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Nakatsuka, Nathan

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Nakatsuka

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Nathan

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Nakatsuka, Nathan

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2017 - 201912020 - 20232

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Author's Publications: search.filters.isAuthorOfPublication.6490b8d3-3579-4ec0-b5cb-f09f98b3033a

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    Genetic continuity and change among the Indigenous peoples of California
    (Springer Science and Business Media LLC, 2023-11-22) Nakatsuka, Nathan; Holguin, Brian; Sedig, Jakob; Langenwalter, Paul E.; Carpenter, John; Culleton, Brendan J.; García-Moreno, Cristina; Harper, Thomas K.; Martin, Debra; Martínez-Ramírez, Júpiter; Porcayo-Michelini, Antonio; Tiesler, Vera; Villapando-Canchola, M. Elisa; Valdes Herrera, Alejandro; Callan, Kim; Curtis, Elizabeth; Kearns, Aisling; Iliev, Lora; Lawson, Ann Marie; Mah, Matthew; Mallick, Swapan; Micco, Adam; Michel, Megan; Workman, J. Noah; Oppenheimer, Jonas; Qiu, Lijun; Zalzala, Fatma; Rohland, Nadin; Punzo Diaz, Jose Luis; Johnson, John R.; Reich, David
    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 1. We report genome-wide data from 80 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 2-4. 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 1,5. 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.
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    The promise of disease gene discovery in South Asia
    (2017) Nakatsuka, Nathan; Moorjani, Priya; Rai, Niraj; Sarkar, Biswanath; Tandon, Arti; Patterson, Nick; Bhavani, Gandham SriLakshmi; Girisha, Katta Mohan; Mustak, Mohammed S; Srinivasan, Sudha; Kaushik, Amit; Vahab, Saadi Abdul; Jagadeesh, Sujatha M.; Satyamoorthy, Kapaettu; Singh, Lalji; Reich, David; Thangaraj, Kumarasamy
    The more than 1.5 billion people who live in South Asia are correctly viewed not as a single large population, but as many small endogamous groups. We assembled genome-wide data from over 2,800 individuals from over 260 distinct South Asian groups. We identify 81 unique groups, of which 14 have estimated census sizes of more than a million, that 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. We identify multiple examples of recessive diseases in South Asia that are the result of such founder events. This study highlights an under-appreciated opportunity for reducing disease burden among South Asians through the discovery of and testing for recessive disease genes.
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    Publication
    Ethics of DNA Research on Human Remains: Five Globally Applicable Guidelines
    (Nature, 2021-10-20) Alpaslan-Roodenberg, Songül; Anthony, David; Babiker, Hiba; Bánffy, Eszter; Booth, Thomas; Capone, Patricia; Deshpande-Mukherjee, Arati; Eisenmann, Stefanie; Fehren-Schmitz, Lars; Frachetti, Michael; Fujita, Ricardo; Frieman, Catherine J.; Fu, Qiaomei; Gibbon, Victoria; Haak, Wolfgang; Hajdinjak, Mateja; Hofmann, Kerstin; Holguin, Brian; Inomata, Takeshi; Kanzawa-Kiriyama, Hideaki; Keegan, William; Kelso, Janet; Krause, Johannes; Kumaresan, Ganesan; Kusimba, Chapurukha; Kusimba, Sibel; Lalueza-Fox, Carles; Llamas, Bastien; MacEachern, Scott; Mallick, Swapan; Matsumura, Hirofumi; Morales-Arce, Ana Y.; Motuzaite Matuzeviciute, Giedre; Mushrif-Tripathy, Veena; Nakatsuka, Nathan; Nores, Rodrigo; Ogola, Christine; Okumura, Mercedes; Patterson, Nick; Pinhasi, Ron; Prasad, Samayamantri P. R.; Prendergast, Mary E.; Punzo, Jose Luis; Reich, David; Sawafuji, Rikai; Sawchuk, Elizabeth; Schiffels, Stephan; Sedig, Jakob; Shnaider, Svetlana; Sirak, Kendra; Skoglund, Pontus; Slon, Viviane; Snow, Meradeth; Soressi, Marie; Spriggs, Matthew; Stockhammer, Philipp; Szécsényi-Nagy, Anna; Thangaraj, Kumarasamy; Tiesler, Vera; Tobler, Ray; Wang, Chuan-Chao; Warinner, Christina; Yasawardene, Surangi; Zahir, Muhammad
    We are a group of archaeologists, anthropologists, curators, and geneticists representing 24 countries and diverse global communities, most of whom met in November 2020 in a virtual workshop dedicated to ethics in ancient DNA research. 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. After considering diverse contexts, we developed a set of globally applicable guidelines. 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 reexamination 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 going forward.