References

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Datasets

  1. Behar, Doron M., Bayazit Yunusbayev, Mait Metspalu, Ene Metspalu, Saharon Rosset, Juri Parik, Siiri Rootsi, et al. "The genome-wide structure of the Jewish people." Nature 466, no. 7303 (July 8, 2010): 238-242. Paper & Data.
  2. Botigué, Laura R., Brenna M. Henn, Simon Gravel, Brian K. Maples, Christopher R. Gignoux, Erik Corona, Gil Atzmon, et al. "Gene Flow from North Africa Contributes to Differential Human Genetic Diversity in Southern Europe." Proceedings of the National Academy of Sciences (June 3, 2013). doi:10.1073/pnas.1306223110. Paper & Data.
  3. Bryc, K., C. Velez, T. Karafet, A. Moreno-Estrada, A. Reynolds, A. Auton, M. Hammer, C. D. Bustamante, and H. Ostrer. "Colloquium Paper: Genome-wide patterns of population structure and admixture among Hispanic/Latino populations." Proceedings of the National Academy of Sciences 107, no. 2 (2010): 8954-8961. Paper & Data.
  4. Chaubey, Gyaneshwer, Mait Metspalu, Ying Choi, Reedik Mägi, Irene Gallego Romero, Pedro Soares, Mannis van Oven, et al. "Population Genetic Structure in Indian Austroasiatic Speakers: The Role of Landscape Barriers and Sex-Specific Admixture." Molecular Biology and Evolution 28, no. 2 (February 1, 2011): 1013 -1024. Paper.
  5. Consortium, The 1000 Genomes Project. "A Map of Human Genome Variation from Population-scale Sequencing." Nature 467, no. 7319 (October 27, 2010): 1061-1073. Paper & Data.
  6. Di Cristofaro J, Pennarun E, Mazières S, Myres NM, Lin AA, et al. (2013) Afghan Hindu Kush: Where Eurasian Sub-Continent Gene Flows Converge. PLoS ONE 8(10): e76748. doi:10.1371/journal.pone.0076748. Paper & Data
  7. Haber, Marc, Dominique Gauguier, Sonia Youhanna, Nick Patterson, Priya Moorjani, Laura R. Botigué, Daniel E. Platt, et al. "Genome-Wide Diversity in the Levant Reveals Recent Structuring by Culture." PLoS Genet 9, no. 2 (February 28, 2013): e1003316. doi:10.1371/journal.pgen.1003316. Paper & Data.
  8. Henn, Brenna M., Laura R. Botigué, Simon Gravel, Wei Wang, Abra Brisbin, Jake K. Byrnes, Karima Fadhlaoui-Zid, et al. "Genomic Ancestry of North Africans Supports Back-to-Africa Migrations." PLoS Genet 8, no. 1 (January 12, 2012): e1002397. Paper & Data.
  9. Henn, Brenna M., Christopher R. Gignoux, Matthew Jobin, Julie M. Granka, J. M. Macpherson, Jeffrey M. Kidd, Laura Rodri­guez-Botigué, et al. "Hunter-gatherer genomic diversity suggests a southern African origin for modern humans." Proceedings of the National Academy of Sciences 108, no. 13 (March 29, 2011): 5154 -5162. Paper & Data.
  10. Hodoğlugil, Uğur, and Robert W Mahley. "Turkish Population Structure and Genetic Ancestry Reveal Relatedness Among Eurasian Populations." Annals of Human Genetics 76, no. 2 (March 1, 2012): 128-141. Paper.
  11. Li, Jun Z., Devin M. Absher, Hua Tang, Audrey M. Southwick, Amanda M. Casto, Sohini Ramachandran, Howard M. Cann, et al. "Worldwide Human Relationships Inferred from Genome-Wide Patterns of Variation." Science 319, no. 5866 (February 22, 2008): 1100 -1104. Paper & Data.
  12. Metspalu, Mait, Irene Gallego Romero, Bayazit Yunusbayev, Gyaneshwer Chaubey, Chandana Basu Mallick, Georgi Hudjashov, Mari Nelis, et al. "Shared and Unique Components of Human Population Structure and Genome-Wide Signals of Positive Selection in South Asia." The American Journal of Human Genetics 89, no. 6 (December 9, 2011): 731-744. Paper & Data.
  13. Pagani, Luca, Toomas Kivisild, Ayele Tarekegn, Rosemary Ekong, Chris Plaster, Irene Gallego Romero, Qasim Ayub, et al. "Ethiopian Genetic Diversity Reveals Linguistic Stratification and Complex Influences on the Ethiopian Gene Pool." The American Journal of Human Genetics (n.d.). Paper & Data.
  14. Rasmussen, Morten, Yingrui Li, Stinus Lindgreen, Jakob Skou Pedersen, Anders Albrechtsen, Ida Moltke, Mait Metspalu, et al. "Ancient human genome sequence of an extinct Palaeo-Eskimo." Nature 463, no. 7282 (February 11, 2010): 757-762. Paper & Data.
  15. Reich, David, Kumarasamy Thangaraj, Nick Patterson, Alkes L. Price, and Lalji Singh. "Reconstructing Indian population history." Nature 461, no. 7263 (2009): 489-494. Paper.
  16. Schlebusch, Carina M., Pontus Skoglund, Per Sjödin, Lucie M. Gattepaille, Dena Hernandez, Flora Jay, Sen Li, et al. "Genomic Variation in Seven Khoe-San Groups Reveals Adaptation and Complex African History." Science 338, no. 6105 (October 19, 2012): 374-379. doi:10.1126/science.1227721. Paper & Data.
  17. Simonson, Tatum S, Yingzhong Yang, Chad D Huff, Haixia Yun, Ga Qin, David J Witherspoon, Zhenzhong Bai, et al. "Genetic Evidence for High-Altitude Adaptation in Tibet." Science 329, no. 5987 (July 2, 2010): 72-75. Paper & Data.
  18. Teo, Yik-Ying, Xueling Sim, Rick T H Ong, Adrian K S Tan, Jieming Chen, Erwin Tantoso, Kerrin S Small, et al. "Singapore Genome Variation Project: a haplotype map of three Southeast Asian populations." Genome Research 19, no. 11 (November 2009): 2154-2162. Paper & Data.
  19. The HUGO Pan-Asian SNP Consortium. "Mapping Human Genetic Diversity in Asia.” Science 326, no. 5959 (December 11, 2009): 1541 -1545. Paper.
  20. The International HapMap 3 Consortium. "Integrating common and rare genetic variation in diverse human populations." Nature 467, no. 7311 (2010): 52-58. Paper & Data.
  21. Xing, Jinchuan, W Scott Watkins, Adam Shlien, Erin Walker, Chad D Huff, David J Witherspoon, Yuhua Zhang, et al. "Toward a more uniform sampling of human genetic diversity: a survey of worldwide populations by high-density genotyping." Genomics 96, no. 4 (October 2010): 199-210. Paper & Data.
  22. Yunusbayev, Bayazit, Mait Metspalu, Mari Järve, Ildus Kutuev, Siiri Rootsi, Ene Metspalu, Doron M. Behar, et al. "The Caucasus as an Asymmetric Semipermeable Barrier to Ancient Human Migrations." Molecular Biology and Evolution (2011). Paper.

Analysis

  1. Alexander, David H., John Novembre, and Kenneth Lange. "Fast model-based estimation of ancestry in unrelated individuals." Genome Research 19, no. 9 (2009): 1655 -1664. http://genome.cshlp.org/content/19/9/1655.abstract.
  2. Browning, Sharon R., and Brian L. Browning. "Rapid and Accurate Haplotype Phasing and Missing-Data Inference for Whole-Genome Association Studies By Use of Localized Haplotype Clustering." The American Journal of Human Genetics 81, no. 5 (November 1, 2007): 1084-1097. http://www.cell.com/AJHG/retrieve/pii/S0002929707638828.
  3. Delaneau, Olivier, Jonathan Marchini, and Jean-Francois Zagury. "A linear complexity phasing method for thousands of genomes." Nat Meth advance online publication (December 4, 2011). http://dx.doi.org/10.1038/nmeth.1785.
  4. Lawson, Daniel John, Garrett Hellenthal, Simon Myers, and Daniel Falush. "Inference of Population Structure using Dense Haplotype Data." PLoS Genet 8, no. 1 (January 26, 2012): e1002453. http://dx.doi.org/10.1371/journal.pgen.1002453.
  5. Manichaikul, Ani, Josyf C. Mychaleckyj, Stephen S. Rich, Kathy Daly, Michèle Sale, and Wei-Min Chen. "Robust Relationship Inference in Genome-wide Association Studies." Bioinformatics 26, no. 22 (November 15, 2010): 2867 -2873. http://bioinformatics.oxfordjournals.org/content/26/22/2867.abstract.
  6. Patterson, Nick, Alkes L Price, and David Reich. "Population Structure and Eigenanalysis." PLoS Genet 2, no. 12 (December 22, 2006): e190. http://dx.plos.org/10.1371/journal.pgen.0020190.
  7. Patterson, Nick, Priya Moorjani, Yontao Luo, Swapan Mallick, Nadin Rohland, Yiping Zhan, Teri Genschoreck, Teresa Webster, and David Reich. “Ancient Admixture in Human History.” Genetics 192, no. 3 (November 1, 2012): 1065–1093. doi:10.1534/genetics.112.145037.
  8. Price, Alkes L, Nick J Patterson, Robert M Plenge, Michael E Weinblatt, Nancy A Shadick, and David Reich. "Principal components analysis corrects for stratification in genome-wide association studies." Nat Genet 38, no. 8 (2006): 904-909. http://dx.doi.org/10.1038/ng1847.
  9. Purcell, Shaun, Benjamin Neale, Kathe Todd-Brown, Lori Thomas, Manuel A. R. Ferreira, David Bender, Julian Maller, et al. "PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses." American Journal of Human Genetics 81, no. 3 (September 2007): 559-575. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1950838/

Software

  1. Admixture
  2. Eigensoft
  3. ADMIXTOOLS
  4. Plink
  5. Plink2
  6. ChromoPainter/fineSTRUCTURE
  7. BEAGLE
  8. SHAPEIT
  9. KING
  10. R
  11. MClust
  12. Google Visualization API

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