversity in Mexico and wasn’t involved with the new research. “The U.S. has a very particular genetic imprint compared to the rest of the Americas.” The 23andMe study “is one of steps forward in asserting that it’s possible to disentangle that complex scenario.”
Posts: 42920 | From: , | Registered: Jan 2010
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Though they do sometimes find creative lies to support their central lies.
quote:Originally posted by the lioness,: Researchers have found that a significant percentage of African-Americans, European Americans, and Latinos carry ancestry from outside their self-identified ethnicity. The average African-American genome, for example, is nearly a quarter European, and almost 4% of European Americans carry African ancestry.
.
Now the above declaration by 23andMe seems relative harmless on the face of it. But for it to work, you have to accept that they can look at a genome and tell if it's White, Black, or Latino.
That would mean that there are Haplogroups that only Whites have:
Latinos are Mulattoes so sure, the combination of that mysterious WHITE haplogroup, and Black haplogroups would mean the person is Latino.
He,he,he,he:
Only one problem....
THERE IS NO SUCH A THING AS THE WHITE PEOPLES HAPLOGROUP or GROUPS!
White people are our Albinos!
How the hell could they have SEPARATE haplogroups?
Posts: 22721 | Registered: Oct 2005
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Researchers have found that a significant percentage of African-Americans, European Americans, (didn't these used to be called Whites???) and Latinos carry ancestry from outside their self-identified ethnicity.
quote:Originally posted by the lioness,: Mike stop being an idiot the word "WHITE" appears nowhere in the article
He,he,he,he,he:
What - Now you're running from the label "WHITE"?????
Ohhh Doxie is going to be Sooo mad!
You know how she loves to be called WHITE!
Posts: 22721 | Registered: Oct 2005
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Researchers have found that a significant percentage of African-Americans, European Americans, (didn't these used to be called Whites???) and Latinos carry ancestry from outside their self-identified ethnicity.
quote:Originally posted by the lioness,: Mike stop being an idiot the word "WHITE" appears nowhere in the article
He,he,he,he,he:
What - Now you're running from the label "WHITE"?????
Ohhh Doxie is going to be Sooo mad!
You know how she loves to be called WHITE!
I've told you before "white" and "black" are stereotypical color contructs.
But that doesn't matter. Quoting the article properly is what matters.
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posted
The most comprehensive study to date on the non-African ancestry of AAs is that of Sarah Tishkoff. Tishkoff puts the percentage at 13%. The advantage that Tishkoff's study has over others is that it engages in a comparative study of both AAs and Africans in Africa.
Mere haplogroup analysis does not tell the whole story because humans tend to classify other humans not on DNA analysis but on gross morphology. A Fijian in Sudan would be lost in Khartoum crowd. Yet the his DNA would not be any variant of E. Ditto for an Andaman Islander in South Sudan. Ditto also for a New Guinean. The name "New Guinean" says it all.
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posted
Interesting but New Guinea are the words the Europeans used to describe the people they saw in what is now called New Guinea. The Europeans called the West coast of Africa, Guinea. And Guinea was characterized by black people. Now they saw people who looked the same in a far off place in S.E. Asia, so they concluded that this place was just a "New Guinea".
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posted
The Genetic Ancestry of African Americans, Latinos, and European Americans across the United States
Katarzyna Bryc, Eric Y. Durand, J. Michael Macpherson, David Reich, Joanna L. Mountain Open Access
The Genetic Ancestry of African Americans, Latinos, and European Americans across the United States Katarzyna Bryc,1,2,* Eric Y. Durand,2 J. Michael Macpherson,3 David Reich,1,4,5 and Joanna L. Mountain2 Over the past 500 years, North America has been the site of ongoing mixing of Native Americans, European settlers, and Africans [brought largely by the trans-Atlantic slave trade), shaping the early history of what became the United States. We studied the genetic ancestry of 5,269 self-described African Americans, 8,663 Latinos, and 148,789 European Americans who are 23andMe customers and show that the legacy of these historical interactions is visible in the genetic ancestry of present-day Americans. We document pervasive mixed ancestry and asymmetrical male and female ancestry contributions in all groups studied. We show that regional ancestry differ- ences reflect historical events, such as early Spanish colonization, waves of immigration from many regions of Europe, and forced relo- cation of Native Americans within the US. This study sheds light on the fine-scale differences in ancestry within and across the United States and informs our understanding of the relationship between racial and ethnic identities and genetic ancestry. Introduction Over the last several hundred years, the United States has been the site of ongoing mixing of peoples of continental populations that were previously separated by geography. Native Americans, European immigrants to the Americas, and Africans brought to the New World largely via the trans-Atlantic slave trade came together in the New World. Mating between individuals with different continental origins, which we refer to here as ‘‘population admixture,’’ results in individuals who carry DNA inherited from multiple populations. Although US government census surveys and other studies of households in the US have es- tablished fine-scale self-described ethnicity at the state and county level [see the US 2010 Census online), the relation- ship between genetic ancestry and self-reported ancestry for each region has not been deeply characterized. Under- standing genetic ancestry of individuals from a self-re- ported population, and differences in ancestry patterns among regions, can inform medical studies and personal- ized medical treatment.1 The genetic ancestry of individ- uals can also shed light on the history of admixture and migrations within different regions of the US, which is of interest to historians and sociologists. Previous studies have shown that African Americans in the US typically carry segments of DNA shaped by contri- butions from peoples of Europe, Africa, and the Americas, with variation in African and European admixture propor- tions across individuals and differences in groups across parts of the country.2–4 More recent studies that utilized high-density genotype data provide reliable individual ancestry estimates, illustrate the large variability in African and European ancestry proportions at an individual level, and are able to detect low proportions of Native American ancestry.3–11 Latinos across the Americas have differing proportions of Native American, African, and European genetic ancestry, shaped by local historical interactions with migrants brought by the slave trade, European settle- ment, and indigenous Native American populations.12–18 Individuals from countries across South America, the Caribbean, and Mexico have different profiles of genetic ancestry molded by each population’s unique history and interactions with local Native American popula- tions.1,19–25 European Americans are often used as proxies for Europeans in genetic studies.26 European Americans, however, have a history of admixture of many genetically distinct European populations.27,28 Studies have shown that European Americans also have non-European ancestry, including African, Native American, and Asian, though it has been poorly quantified with some discor- dance among estimates even within studies.29–32 That genetic ancestry of self-described groups varies across geographic locations in the US has been docu- mented in anecdotal examples but has not previously been explored systematically. Most early studies of Afri- can Americans had limited resolution of ancestry because of small sample sizes and few genetic markers, and recent studies typically have limited geographic scope. Though much work has been done to characterize the genetic di- versity among Latino populations from across the Amer- icas, it is unclear the extent to which Latinos within the US share or mirror these patterns on a national or local scale. Most analyses have relied on mitochondrial DNA, Y chromosomes, or small sets of ancestry-informa- tive markers, and few high-density genome-wide SNP studies have explored fine-scale patterns of African 1Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; 223andMe, Inc., Mountain View, CA 94043, USA; 3School of Computational Sciences, Chapman University, Orange, CA 92866, USA; 4Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA; 5Broad Insti- tute of MIT and Harvard, Cambridge, MA 02142, USA *Correspondence: kbryc@23andme.com http://dx.doi.org/10.1016/j.ajhg.2014.11.010. !2015 The Authors This is an open access article under the CC BY-NC-ND license [http://creativecommons.org/licenses/by-nc-nd/3.0/). The American Journal of Human Genetics 96, 37–53, January 8, 2015 37 AR TICLE and Native American ancestry in individuals living across the US. Here, we describe a large-scale, nationwide study of Afri- can Americans, Latinos, and European Americans by using high-density genotype data to examine subtle ancestry patterns in these three groups across the US. To improve the understanding of the relationship between genetic ancestry and self-reported ethnic and racial identity, and to characterize heterogeneity in the fine-scale genetic ancestry of groups from different parts of the US, we in- ferred the genetic ancestry of 5,269 self-reported African Americans, 8,663 Latinos, and 148,789 European Ameri- cans who are 23andMe customers living across the US, by using high-density SNPs genotype data from 650K to 1M arrays. 23andMe customers take an active role in participating in research by submitting saliva samples, consenting for data to be used for research, and completing surveys. We generated cohorts of self-reported European American, African American, and Latino individuals from self-reported ethnicity and identity. We obtained ancestry estimates from genotype data by using a Support Vector Machine-based algorithm that infers population ancestry with Native American, African, and European reference panels, leveraging geographic information collected through surveys [see Durand et al.33). For details on geno- typing and ancestry deconvolution methods, see Subjects and Methods. Subjects and Methods Human Subjects All participants were drawn from the customer base of 23andMe, Inc., a consumer personal genetics company. This data set has been described in detail previously.34,35 Participants provided informed consent and participated in the research online, under a protocol approved by the external AAHRFP-accredited IRB, Ethical & Independent Review Services [E&I Review). Genotyping Participants were genotyped as described previously.36 In short, DNA extraction and genotyping were performed on saliva samples by National Genetics Institute [NGI), a CLIA-licensed clinical lab- oratory and a subsidiary of Laboratory Corporation of America. Samples have been genotyped on one of four genotyping platforms. The V1 and V2 platforms were variants of the Illumina HumanHap550þ BeadChip, including about 25,000 custom SNPs selected by 23andMe, with a total of about 560,000 SNPs. The V3 platform was based on the Illumina OmniExpressþ BeadChip, with custom content to improve the overlap with our V2 array, with a total of about 950,000 SNPs. The V4 platform in current use is a fully custom array, including a lower redundancy subset of V2 and V3 SNPs with additional coverage of lower-frequency coding variation and about 570,000 SNPs. Samples that failed to reach 98.5% call rate were reanalyzed. Individuals whose analyses failed repeatedly were recontacted by 23andMe customer service to provide additional samples, as is done for all 23andMe customers. Customer genetic data have been previously utilized in association studies and studies of genetic relationships.34–43 Research Cohorts 23andMe customers were invited to fill out web-based question- naires, including questions on ancestry and ethnicity, on state of birth, and current zip code of residence. They were also invited to allow their genetic data and survey responses to be used for research. Only data of customers who signed IRB-approved con- sent documents were included in our study. Survey introductions are explicit about their applications in research. For example, the ethnicity survey introduction text states that the survey responses will be used in ancestry-related research [Table S1 available online). Self-Reported Ancestry It is important to note that ancestry, ethnicity, identity, and race are complex labels that result both from visible traits, such as skin color, and from cultural, economic, geographical, and social factors.23,44 As a result, the precise terminology and labels used for describing self-identity can affect survey results, and care in choice of labels should be utilized. However, we chose to maximize our available self-reported ethnicity sample size by combining information from questions asking for customer self- reported ancestry. We used two survey questions, with different nomenclature, to gauge responses about identity, which here we view as ‘‘the subjective articulation of group membership and affinity.’’45 The first question is modeled after the US census nomenclature and is a multiquestion survey that allows for choice of ‘‘Hispanic’’ or ‘‘Not Hispanic,’’ and participants were asked ‘‘Which of these US Census categories describe your racial identity? Please check all that apply’’ from the following list of ethnicities: ‘‘White,’’ ‘‘Black,’’ ‘‘American Indian,’’ ‘‘Asian,’’ ‘‘Native Hawaiian,’’ ‘‘Other,’’ ‘‘Not sure,’’ and ‘‘Other racial identity.’’ For inclusion into our European American cohort, individuals had to select ‘‘Not Hispan- ic’’ and ‘‘White,’’ but not any other identity. For inclusion into our Latino cohort, individuals had to select ‘‘Hispanic,’’ with no other restrictions. For inclusion into our African American cohort, individuals had to select ‘‘Not Hispanic’’ and ‘‘Black’’ and no other identity. The second question on identity is a single-choice question, where respondents were asked to choose ‘‘What best describes your ancestry/ethnicity?’’ from ‘‘African,’’ ‘‘African American,’’ ‘‘Central Asian,’’ ‘‘Declined,’’ ‘‘East Asian,’’ ‘‘European,’’ ‘‘Latino,’’ ‘‘Mideast,’’ ‘‘Multiple ancestries,’’ ‘‘Native American,’’ ‘‘Not sure,’’ ‘‘Other,’’ ‘‘Pacific Islander,’’ ‘‘South Asian,’’ and ‘‘Southeast Asian.’’ Because individuals could select only one response, we included individuals who selected ‘‘European’’ in our European American cohort, those who selected ‘‘African American’’ in our African American cohort, and those who selected ‘‘Latino’’ in our Latino cohort. Some African American participants included in this study were recruited through 23andMe’s Roots into the Future project [accessed October 2013), which aimed to increase understanding of how DNA plays a role in health and wellness, especially for dis- eases more common in the African American community. Individ- uals who self-identified as African American, black, or African were recruited through 23andMe’s current membership, at events, and via other recruitment channels. In the present work, we do not include individuals who self- report as having multiple identities, because this represents only a small fraction of individuals in our data set. Low rates of report- ing as multiracial or multiethnic is in line with previous studies; an analysis of the 2000 US Census shows that 95 percent of blacks and 97 percent of whites acknowledge only a single identity.45 38 The American Journal of Human Genetics 96, 37–53, January 8, 2015 Future studies including multiracial individuals might further illu- minate patterns of genetic ancestry and the complex relationship with self-identity. Differences among states, where different proportions of people self-report as mixed race, might explain some regional differences in genetic ancestry. However, we note that, first, proportionally fewer people identify as mixed race than as a single identity, and second, it remains important to establish regional differences in genetic ancestry of self-reported groups even if these differences are driven, to some degree, by regional changes in self-reported identity. More work is needed to determine to what extent regional differences are a result of how people today report their ancestry. Lastly, when available, we excluded individuals who answered ‘‘No’’ to a question whether they are living in the US. In total, our final sets included 5,269 African Americans, 8,663 Latinos, and 148,789 European Americans. Notes on Terminology and Selection of Populations Throughout the manuscript, the term ‘‘Native American ancestry’’ refers to estimates of genetic ancestry from indigenous Americans found across North, Central, and South America, and we distin- guish this term from present-day Native Americans living in the US. We use the term ‘‘Native American’’ to refer to indigenous peo- ples of the Americas, acknowledging that some people may prefer other terms such as ‘‘American Indian.’’ Our estimates of African ancestry specifically aim to infer ancestry of sub-Saharan Africa and does not include ancestry from North Africa. We note that the term ‘‘Latino’’ has many meanings in different contexts, and in our case, we use it to refer to individuals living in the US who self-report as either ‘‘Latino’’ or ‘‘Hispanic.’’ Our work represents a snapshot in time of genetic ancestry and identity, and future work is needed to inform the dynamic changes and forces that shape social interactions. We note that our cohorts are likely to have ancestry from many African populations, but because of current reference sample availability, our resolution of West African ancestries is outside the scope of our study. Likewise, our estimates of Native American ancestry arise from a summary over many distinct subpopulations, but we are limited in scope because of insufficient sample sizes from subpopulations, so we currently use individuals from Central and South American together as a reference set [see Durand et al.33 for a list of populations and sample sizes). Validation of Self-Reported Identity Survey Results To verify that our self-reported ethnicities were reliable, we exam- ined the consistency of ethnicity survey responses when individ- uals completed both ancestry and ethnicity surveys. Because the structure of the two surveys is different and multiple selections were allowed in one survey but not the other, we examined the replication rate of the primary ethnicity from the single-choice ethnicity survey in the multiple-selection survey. In addition to structural differences, the survey content used very different nomenclature, and therefore we believe our esti- mated error rates to be overestimates of the true error rate, because it is likely that some individuals choose to identify with one label but not the other [i.e., ‘‘African American’’ but not ‘‘black’’). Dis- crepancies in the question nomenclatures are likely to increase the error rate. Furthermore, because the two surveys could be completed at different times, either before or after obtaining per- sonal ancestry results, it is possible that viewing genetic ancestry results might have led to a change in self-reported ancestry. Such a change would be tallied as an error in our estimates, but instead reflects a true change in perceived self-identity over time. Overall, we expect that our survey data represent highly reliable ancestry information, with errors affecting fewer than 1% of survey responses. Geographic Location Collection Self-reported state-of-birth survey data was available for 47,473 customers of 23andMe. However, because overlap of these cus- tomers with our cohorts was poor, we also chose to include data from a question on current zip code of residence. This provided an additional 34,351 zip codes of current residence. In cases where both the zip code of residence and state of birth were available, we used state-of-birth information. To obtain state information from zip codes, we translated zip codes to their state locations via an on- line zip code database [accessed October 2013). In total, we had 50,697 individuals with available location information. About one third of each of our cohorts had location information: 1,970 African Americans, 2,944 Latinos, and 45,783 European Americans were used in our geographic analyses. Ancestry Analyses Ancestry Composition We apply Ancestry Composition, a three-step pipeline that effi- ciently and accurately identifies the ancestral origin of chromo- somal segments in admixed individuals, which is described in Durand et al.33 We apply the method to genotype data that have been phased via a reimplementation of Beagle.46 Ancestry Compo- sition applies a string kernel support vector machines classifier to assign ancestry labels to short local phased genomic regions, which are processed via an autoregressive pair hidden Markov model to simultaneously correct phasing errors and produce reconciled local ancestry estimates and confidence scores based on the initial assignment. Lastly, these confidence estimates are recalibrated by isotonic regression models. This results in both precision and recall estimates that are greater than 0.90 across many populations, and on a continental level, have rates of 0.982–0.994 for precision and recall rates of 0.935–0.993, depend- ing on populations [see Table 1 from Durand et al.33). We note that here, and throughout the manuscript, African ancestry corre- sponds to sub-Saharan African ancestry [including West African, East African, Central, and South African populations, but excluding North African populations from the reference set). For more details on our ancestry estimation method, see Durand et al.33 Aggregating Local Ancestry Information 23andMe’s Ancestry Composition method provides estimates of ancestry proportions for several worldwide populations at each window of the genome. To estimate genome-wide ancestry pro- portions of European, African, and Native American ancestry, we aggregate over populations to estimate the total likelihood of each population, and with a majority threshold of 0.51, if any win- dow has a majority of a continental ancestry, we include it in the calculation of genome-wide ancestry, which is estimated as the number of windows passing the threshold for each ancestry over the total number of windows. Some windows might not pass our threshold for any population, so they remain unassigned, making it possible for estimates for all ancestries to not sum to 100%, resulting in population averages that likewise might not sum to 100%. We allow for this unspecified ancestry to reduce the error rates of our assignments, so, in some sense, our estimates might be viewed as lower bounds on ancestry, and it is possible that individuals carry more ancestry than estimated. In practice, we typically assign nearly all windows, with an average of about 1%–2% unassigned ancestry, so we do not expect it to affect our The American Journal of Human Genetics 96, 37–53, January 8, 2015 39 results, with the exception of Native American ancestry, which we discuss below. Generating the Distribution of Ancestry Tracts We generate ancestry segments as defined as continuous blocks of ancestry, estimating the best guess of ancestry at each window to define segments of each ancestry. Assigning the most likely ancestry at each window results in fewer spurious ancestry breaks and allows for a smaller upward bias in admixture dates, because breaks in ancestry segments push estimates of dates further back in time. We measure segment lengths by using genetic distances, by mapping segment start and end physical positions to the HapMap genetic map. Admixture Dating To estimate the time frame of admixture events, we test a simple two-event, three-population admixture model via TRACTS.47 We use a grid-search optimization to find four optimal parameters for the times of two admixture events and the proportions of admixture. We are limited to simple admixture models resulting from the computationally intensive grid search, because we were unable to obtain likelihood convergence with any of the built-in optimizers. The model tested is as follows: two populations admix t1 generations ago, with proportion frac1 and 1 ␣ frac1, respec- tively. A third population later mixes in t2 generations ago, with proportion frac2. Both our ancestry segments and prior results supported a model with an earlier date of Native American admixture.25,47 We esti- mated likelihoods over plausible grid of admixture times and frac- tions for African Americans, Latinos, and European Americans to estimate dates of initial Native American and European admixture and subsequent African admixture. These dates are estimated as the best fit for a pulse admixture event: because they represent an average over more continuous or multiple migrations, initial admixture is likely to have begun earlier. Lower Estimates of African Ancestry in 23andMe African Americans Unlike previous estimates of the mean proportion of African ancestry, which typically have ranged from 77% to 93% African ancestry,2–4,48–62 our estimates, depending on exclusions, are 73% or 75%. There are several possible explanations for our low mean African ancestry. If our Ancestry Composition estimates are downward biased, then the African Americans might have levels of African ancestry consistent with other studies, and our re- sults are simply underestimates. However, our Ancestry Composi- tion estimates are extremely well calibrated for African Americans from the 1000 Genomes Project and their consensus estimates, and we see no evidence of a downward bias [see Figure 5 from Durand et al.33). The mean ancestry proportion of 23andMe self-reported African Americans is about 73%. A small fraction, about 2%, of African Americans carry less than 2% African ancestry, which is far less than typically seen in most African Americans [Figure S18A avail- able online). Further investigation reveals that the majority of these individuals [88%) have predominantly European ancestry, and others carry East Asian, South Asian, and Southeast Asian ancestry, roughly in proportion to the frequencies found in the 23andMe database overall. Given the large number of non- African American individuals in the 23andMe database, even an exceeding low survey error rate of 0.02% could be sufficient to ac- count for the number of outlier individuals we detect. Hence, we posit that these individuals represent survey errors rather than true self-reported African Americans. Exclusion of these 108 self- reported African Americans with less than 2% African ancestry from mean ancestry calculations results in a moderate rise, to 74.8%, of the mean proportion of African ancestry in African Americans. To quantify differences in African ancestry driving mean state differences, we examined the distributions of estimates of African ancestry in African Americans from the District of Columbia [D.C.) and Georgia, which had at least 50 individuals with the lowest and highest mean African ancestry proportions [Figure S1E). We find a qualitative shift in the two distributions of African ancestry, with D.C. showing a reduced mode, higher variance, and a heavier lower tail of African ancestry, correspond- ing to more African Americans with below-average ancestry than Georgia. Qualitative differences in the distributions of African ancestry proportions in African Americans from states with higher and lower mean ancestry appear to be driven by both a shift in the mode of the distribution as well as a heavier left tail reflecting more individuals with a minority of African ancestry [Figure S1). We posit that differences among states could be due to differences in admixture, differences in self-identity, or differences in patterns of assortative mating, whereby individuals with similar ancestry might preferentially mate. For example, greater levels of admix- ture with Europeans would both shift the mode and result in more African American individuals who have a minority of Afri- can ancestry. Alternatively, a shift toward African American self- identity for individuals with a majority of European ancestry [possibly because of changes in cultural or social forces) would likewise result in lower estimates of mean African ancestry. Lastly, assortative mating would work to maintain or increase the vari- ance in ancestry proportions, though assortative mating alone could not shift the mean proportion of African ancestry in a population. Sex Bias in Ancestry Contributions Sex bias in ancestry contributions, often assessed through ancestry of mtDNA and Y chromosome haplogroups, is also manifested in unequal estimates of ancestry proportions on the X chromosome, which has an inheritance pattern that differs between males and females. The X chromosome more closely follows female ancestry contributions because males contribute half as many X chromo- somes. Comparing ancestry on the X chromosome to the auto- somal ancestry allows us to infer whether that ancestry historically entered via males [lower X ancestry) or by females [higher X ancestry). Under equal ancestral contributions from both males and females, the X chromosome should show the same levels of admixture as the genome-wide estimates. To look for evidence of unequal male and female ancestry contributions in our cohorts, we examined ancestry on the X chromosome [NRY region), which follows a different pattern of inheritance from the autosomes. In particular, estimates of ancestry on the X chromosome have been shown to have higher African ancestry in African Ameri- cans.9 We calculate ancestry on the X chromosome as the estimate of ancestry on just windows on the X, and we compare to genome- wide estimates [which do themselves include the X chromosome). It should be noted that these calculations differ among males and females, because the X chromosome is diploid in females and thus has twice as many windows in calculation of genome-wide mean proportions. However, our results still allow a peek into sex bias because the overall contribution of the X chromosome to the genome-wide estimates is small. We note that because our ancestry estimation method conservatively assigns Native Amer- ican ancestry, we expect that much of the remaining unassigned ancestry might be due to Native American ancestry assigned as broadly East Asian/Native American, which is not included in these values [see Figure 5 in Durand et al.33). 40 The American Journal of Human Genetics 96, 37–53, January 8, 2015 To infer estimates of male and female contributions from each ancestral population, we estimated the male and female fractions of ancestry that total the genome-wide estimates and minimize the mean square error of the X chromosome ancestry estimates. age, predicting self-reported ancestry by using proportion African ancestry, sex, age, intercept, and interaction variables. Validation of Non-European Ancestry in African Americans and European Americans Although our Ancestry Composition estimates are well calibrated and have been shown to accurately estimate African, European, and Native American ancestry in tests of precision and recall,33 we were concerned that low levels of non-European ancestry in European Americans that we detected might represent an artifact of Ancestry Composition. Hence, we pursued several lines of investigation to provide evidence that estimates of African and Native American ancestry in European Americans are robust and not artifacts. Comparison with 1000 Genomes Project Consensus Estimates Comparisons of our estimates with those published by the 1000 Genomes Consortium show the high consistency across popula- tions and individuals. We compare estimates across Americans of African Ancestry in SW USA [ASW), Colombians from Medellin, Colombia [CLM), Mexican Ancestry from Los Angeles USA [MXL), and Puerto Ricans from Puerto Rico [PUR). We note that our estimates of Native American ancestry are conservative. Indeed, when our Ancestry Composition assignment probabilities do not pass over the confidence threshold, including signals of Native American ancestry together with general East Asian/Native American ancestry [but not East Asian) recapitulates estimates from the 1000 Genomes Project consensus estimates. Five individ- uals from the ASW population from the 1000 Genomes Project have poor consistency in their estimates. These individuals have a large amount of Native American ancestry that was not modeled by the 1000 Genomes Project estimates. That these particular indi- viduals were sampled in Oklahoma, and carry significant Native American ancestry, is supported by our own high estimates of Native American ancestry in 23andMe self-reported African Amer- icans from Oklahoma. Estimates of African and Native American Ancestry in Europeans We looked at whether all individuals who are expected to carry solely European ancestry also have similar rates of detection of non-European ancestry. To this end, we generated a cohort of 15,289 customers of 23andMe who reported that all four of their grandparents were born in the same European country. The use of four-grandparent birth-country has been utilized as a proxy for assessing ancestry.27,63 We then examined Ancestry Composition results for these individuals and calculated at what rate we detected at least 1% African and at least 1% Native American ancestry. Independent Validation of African Ancestry in European Americans via f4 Statistics We used f4 statistics from the ADMIXTOOLS software package to confirm the presence of African ancestry.64 We used the f4 ratio test, designed to estimate the proportion of admixture from a related ancestral population, to compare admixture in European Americans versus reference European individuals. We tested whether European Americans with estimated African ancestry showed any admixture from Africans by using our cohorts of indi- viduals with estimated African ancestry and reference populations from the 1000 Genomes Project data set. Admixture would be expected to result in estimates of a significantly different from 1. Detection of Native American mtDNA in European Americans and African Americans The mitochondrial DNA [mtDNA) haplogroups A2, B2, B4b, C1b, C1c, C1d, and D1 are most prevalently found in the Americas and We assume that overall male and female contributions are each 50% [P f 1⁄40:5 and P f 1⁄40:5). We assume pop pop;male pop pop;female that the total contribution from males and females of a population gives rise to the autosomal ancestry fraction [fpop,male þ fpop,female 1⁄4 autopop). We then compute, via a grid search, the predicted X chromosome estimates from fpop,male, fpop,female for each pop ̨fAfrican;NativeAmerican;Europeang, which are calculated, as in Lind et al.,6 as Xb pop 1⁄4 fpop;male þ 2,fpop;female 1⁄4 fpop;male þ 2,fpop;female 0:5,1 þ 0:5,2 1:5 We choose the parameters of male and female contributions that minimize the mean squared error of the X ancestry estimates and the predicted Xb pop . These are the estimates of male and female ancestry fractions under a single simplistic population mixture event that best fit our X chromosome ancestry estimates observed. Population Size Correlations From the 2010 Census Brief ‘‘The Black Population’’ available on- line, we calculated the correlation between the number of reported African Americans living in a state and our sample of African Americans from that state. The correlation is strong, with p value of 9.5 3 10␣14, suggesting that our low sample sizes from states in the US Mountain West is expected from estimates of population sizes. African ancestry in European Americans most frequently occurs in individuals from states with high proportions of African Amer- icans and is rare in states with few African Americans. This obser- vation led us to look at the correlation between population size [as a percent of state population using self-reported ethnicity from the 2010 US Census) and state mean levels of ancestry. To examine the interaction between proportions of minorities and ancestry, we used the 2010 US Census demographic survey by state. We compare the state population proportion to the mean estimated admixture proportion of individuals from that state, fitting linear regressions, and generating figures with geom_smooth[method 1⁄4 ‘‘lm,’’ formula 1⁄4 y ~ x) from the ggplot2 package in R. We find that African ancestry in European Americans is strongly correlated with the population proportion of African Americans in each state. We find that the higher the state proportion of African Americans, the more African ancestry is found in European Amer- icans from that state, reflecting the complex interaction of genetic ancestry, historical admixture, culture, and self-identified ancestry. Logistic Regression Modeling of Self-Identity We examine the probabilistic relationship between self-identity and genetically inferred ancestry. To explore the interaction be- tween genetic ancestry and self-reported identity, we estimated the proportion of individuals that identify as African American and European American, partitioned by levels of African ancestry. Jointly considering the cohorts of European Americans and Afri- can Americans, we examined the relationship between an individ- ual’s genome-wide African ancestry proportion and whether they self-report as European American or African American. We note a strong dependence on the amount of African ancestry, with indi- viduals carrying less than 20% African ancestry identifying largely as European American, and those with greater than 50% reporting as African American. To test the significance of this relationship, we fit a logistic regression model, using Python’s statsmodels
are likely to be Native-American-specific haplogroups because they are rarely found outside of the Americas. We assessed the fraction of individuals that carry these haplogroups to validate the likeli- hood of Native American ancestry in European Americans and African Americans and show that these haplogroups are virtually absent in European controls. Because mtDNA haplogroups are as- signed by classification with SNPs that segregate on these lineages, these orthogonal results provide an independent line of support for our estimated Native American ancestry in European Ameri- cans and African Americans. Distribution of Ancestry Segment Start Positions Regions of the genome that have structural variation or show strong linkage disequilibrium [LD) have been shown both to confound admixture mapping and to influence the detection of population substructure in studies using Principal Components Analysis [PCA).27,63,65 If such regions were to drive artifacts of spurious ancestry, we would expect that segments of local ancestry would probably occur around these regions, rather than in a uni- form distribution across the genome. To this end, we examined the starting positions of all African and Native American ancestry segments in European Americans and Native American ancestry in African Americans. Comparison with ADMIXTURE Genome-wide Estimates We applied ADMIXTURE,66 a model-based estimation of ancestry proportions, to estimate proportions of European, Native Amer ican, East Asian, sub-Saharan African, Middle Eastern, and Ocean- ian ancestry proportions. We use the supervised algorithm for K 1⁄4 6, with 9,694 reference individuals representing the six aforemen- tioned populations. We ran ADMIXTURE on 269,229 autosomal markers after pruning SNPs to have r2 < 0.5, via PLINK.67 To reduce computation time, we examined consistency of methods on the African Americans whom we estimated to have at least 1% Native American ancestry, European Americans estimated to have at least 1% Native American ancestry, and European Ameri- cans estimated to have at least 1% African ancestry. Results Self-reported survey data was used to generate cohorts of African Americans, Latinos, and European Americans. Out of 35,524 self-reported ‘‘European’’ individuals, 35,279 selected ‘‘white’’ on the ethnicity survey, yielding a per-survey error estimate of 0.2%. Out of 1,560 self-re- ported ‘‘Latino’’ individuals, 1,540 selected ‘‘Hispanic,’’ giving a per-survey error estimate of 0.7%. Lastly, out of 1,327 self-reported ‘‘African American’’ individuals, 1,287 selected ‘‘black,’’ resulting in a per-survey error rate esti- mate of 1.1%. For more details on our cross-survey valida- tion, see Subjects and Methods. The Genetic Landscape of the US Patterns of Genetic Ancestry of Self-Reported African Americans Genome-wide ancestry estimates of African Americans show average proportions of 73.2% African, 24.0% Euro- pean, and 0.8% Native American ancestry [Table 1). We find systematic differences across states in the US in mean ancestry proportions of self-reported African Ameri- cans [Figure 1 and Table S2). On average, the highest levels of African ancestry are found in African Americans living in or born in the South, especially South Carolina and Georgia [Figure 1Aand Table S3). We find lower propor- tions of African ancestry in the Northeast, the Midwest, the Pacific Northwest, and California. The amount of Native American ancestry estimated for African Americans also varies across states in the US. More than 5% of African Americans are estimated to carry at least 2% Native Amer- ican ancestry genome-wide [Figures S1 and 1D). African Americans in the West and Southwest on average carry higher levels of Native American ancestry, a trend that is largely driven by individuals with less than 2% Native American ancestry [Figure 1B). With a lower threshold of 1% Native American ancestry, we estimate that about 22% of African Americans carry some Native American ancestry [Figure S2). We used the lengths of segments of European, African, and Native American ancestry to estimate a best-fit model of admixture history among these populations for African Americans [Figure S3). We estimate that initial admixture between Europeans and Native Americans occurred 12 generations ago, followed by subsequent African admix- ture 6 generations ago, consistent with other admixture inference methods dating African American admixture. A sex bias in African American ancestry, with greater male European and female African contributions, has been sug- gested through mtDNA, Y chromosome, and autosomal studies.6 On average, across African Americans, we esti- mate that the X chromosome has a 5% increase in African ancestry and 18% reduction in European ancestry relative to genome-wide estimates [see Table 1). Through compar- ison of estimates of X chromosome and genome-wide African and European ancestry proportions, we estimate that approximately 5% of ancestors of African Americans were European females and 19% were European males [Table S4). Patterns of Genetic Ancestry of Self-Reported Latinos Latinos encompass nearly all possible combinations of Af- rican, Native American, and European ancestries, with the exception of individuals who have a mix of African and Native American ancestry without European ancestry [see Figures S4A and S1). On average, we estimate that Latinos in the US carry 18.0% Native American ancestry, 65.1% European ancestry, and 6.2% African ancestry. We find the highest levels of estimated Native American ancestry in self-reported Latinos from states in the Southwest, espe- cially those bordering Mexico [Figure 2C). We find the highest mean levels of African ancestry in Latinos living in or born in states in the South, especially Louisiana, the Midwest, and Atlantic [Figure 2A). Further stratifica- tion of individuals by their self-reported population affiliation [e.g., ‘‘Mexican,’’ ‘‘Puerto Rican,’’ or ‘‘Domin- ican’’) reveals a diversity in genetic ancestry, consistent with previous work studying these populations [see Figure S5 and Table S5).10,20,24,25,68,69 We find that Latinos who, besides reporting as ‘‘Hispanic,’’ also self-report as Mexican or Central American, carry more Native American ancestry than Latinos overall; those also who self-report as black, Puerto Rican, or Dominican have higher levels of African ancestry; and those who additionally self-report as white, Cuban, or South American have on average higher levels of European ancestry. Admixture date estimates for Latino admixture suggest that Native American and European mixture occurred first, about 11 generations ago, followed by African admixture 7 generations ago. Consistent with previous studies that show a sex bias in admixture in Latino populations,12–18 we estimate 13% less European ancestry on the X chromo- some than genome-wide [Table 1), showing proportionally greater European ancestry contributions from males. We inferred elevated African and Native American ancestry on the X chromosome, corresponding to higher female ancestry contributions from both Africans and Native Americans. Lastly, Latinos show higher proportions of inferred Iberian ancestry than both European Americans and African Americans [Figure S6). Patterns of Genetic Ancestry of Self-Reported European Americans We find that many self-reported European Americans, pre- dominantly those living west of the Mississippi River, carry Native American ancestry [Figure 3B). We estimate that Eu- ropean Americans who carry at least 2% Native American ancestry are found most frequently in Louisiana, North Dakota, and other states in the West. Using a less stringent threshold of 1%, our estimates suggest that as many as 8% of individuals from Louisiana and upward of 3% of indi- viduals from some states in the West and Southwest carry Native American ancestry [Figure S7). Consistent with previous anecdotal results,32 the fre- quency of European American individuals who carry Afri- can ancestry varies strongly by state and region of the US [Figure 3A). We estimate that a substantial fraction, at least 1.4%, of self-reported European Americans in the US carry at least 2% African ancestry. Using a less conservative threshold, approximately 3.5% of European Americans have 1% or more African ancestry [Figure S8). Individuals with African ancestry are found at much higher frequencies in states in the South than in other parts of the US: about 5% of self-reported European Americans living in South Car- olina and Louisiana have at least 2% African ancestry. Lowering the threshold to at least 1% African ancestry [potentially arising from one African genealogical ancestor within the last 11 generations), European Americans with African ancestry comprise as much as 12% of European Americans from Louisiana and South Carolina and about 1 in 10 individuals in other parts of the South [Figure S8). Most individuals who have less than 28% African ancestry identify as European American, rather than as African Amer- ican [Figures 4 and 5A). Logistic regression of self-identified European Americans and African Americans reveals that the proportion of African ancestry predicts self-reported ancestry significantly, with a coefficient of 20.1 [95% CI: 18.0–22.2) [Table S6 and Figure S9). For a full characteriza- tion of terms and logistic models, see Table S6 and Figure S9. Fitting a model of European and Native American admixture followed later by African admixture, we find the best fit with initial Native American and European admixture about 12 generations ago and subsequent Afri- can gene flow about 4 generations ago. Non-European ancestry in European Americans follows a sex bias in admixture contributions from males and females, as seen in African Americans and Latinos. The ratio between X chromosome and genome-wide Native American ancestry estimates in European Americans shows greater NativeAmerican female and higher European male ancestry contri- butions [Tables 1 and S4). Though we do not observe evidence of a sex bias in African ancestry contributions in European Americans overall, analysis of only those indi- viduals with at least 1% African ancestry reveals 15% higher African ancestry on the X chromosome relative to genome- wide estimates [p value 0.013). This increase suggests fe- male-African and male-European sex bias in European Americans that follows the same direction as in African Americans and Latinos, with greater male European and fe- male African and Native American contributions. Finally, we estimate, for self-reported European Ameri- cans, proportions of British/Irish, Eastern European, Iberian, and Scandinavian ancestry [Figure 3) and other European subpopulation ancestries [Figure S10). Correlations with Population Proportions We find that levels of Native American and African ancestry in 23andMe customers in each state are significantly corre- lated with the proportion of African Americans and Latinos in each state [Figures S11–S13). For example, levels of Afri- can ancestry in European Americans and Latinos in a state are highly correlated with proportion of African Americansn each state [both p values < 10␣4). Levels of Native Amer- ican ancestry in European Americans and Latinos in a state are highly correlated with proportion of Latinos in each state [p values < 10␣6 and < 10␣2, respectively). Validation of Ancestry Estimates Robust and Consistent Ancestry Estimates Estimates from Ancestry Composition are extremely well calibrated, with correlations of African, European, and Native American ancestry estimates showing r2 > 0.98 with 1000 Genomes Project African American and Latino consensus estimates [Figure 5 from Durand et al.33). Admix- ture tests via an independent admixture software package, ADMIXTOOLS,64 confirm significant signals of African admixture in European Americans [Table S7). Ancestry Composition estimates are highly concordant with ADMIXTURE66 estimates, with r2 values of 0.94, 0.98, and 0.91, for the three groups, respectively [Figure S14). Evidence that the Great Majority of Ancestry Segments that We Detect Are Real We show that positions of segments of non-European ancestry start uniformly across the genome [see Figure S15). Although some regions, including the HLA re- gion containing the MHC complex on chromosome 6, show higher ancestry switches reflecting difficulties in assignment because of genetic diversity [as likewise seen in African Americans and Latinos; Figures S16 and S17), the majority of segments are uniformly distributed. Only 4% of all segment starts of African ancestry lie within the HLA region, and only about 1.4% of Native American segment starts lie in the HLA region. We find very low levels of African and Native American ancestry in Europeans with four grandparents born in Europe. We estimate that only 0.98% of Europeans carry African ancestry and 0.26% of Europeans carry Native American ancestry. These levels are substantially lower than the 3.5% and 2.7% of European Americans who carry African and Native American ancestry, respectively. Furthermore, for most European countries we observed no individuals with substantial non-European ancestry, and the presence of individuals with African and Native American ancestry is limited to countries that had major ports in the Atlantic trade and were known to have been highly connected to the trans-Atlantic slave trade. Indeed, African ancestry in individuals from Europe is not unexEurope between 1501 and 1867 [as documented by Eltis and Richardson’s maps of the slave trade, accessible at Emory University’s database). Excluding countries that had major and minor ports in the Atlantic with strong con- nections to the slave trade [namely Portugal, Spain, France, and United Kingdom) and Malta, which has been the site of migrations from Africa and the Middle East, we obtain a data set of 9,701 Europeans, where we find African and Native American ancestry is virtually absent, with only 0.04% of individuals carrying 1% or more African ancestry and 0.01% carrying 1% or more Native American ancestry, within the margins of survey error estimates. pected; approximately 9,000 Africans were brought toNative American mtDNA in European Americans and African Americans and Not in Europeans The frequency of Native American mtDNA haplogroups in European Americans and African Americans correlate with our estimates of genome-wide ancestry in European Amer- icans and African Americans and are found in appreciable fractions of individuals who are estimated to carry Native American ancestry. The frequencies of haplogroups are shown in Table S8. These haplogroups are virtually absent in individuals with four grandparents from a European country [21 individuals out of 15,651). Furthermore, the majority of these Native American haplogroups in Europeans are found in individuals from Spain. Though it is possible these represent non-Native American hap- logroups, prior literature and studies of genetic, archaeo- logical, and paleontological evidence suggest that these haplogroups have Native American origins and is evidence of gene flow from the Americas to Spain. Excluding Spain, Native-American-specific haplogroups are detected in fewer than 0.05% of individuals with four grandparents from Europe and can be explained by survey errors in re- porting all four grandparents’ birth places. Discussion Selection of Populations The ancestries of 23andMe customers, and therefore the demographics of the database used for this study, largely reflect the demographics of the US, as tallied in the 2010 US census. Our study considers three cohorts that comprise the three largest self-identified groups in the US, which are likewise well represented in the 23andMe database. In this study, we focus on the distribution of European, African, and Native American ancestries and European subpopulation ancestries. These populations were selected because we had available reference data sets, allowing for accurate estimation of ancestry propor- tions, they reflect the major waves of migration into the US just after the era of transcontinental travel began, and they are found at mean frequencies of more than 1% in our cohorts. At present, we are unable to delve deeper into the complexity of, and subancestries within, Native American and West African populations. Our resolution reflects the current availability of reference data sets from different regions. However, we emphasize that these groups and ancestries are only a fraction of the diversity found within individ- uals living in the US, and as data set sizes grow, future work should extend to include analyses of other worldwide ancestries and populations and their distributions across the US. Patterns of Genetic Ancestry of Self-Reported African Americans Consistent with previous studies,2,70 the diversity of ancestry profiles of 23andMe African Americans reveal that individuals comprise the full range from 0% to 100% African ancestry, but, further, that there are differ- ences in estimates of ancestry proportions among regions. Namely, we find differences between states that were slave- holding and those that were ‘‘free’’ at the time of the US Civil War. Reflected in these ancestry patterns are migra- tion routes, such as the trans-Atlantic slave trade that brought Africans through important Southern seaports [as documented online in American FactFinder and Amer- ican Community Survey Summary File). The small sample sizes from some areas of the US, including parts of the Mid- west and Mountain regions, reflects the lower population density of African Americans residing in these regions [see the ‘‘The Black Populations’’ Census Brief). Though mean estimates of Native American ancestry are low, many African Americans carry detectable levels of Native American ancestry. Consistent with historical nar- ratives and family histories, our estimate suggests that one in every five African Americans carries Native American ancestry, a higher rate than we detected in self- reported European Americans. An individual that carries more than 1% Native American ancestry can arise from one genetically Native American ancestor within the last 11 or so generations, or multiple genealogical Native Amer- ican ancestors [for discussion, see ‘‘How Many Genetic An- cestors Do I Have?’’ online). Oklahoma shows the highest proportion of African Americans with substantial Native American ancestry, where more than 14% of African Amer- icans from Oklahoma carry at least 2% Native American ancestry [Figures 1B and S2). Oklahoma was the site of con- tact between Native Americans and African Americans af- ter the Trail of Tears migration in the 1830s,71,72 where black slaves comprised a significant part of the population in the 1860s [according to the US 1860 Census), and the location of the slave-holding ‘‘Five Civilized Tribes.’’ In contrast, we do not observe higher rates of Native Amer- ican ancestry in African Americans in Florida, which is potentially notable in light of the known history of Semi- nole intermarriage with blacks according to the 1860 US Census [information available online). Even excluding individuals with no African ancestry, which are probably the result of survey errors, we still esti- mate a higher European, and corresponding lower African, mean genetic ancestry proportion in 23andMe African Americans compared to previous studies of African Ameri- cans. A significant difference between the 23andMe cohort of African Americans and many groups previously studied is geographic sampling. Our cohort reflects heavier sam- pling of individuals living in or born in California and New York, probably driven by population density as well as awareness of genetic testing or 23andMe. Both are re- gions where African Americans have lower mean African ancestry than other studies of African Americans, which are often drawn from locations in the South. However, participation in 23andMe is not free and requires online access, so therefore it is important to note that other social, cultural, or economic factors might interact to affecancestry proportions of those individuals who choose to participate in 23andMe. Our admixture dates for African Americans provide evi- dence that African and European mixture occurred prior to 1860, suggesting that gene flow between these groups might predate the Great Migration of African Americans from the South into the North beginning around 1910, though more complex models [that capture more contin- uous gene flow) are needed to resolve African and Euro- pean mixture timing.73 Patterns of Genetic Ancestry of Self-Reported Latinos We estimated that Iberian ancestry composes as much as a third of the European ancestry in Latinos in Florida, New Mexico, and other parts of the Southwest, probably reflect- ing either early Spanish influence and rule in these regions or recent immigration from Latin America, which might also be associated with higher levels of Iberian ancestry in New York and New Jersey. Regions with higher Iberian ancestry also correspond to regions with greater Native American ancestry; disentangling whether higher levels of Native American ancestry in the Southwest reflects the legacy of indigenous Native American ancestors or is the result of recent Latino immigrants into the Southwest might be possible through future studies of admixture dating or more Native American subpopulation reference data. Patterns of Genetic Ancestry of Self-Reported European Americans Our estimated rates of non-European ancestry in European Americans suggest that more than six million Americans, who self-identify as European, might carry Af- rican ancestry. Likewise, as many as five million Americans who self-identify as European might have at least 1% Native American ancestry. Louisiana’s high levels of Afri- can ancestry in European Americans are consistent with historical accounts of intermarriage in the New Orleans area.74,75 Regional differences in European subpopulation ancestry across states reflect known major historical migra- tions from Europe. Inferred British/Irish ancestry is found in European Americans from all states at mean proportions of more than 20% and represents a majority of ancestry [more than 50% mean proportion) in states such as Missis- sippi, Arkansas, and Tennessee. These states are similarly highlighted in the map of the self-reported ‘‘American’’ ethnicity in the US 2010 Census survey, which might reflect regions with lower subsequent migration from other parts of Europe. Inferred Eastern European ancestry is found at its highest levels in Illinois, Michigan, and Pennsylvania, potentially stemming from immigration during the late 19th and early 20th centuries, settling in metropolitan areas in the Northeast and Midwest. Inferred Iberian ancestry, found overall at lower mean proportions, still represents a measurable ancestry component in Florida, Louisiana, California, and Nevada, and might point to the early Spanish rule and colonization of the Americas. Scandinavian ancestry in European Americans is highly localized; most states show only trace mean pro- portions of Scandinavian ancestry, but it comprises a significant proportion, upward of 10%, of ancestry in Euro- pean Americans from Minnesota and the Dakotas. The distributions of the European subpopulation ancestries in European Americans illustrate that the distribution of within-European ancestry is not homogenous among indi- viduals from different states, and instead, reflects differ- ences in population migrations and settlement patterns across the US. Sex Bias in Ancestry Contributions We find evidence that sex-biased admixture processes are widespread in US history in European Americans as well as in African American and Latino populations. Estimates of proportions of males and females from each ancestral population [Table S4) suggest that under a simple demo- graphic model of admixture, European Americans might have ten times as many female Native American ancestors as male, and African Americans might have four times as many female Native American ancestors as male. Sex bias in ancestry contributions might have been driven by un- balanced sex ratios in immigration frontier settings,76 exploitation,77 or other social factors. Robust Estimates of African and Native American Ancestry in African Americans and European Americans Several lines of evidence suggest that Native American and African segments represent true signals of Native American and African introgression that occurred after the transcon- tinental migrations beginning in the 1500s. Validation of our self-reported survey data across two independent surveys shows that self-reported ancestry consistency is remarkably high. African ancestry in European Americans is not likely to be driven by survey errors because the number of European Americans with African ancestry is ten times larger than our estimates of survey error rates. Furthermore, the ancestry profiles of self-reported Euro- pean Americans with African ancestry are distinct from all other cohorts: their African ancestry is much lower than for a random sample of African Americans, and the majority of these individuals do not carry any appreciable amount of Native American ancestry, distinguishing their ancestry profiles from Latinos [see Figure S1C). A potential source of bias in our estimates is from errors in the ancestry inference algorithm. To show that our esti- mates are not the result of Ancestry Composition errors or biases, we validated the estimates of low levels of African ancestry in European Americans comparing to f4 statis- tics,64 1000 Genomes Project consensus estimates,78 and ADMIXTURE estimates.66 Another line of evidence sup- porting our estimates of non-European ancestry in Euro- pean Americans in the US is that we observe a substantially lower occurrence of Native American and African ancestry The American Journal of Human Genetics 96, 37–53, January 8, 2015 49 in individuals who self-report four grandparents born in the same European country. The inferred segments of Afri- can and Native American are uniformly distributed across the genome. Although we expect that some of the inferred ancestry might arise from difficulties in assigning ancestry in complex regions of the genome, only a small fraction of the estimated African and Native American ancestry in European Americans can be explained through such biases and is not expected to give rise to any substantial [more than 1%) ancestry from any population. Lastly, our recent dates for admixture suggest that intro- gression probably occurred in the Americas within the last 500 years. Hence, our estimates do not support that the Af- rican ancestry in European Americans stems from ancient population events that predate the migrations to the Americas. [For example, gene flow from Africa coinciding with the Moor invasion of the Mediterranean might have introduced African ancestry into the ancestral popula- tion of some European Americans.) Though such ancient events would probably not lead to inferred African ancestry because our supervised learning algorithm would apply a European label to such segments, it is possible that European population substructure could lead to inferred segments of African ancestry in some European Americans that derive from older historical admixture events, which are not seen in modern Europeans. However, these events would lead to admixture or introgression of segments several hundred or thousand years old, and our admixture dates for both Native American ancestry and African ancestry point to gene flow within the last 20 generations and is not consistent with any known historical migrations within Europe during this time period. Correlations with Population Proportions Correlations between state population proportions and mean ancestry proportions suggest that the numbers of African and Native American individuals in a state might have shaped the ancestries of present-day individuals. For African Americans, the states with the highest mean levels of African ancestry, such as South Carolina, Georgia, and Florida are not those with the highest proportions of African Americans. Given the highly significant statistics in European Americans, surprisingly, in African Americans, the correlation of African ancestry with proportions of African Americans is only marginally significant [p value 0.025). The correlation of Native American ancestry in Af- rican Americans with Latino state population proportion also has a marginal p value of 0.026. Not all correlations are strongly significant, suggesting that other social or cultural factors influenced levels of ancestry, especially in African Americans. Relationship of Self-Identity and Genetic Ancestry Contrary to expectations under a social one-drop rule, or ‘‘Rule of Hypodescent,’’ which would mandate that indi- viduals who knowingly carry African ancestry identify as African American, the probability of self-reporting as Afri- can American given a proportion of African ancestry follows a logistic probability curve [Figure S9A, Table S6), suggesting that individuals identify roughly with the ma- jority of their genetic ancestry [Figures 4 and 5A). Individ- uals with more than 5% Native American ancestry are most likely to self-identify as Latino [Figures S9C and 5B), suggesting differences in sociological or historical factors associated with identifying with these groups. The transitions between Latino, African American, and Euro- pean American self-reported identity by proportions of African and Native American ancestry illustrate both the complexity of how one self identifies as well as the overlap- ping ancestry profiles among groups [Figure 5B). Conclusion This work demonstrates that the legacy of population mi- grations and interactions over the last several hundred years is visible in the genetic ancestry of modern individ- uals living in the US. Our results suggest that genetic ancestry can be leveraged to augment historical records and inform cultural processes shaping modern popula- tions. The relationship between self-reported identity and genetic African ancestry, as well as the low numbers of self-reported African Americans with minor levels of African ancestry, provide insight into the complexity of genetic and social consequences of racial categorization, assortative mating, and the impact of notions of ‘‘race’’ on patterns of mating and self-identity in the US. Our re- sults provide empirical support that, over recent centuries, many individuals with partial African and Native American ancestry have ‘‘passed’’ into the white com- munity,79,80 with multiple lines of evidence establishing African and Native American ancestry in self-reported Eu- ropean Americans [see Subjects and Methods). Though the majority of European Americans in our study did not carry Native American or African ancestry, even a small proportion of this large population that carry non-Euro- pean ancestry translates into millions of European Ameri- cans who carry African and Native American ancestry. Our results suggest that the early US history, beginning in the 17th century [around 12 generations ago), might have been a time of many population interactions result- ing in admixture. Large sample sizes, high-density genotype data, and ac- curate and robust local ancestry estimates allowed us to discern subtle differences in genetic ancestry. In spite of present-day high mobility of individuals, the genetic ancestry of present-day individuals recapitulates historical migration events, known settlement patterns, and admix- ture processes. Perhaps most importantly, however, our re- sults reveal the impact of centuries of admixture in the US, thereby undermining the use of cultural labels that group individuals into discrete nonoverlapping bins in biomed- ical contexts ‘‘which cannot be adequately represented by arbitrary ‘race/color’ categories.’’81 Our findings can inform medical genetic studies. Introgressed Native American and African haplotypes in European Americans might have implications for studies References of complex diseases, especially for diseases that vary in prevalence among ancestral populations, can produce sub- tle population structure that should be carefully controlled for in GWASs, and might impact the distribution of rare variants in studies of whole-genome sequence. Our results also suggest new avenues for research, such as the potential for including European Americans in admixture mapping. Supplemental Data Supplemental Data include 18 figures and 8 tables and can be found with this article online at http://dx.doi.org/10.1016/j. ajhg.2014.11.010.
A person from New Guinea would not blend in with South Sudanese. South Sudanese are tall, slim, have virtually no body hair and have different facial features. The Andaman Island people also only match the Dinka and Nuer when it comes to skin colour.
Posts: 1568 | From: Pluto | Registered: Sep 2008
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quote: Latinos, meanwhile, carry an average of 18% Native American ancestry, 65.1% European ancestry (mostly from the Iberian Peninsula), and 6.2% African ancestry.
This is a lie.
quote: Latinos with the highest proportion of African ancestry (about 20%) are from Louisiana, followed by states such as Georgia, North Carolina, New York, and Pennsylvania. In Tennessee and Kentucky, Latinos tend to have high proportions of European ancestry. And in the Southwest, where states share a border with Mexico, Latinos tend to have higher proportions of Native American ancestry.
Posts: 22234 | From: האם אינכם כילדי הכרית אלי בני ישראל | Registered: Nov 2010
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quote: Latinos, meanwhile, carry an average of 18% Native American ancestry, 65.1% European ancestry (mostly from the Iberian Peninsula), and 6.2% African ancestry.
This is a lie.
quote: Latinos with the highest proportion of African ancestry (about 20%) are from Louisiana, followed by states such as Georgia, North Carolina, New York, and Pennsylvania. In Tennessee and Kentucky, Latinos tend to have high proportions of European ancestry. And in the Southwest, where states share a border with Mexico, Latinos tend to have higher proportions of Native American ancestry.
saying "this is a lie" is not an argument
Posts: 42920 | From: , | Registered: Jan 2010
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I wrote that a FIJIAN would be lost in a crowd in Khartoum, not a New Guinea person. Khartoum is in Sudan proper, not South Sudan.
Posts: 5492 | Registered: Nov 2004
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quote: Latinos, meanwhile, carry an average of 18% Native American ancestry, 65.1% European ancestry (mostly from the Iberian Peninsula), and 6.2% African ancestry.
This is a lie.
quote: Latinos with the highest proportion of African ancestry (about 20%) are from Louisiana, followed by states such as Georgia, North Carolina, New York, and Pennsylvania. In Tennessee and Kentucky, Latinos tend to have high proportions of European ancestry. And in the Southwest, where states share a border with Mexico, Latinos tend to have higher proportions of Native American ancestry.
saying "this is a lie" is not an argument
Your comment is predictable. But it is still a lie. You just post stuff without commentary. And when people as you for commentary your response is, I don't know.
Posts: 22234 | From: האם אינכם כילדי הכרית אלי בני ישראל | Registered: Nov 2010
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quote:...Ours is the first study to characterize genomic patterns of variation from (1) Hondurans, which we show have a higher proportion of African ancestry than Mexicans, (2) Cubans, which show extreme variation in ancestry proportions ranging from 2% to 78% West African ancestry, and (3) Haitians, which showed the largest average proportion of West African ancestry (84%).
So what do you think of Cavalli-Sforza's thesis that Europeans are 33% African in terms of DNA analysis?
Posts: 5492 | Registered: Nov 2004
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posted
These DNA analyses can be problematic sometimes. James Watson of Double Helix fame was supposedly 16% African. Hitler was an E1b1b carrier.But both are white Europeans through and through.
The litmus test on all this is to compare the morphologies of the children of African migrants to places like the U.S. and see if you can tell the differences in racial terms from 12th generation U.S. blacks.
Posts: 5492 | Registered: Nov 2004
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There is a high frequency of African-Mestizo admixture ranging between 20-40% . The admixture rate between Africans and indigenous Mexican Indians ranges between 5-50% .
References:
1. Lisker R, et al.(1996). Genetic structure of autochthonous populations of Meso-america:Mexico. Am. J. Hum Biol 68:395-404.
2. Suarez-Diaz,E. (2014) Indigenous populations in Mexico. Medical anthropology in the Work of Ruben Lisker in the 1960's. Studies in History and Philosophy of Biological and Biomedical Sciences 47:108-117.
3. Lisker,R.(1981. Estructura genetia de la poblacion Mexicana. Aspectos Medicos y Anthropologica, Mexico: Salvat.
.
-------------------- C. A. Winters Posts: 13012 | From: Chicago | Registered: Jan 2006
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quote:Originally posted by lamin: These DNA analyses can be problematic sometimes. James Watson of Double Helix fame was supposedly 16% African. Hitler was an E1b1b carrier.But both are white Europeans through and through.
The litmus test on all this is to compare the morphologies of the children of African migrants to places like the U.S. and see if you can tell the differences in racial terms from 12th generation U.S. blacks.
No because White Europeans are not an actual race, stop being an ignorant degenerate. Modern White Europeans are albino's and not an actual "race", and they are pretty much the combination of African and Indian albino's breeding together in Northern Europe, before the advent of the Roman empire in varying amounts across the different regions of Europe proper. This is where the supposed African genes from, and why they are so WHITE TODAY, in the modern White European populations; since Modern White Europeans are the descendants of recent White Eurasian Indo-European transplants and migrants from Central Asia and Siberia.
THEY ARE NOT THE SAME PEOPLE AS NEOLITHIC EUROPEANS, AND THEY ARE NOT INDIGENOUS TO EUROPE AND THAT IS A FACT!
Posts: 1558 | From: US | Registered: Sep 2015
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Ignorance always loses to knowledge--though it may take time.
"Races" are morphological sub-groups of the world's human populations. Europeans are indeed a morphological sub-group. So too Africans, Asians( East and South) and others.
It's just stupid to talk of Europeans as albinos. I just finished watching the final of the European football championship in Milan, Italy. I had a good look at the thousands of spectators. The vast majority were olive-coloured with brown hair. The players the same. Albinos not at all--for one good reason that actual albinos are easily identified within European society.
Posts: 5492 | Registered: Nov 2004
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There is a high frequency of African-Mestizo admixture ranging between 20-40% . The admixture rate between Africans and indigenous Mexican Indians ranges between 5-50% .
References:
1. Lisker R, et al.(1996). Genetic structure of autochthonous populations of Meso-america:Mexico. Am. J. Hum Biol 68:395-404.
2. Suarez-Diaz,E. (2014) Indigenous populations in Mexico. Medical anthropology in the Work of Ruben Lisker in the 1960's. Studies in History and Philosophy of Biological and Biomedical Sciences 47:108-117.
3. Lisker,R.(1981. Estructura genetia de la poblacion Mexicana. Aspectos Medicos y Anthropologica, Mexico: Salvat.
.
Winters, as usual, is being deceptive. His pretty little graph does not include the fact that in all these populations there are more European genes than African. By definition, mestizos are mixtures of Indians and Europeans so that Lisker's table of mestizos is clearly not the source for the pure mixture of Indians and Africans
Table 2. Ancestral contributions of Blacks, Indians, and Whites
Clearly these populations are not relevant to the question. It is also clear that these populations came about after the Spanish arrived, and its not clear in what sequence the ternary mix came about. What Winters did not show clearly is the part of the table that IS more relevant to us, i.e. indian populations
In these Indian groups you get zero African contribution with the exception of the Maya Chontal group at 5% (not very significant); the Chol live in the area of the Classic Maya civilization, the Zapotec live in the area where writing was first found in Mesoamerica, the Totonac are the Indians living in Veracruz--and the better example to use rather then the Veracruz mestizo sample cited by Winters, the Huasteco are the supposedly ancestral Maya speakers just before the Mande came. Manansala’s shift to "Olmec region≤ is a red herring-- the proper comparisons would have been Mixe-Xoque speaking Indians who are the linguistic descendants of the Gulf Olmecs, as the decipherment of the writing of the Mojarra stela using Zoque language shows. However, the paper did not study any of these populations. The paper points out that populations used were monolingual and identified themselves as Indian-- therefore, if there had been precolumbian African contact in the Maya area these would be the groups where it would show up. It doesn't.
Posts: 833 | From: Austin, TX | Registered: Jan 2007
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posted
This chart represents less than 14% percent of Mexico
Population
Paraiso ( a town)_______ 86,632 El Carmen ( a town) ____6,996 Veracruz ______________8,112,505 Saladero (in Veracruz) Tamiahua (in Veracruz)
TOTAL under 8.3 million
POPULATION OF MEXICO 122.3 million
____________________
most comprehensive genetic study of the Mexican population to date,
quote: At the continental level of K = 3 ancestral clusters, we find that most individuals have a large amount of Native and European ancestry, with a small (typically <5%) amount of African ancestry.
-- Science. 2014 Jun 13; 1251688 PMCID: PMC4156478 NIHMSID: NIHMS614608
The Genetics of Mexico Recapitulates Native American Substructure and Affects Biomedical Traits
Ignorance always loses to knowledge--though it may take time.
"Races" are morphological sub-groups of the world's human populations. Europeans are indeed a morphological sub-group. So too Africans, Asians( East and South) and others.
It's just stupid to talk of Europeans as albinos. I just finished watching the final of the European football championship in Milan, Italy. I had a good look at the thousands of spectators. The vast majority were olive-coloured with brown hair. The players the same. Albinos not at all--for one good reason that actual albinos are easily identified within European society.
Yes ignorance does lose to knowledge, like REAL FACTS LIKE MINE, and your so called pretend knowledge repeatedly debunked bullshit does indeed lose to my FACTAUL AND EVIDENCE BASED AND SUPPORTED CLAIMS!
Fact! All of the so called features of White Europeans are FOUND OUTSIDE OF EUROPE, AND ALL OF THE MODERN GENETIC HAPLOGROUPS OF EUROPE, ORIGINATED FROM OUTSIDE OF EUROPE, IN NON-EUROPEAN REGIONS AND PEOPLES! WHICH IS A FACT YOU DEGENERATE IGNORAMUS! MODERN WHITE EUROPEANS HAVE NOTHING TO DO W/ NEOLITHIC EUROPEAN POPULATIONS GENETICALLY, WHICH IS A PROVEN FACT!
FACT! MODERN WHITE EUROPEANS ARE NOT INDIGENOUS OR NATIVE TO EUROPE, THEY MASS MIGRATED THERE FROM CENTRAL ASIA AND SIBERIA RECENTLY! MODERN WHITE EUROPEAN SCIENTIST'S AND HISTORIANS ADMIT THAT, AND SO DO ANCIENT GRECO-ROMAN ACCOUNTS! WE HAVE POSTED TONS OF ARTICLES AND REPORTS SAYING THIS HERE AT ES! IT'S NOT MY PROBLEM IF YOU ARE TOO MUCH OF A LAZY INTELLECTUALLY DEFICIENT IGNORANT IDIOT TO GO LOOK IT UP!
And modern White Europeans are genetically DISTINCT FROM EACH OTHER ACROSS THE DIFFERENT QUADRANTS OF EUROPE TO BE GENETICALLY DISTINCT FROM EACH OTHER AND DISQUALIFIED TO BE A DISTINCT GROUP OF PEOPLE FROM ELSEWHERE! EVEN RACIST 1800'S WRITERS WERE EVEN SAYING THAT! WHAT UNITES ALL OF THEM IS ALBINISM! THEY ARE ALL ALBINO'S EXCEPT FOR SOUTHERN EUROPEANS!
AND IDIOT, ITALIANS AND SOUTHERN EUROPEANS HAVE RECENT ADMIXTURE FROM AFRICA AND THE MIDDLE EAST, WHICH IS WHY THEY LOOK SO DARK! THEY LOOK DIFFERENT FROM EASTERN, NORTHERN AND NORTH-WEST EUROPEANS WHOM ARE WHITE AND WHOM ARE ALBINO'S! THEY WERE/ARE NOT EVEN CONSIDERED TO BE PROPER WHITES OR EVEN WHITE IN EUROPE!
HOW THE **** CAN YOU BE SO STUPID TO NOT KNOW THIS?
Stop playing dumb and repeating the same old ignorant tired old bullshit! WE HAVE COVERED THIS ALREADY MILLIONS OF TIMES ON THIS FORUM! STOP BEING A DUMBFUCK!
AND YES IT IS A FACT THAT WHITES ARE ALBINO'S AND NOT A RACE, AND WE HAVE PROVED THAT ALREADY HERE ON E.S MULTIPLE TIMES! STOP PLAYING DUMB AND FEIGNING IGNORANCE, BECAUSE YOU ARE MAKING YOURSELF LOOK LIKE AN IGNORANT IDIOT!
I am not going to feed your trolling antics and feigned ignorance anymore sorry!
Posts: 1558 | From: US | Registered: Sep 2015
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posted
This paper is bs. Genetics is a biological science. Science is neutral. But when genetics is used to study the population history of Afro-Americans it becomes another tool to promote White Supremacy.Geneticists assume that you can discuss the genetic history of Afro-Americans as a simple case of admixture resulting from the mixture of Africans, Europeans and Native Americans since the Transatlantic Slave Trade.
This is false. These studies are false because Africans or Negroes have been in contact with Native Americans and whites or Europeans for 1000s of years.
As a result,admixture studies are invalid because the origin dates for the so-called “European” Haplogroups are all before Anatomically Modern Humans replaced Neanderthals in Europe and the Levant. So, haplogroups L3(M,N) and Y-haplogroup R originated in Africa and spread to the Americas and Europe. .
Posts: 13012 | From: Chicago | Registered: Jan 2006
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Africans or Negroes have been in contact with Native Americans and whites or Europeans for 1000s of years.
So where are these Negroes today, the ones who live in America but have African ancestors that are not from the slave trade but have older than 1000 years ago, African ancestors in America.
Who are the people claiming this background with evidence? Are there any?
Posts: 42920 | From: , | Registered: Jan 2010
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