Publications

2021
S. Alpaslan-Roodenberg, (33 authors), N. Nakatsuka, (28 authors), and M. Zahir. 11/2021. “Ethics of DNA research on human remains: five globally applicable guidelines.” Nature, 599, 7883, Pp. 41-46. Publisher's VersionAbstract
We are a group of archaeologists, anthropologists, curators and geneticists representing diverse global communities and 31 countries. All of us met in a virtual workshop dedicated to ethics in ancient DNA research held in November 2020. There was widespread agreement that globally applicable ethical guidelines are needed, but that recent recommendations grounded in discussion about research on human remains from North America are not always generalizable worldwide. Here we propose the following globally applicable guidelines, taking into consideration diverse contexts. These hold that: (1) researchers must ensure that all regulations were followed in the places where they work and from which the human remains derived; (2) researchers must prepare a detailed plan prior to beginning any study; (3) researchers must minimize damage to human remains; (4) researchers must ensure that data are made available following publication to allow critical re-examination of scientific findings; and (5) researchers must engage with other stakeholders from the beginning of a study and ensure respect and sensitivity to stakeholder perspectives. We commit to adhering to these guidelines and expect they will promote a high ethical standard in DNA research on human remains going forward.
ethicsofdnaresearch_nature2021.pdf
D. Popovic, M. Molak, M. Ziolkowski, A. Vranich, M. Sobczyk, D. Vidaurre, G. Agresti, M. Skrzypczak, K. Ginalski, T. Lamnidis, N. Nakatsuka, S. Mallick, and M. Baca. 9/24/2021. “Ancient genomes reveal long range influence of the site and culture of Tiwanaku.” Science Advances, 7, 39. Publisher's VersionAbstract
Tiwanaku civilization flourished in the Lake Titicaca basin between 500 and 1000 CE and at its apogee influenced wide areas across the southern Andes. Despite a considerable amount of archaeological data, little is known about the Tiwanaku population. We analyzed 17 low-coverage genomes from individuals dated between 300 and 1500 CE and demonstrated genetic continuity in the Lake Titicaca basin throughout this period, which indicates that the substantial cultural and political changes in the region were not accompanied by large-scale population movements. Conversely, the ritual center of Tiwanaku revealed high diversity, including individuals with primarily local genetic ancestry and those with foreign admixture or provenance from as far as the Amazon. Nonetheless, most human offerings associated with the Akapana platform exhibited pure Titicaca basin ancestry and dated to ca. 950 CE—the onset of Tiwanaku’s decline as a sociopolitical center. Our results strengthen the view of Tiwanaku as a complex and far-reaching polity.
popovic2021_tiwanaku.pdf
2020
Nathan Nakatsuka, Nick Patterson, Nikolaos Patsopoulos, Nicholas Altemose, Arti Tandon, Ashley Beecham, Jacob McCauley, Noriko Isobe, Stephen Hauser, Philiip De Jager, David Hafler, Jorge Oksenberg, and David Reich. 10/9/2020. “Two Genetic Variants Explain the Association of European Ancestry with Multiple Sclerosis Risk in African-Americans.” Scientific Reports, 10, 1, Pp. 16902. Publisher's VersionAbstract
Epidemiological studies have suggested differences in the rate of multiple sclerosis (MS) in individuals of European ancestry compared to African ancestry, motivating genetic scans to identify variants that could contribute to such patterns. In a whole-genome scan in 899 African-American cases and 1155 African-American controls, we confirm that African-Americans who inherit segments of the genome of European ancestry at a chromosome 1 locus are at increased risk for MS [logarithm of odds (LOD) = 9.8], although the signal weakens when adding an additional 406 cases, reflecting heterogeneity in the two sets of cases [logarithm of odds (LOD) = 2.7]. The association in the 899 individuals can be fully explained by two variants previously associated with MS in European ancestry individuals. These variants tag a MS susceptibility haplotype associated with decreased CD58 gene expression (odds ratio of 1.37; frequency of 84% in Europeans and 22% in West Africans for the tagging variant) as well as another haplotype near the FCRL3 gene (odds ratio of 1.07; frequency of 49% in Europeans and 8% in West Africans). Controlling for all other genetic and environmental factors, the two variants predict a 1.44-fold higher rate of MS in European-Americans compared to African-Americans.
ScientificReports2020_MS.pdf
Nathan Nakatsuka*, Éadaoin Harney*, Swapan Mallick, Matthew Mah, Nick Patterson, and David Reich. 8/10/2020. “ContamLD: estimation of ancient nuclear DNA contamination using breakdown of linkage disequilibrium.” Genome Biology, 21, 1, Pp. 199. Publisher's VersionAbstract
We report a method called 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. ContamLD leverages the idea that contaminants should have haplotypes uncorrelated to those of the studied individual. Using simulated data, we confirm that ContamLD accurately infers contamination rates with low standard errors: for example, less than 1.5% standard error in cases with less than 10% contamination and 500,000 sequences covering SNPs. This method is optimized for application to aDNA, taking advantage of characteristic aDNA damage patterns to provide calibrated contamination estimates, and is available at https://github.com/nathan-nakatsuka/ContamLD.
GenomeBiology2020_ContamLD.pdf
Jacob L Bongers, Nathan Nakatsuka, Colleen O'Shea, Thomas K Harper, Henry Tantaleán, Charles Stanish, and Lars Fehren-Schmitz. 8/4/2020. “Integration of ancient DNA with transdisciplinary dataset finds strong support for Inca resettlement in the south Peruvian coast.” PNAS, 117, 31, Pp. 18359-18368. Publisher's VersionAbstract
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.
PNAS2020_ChinchaValley.pdf
Nathan Nakatsuka*, Pierre Luisi*, Josefina MB Motti, Mónica Salemme, Fernando Santiago, Manuel D'Angelo Del D Campo, Rodrigo J Vecchi, Yolanda Espinosa-Parrilla, Alfredo Prieto, Nicole Adamski, Ann Marie Lawson, Thomas K Harper, Brendan J Culleton, Douglas J Kennett, Carles Lalueza-Fox, Swapan Mallick, Nadin Rohland, Ricardo A Guichón, Graciela S Cabana, Rodrigo Nores, and David Reich. 8/3/2020. “Ancient genomes in South Patagonia reveal population movements associated with technological shifts and geography.” Nature Communications, 11, 1, Pp. 3868. Publisher's VersionAbstract
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.
NatureCommunications2020_Patagonia.pdf
Nathan Nakatsuka, Iosif Lazaridis, Chiara Barbieri, Pontus Skoglund, Nadin Rohland, Swapan Mallick, Cosimo Posth, Kelly Harkins-Kinkaid, Matthew Ferry, Éadaoin Harney, Megan Michel, Kristin Stewardson, Jannine Novak-Forst, José M Capriles, Marta Alfonso Durruty, Karina Aranda Álvarez, David Beresford-Jones, Richard Burger, Lauren Cadwallader, Ricardo Fujita, Johny Isla, George Lau, Carlos Lémuz Aguirre, Steven LeBlanc, Sergio Calla Maldonado, Frank Meddens, Pablo G Messineo, Brendan J Culleton, Thomas K Harper, Jeffrey Quilter, Gustavo Politis, Kurt Rademaker, Markus Reindel, Mario Rivera, Lucy Salazar, José R Sandoval, Calogero M Santoro, Nahuel Scheifler, Vivien Standen, Maria Ines Barreto, Isabel Flores Espinoza, Elsa Tomasto-Cagigao, Guido Valverde, Douglas J Kennett, Alan Cooper, Johannes Krause, Wolfgang Haak, Bastien Llamas, David Reich, and Lars Fehren-Schmitz. 5/28/2020. “A Paleogenomic Reconstruction of the Deep Population History of the Andes.” Cell, 181, 5, Pp. 1131-1145. Publisher's VersionAbstract
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 ∼9,000-500 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 5,800 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 ∼2,000-500 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 highlight cases of long-range mobility connecting the Andes to Argentina and the Northwest Andes to the Amazon Basin. https://www.youtube.com/watch?v=S-ra2eDF16U
Cell2020_Andes.pdf
2019
V. Narasimhan*, N. Patterson*, P. Moorjani+, N. Rohland+, R. Bernardos, S. Mallick, I. Lazaridis, N. Nakatsuka, [104 authors], N. Boivin, K. Thangaraj+, D. Kennett+, M. Frachetti+, R. Pinhasi+, and D. Reich+. 9/6/2019. “The formation of human populations in South and Central Asia.” Science, 365, 6457. Publisher's Version Science2019_SouthCentralAsia.pdf
V. Shinde*, V. Narasimhan*, N. Rohland, S. Mallick, M. Mah, M. Lipson, N. Nakatsuka, [19 authors], N. Rai+, and D. Reich+. 9/4/2019. “An Ancient Genome from the Indus Valley Civilization Lacks Ancestry from Steppe Pastoralists or Western Iranian Farmers.” Cell, 8674, 19, Pp. 30967-5. Publisher's Version Cell2019_AncientHarappanGenome.pdf
2018
C. Posth*, N. Nakatsuka*, I. Lazaridis, P. Skoglund, S. Mallick, T. Lamnidis, N. Rohland, K. Nagele, N. Adamski, E. Bertolini, N. Broomandkhoshbacht, A. Cooper, B. Culleton, T. Ferraz, M. Ferry, A. Furtwangler, W. Haak, K. Harkins, T. Harper, T. Hunemeier, A. Lawson, B. Llamas, M. Michel, E. Nelson, J. Oppenheimer, N. Patterson, S. Schiffels, J. Sedig, K. Stewardson, S. Talamo, C. Wang, J. Hublin, M. Hubbe, K. Harvati, A. Nuevo Delaunay, J. Beier, M. Francken, P. Kaulicke, H. Reyes-Centeno, K. Rademaker, W. Trask, M. Robinson, S. Gutierrez, K. Prufer, D. Salazar-Garcia, E. Chim, L. Muller Plumm Gomes, M. Alves, A. Liryo, M. Inglez, R. Oliveira, D. Bernardo, A. Barioni, V. Wesolowski, N. Scheifler, M. Rivera, C. Plens, P. Messineo, L. Figuti, D. Corach, C. Scabuzzo, S. Eggers, P. DeBlasis, M. Reindel, C. Mendez, G. Politis, E. Tomasto-Cagigao, D. Kennett, A. Strauss, L. Fehren-Schmitz, J. Krause, and D. Reich. 9/15/2018. “Reconstructing the Deep Population History of Central and South America.” Cell, 175, 5, Pp. 1185-1197. Publisher's Version Cell2018_CentralSouthAmerica.pdf
K. Claw, M. Anderson, R. Begay, K. Tsosie, K. Fox, N. Garrison, and Summer INdigenous Genomics (SING) the internship for peoples in Consortium. 7/27/2018. “A framework for enhancing ethical genomic research with indigenous communities.” Nature Communications, 9, 1, Pp. 2957. Publisher's Version NatureCommunications2018GenomicsResearchIndigenousCommunities.pdf
J. Bardill, A. Bader, N. Garrison, D. Bolnick, J. Raff, A. Walker, R. Malhi, and Summer Internship INdigenous Genomics (SING) the for peoples in Consortium. 4/27/2018. “Advancing the ethics of paleogenomics.” Science: Policy Forum, 360, 6387, Pp. 384-385. Publisher's Version Science_AdvancingEthicsofPaleogenomics.pdf
2017
N. Nakatsuka, P. Moorjani, N. Rai, B. Sarkar, A. Tandon, N. Patterson, G. Bhavani, K. Girisha, N. Mustak, S. Srinivasan, A. Kaushik, S. Vahab, S. Jagadeesh, K. Satyamoorthy, L. Singh, D. Reich+, and K. Thangaraj+. 9/1/2017. “The Promise of Discovering Population-Specific Disease-Associated Genes in South Asia.” Nature Genetics, 49, 9, Pp. 1403-1407. Publisher's Version NatGenetics2017_DiseaseGenesSouthAsia.pdf
2014
L. Strittmatter, Y. Li, N. Nakatsuka, S. Calvo, Z. Grabarek, and V. Mootha. 5/1/2014. “CLYBL is a polymorphic human enzyme with malate synthase and β-methylmalate synthase activity.” Human Molecular Genetics, 23, 9, Pp. 2313-23. Publisher's Version HumanMolecularGenetics_CLYBL.pdf
2013
N. Nakatsuka, L. Esquivel, M. Levin, C. Browne, and K. Braun. 2/2013. “Identifying the Unique Challenges Facing Kanaka Maoli Kūpuna Residing Outside of Hawaiʻi.” Hulili Journal for Multidisciplinary Research on Hawaiian Well-Being, 9, Pp. 133-151. Hulili_KanakaMaoliKupuna.pdf
2011
R. Xie, J. Chung, K. Ylaya, R. Williams, N. Guerrero, N. Nakatsuka, C. Badie, and S. Hewitt. 4/2011. “Factors influencing the degradation of archival formalin-fixed paraffin-embedded tissue sections.” Journal of Histochemistry and Cytochemistry, 59, 4, Pp. 356-65. Publisher's Version JournalofHistochemistryandCytochemistry_FFPETissue.pdf