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453 results on '"Malhi, Ripan S."'

3. Chaco Canyon Dig Unearths Ethical Concerns

Author

Claw, Katrina G., Lippert, Dorothy, Bardill, Jessica, Cordova, Anna, Fox, Keolu, Yracheta, Joseph M., Bader, Alyssa C., Bolnick, Deborah A., Malhi, Ripan S., TallBear, Kimberly, Garrison, Nanibaa' A., and Garrison, Nanibaa' A.

Published
2018

12. A comparison of proteomic, genomic, and osteological methods of archaeological sex estimation.

Author

Buonasera, Tammy, Eerkens, Jelmer, de Flamingh, Alida, Engbring, Laurel, Yip, Julia, Li, Hongjie, Haas, Randall, DiGiuseppe, Diane, Grant, Dave, Salemi, Michelle, Nijmeh, Charlene, Arellano, Monica, Leventhal, Alan, Phinney, Brett, Byrd, Brian F, Malhi, Ripan S, and Parker, Glendon

Subjects
Humans, Peptides, DNA, Proteomics, Base Sequence, Geography, Archaeology, California, Female, Male, Amelogenin, Sex Determination by Skeleton, Osteology
Abstract

Sex estimation of skeletons is fundamental to many archaeological studies. Currently, three approaches are available to estimate sex-osteology, genomics, or proteomics, but little is known about the relative reliability of these methods in applied settings. We present matching osteological, shotgun-genomic, and proteomic data to estimate the sex of 55 individuals, each with an independent radiocarbon date between 2,440 and 100 cal BP, from two ancestral Ohlone sites in Central California. Sex estimation was possible in 100% of this burial sample using proteomics, in 91% using genomics, and in 51% using osteology. Agreement between the methods was high, however conflicts did occur. Genomic sex estimates were 100% consistent with proteomic and osteological estimates when DNA reads were above 100,000 total sequences. However, more than half the samples had DNA read numbers below this threshold, producing high rates of conflict with osteological and proteomic data where nine out of twenty conditional DNA sex estimates conflicted with proteomics. While the DNA signal decreased by an order of magnitude in the older burial samples, there was no decrease in proteomic signal. We conclude that proteomics provides an important complement to osteological and shotgun-genomic sex estimation.

Published
2020

14. The population history of northeastern Siberia since the Pleistocene

Author

Sikora, Martin, Pitulko, Vladimir V, Sousa, Vitor C, Allentoft, Morten E, Vinner, Lasse, Rasmussen, Simon, Margaryan, Ashot, de Barros Damgaard, Peter, de la Fuente, Constanza, Renaud, Gabriel, Yang, Melinda A, Fu, Qiaomei, Dupanloup, Isabelle, Giampoudakis, Konstantinos, Nogués-Bravo, David, Rahbek, Carsten, Kroonen, Guus, Peyrot, Michaël, McColl, Hugh, Vasilyev, Sergey V, Veselovskaya, Elizaveta, Gerasimova, Margarita, Pavlova, Elena Y, Chasnyk, Vyacheslav G, Nikolskiy, Pavel A, Gromov, Andrei V, Khartanovich, Valeriy I, Moiseyev, Vyacheslav, Grebenyuk, Pavel S, Fedorchenko, Alexander Yu, Lebedintsev, Alexander I, Slobodin, Sergey B, Malyarchuk, Boris A, Martiniano, Rui, Meldgaard, Morten, Arppe, Laura, Palo, Jukka U, Sundell, Tarja, Mannermaa, Kristiina, Putkonen, Mikko, Alexandersen, Verner, Primeau, Charlotte, Baimukhanov, Nurbol, Malhi, Ripan S, Sjögren, Karl-Göran, Kristiansen, Kristian, Wessman, Anna, Sajantila, Antti, Lahr, Marta Mirazon, Durbin, Richard, Nielsen, Rasmus, Meltzer, David J, Excoffier, Laurent, and Willerslev, Eske

Subjects
Asia, DNA, Ancient, Europe, Gene Pool, Genome, Human, Haplotypes, History, 15th Century, History, Ancient, History, Medieval, Human Migration, Humans, Indians, North American, Male, Siberia, General Science & Technology
Abstract

Northeastern Siberia has been inhabited by humans for more than 40,000 years but its deep population history remains poorly understood. Here we investigate the late Pleistocene population history of northeastern Siberia through analyses of 34 newly recovered ancient genomes that date to between 31,000 and 600 years ago. We document complex population dynamics during this period, including at least three major migration events: an initial peopling by a previously unknown Palaeolithic population of 'Ancient North Siberians' who are distantly related to early West Eurasian hunter-gatherers; the arrival of East Asian-related peoples, which gave rise to 'Ancient Palaeo-Siberians' who are closely related to contemporary communities from far-northeastern Siberia (such as the Koryaks), as well as Native Americans; and a Holocene migration of other East Asian-related peoples, who we name 'Neo-Siberians', and from whom many contemporary Siberians are descended. Each of these population expansions largely replaced the earlier inhabitants, and ultimately generated the mosaic genetic make-up of contemporary peoples who inhabit a vast area across northern Eurasia and the Americas.

Published
2019

15. Evolutionary and phylogenetic insights from a nuclear genome sequence of the extinct, giant, “subfossil” koala lemur Megaladapis edwardsi

Author

Marciniak, Stephanie, Mughal, Mehreen R., Godfrey, Laurie R., Bankoff, Richard J., Randrianatoandro, Heritiana, Crowley, Brooke E., Bergey, Christina M., Muldoon, Kathleen M., Randrianasy, Jeannot, Raharivololona, Brigitte M., Schuster, Stephan C., Malhi, Ripan S., Yoder, Anne D., Louis, Edward E., Kistler, Logan, and Perry, George H.

Published
2021

16. Early human dispersals within the Americas

Author

Moreno-Mayar, J Víctor, Vinner, Lasse, de Barros Damgaard, Peter, de la Fuente, Constanza, Chan, Jeffrey, Spence, Jeffrey P, Allentoft, Morten E, Vimala, Tharsika, Racimo, Fernando, Pinotti, Thomaz, Rasmussen, Simon, Margaryan, Ashot, Iraeta Orbegozo, Miren, Mylopotamitaki, Dorothea, Wooller, Matthew, Bataille, Clement, Becerra-Valdivia, Lorena, Chivall, David, Comeskey, Daniel, Devièse, Thibaut, Grayson, Donald K, George, Len, Harry, Harold, Alexandersen, Verner, Primeau, Charlotte, Erlandson, Jon, Rodrigues-Carvalho, Claudia, Reis, Silvia, Bastos, Murilo QR, Cybulski, Jerome, Vullo, Carlos, Morello, Flavia, Vilar, Miguel, Wells, Spencer, Gregersen, Kristian, Hansen, Kasper Lykke, Lynnerup, Niels, Mirazón Lahr, Marta, Kjær, Kurt, Strauss, André, Alfonso-Durruty, Marta, Salas, Antonio, Schroeder, Hannes, Higham, Thomas, Malhi, Ripan S, Rasic, Jeffrey T, Souza, Luiz, Santos, Fabricio R, Malaspinas, Anna-Sapfo, Sikora, Martin, Nielsen, Rasmus, Song, Yun S, Meltzer, David J, and Willerslev, Eske

Subjects
Clinical Research, Datasets as Topic, Asia, Eastern, Genome, Human, Genomics, Human Migration, Humans, Indians, North American, North America, Polymorphism, Single Nucleotide, Population Dynamics, Siberia, South America, General Science & Technology
Abstract

Studies of the peopling of the Americas have focused on the timing and number of initial migrations. Less attention has been paid to the subsequent spread of people within the Americas. We sequenced 15 ancient human genomes spanning from Alaska to Patagonia; six are ≥10,000 years old (up to ~18× coverage). All are most closely related to Native Americans, including those from an Ancient Beringian individual and two morphologically distinct "Paleoamericans." We found evidence of rapid dispersal and early diversification that included previously unknown groups as people moved south. This resulted in multiple independent, geographically uneven migrations, including one that provides clues of a Late Pleistocene Australasian genetic signal, as well as a later Mesoamerican-related expansion. These led to complex and dynamic population histories from North to South America.

Published
2018

18. Current evidence allows multiple models for the peopling of the Americas.

Author

Potter, Ben A, Baichtal, James F, Beaudoin, Alwynne B, Fehren-Schmitz, Lars, Haynes, C Vance, Holliday, Vance T, Holmes, Charles E, Ives, John W, Kelly, Robert L, Llamas, Bastien, Malhi, Ripan S, Miller, D Shane, Reich, David, Reuther, Joshua D, Schiffels, Stephan, and Surovell, Todd A

Subjects
Humans, Population Dynamics, Emigration and Immigration, Models, Theoretical, History, Ancient, Americas, Biological Evolution, Models, Theoretical, History, Ancient
Abstract

Some recent academic and popular literature implies that the problem of the colonization of the Americas has been largely resolved in favor of one specific model: a Pacific coastal migration, dependent on high marine productivity, from the Bering Strait to South America, thousands of years before Clovis, the earliest widespread cultural manifestation south of the glacial ice. Speculations on maritime adaptations and typological links (stemmed points) across thousands of kilometers have also been advanced. A review of the current genetic, archeological, and paleoecological evidence indicates that ancestral Native American population expansion occurred after 16,000 years ago, consistent with the archeological record, particularly with the earliest securely dated sites after ~15,000 years ago. These data are largely consistent with either an inland (ice-free corridor) or Pacific coastal routes (or both), but neither can be rejected at present. Systematic archeological and paleoecological investigations, informed by geomorphology, are required to test each hypothesis.

Published
2018

22. Isotopic and genetic analyses of a mass grave in central California: Implications for precontact hunter‐gatherer warfare

Author

Eerkens, Jelmer W, Carlson, Traci, Malhi, Ripan S, Blake, Jennifer, Bartelink, Eric J, Barfod, Gry H, Estes, Alan, Garibay, Ramona, Glessner, Justin, Greenwald, Alexandra M, Lentz, Kari, Li, Hongjie, and Marshall, Charla K

Subjects
Archaeology, Anthropology, History, Heritage and Archaeology, Human Society, Adolescent, Adult, Anthropology, Physical, Bone and Bones, Burial, California, DNA, Mitochondrial, History, Ancient, Humans, Isotopes, Male, Tooth, Violence, Warfare, Young Adult, human provenancing, hunter-gatherer violence, C N O Sr isotopes, ancient mtDNA, California prehistory, Evolutionary Biology, Ecology
Abstract

Analysis of a mass burial of seven males at CA-ALA-554, a prehistoric site in the Amador Valley, CA, was undertaken to determine if the individuals were "locals" or "non-locals," and how they were genetically related to one another.The study includes osteological, genetic (mtDNA), and stable (C, N, O, S) and radiogenic (Sr) isotope analyses of bone and tooth (first and third molars) samples.Isotopes in first molars, third molars, and bone show they spent the majority of their lives living together. They are not locals to the Amador Valley, but were recently living to the east in the San Joaquin Valley, suggesting intergroup warfare as the cause of death. The men were not maternally related, but represent at least four different matrilines. The men also changed residence as a group between age 16 and adult years.Isotope data suggest intergroup warfare accounts for the mass burial. Genetic data suggest the raiding party included sets of unrelated men, perhaps from different households. Generalizing from this case and others like it, we hypothesize that competition over territory was a major factor behind ancient warfare in Central California. We present a testable model of demographic expansion, wherein villages in high-population-density areas frequently fissioned, with groups of individuals moving to lower-population-density areas to establish new villages. This model is consistent with previous models of linguistic expansion.

Published
2016

28. Rights, interests and expectations: Indigenous perspectives on unrestricted access to genomic data

Author

Hudson, Maui, Garrison, Nanibaa’ A., Sterling, Rogena, Caron, Nadine R., Fox, Keolu, Yracheta, Joseph, Anderson, Jane, Wilcox, Phil, Arbour, Laura, Brown, Alex, Taualii, Maile, Kukutai, Tahu, Haring, Rodney, Te Aika, Ben, Baynam, Gareth S., Dearden, Peter K., Chagné, David, Malhi, Ripan S., Garba, Ibrahim, Tiffin, Nicki, Bolnick, Deborah, Stott, Matthew, Rolleston, Anna K., Ballantyne, Leah L., Lovett, Ray, David-Chavez, Dominique, Martinez, Andrew, Sporle, Andrew, Walter, Maggie, Reading, Jeff, and Carroll, Stephanie Russo

Published
2020
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29. Genomic evidence for the Pleistocene and recent population history of Native Americans

Author

Raghavan, Maanasa, Steinrücken, Matthias, Harris, Kelley, Schiffels, Stephan, Rasmussen, Simon, DeGiorgio, Michael, Albrechtsen, Anders, Valdiosera, Cristina, Ávila-Arcos, María C, Malaspinas, Anna-Sapfo, Eriksson, Anders, Moltke, Ida, Metspalu, Mait, Homburger, Julian R, Wall, Jeff, Cornejo, Omar E, Moreno-Mayar, J Víctor, Korneliussen, Thorfinn S, Pierre, Tracey, Rasmussen, Morten, Campos, Paula F, de Barros Damgaard, Peter, Allentoft, Morten E, Lindo, John, Metspalu, Ene, Rodríguez-Varela, Ricardo, Mansilla, Josefina, Henrickson, Celeste, Seguin-Orlando, Andaine, Malmström, Helena, Stafford, Thomas, Shringarpure, Suyash S, Moreno-Estrada, Andrés, Karmin, Monika, Tambets, Kristiina, Bergström, Anders, Xue, Yali, Warmuth, Vera, Friend, Andrew D, Singarayer, Joy, Valdes, Paul, Balloux, Francois, Leboreiro, Ilán, Vera, Jose Luis, Rangel-Villalobos, Hector, Pettener, Davide, Luiselli, Donata, Davis, Loren G, Heyer, Evelyne, Zollikofer, Christoph PE, Ponce de León, Marcia S, Smith, Colin I, Grimes, Vaughan, Pike, Kelly-Anne, Deal, Michael, Fuller, Benjamin T, Arriaza, Bernardo, Standen, Vivien, Luz, Maria F, Ricaut, Francois, Guidon, Niede, Osipova, Ludmila, Voevoda, Mikhail I, Posukh, Olga L, Balanovsky, Oleg, Lavryashina, Maria, Bogunov, Yuri, Khusnutdinova, Elza, Gubina, Marina, Balanovska, Elena, Fedorova, Sardana, Litvinov, Sergey, Malyarchuk, Boris, Derenko, Miroslava, Mosher, MJ, Archer, David, Cybulski, Jerome, Petzelt, Barbara, Mitchell, Joycelynn, Worl, Rosita, Norman, Paul J, Parham, Peter, Kemp, Brian M, Kivisild, Toomas, Tyler-Smith, Chris, Sandhu, Manjinder S, Crawford, Michael, Villems, Richard, Smith, David Glenn, Waters, Michael R, Goebel, Ted, Johnson, John R, Malhi, Ripan S, Jakobsson, Mattias, Meltzer, David J, Manica, Andrea, Durbin, Richard, Bustamante, Carlos D, Song, Yun S, and Nielsen, Rasmus

Subjects
Biological Sciences, Genetics, History, Heritage and Archaeology, Human Society, Historical Studies, Anthropology, Minority Health, Human Genome, American Indian or Alaska Native, Americas, Gene Flow, Genomics, History, Ancient, Human Migration, Humans, Indians, North American, Models, Genetic, Siberia, General Science & Technology
Abstract

How and when the Americas were populated remains contentious. Using ancient and modern genome-wide data, we found that the ancestors of all present-day Native Americans, including Athabascans and Amerindians, entered the Americas as a single migration wave from Siberia no earlier than 23 thousand years ago (ka) and after no more than an 8000-year isolation period in Beringia. After their arrival to the Americas, ancestral Native Americans diversified into two basal genetic branches around 13 ka, one that is now dispersed across North and South America and the other restricted to North America. Subsequent gene flow resulted in some Native Americans sharing ancestry with present-day East Asians (including Siberians) and, more distantly, Australo-Melanesians. Putative "Paleoamerican" relict populations, including the historical Mexican Pericúes and South American Fuego-Patagonians, are not directly related to modern Australo-Melanesians as suggested by the Paleoamerican Model.

Published
2015

30. POPULATION GENETICS. Genomic evidence for the Pleistocene and recent population history of Native Americans.

Author

Raghavan, Maanasa, Steinrücken, Matthias, Harris, Kelley, Schiffels, Stephan, Rasmussen, Simon, DeGiorgio, Michael, Albrechtsen, Anders, Valdiosera, Cristina, Ávila-Arcos, María C, Malaspinas, Anna-Sapfo, Eriksson, Anders, Moltke, Ida, Metspalu, Mait, Homburger, Julian R, Wall, Jeff, Cornejo, Omar E, Moreno-Mayar, J Víctor, Korneliussen, Thorfinn S, Pierre, Tracey, Rasmussen, Morten, Campos, Paula F, de Barros Damgaard, Peter, Allentoft, Morten E, Lindo, John, Metspalu, Ene, Rodríguez-Varela, Ricardo, Mansilla, Josefina, Henrickson, Celeste, Seguin-Orlando, Andaine, Malmström, Helena, Stafford, Thomas, Shringarpure, Suyash S, Moreno-Estrada, Andrés, Karmin, Monika, Tambets, Kristiina, Bergström, Anders, Xue, Yali, Warmuth, Vera, Friend, Andrew D, Singarayer, Joy, Valdes, Paul, Balloux, Francois, Leboreiro, Ilán, Vera, Jose Luis, Rangel-Villalobos, Hector, Pettener, Davide, Luiselli, Donata, Davis, Loren G, Heyer, Evelyne, Zollikofer, Christoph PE, Ponce de León, Marcia S, Smith, Colin I, Grimes, Vaughan, Pike, Kelly-Anne, Deal, Michael, Fuller, Benjamin T, Arriaza, Bernardo, Standen, Vivien, Luz, Maria F, Ricaut, Francois, Guidon, Niede, Osipova, Ludmila, Voevoda, Mikhail I, Posukh, Olga L, Balanovsky, Oleg, Lavryashina, Maria, Bogunov, Yuri, Khusnutdinova, Elza, Gubina, Marina, Balanovska, Elena, Fedorova, Sardana, Litvinov, Sergey, Malyarchuk, Boris, Derenko, Miroslava, Mosher, MJ, Archer, David, Cybulski, Jerome, Petzelt, Barbara, Mitchell, Joycelynn, Worl, Rosita, Norman, Paul J, Parham, Peter, Kemp, Brian M, Kivisild, Toomas, Tyler-Smith, Chris, Sandhu, Manjinder S, Crawford, Michael, Villems, Richard, Smith, David Glenn, Waters, Michael R, Goebel, Ted, Johnson, John R, Malhi, Ripan S, Jakobsson, Mattias, Meltzer, David J, Manica, Andrea, Durbin, Richard, Bustamante, Carlos D, Song, Yun S, and Nielsen, Rasmus

Subjects
Humans, Genomics, Models, Genetic, History, Ancient, Indians, North American, Americas, Siberia, Gene Flow, Human Migration, Human Genome, Genetics, General Science & Technology
Abstract

How and when the Americas were populated remains contentious. Using ancient and modern genome-wide data, we found that the ancestors of all present-day Native Americans, including Athabascans and Amerindians, entered the Americas as a single migration wave from Siberia no earlier than 23 thousand years ago (ka) and after no more than an 8000-year isolation period in Beringia. After their arrival to the Americas, ancestral Native Americans diversified into two basal genetic branches around 13 ka, one that is now dispersed across North and South America and the other restricted to North America. Subsequent gene flow resulted in some Native Americans sharing ancestry with present-day East Asians (including Siberians) and, more distantly, Australo-Melanesians. Putative "Paleoamerican" relict populations, including the historical Mexican Pericúes and South American Fuego-Patagonians, are not directly related to modern Australo-Melanesians as suggested by the Paleoamerican Model.

Published
2015

31. The ancestry and affiliations of Kennewick Man

Author

Rasmussen, Morten, Sikora, Martin, Albrechtsen, Anders, Korneliussen, Thorfinn Sand, Moreno-Mayar, J Víctor, Poznik, G David, Zollikofer, Christoph PE, Ponce de León, Marcia S, Allentoft, Morten E, Moltke, Ida, Jónsson, Hákon, Valdiosera, Cristina, Malhi, Ripan S, Orlando, Ludovic, Bustamante, Carlos D, Stafford, Thomas W, Meltzer, David J, Nielsen, Rasmus, and Willerslev, Eske

Subjects
Biological Sciences, Anthropology, History, Heritage and Archaeology, Human Society, Clinical Research, Americas, Genome, Human, Genomics, Humans, Indians, North American, Male, Phylogeny, Skeleton, Skull, Washington, General Science & Technology
Abstract

Kennewick Man, referred to as the Ancient One by Native Americans, is a male human skeleton discovered in Washington state (USA) in 1996 and initially radiocarbon dated to 8,340-9,200 calibrated years before present (BP). His population affinities have been the subject of scientific debate and legal controversy. Based on an initial study of cranial morphology it was asserted that Kennewick Man was neither Native American nor closely related to the claimant Plateau tribes of the Pacific Northwest, who claimed ancestral relationship and requested repatriation under the Native American Graves Protection and Repatriation Act (NAGPRA). The morphological analysis was important to judicial decisions that Kennewick Man was not Native American and that therefore NAGPRA did not apply. Instead of repatriation, additional studies of the remains were permitted. Subsequent craniometric analysis affirmed Kennewick Man to be more closely related to circumpacific groups such as the Ainu and Polynesians than he is to modern Native Americans. In order to resolve Kennewick Man's ancestry and affiliations, we have sequenced his genome to ∼1× coverage and compared it to worldwide genomic data including for the Ainu and Polynesians. We find that Kennewick Man is closer to modern Native Americans than to any other population worldwide. Among the Native American groups for whom genome-wide data are available for comparison, several seem to be descended from a population closely related to that of Kennewick Man, including the Confederated Tribes of the Colville Reservation (Colville), one of the five tribes claiming Kennewick Man. We revisit the cranial analyses and find that, as opposed to genome-wide comparisons, it is not possible on that basis to affiliate Kennewick Man to specific contemporary groups. We therefore conclude based on genetic comparisons that Kennewick Man shows continuity with Native North Americans over at least the last eight millennia.

Published
2015

34. The genome of a Late Pleistocene human from a Clovis burial site in western Montana

Author

Rasmussen, Morten, Anzick, Sarah L, Waters, Michael R, Skoglund, Pontus, DeGiorgio, Michael, Stafford, Thomas W, Rasmussen, Simon, Moltke, Ida, Albrechtsen, Anders, Doyle, Shane M, Poznik, G David, Gudmundsdottir, Valborg, Yadav, Rachita, Malaspinas, Anna-Sapfo, V, Samuel Stockton White, Allentoft, Morten E, Cornejo, Omar E, Tambets, Kristiina, Eriksson, Anders, Heintzman, Peter D, Karmin, Monika, Korneliussen, Thorfinn Sand, Meltzer, David J, Pierre, Tracey L, Stenderup, Jesper, Saag, Lauri, Warmuth, Vera M, Lopes, Margarida C, Malhi, Ripan S, Brunak, Søren, Sicheritz-Ponten, Thomas, Barnes, Ian, Collins, Matthew, Orlando, Ludovic, Balloux, Francois, Manica, Andrea, Gupta, Ramneek, Metspalu, Mait, Bustamante, Carlos D, Jakobsson, Mattias, Nielsen, Rasmus, and Willerslev, Eske

Subjects
Genetics, Biotechnology, American Indian or Alaska Native, Human Genome, Archaeology, Asia, Bone and Bones, Burial, Chromosomes, Human, Y, DNA, Mitochondrial, Emigration and Immigration, Europe, Gene Flow, Genome, Human, Haplotypes, History, Ancient, Humans, Indians, North American, Infant, Male, Models, Genetic, Molecular Sequence Data, Montana, Phylogeny, Population Dynamics, Radiometric Dating, General Science & Technology
Abstract

Clovis, with its distinctive biface, blade and osseous technologies, is the oldest widespread archaeological complex defined in North America, dating from 11,100 to 10,700 (14)C years before present (bp) (13,000 to 12,600 calendar years bp). Nearly 50 years of archaeological research point to the Clovis complex as having developed south of the North American ice sheets from an ancestral technology. However, both the origins and the genetic legacy of the people who manufactured Clovis tools remain under debate. It is generally believed that these people ultimately derived from Asia and were directly related to contemporary Native Americans. An alternative, Solutrean, hypothesis posits that the Clovis predecessors emigrated from southwestern Europe during the Last Glacial Maximum. Here we report the genome sequence of a male infant (Anzick-1) recovered from the Anzick burial site in western Montana. The human bones date to 10,705 ± 35 (14)C years bp (approximately 12,707-12,556 calendar years bp) and were directly associated with Clovis tools. We sequenced the genome to an average depth of 14.4× and show that the gene flow from the Siberian Upper Palaeolithic Mal'ta population into Native American ancestors is also shared by the Anzick-1 individual and thus happened before 12,600 years bp. We also show that the Anzick-1 individual is more closely related to all indigenous American populations than to any other group. Our data are compatible with the hypothesis that Anzick-1 belonged to a population directly ancestral to many contemporary Native Americans. Finally, we find evidence of a deep divergence in Native American populations that predates the Anzick-1 individual.

Published
2014

35. The evolutionary history of dogs in the Americas

Author

Leathlobhair, Máire Ní, Perri, Angela R., Irving-Pease, Evan K., Witt, Kelsey E., Linderholm, Anna, Haile, James, Lebrasseur, Ophelie, Ameen, Carly, Blick, Jeffrey, Boyko, Adam R., Brace, Selina, Cortes, Yahaira Nunes, Crockford, Susan J., Devault, Alison, Dimopoulos, Evangelos A., Eldridge, Morley, Enk, Jacob, Gopalakrishnan, Shyam, Gori, Kevin, Grimes, Vaughan, Guiry, Eric, Hansen, Anders J., Hulme-Beaman, Ardern, Johnson, John, Kitchen, Andrew, Kasparov, Aleksei K., Kwon, Young-Mi, Nikolskiy, Pavel A., Lope, Carlos Peraza, Manin, Aurélie, Martin, Terrance, Meyer, Michael, Myers, Kelsey Noack, Omura, Mark, Rouillard, Jean-Marie, Pavlova, Elena Y., Sciulli, Paul, Sinding, Mikkel-Holger S., Strakova, Andrea, Ivanova, Varvara V., Widga, Christopher, Willerslev, Eske, Pitulko, Vladimir V., Barnes, Ian, Gilbert, M. Thomas P., Dobney, Keith M., Malhi, Ripan S., Murchison, Elizabeth P., Larson, Greger, and Frantz, Laurent A. F.

Published
2018

36. Ancient human parallel lineages within North America contributed to a coastal expansion

Author

Scheib, C. L., Li, Hongjie, Desai, Tariq, Link, Vivian, Kendall, Christopher, Dewar, Genevieve, Griffith, Peter William, Mörseburg, Alexander, Johnson, John R., Potter, Amiee, Kerr, Susan L., Endicott, Phillip, Lindo, John, Haber, Marc, Xue, Yali, Tyler-Smith, Chris, Sandhu, Manjinder S., Lorenz, Joseph G., Randall, Tori D., Faltyskova, Zuzana, Pagani, Luca, Danecek, Petr, O’Connell, Tamsin C., Martz, Patricia, Boraas, Alan S., Byrd, Brian F., Leventhal, Alan, Cambra, Rosemary, Williamson, Ronald, Lesage, Louis, Holguin, Brian, Soto, Ernestine Ygnacio-De, Rosas, JohnTommy, Metspalu, Mait, Stock, Jay T., Manica, Andrea, Scally, Aylwyn, Wegmann, Daniel, Malhi, Ripan S., and Kivisild, Toomas

Published
2018

37. Advancing the ethics of paleogenomics

Author

Summer internship for INdigenous peoples in Genomics (SING) Consortium, Bardill, Jessica, Bader, Alyssa C., Garrison, Nanibaa’ A., Bolnick, Deborah A., Raff, Jennifer A., Walker, Alexa, and Malhi, Ripan S.

Published
2018

43. Terminal Pleistocene Alaskan genome reveals first founding population of Native Americans

Author

Moreno-Mayar, J. Vctor, Potter, Ben A., Vinner, Lasse, Steinrcken, Matthias, Rasmussen, Simon, Terhorst, Jonathan, Kamm, John A., Albrechtsen, Anders, Malaspinas, Anna-Sapfo, Sikora, Martin, Reuther, Joshua D., Irish, Joel D., Malhi, Ripan S., Orlando, Ludovic, Song, Yun S., Nielsen, Rasmus, Meltzer, David J., and Willerslev, Eske

Subjects
Alaska -- Natural history, Native Americans -- Genetic aspects -- Natural history, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): J. Vctor Moreno-Mayar [1]; Ben A. Potter [2]; Lasse Vinner [1]; Matthias Steinrcken [3, 4]; Simon Rasmussen [5]; Jonathan Terhorst [6, 7]; John A. Kamm [6, 8]; Anders Albrechtsen [...]

Published
2018
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45. Combining methods for non-invasive fecal DNA enables whole genome and metagenomic analyses in wildlife biology

Author

de Flamingh, Alida, Ishida, Yasuko, Pečnerová, Patrícia, Vilchis, Sahara, Siegismund, Hans R., van Aarde, Rudi J., Malhi, Ripan S., Roca, Alfred L., de Flamingh, Alida, Ishida, Yasuko, Pečnerová, Patrícia, Vilchis, Sahara, Siegismund, Hans R., van Aarde, Rudi J., Malhi, Ripan S., and Roca, Alfred L.

Abstract

Non-invasive biological samples benefit studies that investigate rare, elusive, endangered, or dangerous species. Integrating genomic techniques that use non-invasive biological sampling with advances in computational approaches can benefit and inform wildlife conservation and management. Here, we used non-invasive fecal DNA samples to generate low- to medium-coverage genomes (e.g., >90% of the complete nuclear genome at six X-fold coverage) and metagenomic sequences, combining widely available and accessible DNA collection cards with commonly used DNA extraction and library building approaches. DNA preservation cards are easy to transport and can be stored non-refrigerated, avoiding cumbersome or costly sample methods. The genomic library construction and shotgun sequencing approach did not require enrichment or targeted DNA amplification. The utility and potential of the data generated was demonstrated through genome scale and metagenomic analyses of zoo and free-ranging African savanna elephants (Loxodonta africana). Fecal samples collected from free-ranging individuals contained an average of 12.41% (5.54–21.65%) endogenous elephant DNA. Clustering of these elephants with others from the same geographic region was demonstrated by a principal component analysis of genetic variation using nuclear genome-wide SNPs. Metagenomic analyses identified taxa that included Loxodonta, green plants, fungi, arthropods, bacteria, viruses and archaea, showcasing the utility of this approach for addressing complementary questions based on host-associated DNA, e.g., pathogen and parasite identification. The molecular and bioinformatic analyses presented here contributes towards the expansion and application of genomic techniques to conservation science and practice., Non-invasive biological samples benefit studies that investigate rare, elusive, endangered, or dangerous species. Integrating genomic techniques that use non-invasive biological sampling with advances in computational approaches can benefit and inform wildlife conservation and management. Here, we used non-invasive fecal DNA samples to generate low- to medium-coverage genomes (e.g., >90% of the complete nuclear genome at six X-fold coverage) and metagenomic sequences, combining widely available and accessible DNA collection cards with commonly used DNA extraction and library building approaches. DNA preservation cards are easy to transport and can be stored non-refrigerated, avoiding cumbersome or costly sample methods. The genomic library construction and shotgun sequencing approach did not require enrichment or targeted DNA amplification. The utility and potential of the data generated was demonstrated through genome scale and metagenomic analyses of zoo and free-ranging African savanna elephants (Loxodonta africana). Fecal samples collected from free-ranging individuals contained an average of 12.41% (5.54–21.65%) endogenous elephant DNA. Clustering of these elephants with others from the same geographic region was demonstrated by a principal component analysis of genetic variation using nuclear genome-wide SNPs. Metagenomic analyses identified taxa that included Loxodonta, green plants, fungi, arthropods, bacteria, viruses and archaea, showcasing the utility of this approach for addressing complementary questions based on host-associated DNA, e.g., pathogen and parasite identification. The molecular and bioinformatic analyses presented here contributes towards the expansion and application of genomic techniques to conservation science and practice.

Published
2023

46. Anthropological Genetics

Author

Kitchen, Andrew, Non, Amy L., Gravlee, Clarence C., Mulligan, Connie J., warinner, Christina, Lewis, Cecil M., Bankoff, Richard J., Randrianatoandro, Heritiana D. D., Perry, George H., Malhi, Ripan S., Bader, Alyssa C., and Raff, Jennifer

Published
2015

50. Community partnerships are fundamental to ethical ancient DNA research

Author

Kowal, Emma, primary, Weyrich, Laura S., additional, Argüelles, Juan Manuel, additional, Bader, Alyssa C., additional, Colwell, Chip, additional, Cortez, Amanda Daniela, additional, Davis, Jenny L., additional, Figueiro, Gonzalo, additional, Fox, Keolu, additional, Malhi, Ripan S., additional, Matisoo-Smith, Elizabeth, additional, Nayak, Ayushi, additional, Nelson, Elizabeth A., additional, Nicholas, George, additional, Nieves-Colón, Maria A., additional, Russell, Lynette, additional, Ulm, Sean, additional, Vergara-Silva, Francisco, additional, Villanea, Fernando A., additional, Wagner, Jennifer K., additional, Yracheta, Joseph M., additional, and Tsosie, Krystal S., additional

Published
2023
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