7,000 years of change: Migration and admixture in the population history of the Caribbean
Maria A Nieves-Colon1,*, William J Pestle2, Jada Benn-Torres3, Carlos D Bustamante4, Anne C Stone1
1 School of Human Evolution and Social Change, Arizona State University, Tempe, AZ,
2 Department of Anthropology, University of Miami, Coral Gables, FL,
3 Vanderbilt University, Nashville, TN,
4 Department of Genetics, Stanford University, Stanford, CA, United States
Abstract: Although the Caribbean has been continuously inhabited for the last 7,000 years, European contact in the last 500 years dramatically reshaped the cultural and genetic makeup of island populations. Several recent studies have explored the genetic diversity of Caribbean Latinos, and have characterized Native American variation present within their genomes. However, the difficulty of obtaining ancient DNA from pre-contact populations and the underrepresentation of non-Latino Caribbean islanders in genetic research, have prevented a complete understanding of genetic variation over time and space in the Caribbean basin. Here we discuss research that takes two approaches towards characterizing migration and admixture in Caribbean populations: an ancient DNA analysis of 139 individuals from three pre-contact archaeological sites in Puerto Rico (A.D. 500–1300), and an analysis of whole genome variants from 55 Afro-Caribbeans in five Lesser Antillean populations. Our ancient DNA analysis traces the origin and number of pre-contact migrations to Puerto Rico and examines the extent of genetic continuity between ancient and modern populations. In contrast, our modern DNA work analyzes autosomal SNP genotypes to characterize complex patterns of admixture since European contact among Lesser Antillean Afro-Caribbeans. Our findings characterize how ancient indigenous groups, European colonial regimes, the African Slave Trade and modern labor movements have shaped the genomic diversity of Caribbean islanders. In addition to its anthropological or historical importance, such knowledge is also essential for informing the identification of medically relevant genetic variation in these populations.
Expanded summary*: Characterizing how migration and admixture shapes human genetic diversity is vital for understanding human evolution, history and health. This is especially true in world regions that have undergone recent and dramatic demographic shifts, such as the Caribbean. Previous research with admixed Caribbean populations has shown that many islanders retain genomic variation from pre-Columbian indigenous groups, but also carry signatures of more recent admixture events fostered by European colonization and the African Slave Trade. However, a complete understanding of human genomic diversity across the Caribbean region is hampered by sampling gaps of both past and present populations. Due to the difficulties of obtaining ancient DNA (aDNA) from the tropics, the genetic diversity of pre-Columbian Caribbean groups is not well characterized. Efforts have been made to address this problem by studying Native American fragments in the genomes of admixed islanders. But, because modern populations do not retain all the genomic diversity of ancient groups, this approach provides limited resolution for reconstructing ancient demographic events. Further, many Caribbean populations remain underrepresented in large catalogs of genomic variation. Except for Barbadian Afro-Caribbeans, recently included in 1000 Genomes Phase 3, genetics research on Lesser Antillean populations has been limited to uni-parental loci and low-density ancestry informative markers. The present research seeks to fill in these gaps through two approaches: an aDNA analysis of 139 individuals from three archaeological sites in Puerto Rico (A.D. 500–1300), and an analysis of genome-wide SNP variants from 55 Afro-Caribbeans in five Lesser Antillean (LA) populations.
The aDNA investigation characterizes patterns of migration and genetic admixture in pre-Columbian Puerto Rico, and examines the extent of genetic continuity between ancient groups and modern islanders. In-solution capture and next-generation sequencing were used to obtain ancient DNA from 139 human skeletal remains (dated between A.D. 500–1300), from the sites of Tibes (n=52), Paso del Indio (n=50) and Punta Candelero (n=37). Preliminary data obtained from 24 complete mitochondrial genomes (mean read depth: 9.8x) suggest that pre-Columbian communities in Puerto Rico share genetic affinity with several extant South American and Mesoamerican indigenous populations. We also find that most pre-Columbian mtDNA lineages are not present in the Americas today, except for one, which is found almost exclusively in modern Puerto Ricans. These data support an origins scenario of complex and continuous admixture for ancient Caribbean groups but also underscore the large effect that contact-era population declines had on indigenous communities. Autosomal genotypes currently being generated from these remains will further inform these issues.
The second part of our project analyzes autosomal SNP genotypes in 55 self-identified Afro-Caribbeans from St. Kitts (n=5), St. Lucia (n=10), St. Vincent (n=15), Grenada (n=6), and Trinidad (n=19). We characterize patterns of genome-wide variation and ancestry in these individuals and compare them to exising data from other recently admixed American populations. We observe a complex pattern of admixture among in the LA Afro-Caribbeans with inputs from up to five continental sources and strong signatures of sex-biased mating. African ancestry proportions are high, but Native American ancestry is extremely low. This pattern contrasts sharply with that observed in Caribbean Latinos and is more similar to that observed in Haitians and Barbadians. We further observe that Trinidadian Afro-Caribbeans have the highest proportion of admixture with East and South Asian populations of all Caribbean populations studied to date.
Overall, our findings underscore the large impact of post-contact demographic shifts on Caribbean population history and illustrate how genomic diversity has changed in this region over the last 7,000 years. In addition, this work increases the representation of admixed and diverse populations in available genomic datasets and has the potential to inform future functional and clinical genetics research with admixed Caribbean islanders.
Genome wide data from the Iron Age provides insights into the population history of Finland.
Thiseas Christos Lamnidis1,*, Kerttu Majander2, Elina Salmela1 3, Anna Wessman4, Antti Sajantila5, Päivi Onkamo3, Stephan Schiffels1, Johannes Krause1 2
1Department of Archaogenetics, Max Planck Institute for the Science of Human History, Jena,
2Institute for Archaeological Sciences, Archaeo-and Palaeogenetics, University of Tübingen, Tübingen, Germany,
3 Department of Biosciences,
4 Department of Archaeology,
5 Department of Forensic Medicine, University of Helsinki, Helsinki, Finland
Abstract: The population history of Finland is subject of an ongoing debate, in particular with respect to the relationship and origins of modern Finnish and Saami people. Here we analyse genome-wide data, extracted from three teeth found in the archaeological site of Levänluhta, in southern Ostrobothnia. The site dates back to the Iron Age between 550-800 AD, according to the artefacts recovered, while radiocarbon dating on scattered femurs from the site span 350-730 AD. When analysed together with previously published ancient European samples and with modern European populations, the ancient Finnish samples lack a genetic component found in early Neolithic Farmers and all modern European populations today. Instead, we find that they are more closely related to modern Siberian and East Asian populations than modern Finnish are, a pattern also observed in genetic data from modern Saami. Our results suggest that the ancestral Saami population 1500 years ago, inhabited a larger region than today, extending as far south as Levänluhta. Such a scenario is also supported by linguistic evidence suggesting most of Finland to have been speaking Saami languages before 1000 AD. We also observe genetic differences between modern Saami and our ancient samples, which are likely to have arisen due to admixture with Finnish people during the last 1500 years.
The genetic history of the Indonesian Pygmies of Flores
Serena Tucci1 2,*, Benjamin Vernot3, Rajiv C. McCoy1, Samuel Vohr4, Matthew R. Robinson5, Chiara Barbieri6, Joshua Schraiber7 8, Herawati Sudoyo9 10, Peter M. Visscher5 11, Guido Barbujani2, Richard E. Green4, Joshua M. Akey1
1 Department of Genome Sciences, University of Washington, Seattle, United States,
2 Department of Life Sciences and Biotechnologies, University of Ferrara, Ferrara, Italy,
3 Department of Evolutionary Genetics, Max Planck Institute for
Evolutionary Anthropology, Leipzig, Germany,
4 Department of Biomolecular Engineering, University of California, Santa
Cruz, United States,
5 Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia,
6 Department of Linguistic and Cultural Evolution, Max Planck Institute for the Science of Human History, Jena, Germany,
7 Institute for Genomics and Evolutionary Medicine,
8 Department of Biology, Temple University, Temple, United States,
9 Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology,
10 Department of Medical Biology, Faculty of Medicine, University of Indonesia, Jakarta, Indonesia,
11 Queensland Brain Institute, The University of Queensland, Brisbane, Australia
Abstract: Modern human pygmy populations are distributed globally, and their short stature is hypothesized to represent one aspect of a complex eco-geographic adaptation to rainforest or island environments. Although numerous genetic studies have been conducted on pygmies in Africa and Southeast Asia, to date, there have been no genome-scale analyses of the pygmy population living on the island of Flores, Indonesia. Intriguingly, this population lives in a village near the cave where remains of a small-bodied human species, Homo floresiensis, were recently found. Here, we describe whole-genome sequences (>40x) from 10 Flores pygmy individuals, as well as genome-wide SNP data from 35 individuals. The Flores genomes harbor on average 48 Mb and 4.4 Mb of Neandertal and Denisovan sequence, respectively. Height-associated loci identified in European populations are significantly differentiated in the Flores pygmies, who possess an excess of height-decreasing alleles and a deficiency of height-increasing alleles. This result is consistent with a hypothesis of polygenic selection acting on standing variation for reduced stature in Flores. Finally, we identify a strong signature of recent positive selection encompassing the FADS gene cluster on chromosome 11, encoding for fatty acid desaturases that regulate the metabolism of long-chain polyunsaturated fatty acids (LC-PUFA). Flores individuals are nearly fixed for an ancestral haplotype that is predicted to confer reduced capacity to synthesize LC-PUFA from plant-based precursors. Our results add to emerging evidence that the FADS region has been a recurrent target of selection in diverse human populations, possibly in response to changing diets.