A multidisciplinary review of the Inka imperial resettlement policy and implications for future investigations

The rulers of the Inka empire conquered approximately 2 million km² of the South American Andes in just under 100 years from 1438-1533 CE. Inside the empire, the elite conducted a systematic resettlement of the many Indigenous peoples in the Andes that had been rapidly colonised. The nature of this resettlement phenomenon is recorded within the Spanish colonial ethnohistorical record. Here we have broadly characterised the resettlement policy, despite the often incomplete and conflicting details in the descriptions. We then review research from multiple disciplines that investigate the empirical reality of the Inka resettlement policy, including stable isotope analysis, intentional cranial deformation morphology, ceramic artefact chemical analyses and genetics. Further, we discuss the benefits and limitations of each discipline for investigating the resettlement policy and emphasise their collective value in an interdisciplinary characterisation of the resettlement policy.Roberta Davidson, Lars Fehren-Schmitz and Bastien Llama

Allelic bias when performing in-solution enrichment of ancient human DNA

First published: 15 September 2023In-solution hybridisation enrichment of genetic variation is a valuable methodology in human paleogenomics. It allows enrichment of endogenous DNA by targeting genetic markers that are comparable between sequencing libraries. Many studies have used the 1240k reagent-which enriches 1,237,207 genome-wide SNPs-since 2015, though access was restricted. In 2021, Twist Biosciences and Daicel Arbor Biosciences independently released commercial kits that enabled all researchers to perform enrichments for the same 1240 k SNPs. We used the Daicel Arbor Biosciences Prime Plus kit to enrich 132 ancient samples from three continents. We identified a systematic assay bias that increases genetic similarity between enriched samples and that cannot be explained by batch effects. We present the impact of the bias on population genetics inferences (e.g. Principal Components Analysis, ƒ-statistics) and genetic relatedness (READ). We compare the Prime Plus bias to that previously reported of the legacy 1240k enrichment assay. In ƒ-statistics, we find that all Prime-Plus-generated data exhibit artefactual excess shared drift, such that within-continent relationships cannot be correctly determined. The bias is more subtle in READ, though interpretation of the results can still be misleading in specific contexts. We expect the bias may affect analyses we have not yet tested. Our observations support previously reported concerns for the integration of different data types in paleogenomics. We also caution that technological solutions to generate 1240k data necessitate a thorough validation process before their adoption in the paleogenomic community.Roberta Davidson, Matthew P. Williams, Xavier Roca-Rada, Kalina Kassadjikova, Raymond Tobler, Lars Fehren-Schmitz, Bastien Llama

Ancient mitochondrial genomes from the Argentinian Pampas inform the early peopling of the Southern Cone of South America

The Southern Cone of South America (SCSA) is a key region for investigations about the peopling of the Americas. However, little is known about the eastern sector, the Argentinian Pampas. We analyzed 18 mitochondrial genomes?7 of which are novel?from human skeletal remains from 3 Early to Late Holocene archaeological sites. The Pampas present a distinctive genetic makeup compared to other Middle to Late Holocene pre-Columbian SCSA populations. We also report the earliest individuals carrying SCSA-specific mitochondrial haplogroups D1j and D1g fromEarly andMiddle Holocene, respectively. Using these deep calibration time points in Bayesian phylogenetic reconstructions, we suggest that the first settlers of the Pampas were part of a single and rapid dispersal 15,600 years ago. Finally, we propose that present-day genetic differences between the Pampas and the rest of the SCSA are due to founder effects, genetic drift, and a partial population replacement 9,000 years ago.Fil: Roca Rada, Xavier. Centre For Ancient Dna, University Of Adelaide; AustraliaFil: Politis, Gustavo Gabriel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tandil. Investigaciones Arqueológicas y Paleontológicas del Cuaternario Pampeano. Universidad Nacional del Centro de la Provincia de Buenos Aires. Investigaciones Arqueológicas y Paleontológicas del Cuaternario Pampeano; ArgentinaFil: Messineo, Pablo Geronimo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tandil. Investigaciones Arqueológicas y Paleontológicas del Cuaternario Pampeano. Universidad Nacional del Centro de la Provincia de Buenos Aires. Investigaciones Arqueológicas y Paleontológicas del Cuaternario Pampeano; ArgentinaFil: Scheifler, Nahuel Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tandil. Investigaciones Arqueológicas y Paleontológicas del Cuaternario Pampeano. Universidad Nacional del Centro de la Provincia de Buenos Aires. Investigaciones Arqueológicas y Paleontológicas del Cuaternario Pampeano; ArgentinaFil: Scabuzzo, Clara. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro de Investigaciones y Transferencia de Entre Ríos. Universidad Nacional de Entre Ríos. Centro de Investigaciones y Transferencia de Entre Ríos; ArgentinaFil: Gonzalez, Mariela Edith. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tandil. Investigaciones Arqueológicas y Paleontológicas del Cuaternario Pampeano. Universidad Nacional del Centro de la Provincia de Buenos Aires. Investigaciones Arqueológicas y Paleontológicas del Cuaternario Pampeano; ArgentinaFil: Harkins, Kelly M.. University of California; Estados UnidosFil: Reich, David. Harvard Medical School; Estados UnidosFil: Souilmi, Yassine. University of Adelaide; AustraliaFil: Teixeira, Joao C. T.. University of Adelaide; AustraliaFil: Llamas, Bastien. University of Adelaide; AustraliaFil: Fehren Schmitz, Lars. University of California; Estados Unido

Comparing Genetic Variation among Latin American Immigrants: Implications for Forensic Casework in the Arizona- and Texas-México Borderlands

The humanitarian crisis on the United States-México border is a long standing and evolving crisis in which nearly 8,000 deaths have been reported in the last two decades. These deaths are largely distributed across the Arizona-México and Texas-México border regions where demographic trends for immigrants attempting to cross into the U.S. have shifted dramatically. The demographic change and volume of immigrants seeking shelter in the U.S. presents new challenges for the forensic practitioners entrusted with the identification of individuals who lose their lives during the final segment of their journey. Within this Border context, the present study investigates how genetic variation inferred from forensically significant microsatellites can provide valuable information on regions of origin for unidentified remains on the group level. To explore how we can mobilize these genetic data to inform identification strategies, we conduct a comparative genetic analysis of identified and unidentified immigrant cases from the Arizona- and Texas-México contexts, as well as 27 other Latin American groups. Allele frequencies were utilized to calculate FST, and relationships were visually depicted in a multidimensional scaling plot. A Spearman correlation coefficient analysis assessed the strength and significance of population relationships and an agglomerative clustering analysis assessed population clusters. Results indicate that Arizona-México immigrants have the strongest relationship (\u3e80%) with groups from El Salvador, Guatemala, México, and an indigenous group from Southern México. Texas-México immigrants have the strongest relationships (\u3e80%) with groups from Belize, Colombia, Costa Rica, El Salvador, Guatemala, Honduras, and Nicaragua. These findings agree with, and are discussed in comparison to, previously reported demographic trends, population genetics research, and population history analyses. We emphasize the utility and necessity of coupling genetic variation research with a nuanced anthropological perspective for identification processes in the U.S-México border context

Ancient DNA analysis suggests negligible impact of the Wari Empire expansion in Peru's Central Coast during the Middle Horizon

The analysis of ancient human DNA from South America allows the exploration of pre-Columbian population history through time and to directly test hypotheses about cultural and demographic evolution. The Middle Horizon (650-1100 AD) represents a major transitional period in the Central Andes, which is associated with the development and expansion of ancient Andean empires such as Wari and Tiwanaku. These empires facilitated a series of interregional interactions and socio-political changes, which likely played an important role in shaping the region's demographic and cultural profiles. We analyzed individuals from three successive pre-Columbian cultures present at the Huaca Pucllana archaeological site in Lima, Peru: Lima (Early Intermediate Period, 500-700 AD), Wari (Middle Horizon, 800-1000 AD) and Ychsma (Late Intermediate Period, 1000-1450 AD). We sequenced 34 complete mitochondrial genomes to investigate the potential genetic impact of the Wari Empire in the Central Coast of Peru. The results indicate that genetic diversity shifted only slightly through time, ruling out a complete population discontinuity or replacement driven by the Wari imperialist hegemony, at least in the region around present-day Lima. However, we caution that the very subtle genetic contribution of Wari imperialism at the particular Huaca Pucllana archaeological site might not be representative for the entire Wari territory in the Peruvian Central Coast.Guido Valverde, María Inés Barreto Romero, Isabel Flores Espinoza, Alan Cooper, Lars Fehren-Schmitz, Bastien Llamas, Wolfgang Haa

Ancient mitochondrial DNA provides high-resolution time scale of the peopling of the Americas

The exact timing, route, and process of the initial peopling of the Americas remains uncertain despite much research. Archaeological evidence indicates the presence of humans as far as southern Chile by 14.6 thousand years ago (ka), shortly after the Pleistocene ice sheets blocking access from eastern Beringia began to retreat. Genetic estimates of the timing and route of entry have been constrained by the lack of suitable calibration points and low genetic diversity of Native Americans. We sequenced 92 whole mitochondrial genomes from pre-Columbian South American skeletons dating from 8.6 to 0.5 ka, allowing a detailed, temporally calibrated reconstruction of the peopling of the Americas in a Bayesian coalescent analysis. The data suggest that a small population entered the Americas via a coastal route around 16.0 ka, following previous isolation in eastern Beringia for ~2.4 to 9 thousand years after separation from eastern Siberian populations. Following a rapid movement throughout the Americas, limited gene flow in South America resulted in a marked phylogeographic structure of populations, which persisted through time. All of the ancient mitochondrial lineages detected in this study were absent from modern data sets, suggesting a high extinction rate. To investigate this further, we applied a novel principal components multiple logistic regression test to Bayesian serial coalescent simulations. The analysis supported a scenario in which European colonization caused a substantial loss of pre-Columbian lineages.Bastien Llamas, Lars Fehren-Schmitz, Guido Valverde, Julien Soubrier, Swapan Mallick, Nadin Rohland, Susanne Nordenfelt, Cristina Valdiosera, Stephen M. Richards, Adam Rohrlach, Maria Inés Barreto Romero, Isabel Flores Espinoza, Elsa Tomasto Cagigao, Lucía Watson Jiménez, Krzysztof Makowski, Ilán Santiago Leboreiro Reyna, Josefina Mansilla Lory, Julio Alejandro Ballivián Torrez, Mario A. Rivera, Richard L. Burger, Maria Constanza Ceruti, Johan Reinhard, R. Spencer Wells, Gustavo Politis, Calogero M. Santoro, Vivien G. Standen, Colin Smith, David Reich, Simon Y. W. Ho, Alan Cooper and Wolfgang Haa

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