Exploring the legacy of African and Indigenous Caribbean admixture in Puerto Rico.

OBJECTIVES: From an anthropological genetic perspective, little is known about the ethnogenesis of African descendants in Puerto Rico. Furthermore, historical interactions between Indigenous Caribbean and African descendant peoples that may be reflected in the ancestry of contemporary populations are understudied. Given this dearth of genetic research and the precedence for Afro-Indigenous interactions documented by historical, archeological, and other lines of evidence, we sought to assess the biogeographic origins of African descendant Puerto Ricans and to query the potential for Indigenous ancestry within this community. MATERIALS AND METHODS: Saliva samples were collected from 58 self-identified African descendant Puerto Ricans residing in Puerto Rico. We sequenced whole mitochondrial genomes and genotyped Y chromosome haplogroups for each male individual (n = 25). Summary statistics, comparative analyses, and network analysis were used to assess diversity and variation in haplogroup distribution between the sample and comparative populations. RESULTS: As indicated by mitochondrial haplogroups, 66% had African, 5% had European, and 29% had Indigenous American matrilines. Along the Y chromosome, 52% had African, 28% had Western European, 16% had Eurasian, and, notably, 4% had Indigenous American patrilines. Both mitochondrial and Y chromosome haplogroup frequencies were significantly different from several comparative populations. DISCUSSION: Biogeographic origins are consistent with historical accounts of African, Indigenous American, and European ancestry. However, this first report of Indigenous American paternal ancestry in Puerto Rico suggests distinctive features within African descendant communities on the island. Future studies expanding sampling and incorporating higher resolution genetic markers are necessary to more fully understand African descendant history in Puerto Rico.

Racial Experience as an Alternative Operationalization of Race.

The study of human variation is central to both social and biomedical sciences, but social and biomedical scientists diverge in how variation is theorized and operationalized. Race is especially problematic because it is a cultural concept that contains implicit and explicit understandings of how collective bodies differ. In this moderately updated article, originally published in Human Biology in 2015 (vol. 87, no. 4, pp. 306-312), we propose an operationalization of race that addresses both racial experience and human biological diversity, placing them within the same ontological sphere. Furthermore, this approach can more effectively advance antiracist pedagogy and politics. We argue that human biological diversity does not have to be in opposition to constructivist notions of race. Rather, racial experience is emphasized as an embodied experience that is as real and as valid as biological variation. By focusing on both racial experience and biological diversity, it becomes more feasible to operationalize race to fruitfully inform the pedagogy and politics of antiracism. To do so, racial experience must be more broadly conceived and should not always equate to negative outcomes. With the recognition that racial experience has the potential to be something other than damaging, an antiracist anthropology can more effectively address issues pertaining to racial health disparities.

Racial Experience as an Alternative Operationalization of Race.

The study of human variation is central to both social and biomedical sciences, but social and biomedical scientists diverge in how variation is theorized and operationalized. Race is especially problematic because it is a cultural concept that contains implicit and explicit understandings of how collective bodies differ. In this article, we propose an operationalization of race that addresses both racial experience and human biological diversity, placing them within the same ontological sphere. Furthermore, this approach can more effectively advance antiracist pedagogy and politics. We argue that human biological diversity does not have to be in opposition to constructivist notions of race. Rather, racial experience is emphasized as an embodied experience that is as real and as valid as biological variation. By focusing on both racial experience and biological diversity, it becomes more feasible to operationalize race to fruitfully inform the pedagogy and politics of antiracism. To do so, racial experience must be more broadly conceived and should not always equate to negative outcomes. With the recognition that racial experience has the potential to be something other than damaging, an antiracist anthropology can more effectively address issues pertaining to racial health disparities.

Origins of marronage: Mitochondrial lineages of Jamaica's Accompong Town Maroons.

OBJECTIVES: The Accompong Town Maroons are descendants of enslaved Africans who successfully waged war against British colonial rule and established an independent community in western Jamaica. There are discrepancies regarding Accompong Town Maroon ancestry with some scholars noting ancestry from both Africans and Taínos, Jamaica's indigenous population, while other scholars only acknowledge African ancestry. We considered the mitochondrial lineages of contemporary Accompong Town Maroons to address the question of ancestral origins. METHODS: We sequenced a section of the mitochondrial DNA control region (np 16,024-16,569) and genotyped a panel of hierarchically selected haplogroup diagnostic SNPs for 50 individuals with genealogical ties to Accompong Town. Mitochondrial haplotypes were also compared with publically available Jamaican mitochondrial haplotypes using an exact test as well as haplotypes within the EMPOP public database to further access biogeographic origins. RESULTS: L-type mitochondrial haplogroups were observed in 96% of samples, and the remaining 4% belonged to haplogroup B2. Haplotype diversity was 0.922 (SD = 0.024) and not significantly different than the comparable Jamaican population. Of the two B2 haplotypes, one matched haplotypes throughout the Americas and East Asia and the other matched only in East Asia. These results suggest both African and indigenous American maternal ancestries within Accompong Town. CONCLUSIONS: Our data suggested that the maternal ancestry of contemporary Accompong Town Maroons is predominantly African and, despite claims to suggest otherwise, also indigenous American. Our study complemented Maroon oral histories, archeological data, and illuminated how colonization shaped human genetic variation within the Caribbean.

An anthropological genetic perspective on Creolization in the Anglophone Caribbean.

Variable socio-cultural influences developed in the colonial Caribbean as a result of competing European hegemonic rule. In this study, we examine how colonial regulations regarding social hierarchies and mate choice worked to influence the genetic landscape of contemporary African Caribbean populations. To this end, 420 individuals from Dominica, Grenada, St. Kitts, St. Lucia, St. Thomas, St. Vincent, Jamaica, and Trinidad were genotyped for 105 autosomal ancestry informative markers. Based on these data, population substructure and admixture were assessed using an exact test, a model-based clustering method, and principal components analysis. On average, individual admixture estimates of the pooled African Caribbean sample were 77% (SD ± 18%) West African, 15% (SD ± 15%) European, and 7.7% (SD ± 8%) Native American. In general, ancestry estimates were significantly different between Dominica and all other islands. Genetic structure analyses indicated subdivision into two subpopulations on most islands. Finally, unlike all of the other Caribbean populations that clustered adjacent to African populations, the Dominican population was more intermediate between the three parental groups in the principal components plot. As a result of the significant French influence throughout Dominican history, Dominica did not have the same cultural influences that typified other Anglophone colonies. Consequently, there were different social hierarchies and resulting mate choices on Dominica compared with the other considered islands. This study highlights the complex socio-cultural history of a broad region of the Caribbean and attests to the interplay between social and biological factors in shaping the genetic diversity present in present-day communities.

Y chromosome lineages in men of west African descent.

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.

Replication of prostate cancer risk loci on 8q24, 11q13, 17q12, 19q33, and Xp11 in African Americans.

BACKGROUND: Prostate cancer (Pca) is a common malignancy that disproportionately affects African American men (AA). Recently there have been several genome-wide association studies (GWAS) implicating new prostate cancer risk loci along chromosomes 2, 3, 6, 7, 8, 10, 11, 12, 17, 19, and X in populations of European ancestry. Given the higher incidence and mortality for AAs, and differences in allele frequencies and haplotype structures between African and European descent populations, it is important to assess the impact of these candidate risk loci in AAs. METHODS: Here we evaluated 20 single nucleotide polymorphisms (SNPs) associated with prostate cancer risk in recent GWAS studies, in AA prostate cancer cases and controls. RESULTS: We replicated five of the SNPs in our AA population, rs10896449 on 11q13.2 (P = 0.009), rs2735839 on 19q33.33 region, (P = 0.04), rs443076 on chromosome 17q12 (P = 0.008), rs5945572 on Xp11.22 (P = 0.05), as well as the rare variant specific to west African ancestry, bd11934905 in region 2 of 8q24 (P = 1 x 10(-4)). CONCLUSIONS: While we were able to replicate a few of the previous GWAS SNPs, we were not able to confirm the vast majority of these associations in our AA population. This finding further supports the need to perform GWAS and additional fine mapping in AAs to locate additional susceptibility loci.

Novel single nucleotide polymorphism associations with colorectal cancer on chromosome 8q24 in African and European Americans.

Regions on chromosome 8q24 harbor susceptibility alleles for multiple cancers including colorectal (region 3) and prostate cancer (regions 1-4). The objectives of the present study were (i) to test whether single-nucleotide polymorphisms (SNPs) in region 4 are associated with colorectal cancer (CRC) in European or African Americans; (ii) to test whether 8q24 SNPs previously shown to be associated with colorectal and prostate cancer also show association in our multiethnic series and (iii) to test for association between 100 ancestry informative markers (AIMs) and CRC in both the African American and European American cohorts. In total, we genotyped nine markers on 8q24 and 100 unlinked AIMs in 569 CRC cases and 439 controls (490 European Americans and 518 African Americans) obtained retrospectively from a hospital-based sample. We found rs7008482 in 8q24 region 4 to be significantly associated with CRC in European Americans (P = 0.03). Also in region 4, we found that a second SNP, rs16900305, trended toward association with CRC in African Americans. The rs6983267 in region 3, previously implicated in CRC risk, trended toward association with disease in European Americans but not in African Americans. Finally, none of the 100 AIMs tested for association reached statistical significance after correction for multiple hypothesis testing. In summary, these results are evidence that 8q24 region 4 contains novel CRC-associated alleles in European and African Americans.

Race, genetic West African ancestry, and prostate cancer prediction by prostate-specific antigen in prospectively screened high-risk men.

"Race-specific" prostate-specific antigen (PSA) needs evaluation in men at high risk for prostate cancer for optimizing early detection. Baseline PSA and longitudinal prediction for prostate cancer were examined by self-reported race and genetic West African (WA) ancestry in the Prostate Cancer Risk Assessment Program, a prospective high-risk cohort. Eligibility criteria were age 35 to 69 years, family history of prostate cancer, African American race, or BRCA1/2 mutations. Biopsies were done at low PSA values (<4.0 ng/mL). WA ancestry was discerned by genotyping 100 ancestry informative markers. Cox proportional hazards models evaluated baseline PSA, self-reported race, and genetic WA ancestry. Cox models were used for 3-year predictions for prostate cancer. Six hundred forty-six men (63% African American) were analyzed. Individual WA ancestry estimates varied widely among self-reported African American men. Race-specific differences in baseline PSA were not found by self-reported race or genetic WA ancestry. Among men with > or =1 follow-up visit (405 total, 54% African American), 3-year prediction for prostate cancer with a PSA of 1.5 to 4.0 ng/mL was higher in African American men with age in the model (P = 0.025) compared with European American men. Hazard ratios of PSA for prostate cancer were also higher by self-reported race (1.59 for African American versus 1.32 for European American, P = 0.04). There was a trend for increasing prediction for prostate cancer with increasing genetic WA ancestry. "Race-specific" PSA may need to be redefined as higher prediction for prostate cancer at any given PSA in African American men. Large-scale studies are needed to confirm if genetic WA ancestry explains these findings to make progress in personalizing prostate cancer early detection.

Confirmation study of prostate cancer risk variants at 8q24 in African Americans identifies a novel risk locus.

Prostate cancer is a common complex disease that disproportionately affects men of African descent. Recently, several different common variants on chromosome 8q24 have been shown to be associated with prostate cancer in multiple studies and ethnic groups. The objective of this study was to confirm the association of 8q24 markers with prostate cancer in African Americans. We genotyped 24 markers along 8q24 and 80 unlinked ancestry informative markers in a hospital-based case-control sample of 1057 African American men (490 prostate cancer cases and 567 controls). Association analyses of 8q24 markers with prostate cancer risk were adjusted for both global and local 8q24 admixture stratification using estimates from ancestry informative markers. We report that rs7008482, which maps to the 8q24.13 region, is an additional independent prostate cancer risk variant (P = 5 x 10(-4)), and we also replicate the association of rs16901979 with prostate cancer (P = 0.002). Other published risk variants in the region such as rs1447295 and rs6983267 showed a similar direction and magnitude of effect, but were not significant in our population. Both rs7008482 and rs16901979 independently predicted risk and remained significant (P < 0.001) after controlling for each other. Our data combined with additional replications of 8q24 markers provide compelling support for multiple regions of risk for prostate cancer on 8q24.

The relationship between "race" and genetics in biomedical research.

The post-human genome sequencing era has presented several daunting challenges for biomedical research. How do we begin to quantify the level of sequence variation that exists within and between human populations? This challenge has serious implications for the enigma called "race," genetic ancestry, group definition, and membership. Another challenge has been the attempt to understand the role DNA sequence variation contributes to variation in susceptibility to common complex diseases. How these challenges are met will have an impact on our ability to determine if health disparities (eg, cardiovascular disease) are due to biological differences. Here we discuss genetic variation among African Americans and Hispanic Americans and its implications for "race." We believe that the casual use of "race" to define groups in biomedical research has contributed to our limited understanding of complex disease etiology and risk factors driving health disparities.