Historical Genetics

05 Feb 2023 23:53

Yet Another Inadequate Placeholder

Partly, I'm interested in the use of genetics as a tool for historical investigation, and what it can tell us about human history. (For instance, migrations, but also traces of, and information about, imperialism, slavery, diseases, conquest, religious conversion, conquest.) Partly, I'm interested in this as an application of statistical methods to inferring latent entities (here, ancestral populations and lineages). Partly, I'm interested in this for what it can tell us about historical methods --- about our ability to reliably reconstruct the past from traces left in the present. And there are some fascinating sociological issues with how ordinary people use the findings of historical genetics, especially when they're presented in personalized ways. (The parts of Nelson's book on this which I've read are very good, but I've not finished it.)

--- I find it interesting that Denisovans are recognized as an entirely new human sub-species, on par with us and Neanderthals, almost entirely on the basis of genetics, and that people then go on to estimate Denisovan ancestry in other populations. I have, of course, no reason to think that they're wrong, but it shows remarkable confidence in the procedures...

Luigi L. Cavalli-Sforza, Genes, Peoples, and Languages
Luigi L. Cavalli-Sforza, Paolo Menozzi and Alberto Piazza
- "Demic Expansions and Human Evolution", Science 259 (1993): 639--646
- The History and Geography of Human Genes

Sharon R. Browning and Brian L. Browning, "Population Structure Can Inflate SNP-Based Heritability Estimates", American Journal of Human Genetics 89 (2011): 191--193
Katarzyna Bryc, Eric Y. Durand, J. Michael Macpherson, David Reich, and Joanna L. Mountain, "The Genetic Ancestry of African Americans, Latinos, and European Americans across the United States", American Journal of Human Genetics 96 (2015): 37--53 [Though there is an important caveat here: people who pay for genetic testing are going to be biased towards those with a reason to be interested in their ancestry, including perhaps suspecting that it's not what it appears...]
C. D. Campbell, E. L. Ogburn, K. L. Lunetta, H. N. Lyon, M. L. Freedman, L. C. Groop, D. Altshuler, K. G. Ardlie and J. N. Hirschhorn, "Demonstrating stratification in a European American population", Nature Genetics 37 (2005): 868--872
John Novembre and Matthew Stephens, "Interpreting principal component analyses of spatial population genetic variation", Nature Genetics 40 (2008): 646--649
J. K. Pritchard, M. Stephens, N. A. Rosenberg and P. Donnelly, "Association mapping in structured populations", American Journal of Human Genetics 67 (2000): 170--181
J. K. Pritchard, M. Stephens and P. Donnelly, "Inference of population structure using multilocus genotype data", Genetics 155 (2000): 945--959
Robert P. Stuckert, "African Ancestry of the White American Population", The Ohio Journal of Science 58 (1958): 155--160

Gaurav Bhatia, Arti Tandon, Melinda C. Aldrich, Christine B. Ambrosone, Christopher Amos, Elisa V. Bandera, Sonja I. Berndt, Leslie Bernstein, William J. Blot, Cathryn H. Bock, Neil Caporaso, Graham Casey, Sandra L. Deming, W. Ryan Diver, Susan M. Gapstur, Elizabeth M. Gillanders, Curtis C. Harris, Brian E. Henderson, Sue A. Ingles, William Isaacs, Esther M. John, Rick A. Kittles, Emma Larkin, Lorna H. McNeill, Robert C. Millikan, Adam Murphy, Christine Neslund-Dudas, Sarah Nyante, Michael F. Press, Jorge L. Rodriguez-Gil, Benjamin A. Rybicki, Ann G. Schwartz, Lisa B. Signorello, Margaret Spitz, Sara S. Strom, Margaret A. Tucker, John K. Wiencke, John S. Witte, Xifeng Wu, Yuko Yamamura, Krista A. Zanetti, Wei Zheng, Regina G. Ziegler, Stephen J. Chanock, Christopher A. Haiman, David Reich, Alkes L. Price, "Genome-wide scan of 29,141 African Americans finds no evidence of selection since admixture", arxiv:1312.2675
Peter de Barros Damgaard et al., "137 ancient human genomes from across the Eurasian steppes", Nature 557 (2018): 369--374
Garrett Hellenthal, George B. J. Busby, Gavin Band, James F. Wilson, Cristian Capelli, Daniel Falush, Simon Myers, "A Genetic Atlas of Human Admixture History", Science 343 (2014): 747--751
Choongwon Jeong et al., "The genetic history of admixture across inner Eurasia", Nature Ecology and Evolution 3 (2019): 966--976
Carles Lalueza-Fox, Inequality: A Genetic History
Iosif Lazaridis et al., "Genetic origins of the Minoans and Mycenaeans", Nature 548 (2017): 214--218
Mellars, Paul and Gori, Kevin C. and Carr, Martin and Soares, Pedro A. and Richards, Martin B., "Genetic and archaeological perspectives on the initial modern human colonization of southern Asia", Proceedings of the National Academy of Sciences (USA) 110 (2013): 10699--10704
Andres Moreno-Estrada, Simon Gravel, Fouad Zakharia, Jacob L. McCauley, Jake K. Byrnes, Christopher R. Gignoux, Patricia A. Ortiz-Tello, Ricardo J. Martinez, Dale J. Hedges, Richard W. Morris, Celeste Eng, Karla Sandoval, Suehelay Acevedo-Acevedo, Juan Carlos Martinez-Cruzado, Paul J. Norman, Zulay Layrisse, Peter Parham, Esteban Gonzalez Burchard, Michael L. Cuccaro, Eden R. Martin, Carlos D. Bustamante, "Reconstructing the Population Genetic History of the Caribbean", arxiv:1306.0558
Alondra Nelson, The Social Life of DNA: Race, Reparations, and Reconciliation After the Genome
Brendan D. O'Fallon and Lars Fehren-Schmitz, "Native Americans experienced a strong population bottleneck coincident with European contact", Proceedings of the National Academy of Sciences (USA) 108 (2011): 20444--20448
Aaron Panofsky, Joan Donovan, "Genetic ancestry testing among white nationalists: From identity repair to citizen science", Social Studies of Science (2019)
Pontus Skoglund, Helena Malmström, Maanasa Raghavan, Jan Stora, Per Hall, Eske Willerslev, M. Thomas P. Gilbert, Anders Götherström, and Mattias Jakobsson, "Origins and Genetic Legacy of Neolithic Farmers and Hunter-Gatherers in Europe", Science 336 (2012): 466--469
Linda Stone and Paul F. Lurquin, A Genetic and Cultural Odyssey: The Life and Work of L. Luca Cavalli-Sforza
Adam P. Van Arsdale, "Population Demography, Ancestry, and the Biological Concept of Race", Annual Review of Anthropology 48 (2019): 227--241
Wen-Yun Yang, John Novembre, Eleazar Eskin and Eran Halperin, "A model-based approach for analysis of spatial structure in genetic data", Nature Genetics 44 (2012): 725--731