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Research: Worldwide patterns of genomic variation and admixture in gray wolves
- Zhenxin Fan,
- Pedro Silva,
- Ilan Gronau,
- Shuoguo Wang,
- Aitor Serres Armero,
- Rena M. Schweizer,
- Oscar Ramirez,
- John Pollinger,
- Marco Galaverni,
- Diego Ortega Del-Vecchyo,
- Lianming Du,
- Wenping Zhang,
- Zhihe Zhang,
- Jinchuan Xing,
- Carles Vilà,
- Tomas Marques-Bonet,
- Raquel Godinho,
- Bisong Yue,
- and Robert K. Wayne
Genome Res. February 2016 26: 163-173; Published in Advance December 17, 2015, doi:10.1101/gr.197517.115
...evolutionary history without clear worldwide phylogeographic structure (e.g., Wayne et al. 1992; Vilà et al. 1999). However, subsequent studies found subpopulation structure related to local environmental characteristics (e.g., Carmichael et al. 2001; Geffen et al. 2004; Pilot et al. 2006, 2010, 2014; Musiani...
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LETTER: Y Chromosome STR Haplotypes and the Genetic Structure of U.S. Populations of African, European, and Hispanic Ancestry
- Manfred Kayser,
- Silke Brauer,
- Hiltrud Schädlich,
- Mechthild Prinz,
- Mark A. Batzer,
- Peter A. Zimmerman,
- B. A. Boatin,
- and Mark Stoneking
Genome Res. April 1, 2003 13: 624-634; doi:10.1101/gr.463003
...Y Chromosome STR Haplotypes and the Genetic Structure of U.S. Populations of African, European, and Hispanic Ancestry Manfred Kayser 1 , 6 , Silke Brauer 1 , Hiltrud Schädlich 1 , Mechthild Prinz 2 , Mark A. Batzer 3 , Peter A...
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RESOURCE: A Nomenclature System for the Tree of Human Y-Chromosomal Binary Haplogroups
- The Y Chromosome Consortium
Genome Res. February 1, 2002 12: 339-348; doi:10.1101/gr.217602
...A Nomenclature System for the Tree of Human Y-Chromosomal Binary Haplogroups The Y Chromosome Consortium 1 Abstract The Y chromosome contains the largest nonrecombining block in the human genome. By virtue of its many polymorphisms, it is now the most informative haplotyping...
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ARTICLES: Dispersion of human Y chromosome haplotypes based on five microsatellites in global populations.
- R Deka,
- L Jin,
- M D Shriver,
- L M Yu,
- N Saha,
- R Barrantes,
- R Chakraborty,
- and R E Ferrell
Genome Res. December 1996 6: 1177-1184; doi:10.1101/gr.6.12.1177
...method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4 : 406 – 425 . Santos, F.R., Bianchi, N.O. and Pena. S.D.J. 1996 . Worldwide distribution of human Y-chromosome haplotypes. Genome Res. 6 : 601 – 611 . Seielstad, M.T., Hebert, J.M. Lin, A.A. Underhill, P.A. Ibrahim, M. Vollarth, D...
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Research: Inference of selective forces on house mouse genomes during secondary contact in East Asia
- Kazumichi Fujiwara,
- Shunpei Kubo,
- Toshinori Endo,
- Toyoyuki Takada,
- Toshihiko Shiroishi,
- Hitoshi Suzuki,
- and Naoki Osada
Genome Res. March 2024 34: 366-375; Published in Advance March 20, 2024, doi:10.1101/gr.278828.123
..., studies into the demographic history of M. musculus in East Asia using a -wide data set have not been performed.Although the genetic diversity of maternally inherited mitochondrial haplotypes in wild house mice has been well studied, natural variation in the paternally inherited Y Chromosome has remained...
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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
...) have observed greater Y haplotypic diversity in Africa for five biallelic polymorphisms and observe greater Asian diversity in some Y chromosome lineages ( Hammer et al. 1998 ). The availability of microsatellites has allowed the first tests of the significance of excess Y-chromosomal variation...
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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
...) Worldwide distribution of human Y-chromosome haplotypes. Genome Res. 6 : 601 – 611 . ↵ Seielstad M.T. , Hebert J.M. , Lin A.A. , Underhill P.A. , Ibrahim M. , Vollrath D. , Cavalli-Sforza L.L. ( 1994 ) Construction of human Y-chromosomal haplotypes using a new polymorphic A to G transition. Hum. Mol. Genet...
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Method: Taurine pangenome uncovers a segmental duplication upstream of KIT associated with depigmentation in white-headed cattle
- Sotiria Milia,
- Alexander S. Leonard,
- Xena Marie Mapel,
- Sandra Milena Bernal Ulloa,
- Cord Drögemüller,
- and Hubert Pausch
Genome Res. April 2025 35: 1041-1052; Published in Advance December 18, 2024, doi:10.1101/gr.279064.124
...quality even for samples with comparable sequencing coverage. However, this could mostly be explained by the sex of the haplotype (the cattle X Chromosome is roughly three times longer than the cattle Y Chromosome and has ∼350 additional conserved genes), variation in read length/quality (Liao et al. 2023...
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LETTER: The portability of tagSNPs across populations: A worldwide survey
- Anna González-Neira,
- Xiayi Ke,
- Oscar Lao,
- Francesc Calafell,
- Arcadi Navarro,
- David Comas,
- Howard Cann,
- Suzannah Bumpstead,
- Jilur Ghori,
- Sarah Hunt,
- Panos Deloukas,
- Ian Dunham,
- Lon R. Cardon,
- and Jaume Bertranpetit
Genome Res. March 2006 16: 323-330; Published in Advance February 8, 2006, doi:10.1101/gr.4138406
...cases, samples from only two or three populations are studied (usually European, Asian, and African), even though previous worldwide surveys of small genomic regions have shown that haplotype composition, LD structure, and LD decay with physical distance are heterogeneous across populations ( Pritchard...
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Resource: A harmonized public resource of deeply sequenced diverse human genomes
- Zan Koenig,
- Mary T. Yohannes,
- Lethukuthula L. Nkambule,
- Xuefang Zhao,
- Julia K. Goodrich,
- Heesu Ally Kim,
- Michael W. Wilson,
- Grace Tiao,
- Stephanie P. Hao,
- Nareh Sahakian,
- Katherine R. Chao,
- Mark A. Walker,
- Yunfei Lyu,
- gnomAD Project Consortium,
- Heidi L. Rehm,
- Benjamin M. Neale,
- Michael E. Talkowski,
- Mark J. Daly,
- Harrison Brand,
- Konrad J. Karczewski,
- Elizabeth G. Atkinson,
- and Alicia R. Martin
Genome Res. May 2024 34: 796-809; Published in Advance May 15, 2024, doi:10.1101/gr.278378.123
...clustered and resolved into complex events (see the “MakeCohortVcf” function of GATK-SV). We observed mosaicism resulting from gain or loss of X and Y Chromosomes for several samples (Supplemental Table S5), likely owing to a cell line artifact from passaging. Although mosaic loss of the Y Chromosome...

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