Post by Admin on Jul 28, 2020 0:33:27 GMT
Biases in Contributions of Males and Females to Current Gene Pools
We identified a bias toward European male and African female genetic contributions across regions of the Americas using the sex-specific model for admixture,22 which assumes admixture events during the transatlantic slave trade. We observed an African female bias (African sf/sm > 1) in every region of the Americas with highest levels in northern South America (17.17; Table 1; Tables S9 and S10). We also observed a European male sex bias (European sm/sf > 1) in all explored regions except the Latin Caribbean and Central America. Additionally, haplogroup assignments in males indicated that Y chromosome haplogroups tend to be of European origin whereas mitochondrial haplogroups tend to be of African origin across all regions of the Americas (Table S8). Historical documents indicate the overall proportion of enslaved people on voyages were male (Mp > 0.60) across all regions5 (Table 1).
Table 1
Inferred Ancestry Sex Bias versus Documented Sex Bias
America Region African European Native American Mp
sf/sm X A sm/sf X A sf/sm X A
Guianas 1.73 0.65 0.59 4.60 0.12 0.15 – 0.01 0.01 0.64
United States 1.47 0.76 0.71 3.03 0.21 0.25 – 0.02 0.01 0.69
British Caribbean 1.88 0.82 0.75 25.53 0.12 0.18 – <0.01 <0.01 0.62
Latin Caribbean 13.31 0.24 0.19 0.90 0.53 0.52 3.78 0.12 0.06 0.66
C. South America 4.62 0.18 0.12 1.09 0.63 0.64 2.26 0.09 0.04 0.67
N. South America 17.17 0.14 0.11 2.27 0.43 0.49 3.38 0.30 0.17 0.63
Central America 15.60 0.11 0.08 0.89 0.32 0.31 28.04 0.44 0.27 0.68
Cape Verde 22.56 0.59 0.44 71.00 0.35 0.50 – <0.01 <0.01 –
Female to male (sf/sm) and male to female (sm/sf) genetic contribution bias based on ancestry inference of the X chromosome and autosomes, assuming a single admixture event during the transatlantic slave trade (15 generations ago). For example, sf/sm = 2 for African ancestry means ∼2 African women for every African man. Mean Ancestry Composition based solely on the X chromosome (X) and solely on the autosomes (A) for each ancestry category. Mp is the proportion of enslaved males on voyages to each region of the Americas based on historical documents. sf/sm is not calculated for regions with less than 2% mean ancestry in either the X chromosome or autosomes. Assuming more recent admixture generations yielded near-identical results (Table S9).
Discussion
Overall Concordance with Historical Documents
We found that, overall, genetic evidence of Atlantic African ancestry across the Americas is consistent with historical documents of the transatlantic shipping of enslaved Africans.3,5,9 The expectation that more embarkation out of Africa corresponds with more ancestral connections to the Americas is borne out by the comparison between msIBDAfrica-Americas and the number of captives deported from each African region (Figure 2A). For example, the highest proportion of msIBD is found between West Central Africa and the Americas, consistent with the highest proportion of enslaved embarkation from this slave-trading region (5.7 million people5). West Central Africa also experienced the largest proportion of deportations in the mid-1800s5 (Figure 2D), consistent with our finding that people of African descent in the Americas share the most recent common ancestors with people from West Central Africa (Figure 2C). The mean number of IBD connections (mcIBD) between regions of the Americas and Africa also support embarkation estimates from voyage records. The majority of enslaved people arriving in Latin America (Latin Caribbean, Central America, N. South America, and C. South America) were generally deported from one or two slave trading regions, whereas enslaved people arriving in the United States and British Caribbean were taken from all regions of Atlantic Africa (Figure 2B).5,9,10 Consequently, individuals from Latin America tend to have mcIBD with two or three Atlantic African regions, whereas individuals from the United States and the Caribbean tend to have genetic connections to five or six regions (Figure 2B).
Potential Inconsistencies with Historical Documents
While genetic connections between African populations and individuals from the Americas are strongly correlated with historical documents (Figure 2A), a granular breakdown of disembarkation in discrete regions of the Americas identifies discordance. For example, msIBD with the Bights of Benin and Biafra, as well as Nigerian ancestry, is overrepresented in the United States and Latin America considering the recorded number of enslaved people that embarked from ports along the coast of present-day Nigeria into these regions of the Americas (Figures 2B and 3). However, this discordance is explained by records from the intra-American slave trade, an intercolonial trade that occurred primarily between 1619 and 1807 whose impact has recently been understood through collections of port records, newspapers, and merchant accounts from disparate parts of the Americas.5,46 Documented intra-American voyages indicate that the vast majority of enslaved people were transported from the British Caribbean to other parts of the Americas, presumably to maintain the slave economy as transatlantic slave trading was increasingly prohibited (Figure S13).46 These voyages would spread African ancestry common in the British Caribbean to other regions of the Americas that were not in direct trade with specific regions of Africa. In Latin America, transatlantic slave trading voyages virtually ceased between 1660 and 1780, yet a large proportion of all documented captives continued to be transported throughout the early 1800s to Latin America primarily from the British Caribbean.10 In the United States, nearly 10% of the total enslaved population arrived via intra-America trading with the British Caribbean and consequently msIBD between the United States and the British Caribbean (primarily the Bahamas, British Windward, and Leeward Islands) is high (Figure S14). Therefore, embarkation out of Africa and msIBD between Africa and all of the Americas is correlated (Figure 2A), whereas disembarkation in specific regions of the Americas and msIBD with Africa are not consistently correlated (Figure 2B) because of the asymmetric transportation of enslaved people within the Americas.
Another apparent discordance between historical documents and genetic data is seen in msIBD between most regions of the Americas and Senegambia. Senegambia is underrepresented given the overall proportion of enslaved people who were deported from this region to the Americas (Figure 2B). This is likely because Senegambia was one of the first African regions from which large numbers of people were enslaved.5,9,57 Historical documents and TMRCA estimates from IBD segments support this explanation as well, indicating that Senegambia’s connection to the Americas is older (and less well documented) than that of other regions (Figures 2C and 2D). Having distant ancestors from Senegambia would increase the likelihood of people in the Americas sharing very short IBD segments with Senegambians, which, in turn, may be undetected by estimating IBD segments with reduced SNP densities.49 This pattern of reduced msIBD and older TMRCA estimates is most evident in the disembarkation regions of northern South America and Central America where, according to records, nearly half of the enslaved people who disembarked at ports in these regions came from Senegambia, but less than 10% of msIBD between these regions and Africa is with Senegambia (Figure 2B). However, almost no captives from Senegambia disembarked directly in either northern South America or Central America after 1650,5,9,10 consistent with our finding of an older TMRCA between Senegambia and these two regions, and the likelihood that earlier African disembarkation resulted in smaller IBD segments between Africans and Americans of the present day.
The underrepresentation of ancestral connections to Senegambia also occurs in regions of the Americas with more recent (1700–1865) disembarkation from Senegambia, such as the United States and Latin Caribbean. This pattern, in part, may result from the increasing rates of deportation of children from Senegambia over time (Figure S15). Enslavement of children and unsanitary conditions in the holds of ships led to high rates of malnourishment and illness, which in turn led to lower survival rates in later decades of the slave trade.58,59 It is also possible that Senegambians experienced higher mortality due to dangerous plantation conditions. A large proportion of enslaved Senegambians were rice cultivators who worked on rice plantations in the Americas, which were generally rampant with malaria.57,60,61 Clearing of swamplands was also generally performed by men, which could explain higher male mortality.59 While detailed records exist for very few plantations, reduced genetic representation from Senegambia in parts of the Americas is likely correlated with Senegambians being forced to work under life-threatening conditions.
Ancestry Proportions Discordance
Continental African ancestry estimates are unexpected given the number of enslaved people disembarking in the Americas. Nearly 70% of the 10.5 million enslaved people who survived the Middle Passage disembarked in Latin America, yet regions of Latin America have the lowest overall proportion of African ancestry (Figure 3). On the contrary, individuals in this study from the United States and British Caribbean have the highest African ancestry proportion on average. Together, these results indicate that practices and treatment of enslaved people likely varied across the Americas. For instance, literature suggests higher overall mortality and smaller effective population sizes in enslaved populations brought to Latin America,62,63 which would have reduced the contribution of African ancestry to the gene pool. In addition, enslaved indigenous people often admixed with enslaved Africans in Latin America,59 which is evident in the Native American ancestry and haplogroups common in individuals from Latin America (Tables S7 and S8). Other investigations of genetic ancestry have identified comparable estimates of African ancestry across the United States;11, 12, 13, 14, 15 however, other studies have found that African ancestry is higher in admixed populations in Latin America compared to our study.13,64 This is likely due to the non-random representation of global populations in our study cohort, which consists primarily of US customers and does not target specific admixed populations in Latin America. Although our estimates are lower (about 5%–10% on average), the trend of lower African ancestry in Latin America is still supported by other research.64
Sex-Bias Discordance
Despite more than 60% of enslaved people brought to each region of the Americas being men,5 comparisons of ancestry estimates for the X chromosome and autosomes, as well as the comparison of mitochondrial (maternal) and Y (paternal) haplogroups, revealed a bias toward African female contributions to gene pools across all of the Americas.64,65 However, this African female sex bias is more extreme in Latin America (between 4 and 17 African women for every African man contributing to the gene pool) than in British-colonized Americas (between 1.5 and 2 African women for every African man contributing to the gene pool; Table 1). An Americas-wide African female sex-bias can be attributed to known accounts of rape of enslaved African women by slave owners and other sexual exploitation.19,26,62,66 Regional differences may be due to higher mortality in enslaved males in Latin America as well as a common practice called branqueamento, or racial whitening, which involved women marrying lighter-skinned men with the intention of producing lighter-skinned children.1,25,27,62,67 National branqueamento policies were implemented in multiple Latin American countries, funding and subsidizing European immigrant travels with the intention to dilute African Ancestry through reproduction with light-skinned Europeans.68 Conversely, the smaller African female sex-bias seen in former British colonies could be due to the practice of coercing enslaved people to have children as a means of maintaining enslaved workforces nearing the abolition of the transatlantic slave trade.69 In some areas, such as the United States, enslaved women were incentivized to reproduce with the promise of freedom following the birth of many children.20 Furthermore, racist ideologies in the United States led to the segregation of people of African descent as opposed to promotion of European admixture.70 Overall, the inhumane practices associated with institutionalized slavery, though differing across the Americas, all resulted in an African-female sex bias despite the preponderance of males among those enslaved.
We identified a bias toward European male and African female genetic contributions across regions of the Americas using the sex-specific model for admixture,22 which assumes admixture events during the transatlantic slave trade. We observed an African female bias (African sf/sm > 1) in every region of the Americas with highest levels in northern South America (17.17; Table 1; Tables S9 and S10). We also observed a European male sex bias (European sm/sf > 1) in all explored regions except the Latin Caribbean and Central America. Additionally, haplogroup assignments in males indicated that Y chromosome haplogroups tend to be of European origin whereas mitochondrial haplogroups tend to be of African origin across all regions of the Americas (Table S8). Historical documents indicate the overall proportion of enslaved people on voyages were male (Mp > 0.60) across all regions5 (Table 1).
Table 1
Inferred Ancestry Sex Bias versus Documented Sex Bias
America Region African European Native American Mp
sf/sm X A sm/sf X A sf/sm X A
Guianas 1.73 0.65 0.59 4.60 0.12 0.15 – 0.01 0.01 0.64
United States 1.47 0.76 0.71 3.03 0.21 0.25 – 0.02 0.01 0.69
British Caribbean 1.88 0.82 0.75 25.53 0.12 0.18 – <0.01 <0.01 0.62
Latin Caribbean 13.31 0.24 0.19 0.90 0.53 0.52 3.78 0.12 0.06 0.66
C. South America 4.62 0.18 0.12 1.09 0.63 0.64 2.26 0.09 0.04 0.67
N. South America 17.17 0.14 0.11 2.27 0.43 0.49 3.38 0.30 0.17 0.63
Central America 15.60 0.11 0.08 0.89 0.32 0.31 28.04 0.44 0.27 0.68
Cape Verde 22.56 0.59 0.44 71.00 0.35 0.50 – <0.01 <0.01 –
Female to male (sf/sm) and male to female (sm/sf) genetic contribution bias based on ancestry inference of the X chromosome and autosomes, assuming a single admixture event during the transatlantic slave trade (15 generations ago). For example, sf/sm = 2 for African ancestry means ∼2 African women for every African man. Mean Ancestry Composition based solely on the X chromosome (X) and solely on the autosomes (A) for each ancestry category. Mp is the proportion of enslaved males on voyages to each region of the Americas based on historical documents. sf/sm is not calculated for regions with less than 2% mean ancestry in either the X chromosome or autosomes. Assuming more recent admixture generations yielded near-identical results (Table S9).
Discussion
Overall Concordance with Historical Documents
We found that, overall, genetic evidence of Atlantic African ancestry across the Americas is consistent with historical documents of the transatlantic shipping of enslaved Africans.3,5,9 The expectation that more embarkation out of Africa corresponds with more ancestral connections to the Americas is borne out by the comparison between msIBDAfrica-Americas and the number of captives deported from each African region (Figure 2A). For example, the highest proportion of msIBD is found between West Central Africa and the Americas, consistent with the highest proportion of enslaved embarkation from this slave-trading region (5.7 million people5). West Central Africa also experienced the largest proportion of deportations in the mid-1800s5 (Figure 2D), consistent with our finding that people of African descent in the Americas share the most recent common ancestors with people from West Central Africa (Figure 2C). The mean number of IBD connections (mcIBD) between regions of the Americas and Africa also support embarkation estimates from voyage records. The majority of enslaved people arriving in Latin America (Latin Caribbean, Central America, N. South America, and C. South America) were generally deported from one or two slave trading regions, whereas enslaved people arriving in the United States and British Caribbean were taken from all regions of Atlantic Africa (Figure 2B).5,9,10 Consequently, individuals from Latin America tend to have mcIBD with two or three Atlantic African regions, whereas individuals from the United States and the Caribbean tend to have genetic connections to five or six regions (Figure 2B).
Potential Inconsistencies with Historical Documents
While genetic connections between African populations and individuals from the Americas are strongly correlated with historical documents (Figure 2A), a granular breakdown of disembarkation in discrete regions of the Americas identifies discordance. For example, msIBD with the Bights of Benin and Biafra, as well as Nigerian ancestry, is overrepresented in the United States and Latin America considering the recorded number of enslaved people that embarked from ports along the coast of present-day Nigeria into these regions of the Americas (Figures 2B and 3). However, this discordance is explained by records from the intra-American slave trade, an intercolonial trade that occurred primarily between 1619 and 1807 whose impact has recently been understood through collections of port records, newspapers, and merchant accounts from disparate parts of the Americas.5,46 Documented intra-American voyages indicate that the vast majority of enslaved people were transported from the British Caribbean to other parts of the Americas, presumably to maintain the slave economy as transatlantic slave trading was increasingly prohibited (Figure S13).46 These voyages would spread African ancestry common in the British Caribbean to other regions of the Americas that were not in direct trade with specific regions of Africa. In Latin America, transatlantic slave trading voyages virtually ceased between 1660 and 1780, yet a large proportion of all documented captives continued to be transported throughout the early 1800s to Latin America primarily from the British Caribbean.10 In the United States, nearly 10% of the total enslaved population arrived via intra-America trading with the British Caribbean and consequently msIBD between the United States and the British Caribbean (primarily the Bahamas, British Windward, and Leeward Islands) is high (Figure S14). Therefore, embarkation out of Africa and msIBD between Africa and all of the Americas is correlated (Figure 2A), whereas disembarkation in specific regions of the Americas and msIBD with Africa are not consistently correlated (Figure 2B) because of the asymmetric transportation of enslaved people within the Americas.
Another apparent discordance between historical documents and genetic data is seen in msIBD between most regions of the Americas and Senegambia. Senegambia is underrepresented given the overall proportion of enslaved people who were deported from this region to the Americas (Figure 2B). This is likely because Senegambia was one of the first African regions from which large numbers of people were enslaved.5,9,57 Historical documents and TMRCA estimates from IBD segments support this explanation as well, indicating that Senegambia’s connection to the Americas is older (and less well documented) than that of other regions (Figures 2C and 2D). Having distant ancestors from Senegambia would increase the likelihood of people in the Americas sharing very short IBD segments with Senegambians, which, in turn, may be undetected by estimating IBD segments with reduced SNP densities.49 This pattern of reduced msIBD and older TMRCA estimates is most evident in the disembarkation regions of northern South America and Central America where, according to records, nearly half of the enslaved people who disembarked at ports in these regions came from Senegambia, but less than 10% of msIBD between these regions and Africa is with Senegambia (Figure 2B). However, almost no captives from Senegambia disembarked directly in either northern South America or Central America after 1650,5,9,10 consistent with our finding of an older TMRCA between Senegambia and these two regions, and the likelihood that earlier African disembarkation resulted in smaller IBD segments between Africans and Americans of the present day.
The underrepresentation of ancestral connections to Senegambia also occurs in regions of the Americas with more recent (1700–1865) disembarkation from Senegambia, such as the United States and Latin Caribbean. This pattern, in part, may result from the increasing rates of deportation of children from Senegambia over time (Figure S15). Enslavement of children and unsanitary conditions in the holds of ships led to high rates of malnourishment and illness, which in turn led to lower survival rates in later decades of the slave trade.58,59 It is also possible that Senegambians experienced higher mortality due to dangerous plantation conditions. A large proportion of enslaved Senegambians were rice cultivators who worked on rice plantations in the Americas, which were generally rampant with malaria.57,60,61 Clearing of swamplands was also generally performed by men, which could explain higher male mortality.59 While detailed records exist for very few plantations, reduced genetic representation from Senegambia in parts of the Americas is likely correlated with Senegambians being forced to work under life-threatening conditions.
Ancestry Proportions Discordance
Continental African ancestry estimates are unexpected given the number of enslaved people disembarking in the Americas. Nearly 70% of the 10.5 million enslaved people who survived the Middle Passage disembarked in Latin America, yet regions of Latin America have the lowest overall proportion of African ancestry (Figure 3). On the contrary, individuals in this study from the United States and British Caribbean have the highest African ancestry proportion on average. Together, these results indicate that practices and treatment of enslaved people likely varied across the Americas. For instance, literature suggests higher overall mortality and smaller effective population sizes in enslaved populations brought to Latin America,62,63 which would have reduced the contribution of African ancestry to the gene pool. In addition, enslaved indigenous people often admixed with enslaved Africans in Latin America,59 which is evident in the Native American ancestry and haplogroups common in individuals from Latin America (Tables S7 and S8). Other investigations of genetic ancestry have identified comparable estimates of African ancestry across the United States;11, 12, 13, 14, 15 however, other studies have found that African ancestry is higher in admixed populations in Latin America compared to our study.13,64 This is likely due to the non-random representation of global populations in our study cohort, which consists primarily of US customers and does not target specific admixed populations in Latin America. Although our estimates are lower (about 5%–10% on average), the trend of lower African ancestry in Latin America is still supported by other research.64
Sex-Bias Discordance
Despite more than 60% of enslaved people brought to each region of the Americas being men,5 comparisons of ancestry estimates for the X chromosome and autosomes, as well as the comparison of mitochondrial (maternal) and Y (paternal) haplogroups, revealed a bias toward African female contributions to gene pools across all of the Americas.64,65 However, this African female sex bias is more extreme in Latin America (between 4 and 17 African women for every African man contributing to the gene pool) than in British-colonized Americas (between 1.5 and 2 African women for every African man contributing to the gene pool; Table 1). An Americas-wide African female sex-bias can be attributed to known accounts of rape of enslaved African women by slave owners and other sexual exploitation.19,26,62,66 Regional differences may be due to higher mortality in enslaved males in Latin America as well as a common practice called branqueamento, or racial whitening, which involved women marrying lighter-skinned men with the intention of producing lighter-skinned children.1,25,27,62,67 National branqueamento policies were implemented in multiple Latin American countries, funding and subsidizing European immigrant travels with the intention to dilute African Ancestry through reproduction with light-skinned Europeans.68 Conversely, the smaller African female sex-bias seen in former British colonies could be due to the practice of coercing enslaved people to have children as a means of maintaining enslaved workforces nearing the abolition of the transatlantic slave trade.69 In some areas, such as the United States, enslaved women were incentivized to reproduce with the promise of freedom following the birth of many children.20 Furthermore, racist ideologies in the United States led to the segregation of people of African descent as opposed to promotion of European admixture.70 Overall, the inhumane practices associated with institutionalized slavery, though differing across the Americas, all resulted in an African-female sex bias despite the preponderance of males among those enslaved.