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Method: The Mobile Element Locator Tool (MELT): population-scale mobile element discovery and biology
- Eugene J. Gardner,
- Vincent K. Lam,
- Daniel N. Harris,
- Nelson T. Chuang,
- Emma C. Scott,
- W. Stephen Pittard,
- Ryan E. Mills,
- The 1000 Genomes Project Consortium,
- and Scott E. Devine
Genome Res. November 2017 27: 1916-1929; Published in Advance August 30, 2017, doi:10.1101/gr.218032.116
...have been influenced by population bottlenecks duringmigration out of Africa (OOA) or by admixture. Overall, these data reveal complex patterns of Alu subfamily stratification in the 1000 Genomes Project populations, likely reflecting diverse patterns of demographic histories and other population...
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LETTER: Genetic Variation Among World Populations: Inferences From 100 Alu Insertion Polymorphisms
- W. Scott Watkins,
- Alan R. Rogers,
- Christopher T. Ostler,
- Steve Wooding,
- Michael J. Bamshad,
- Anna-Marie E. Brassington,
- Marion L. Carroll,
- Son V. Nguyen,
- Jerilyn A. Walker,
- B.V. Ravi Prasad,
- P. Govinda Reddy,
- Pradipta K. Das,
- Mark A. Batzer,
- and Lynn B. Jorde
Genome Res. July 2003 13: 1607-1618; Published in Advance June 12, 2003, doi:10.1101/gr.894603
..., there is little correlation between geographic and genetic distance in Eurasia. The pairwise comparisons between populations within each of the major groups of Africa, E. Asia, Europe, and India revealed lower, nonsignificant correlations. View larger version: In this window In a new window Figure 7 Geographic...
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LETTER: Patterns of Human Diversity, within and among Continents, Inferred from Biallelic DNA Polymorphisms
- Chiara Romualdi,
- David Balding,
- Ivane S. Nasidze,
- Gregory Risch,
- Myles Robichaux,
- Stephen T. Sherry,
- Mark Stoneking,
- Mark A. Batzer,
- and Guido Barbujani
Genome Res. April 1, 2002 12: 602-612; doi:10.1101/gr.214902
...of their source population for many generations. View larger version: In this window In a new window Figure 1. Relationships between the misclassification rate of the discriminant analysis ( Y axis) and the number of loci used for the discrimination ( X axis), using two different methods and the Alu21 data set...
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Methods: Recent human effective population size estimated from linkage disequilibrium
- Albert Tenesa,
- Pau Navarro,
- Ben J. Hayes,
- David L. Duffy,
- Geraldine M. Clarke,
- Mike E. Goddard,
- and Peter M. Visscher
Genome Res. April 2007 17: 520-526; Published in Advance March 9, 2007, doi:10.1101/gr.6023607
.... Nature 411 : 199 – 204 . ↵ Relethford, J.H. , Harpending, H.C. ( 1994 ) Craniometric variation, genetic theory, and modern human origins . Am. J. Phys. Anthropol. 95 : 249 – 270 . ↵ Relethford, J.H. , Jorde, L.B. ( 1999 ) Genetic evidence for larger African population size during recent human evolution...
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LETTER: Detection of Numerous Y Chromosome Biallelic Polymorphisms by Denaturing High-Performance Liquid Chromatography
- Peter A. Underhill,
- Li Jin,
- Alice A. Lin,
- S. Qasim Mehdi,
- Trefor Jenkins,
- Douglas Vollrath,
- Ronald W. Davis,
- L. Luca Cavalli-Sforza,
- and Peter J. Oefner
Genome Res. October 1, 1997 7: 996-1005; doi:10.1101/gr.7.10.996
...Genetics, School of Pathology, South African Institute for Medical Research, and University of the Witwatersrand, Johannesburg 2000, South Africa;5Department of Biochemistry, Stanford University, Stanford, California 94305 View larger version: In this window In a new window Figure 1. Representative...
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Resource: High-coverage nanopore sequencing of samples from the 1000 Genomes Project to build a comprehensive catalog of human genetic variation
- Jonas A. Gustafson,
- Sophia B. Gibson,
- Nikhita Damaraju,
- Miranda P.G. Zalusky,
- Kendra Hoekzema,
- David Twesigomwe,
- Lei Yang,
- Anthony A. Snead,
- Phillip A. Richmond,
- Wouter De Coster,
- Nathan D. Olson,
- Andrea Guarracino,
- Qiuhui Li,
- Angela L. Miller,
- Joy Goffena,
- Zachary B. Anderson,
- Sophie H.R. Storz,
- Sydney A. Ward,
- Maisha Sinha,
- Claudia Gonzaga-Jauregui,
- Wayne E. Clarke,
- Anna O. Basile,
- André Corvelo,
- Catherine Reeves,
- Adrienne Helland,
- Rajeeva Lochan Musunuri,
- Mahler Revsine,
- Karynne E. Patterson,
- Cate R. Paschal,
- Christina Zakarian,
- Sara Goodwin,
- Tanner D. Jensen,
- Esther Robb,
- The 1000 Genomes ONT Sequencing Consortium,
- University of Washington Center for Rare Disease Research (UW-CRDR),
- Genomics Research to Elucidate the Genetics of Rare Diseases (GREGoR) Consortium,
- William Richard McCombie,
- Fritz J. Sedlazeck,
- Justin M. Zook,
- Stephen B. Montgomery,
- Erik Garrison,
- Mikhail Kolmogorov,
- Michael C. Schatz,
- Richard N. McLaughlin, Jr.,
- Harriet Dashnow,
- Michael C. Zody,
- Matt Loose,
- Miten Jain,
- Evan E. Eichler,
- and Danny E. Miller
Genome Res. November 2024 34: 2061-2073; Published in Advance October 2, 2024, doi:10.1101/gr.279273.124
..., University of Washington, Seattle, Washington 98195, USA; 5Institute for Public Health Genetics, University of Washington, Seattle, Washington 98195, USA; 6Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa; 7Pacific...
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ARTICLES: Distribution and evolution of CTG repeats at the myotonin protein kinase gene in human populations.
- R Deka,
- P P Majumder,
- M D Shriver,
- D N Stivers,
- Y Zhong,
- L M Yu,
- R Barrantes,
- S J Yin,
- T Miki,
- J Hundrieser,
- C H Bunker,
- S T McGarvey,
- S Sakallah,
- R E Ferrell,
- and R Chakraborty
Genome Res. February 1996 6: 142-154; doi:10.1101/gr.6.2.142
...population has a significantly higher fre- quency of t>19 repeats, which are exclusively as- sociated with the Alu(+) allele. Interestingly, as mentioned above, in two American Indian pop- ulations, the Dogrib and Pehuenche, larger CTG repeat alleles in the >119 class are present at com- paratively higher...
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Method: Mobile element scanning (ME-Scan) identifies thousands of novel Alu insertions in diverse human populations
- David J. Witherspoon,
- Yuhua Zhang,
- Jinchuan Xing,
- W. Scott Watkins,
- Hongseok Ha,
- Mark A. Batzer,
- and Lynn B. Jorde
Genome Res. July 2013 23: 1170-1181; Published in Advance April 18, 2013, doi:10.1101/gr.148973.112
...populations from Africa, South Asia, and Europe, we are able to identify 5799 Alu insertions, including 2524 novel ones, some of which occur in exons. Sub-Saharan populations and a Pygmy group in particular carry numerous intermediate-frequency Alu insertions that are absent in non-African groups...
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LETTER: A View of Modern Human Origins from Y Chromosome Microsatellite Variation
- Mark Seielstad,
- Endashaw Bekele,
- Muntaser Ibrahim,
- Amadou Touré,
- and Mamadou Traoré
Genome Res. June 1, 1999 9: 558-567; doi:10.1101/gr.9.6.558
...populations as widely separated as Basques in the Pyrenees and Quechua in the Andes. Natural selection could remove particular variants from populations, but why would it leave Africa alone unaffected? View larger version: In this window In a new window Figure 2. Neighbor-joining tree constructed from...
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Letter: Fine-scaled human genetic structure revealed by SNP microarrays
- Jinchuan Xing,
- W. Scott Watkins,
- David J. Witherspoon,
- Yuhua Zhang,
- Stephen L. Guthery,
- Rangaswamy Thara,
- Bryan J. Mowry,
- Kazima Bulayeva,
- Robert B. Weiss,
- and Lynn B. Jorde
Genome Res. May 2009 19: 815-825; doi:10.1101/gr.085589.108
...and overall FST values are obtained when HapMap populations are excluded from the analysis (Table 2). This result is comparable to FST values calculated using Alu insertion polymorphisms in a previous study (Table 2; Watkins et al. 2003). Taken together, these results highlight the larger genetic diversity...

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