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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
...reconstruction of human Y chromosome genealogy based on several tens to even hundreds of these important polymorphisms. Despite considerable progress using molecular approaches to analyze mitochondrial and autosomal DNA to decipher evolutionary relationships ( Stoneking 1993 ; von Haeseler et al. 1996 ; Harding...
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RESOURCE: New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree
- Tatiana M. Karafet,
- Fernando L. Mendez,
- Monica B. Meilerman,
- Peter A. Underhill,
- Stephen L. Zegura,
- and Michael F. Hammer
Genome Res. May 2008 18: 830-838; Published in Advance April 2, 2008, doi:10.1101/gr.7172008
.... 2006 ; Regueiro et al. 2006 ; Sengupta et al. 2006 ; Hudjashov et al. 2007 ). Other mutations (e.g., most P mutations from 123–297) were mined from public databases in the following manner. In a recent study aimed at characterizing patterns of common DNA variation in three populations ( Hinds et al...
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LETTER: AluInsertion Polymorphisms and Human Evolution: Evidence for a Larger Population Size in Africa
- Mark Stoneking,
- Jennifer J. Fontius,
- Stephanie L. Clifford,
- Himla Soodyall,
- Santosh S. Arcot,
- Nilmani Saha,
- Trefor Jenkins,
- Mohammad A. Tahir,
- Prescott L. Deininger,
- and Mark A. Batzer
Genome Res. November 1, 1997 7: 1061-1071; doi:10.1101/gr.7.11.1061
.... ( 1995 ) Polynesian genetic affinities with Southeast Asian populations as identified by mtDNA analysis. Am. J. Hum. Genet. 57 : 403 – 414 . ↵ Mountain J.L. , Cavalli-Sforza L.L. ( 1994 ) Inference of human evolution through cladistic analysis of nuclear DNA restriction polymorphisms. Proc. Natl. Acad...
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Research: Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome
- Harsh G. Shukla,
- Mahul Chakraborty,
- and J.J. Emerson
Genome Res. September 2025 35: 2023-2040; Published in Advance July 16, 2025, doi:10.1101/gr.280728.125
...reconstructions of the histone locus and the pericentric heterochromatin of the X Chromosome, spanning the Stellate locus to the distal flank of the rDNA cluster. To infer structural changes in these regions where alignments are often not practicable, we introduce landmark anchors based on unique variants...
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Research: Extensive sampling of Saccharomyces cerevisiae in Taiwan reveals ecology and evolution of predomesticated lineages
- Tracy Jiaye Lee,
- Yu-Ching Liu,
- Wei-An Liu,
- Yu-Fei Lin,
- Hsin-Han Lee,
- Huei-Mien Ke,
- Jen-Pan Huang,
- Mei-Yeh Jade Lu,
- Chia-Lun Hsieh,
- Kuo-Fang Chung,
- Gianni Liti,
- and Isheng Jason Tsai
Genome Res. May 2022 32: 864-877; Published in Advance March 31, 2022, doi:10.1101/gr.276286.121
...analysis for the 105 Taiwanese isolates from this study using propidium iodide (PI) staining assay using previously established protocols (Supplemental Information; Todd et al. 2018).DNA extractionField-collected environmental samples can vary, so we preprocessed these samples and extracted their DNA...
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Method: Determining the impact of uncharacterized inversions in the human genome by droplet digital PCR
- Marta Puig,
- Jon Lerga-Jaso,
- Carla Giner-Delgado,
- Sarai Pacheco,
- David Izquierdo,
- Alejandra Delprat,
- Magdalena Gayà-Vidal,
- Jack F. Regan,
- George Karlin-Neumann,
- and Mario Cáceres
Genome Res. May 2020 30: 724-735; Published in Advance May 18, 2020, doi:10.1101/gr.255273.119
...there is typically no gain or loss of DNA. Here, we tested novel linkage-based droplet digital PCR (ddPCR) assays to study 20 inversions ranging from 3.1 to 742 kb flanked by inverted repeats (IRs) up to 134 kb long. Of those, we validated 13 inversions predicted by different -wide techniques. In addition, we...
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Resource: The landscape of human STR variation
- Thomas Willems,
- Melissa Gymrek,
- Gareth Highnam,
- The 1000 Genomes Project Consortium,
- David Mittelman,
- and Yaniv Erlich
Genome Res. November 2014 24: 1894-1904; Published in Advance August 18, 2014, doi:10.1101/gr.177774.114
...have utilized STRs in a wide range of methods to find signatures of selection and to elucidate mutation patterns in nearby SNPs (Tishkoff et al. 2001; Sun et al. 2012). In DNA forensics, STRs play a significant role as both the United States and the European forensicDNAdatabases rely solely...
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PERSPECTIVE: In Search of Human Variation
- Kenneth M. Weiss
Genome Res. July 1, 1998 8: 691-697; doi:10.1101/gr.8.7.691
...that ABO blood group frequencies differed among human populations. Anthropological genetics has progressed from the dull instrument of blood typing, through protein electrophoresis, to RFLPs, microsatellites, and sequences. Allan Wilson energized the field a decade ago by using mitochondrial DNA (mtDNA...
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Letter: Global diversity in the human salivary microbiome
- Ivan Nasidze,
- Jing Li,
- Dominique Quinque,
- Kun Tang,
- and Mark Stoneking
Genome Res. April 2009 19: 636-643; Published in Advance February 27, 2009, doi:10.1101/gr.084616.108
...continents, inferred from biallelic DNA polymorphisms . Genome Res. 12 : 602 – 612 . ↵ Schipper, R.G. , Silletti, E. , Vingerhoeds, M.H. ( 2007 ) Saliva as research material: Biochemical, physicochemical and practical aspects . Arch. Oral Biol. 52 : 1114 – 1135 . ↵ Slatkin, M. ( 1995 ) A measure...
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Resource: Haplotype-resolved genome and population genomics of the threatened garden dormouse in Europe
- Paige A. Byerly,
- Alina von Thaden,
- Evgeny Leushkin,
- Leon Hilgers,
- Shenglin Liu,
- Sven Winter,
- Tilman Schell,
- Charlotte Gerheim,
- Alexander Ben Hamadou,
- Carola Greve,
- Christian Betz,
- Hanno J. Bolz,
- Sven Büchner,
- Johannes Lang,
- Holger Meinig,
- Evax Marie Famira-Parcsetich,
- Sarah P. Stubbe,
- Alice Mouton,
- Sandro Bertolino,
- Goedele Verbeylen,
- Thomas Briner,
- Lídia Freixas,
- Lorenzo Vinciguerra,
- Sarah A. Mueller,
- Carsten Nowak,
- and Michael Hiller
Genome Res. November 2024 34: 2094-2107; Published in Advance November 14, 2024, doi:10.1101/gr.279066.124
...in garden dormouse conservation (Meinig and Büchner 2012; Büchner et al. 2024), as genetic data could aid in understanding patterns of connectivity and gene flow between regions and uncover past population processes that may help explain current declines. Prior karyotyping and mitochondrial DNA analyses...

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