Integration of ancient DNA with transdisciplinary dataset finds strong support for Inca resettlement in the south Peruvian coast

Ancient DNA (aDNA) analysis provides a powerful means of investigating human migration, social organization, and a plethora of other crucial questions about humanity’s past. Recently, specialists have suggested that the ideal research design involving aDNA would include multiple independent lines of evidence. In this paper, we adopt a transdisciplinary approach integrating aDNA with archaeological, biogeochemical, and historical data to investigate six individuals found in two cemeteries that date to the Late Horizon (1400 to 1532 CE) and Colonial (1532 to 1825 CE) periods in the Chincha Valley of southern Peru. Genomic analyses indicate that these individuals are genetically most similar to ancient and present-day populations from the north Peruvian coast located several hundred kilometers away. These genomic data are consistent with 16th century written records as well as ceramic, textile, and isotopic data. These results provide some of the strongest evidence yet of state-sponsored resettlement in the pre-Colonial Andes. This study highlights the power of transdisciplinary research designs when using aDNA data and sets a methodological standard for investigating ancient mobility in complex societies

Ancient genomes in South Patagonia reveal population movements associated with technological shifts and geography

Archaeological research documents major technological shifts among people who have lived in the southern tip of South America (South Patagonia) during the last thirteen millennia, including the development of marine-based economies and changes in tools and raw materials. It has been proposed that movements of people spreading culture and technology propelled some of these shifts, but these hypotheses have not been tested with ancient DNA. Here we report genome-wide data from 20 ancient individuals, and co-analyze it with previously reported data. We reveal that immigration does not explain the appearance of marine adaptations in South Patagonia. We describe partial genetic continuity since ~6600 BP and two later gene flows correlated with technological changes: one between 4700–2000 BP that affected primarily marine-based groups, and a later one impacting all <2000 BP groups. From ~2200–1200 BP, mixture among neighbors resulted in a cline correlated to geographic ordering along the coast.Fil: Nakatsuka, Nathan. Harvard Medical School; Estados UnidosFil: Luisi, Pierre. Universidad Nacional de Córdoba. Facultad de Filosofía y Humanidades; ArgentinaFil: Motti, Josefina María Brenda. Universidad Nacional del Centro de la Provincia de Buenos Aires; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Salemme, Monica Cira. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Austral de Investigaciones Científicas; Argentina. Universidad Nacional de Tierra del Fuego; ArgentinaFil: Santiago, Fernando Carlos. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Austral de Investigaciones Científicas; ArgentinaFil: D'angelo del Campo, Manuel Domingo. Universidad Nacional del Centro de la Provincia de Buenos Aires. Facultad de Ciencias Sociales. Grupo de Estudios Interdisciplinarios sobre Poblaciones Humanas de Patagonia Austral; Argentina. Universidad Autónoma de Madrid; EspañaFil: Vecchi, Rodrigo Javier. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional del Sur; ArgentinaFil: Espinosa Parrilla, Yolanda. Consejo Superior de Investigaciones Científicas; EspañaFil: Prieto, Alfredo. Universidad de Magallanes; ChileFil: Adamski, Nicole. Harvard Medical School; Estados UnidosFil: Lawson, Ann Marie. Harvard Medical School; Estados UnidosFil: Harper, Thomas K.. University of Pennsylvania; Estados UnidosFil: Culleton, Brendan J.. University of Pennsylvania; Estados UnidosFil: Kennett, Douglas J.. University of California; Estados UnidosFil: Lalueza Fox, Carles. Consejo Superior de Investigaciones Científicas; EspañaFil: Mallick, Swapan. Harvard Medical School; Estados UnidosFil: Rohland, Nadin. Harvard Medical School; Estados UnidosFil: Guichón, Ricardo A.. Universidad Nacional del Centro de la Provincia de Buenos Aires; ArgentinaFil: Cabana, Graciela S.. University of Tennessee; Estados UnidosFil: Nores, Rodrigo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Antropología de Córdoba. Universidad Nacional de Córdoba. Facultad de Filosofía y Humanidades. Instituto de Antropología de Córdoba; ArgentinaFil: Reich, David. Harvard Medical School. Department Of Medicine; Estados Unido

A paleogenomic reconstruction of the deep population history of the andes

There are many unanswered questions about the population history of the Central and South Central Andes, particularly regarding the impact of large-scale societies, such as the Moche, Wari, Tiwanaku, and Inca. We assembled genome-wide data on 89 individuals dating from ~9000-500 years ago (BP), with a particular focus on the period of the rise and fall of state societies. Today’s genetic structure began to develop by 5800 BP, followed by bi-directional gene flow between the North and South Highlands, and between the Highlands and Coast. We detect minimal admixture among neighboring groups between ~2000-500 BP, although we do detect cosmopolitanism (people of diverse ancestries living side-by-side) in the heartlands of the Tiwanaku and Inca polities. We also reveal cases of long-range mobility connecting the Andes to Argentina, and the Northwest Andes to the Amazon Basin

Reconstructing the Deep Population History of Central and South America

We report genome-wide ancient DNA from 49 individuals forming four parallel time transects in Belize, Brazil, the Central Andes, and the Southern Cone, each dating to at least 9,000 years ago. The common ancestral population radiated rapidly from just one of the two early branches that contributed to Native Americans today. We document two previously unappreciated streams of gene flow between North and South America. One affected the Central Andes by 4,200 years ago, while the other explains an affinity between the oldest North American genome associated with the Clovis culture and the oldest Central and South Americans from Chile, Brazil, and Belize. However, this was not the primary source for later South Americans, as the other ancient individuals derive from lineages without specific affinity to the Clovis-associated genome, suggesting a population replacement that began at least 9,000 years ago and was followed by substantial population continuity in multiple regions

Data for Genetic Continuity and Change Among the Indigenous Peoples of California

Prior to colonialism, California harbored more language variation than all of Europe, and linguistic and archaeological analysis have led to many hypotheses to explain this diversity. We report genome-wide data from 79 ancient Californians and 40 ancient northern Mexicans dating to 7400-200 years before present (BP). Our analyses document long-term genetic continuity between people living on California’s Northern Channel Islands and the adjacent Santa Barbara mainland coast from 7400 BP to modern Chumash groups represented by individuals who lived around 200 BP. The distinctive genetic lineages that characterize present-day and ancient people from Northwest Mexico increased in frequency in Southern and Central California by 5200 BP, documenting northward migrations that are candidates for spreading Uto-Aztecan languages prior to the dispersal of maize agriculture from Mexico. Baja Californians share more alleles with the earliest Central Californian in the dataset than with later Central Californians, potentially reflecting an earlier linguistic substrate, whose impact on local ancestry was diluted by later migrations from inland regions. After 1600 BP, ancient Channel Islanders lived in communities with effective sizes similar to those in pre-agricultural Caribbean and Patagonia, and smaller than those on the California mainland and in sampled regions of Mexico

Integrating Ancient and Modern DNA To Study Human History in South Asia and the Americas

In the last two decades, advances in next-generation sequencing, genome-wide genotyping arrays, and methods to obtain DNA from ancient individuals have propelled the field of population genetics such that it is now an extraordinarily powerful tool for inferring human history. This thesis focuses on the study of DNA from both present-day and ancient individuals who existed between 50 to over 10,000 years ago. The analyses focus on South Asian, African-American, and Native American history and some applications of these historical insights for improving human health. Chapter 1.1 provides a background to the field, including a survey of the current methods for obtaining DNA from ancient individuals, the major statistical techniques for using genetics to infer human history, and past ways that archaeological and linguistic information have been integrated with genetics to arrive at more robust, contextualized models of the past. Chapter 1.2 provides a philosophical framework for conducting ethically-responsible genetics research in non-Western cultural contexts with a focus on South Asian and Native American groups. This ethical framework forms the groundwork for the studies in this thesis, and each subsequent section is introduced with a statement on how the study’s approach fits into this framework. Chapter 2 details a study on over 260 distinct present-day South Asian groups, demonstrating that 81 of these groups, including 14 with estimated census sizes over one million, descend from founder events more extreme than those in Ashkenazi Jews and Finns, both of which have high rates of recessive disease due to founder events. These founder events are population bottlenecks that can be detected on the basis of identity-by-descent (IBD) segments shared within the last 100 generations from a common founder, and they highlight an underappreciated opportunity for recessive disease-associated gene mapping in South Asia. Chapter 3 is an admixture mapping study that examines the increased European ancestry at chromosome 1 of African-Americans with Multiple Sclerosis (MS) relative to those without the disease and determines that the signal is due to two genetic variants within the CD58 and FCRL3 genes that together predict a 1.44-fold greater risk for MS in European-Americans compared to African-Africans. Chapter 4 introduces a new software, ContamLD, for estimating contamination in autosomal ancient DNA (aDNA) by measuring the breakdown of linkage disequilibrium in a sequenced individual due to the contaminant DNA. Chapter 5 primarily focuses on three aDNA studies of Central and South America. The first study explores the earliest migrations into Central and South America from 11,000 to 4,000 years ago, while the next two studies focus on the changes in genetic structure over time in the Andes and Patagonia, including genetic analysis of individuals from major Andean cultures, such as the Wari, Tiwanaku, and Inca, as well as ancient individuals from the regions associated with the major Patagonian groups found at the time of European contact with representation of both maritime and terrestrial diet groups. Chapter 6 ties together the insights learned in these studies and compares them to findings of other world regions, highlighting surprising similarities and differences. Overall, this thesis presents just a small snapshot of the power of population genetics for inferring human history and how these insights can sometimes be used in unique ways to advance human health

ContamLD: Estimation of Ancient Nuclear DNA Contamination Using Breakdown of Linkage Disequilibrium

AbstractWe report a method,ContamLD, for estimating autosomal ancient DNA (aDNA) contamination by measuring the breakdown of linkage disequilibrium in a sequenced individual due to the introduction of contaminant DNA, leveraging the idea that contaminants should have haplotypes uncorrelated to those of the studied individual. Using simulated data, we confirm thatContamLDaccurately infers contamination rates with low standard errors (e.g. less than 1.5% standard error in cases with &lt;10% contamination and data from at least 500,000 sequences covering SNPs). This method is optimized for application to aDNA, leveraging characteristic aDNA damage patterns to provide calibrated contamination estimates. Availability:https://github.com/nathan-nakatsuka/ContamLD.</jats:p