DNA of 17th century African slaves frome the Caribbean

PNAS doi: 10.1073/pnas.1421784112

Genome-wide ancestry of 17th-century enslaved Africans from the Caribbean

Hannes Schroeder, María C. Ávila-Arcos et al.

Between 1500 and 1850, more than 12 million enslaved Africans were transported to the New World. The vast majority were shipped from West and West-Central Africa, but their precise origins are largely unknown. We used genome-wide ancient DNA analyses to investigate the genetic origins of three enslaved Africans whose remains were recovered on the Caribbean island of Saint Martin. We trace their origins to distinct subcontinental source populations within Africa, including Bantu-speaking groups from northern Cameroon and non-Bantu speakers living in present-day Nigeria and Ghana. To our knowledge, these findings provide the first direct evidence for the ethnic origins of enslaved Africans, at a time for which historical records are scarce, and demonstrate that genomic data provide another type of record that can shed new light on long-standing historical questions.

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Y chromosomes of West African descendants (Torres et al. 2012)

PLoS ONE 7(1): e29687. doi:10.1371/journal.pone.0029687


Y Chromosome Lineages in Men of West African Descent

Jada Ben Torres et al.

The early African experience in the Americas is marked by the transatlantic slave trade from ~1619 to 1850 and the rise of the plantation system. The origins of enslaved Africans were largely dependent on European preferences as well as the availability of potential laborers within Africa. Rice production was a key industry of many colonial South Carolina low country plantations. Accordingly, rice plantations owners within South Carolina often requested enslaved Africans from the so-called “Grain Coast” of western Africa (Senegal to Sierra Leone). Studies on the African origins of the enslaved within other regions of the Americas have been limited. To address the issue of origins of people of African descent within the Americas and understand more about the genetic heterogeneity present within Africa and the African Diaspora, we typed Y chromosome specific markers in 1,319 men consisting of 508 west and central Africans (from 12 populations), 188 Caribbeans (from 2 islands), 532 African Americans (AAs from Washington, DC and Columbia, SC), and 91 European Americans. Principal component and admixture analyses provide support for significant Grain Coast ancestry among African American men in South Carolina. AA men from DC and the Caribbean showed a closer affinity to populations from the Bight of Biafra. Furthermore, 30–40% of the paternal lineages in African descent populations in the Americas are of European ancestry. Diverse west African ancestries and sex-biased gene flow from EAs has contributed greatly to the genetic heterogeneity of African populations throughout the Americas and has significant implications for gene mapping efforts in these populations.

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Natural selection in African Americans pre- and post-admixture

I have mentioned before that African Americans should not be used to generalize about Africa, not only because of their ~20% European admixture, but also because they live in an environment completely different from the one their African ancestors adapted to: different climate, different set/intensity of pathogens, different social position, different physical requirements and workloads. It is nice to see a paper which attempts to quantify pre- and post-admixture signals of selection in this population; I think this may be a fertile area of future research, and it may also illuminate some of the specificities of the AA population.

Genome Research doi:10.1101/gr.124784.111

Genome-wide detection of natural selection in African Americans pre-and post-admixture

Wenfei Jin et al.

It is particularly meaningful to investigate natural selection in African Americans (AfA) due to the high mortality their African ancestry has experienced in history. In this study, we examined 491,526 autosomal SNPs genotyped in 5,210 individuals and conducted a genome-wide search for selection signals in 1,890 AfA. Several genomic regions showing excess of African or European ancestry, which were thought as the footprints of selection since population admixture, were detected based on a commonly used approach. However, we also developed a new strategy to detect natural selection both pre-and post-admixture by reconstructing an ancestral African population (AAF) from inferred African components of ancestry in AfA and comparing it with indigenous African populations (IAF). Interestingly, many selection-candidate genes identified by the new approach were associated with AfA specific high-risk diseases such as prostate cancer and hypertension, suggesting an important role these disease-related genes might have played in adapting to new environment. CD36 and HBB, whose mutations confer a degree of protection against malaria, were also located in the highly differentiated regions between AAF and IAF. Further analysis showed that the frequencies of alleles protecting against malaria in AAF were lower than that in IAF, which consists with the relaxed selection pressure of malaria in the New World. There is no overlap between the top candidate genes detected by the two approaches, indicating the different environmental pressures AfA experienced pre-and post-population-admixture. We suggest that the new approach is reasonably powerful and can also be applied to other admixed populations such as Latinos and Uyghurs.

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Y-chromosomes of the Bahamas

I like the line about there being substantially more Y-STR variation in E1b1a7a-U174 and E1b1ba8-U175 in the Bahamas than any African collection. I have argued for years that the central assumption of phylogeography, that the location of highest Y-STR diversity is not necessarily the point of origin of a haplogroup, since Y-STR diversity can be affected both by antiquity and by admixture. Nonetheless, I keep reading papers where tiny differences in Y-STR variation, even if we forget about the noisiness of Y-STRs themselves, are taken as evidence of ancient migrations. Thankfully, the time when Y-STRs were used to infer ancient migrations is over, and the huge collection of Y-STR haplotypes amassed by population geneticists, forensic specialists, and genealogists alike can be put to uses for which it is more amenable.

I can't say I know much about the history of the Bahamas, but this was something I had not heard of before:

Over the last 150 years, the Bahamas has been witness to a varied array of settlers, including Chinese immigrant workers, Greek spongers, Jewish business-men and individuals of Lebanese descent fleeing religious persecution. The extent to which each group has contributed genetically to the Bahamian paternal gene pool, however, is unknown. Our findings suggest that the Greeks, which exhibit relatively high frequencies of haplogroups E1b1b1a*-M78, J2a*-M410, and R1b1b1*-L23 (Semino et al., 2004; Myres et al., 2011), are a likely source of these lineages in the Bahamas, although the presence of M78 derived chromosomes may also signal gene flow from Lebanon (Zalloua et al., 2008). J1e-P58 lineages, on the other hand, which are characteristic of Jewish populations (Hammer et al., 2009) and Arab speaking groups (Chiaroni et al., 2010), may represent genetic signatures of Eastern European Jews and/or Lebanese migrants entering the Bahamas in the early twentieth century.

Another interesting tidbit:

Western European colonialism, although short-lived, appears to have left marked genetic imprints throughout the Bahamian archipelago, with Long Island receiving the strongest European genetic signals and Exuma, the weakest; a distribution pattern consistent with our earlier reports utilizing autosomal STR markers (Simms et al., 2008, 2011). The higher frequency of M269 derived individuals in the Long Island population (55.8%), when compared with the other five Bahamian islands surveyed (ranging from 8.5% to 18.3%), suggests higher gene flow from European males (Saunders, 2003b). According to the 1851 census, Long Island possessed one of the smallest European components (13.1%) yet, by 1953, almost 50% of this population was of ‘‘mixed’’ ancestry (Craton, 1998).

R-M269 seems quintessentially European today, and most living R-M269 men probably have West European ancestry. But, the finding of a high frequency in a Bahamian spot ought to remind us that Y-chromosomes can achieve high frequencies in little time, given the right conditions. Indeed, we can very well draw a parallel between the prehistoric spread of R-M269 into Europe, an event that is still shrouded in mystery, with the late historical movement of the same haplogroup into the Americas. Taking the broad view, these two unrelated events represent two pulses of the same westward spread of a successful Y-chromosome lineage.

It is also nice that scientists are beginning to take notice of very basal Y-chromosomes, going back to Y-chromosome Adam.

Two samples that fell outside of haplogroups B-T (defined by M42) were observed in Abaco (1.5%) and New Providence (0.7%), two Bahamian islands separated by a total of 139.4 km, as well as in a single sample from Haiti (unpublished data). When tested for V171, which, according to Cruciani et al. (2011a) defines the A2-T lineage, all three samples exhibited the ancestral allele. Instead, each individual was derived for the paralogous V152 mutation that determines the A1b lineage. It should be noted that each of the three samples possessed an eight base pair long Poly-T stretch at the M91 locus, indicative of the monophyletic haplogroup A defined by Karafet et al. (2008). However, as a result of the rearrangement of the tree by Cruciani et al. (2011a), haplogroup A no longer represents a monophyletic group, as the A2 and A3 lineages are now united with all haplogroup A lineages other than A1 by their shared possession of V171.

Haplogroup A chromosomes have been collected as isolated examples in many genealogical projects and scientific studies. It's a great idea for someone to take the initiative and collect the most divergent ones, invest in genotyping them fully, and push the boundaries of what we know about the most ancient history of modern human patrilineages.

AJPA DOI: 10.1002/ajpa.21616

Paternal lineages signal distinct genetic contributions from British Loyalists and continental Africans among different Bahamian islands

Tanya M. Simms et al.

Over the past 500 years, the Bahamas has been influenced by a wide array of settlers, some of whom have left marked genetic imprints throughout the archipelago. To assess the extent of each group's genetic contributions, high-resolution Y-chromosome analyses were performed, for the first time, to delineate the patriarchal ancestry of six islands in the Northwest (Abaco and Grand Bahama) and Central (Eleuthera, Exuma, Long Island, and New Providence) Bahamas and their genetic relationships with previously published reference populations. Our results reveal genetic signals emanating primarily from African and European sources, with the predominantly sub-Saharan African and Western European haplogroups E1b1a-M2 and R1b1b1-M269, respectively, accounting for greater than 75% of all Bahamian patrilineages. Surprisingly, we observe notable discrepancies among the six Bahamian populations in their distribution of these lineages, with E1b1a-M2 predominating Y-chromosomes in the collections from Abaco, Exuma, Eleuthera, Grand Bahama, and New Providence, whereas R1b1b1-M269 is found at elevated levels in the Long Island population. Substantial Y-STR haplotype variation within sub-haplogroups E1b1a7a-U174 and E1b1ba8-U175 (greater than any continental African collection) is also noted, possibly indicating genetic influences from a variety of West and Central African groups. Furthermore, differential European genetic contributions in each island (with the exception of Exuma) reflect settlement patterns of the British Loyalists subsequent to the American Revolution.

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mtDNA and trans-Saharan slave trade (Harich et al. 2010)

The main trans-Saharan slave routes are shown in Figure 1 (on the left). The paper also contains quite useful interpolation maps of the main Sub-Saharan African mtDNA haplogroups, who should be useful for future reference.

BMC Evolutionary Biology 2010, 10:138 doi:10.1186/1471-2148-10-138

The trans-Saharan slave trade - clues from interpolation analyses and high-resolution characterization of mitochondrial DNA lineages

Abstract

Background
A proportion of 1/4 to 1/2 of North African female pool is made of typical sub-Saharan lineages, in higher frequencies as geographic proximity to sub-Saharan Africa increases. The Sahara was a strong geographical barrier against gene flow, at least since 5,000 years ago, when desertification affected a larger region, but the Arab trans-Saharan slave trade could have facilitate enormously this migration of lineages. Till now, the genetic consequences of these forced trans-Saharan movements of people have not been ascertained.

Results
The distribution of the main L haplogroups in North Africa clearly reflects the known trans-Saharan slave routes: West is dominated by L1b, L2b, L2c, L2d, L3b and L3d; the Center by L3e and some L3f and L3w; the East by L0a, L3h, L3i, L3x and, in common with the Center, L3f and L3w; while, L2a is almost everywhere. Ages for the haplogroups observed in both sides of the Saharan desert testify the recent origin (holocenic) of these haplogroups in sub-Saharan Africa, claiming a recent introduction in North Africa, further strengthened by the no detection of local expansions.

Conclusions
The interpolation analyses and complete sequencing of present mtDNA sub-Saharan lineages observed in North Africa support the genetic impact of recent trans-Saharan migrations, namely the slave trade initiated by the Arab conquest of North Africa in the seventh century. Sub-Saharan people did not leave traces in the North African maternal gene pool for the time of its settlement, some 40,000 years ago.

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