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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
...estimates for 11 of the major clades in the new Y chromosome tree. In 2002, the Y Chromosome Consortium published a single most parsimonious phylogeny of 153 binary haplogroups based on markers genotyped in a globally representative set of samples ( Y Chromosome Consortium 2002 ). A simple set of rules...
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LETTER: mtDNA phylogeny and evolution of laboratory mouse strains
- Ana Goios,
- Luísa Pereira,
- Molly Bogue,
- Vincent Macaulay,
- and António Amorim
Genome Res. March 2007 17: 293-298; Published in Advance February 6, 2007, doi:10.1101/gr.5941007
....M.C. ( 2000 ) Genealogies of mouse inbred strains . Nat. Genet. 24 : 23 – 25 . ↵ Bishop, C.E. , Boursot, P. , Baron, B. , Bonhomme, F. , Hatat, D. ( 1985 ) Most classical Mus musculus domesticus laboratory mouse strains carry a Mus musculus musculus Y chromosome . Nature 315 : 70 – 72 . ↵ Bogue, M. ( 2003...
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Research: The origins and evolution of chromosomes, dosage compensation, and mechanisms underlying venom regulation in snakes
- Drew R. Schield,
- Daren C. Card,
- Nicole R. Hales,
- Blair W. Perry,
- Giulia M. Pasquesi,
- Heath Blackmon,
- Richard H. Adams,
- Andrew B. Corbin,
- Cara F. Smith,
- Balan Ramesh,
- Jeffery P. Demuth,
- Esther Betrán,
- Marc Tollis,
- Jesse M. Meik,
- Stephen P. Mackessy,
- and Todd A. Castoe
Genome Res. April 2019 29: 590-601; Published in Advance March 21, 2019, doi:10.1101/gr.240952.118
..., Arizona 85287, USA; 5Department of Biological Sciences, Tarleton State University, Stephenville, Texas 76402, USA Corresponding author: todd.castoe@uta.eduAbstractHere we use a chromosome-level assembly of a prairie rattlesnake (Crotalus viridis), together with Hi-C, RNA-seq, and whole- resequencing data...
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Resource: An unbiased resource of novel SNP markers provides a new chronology for the human Y chromosome and reveals a deep phylogenetic structure in Africa
- Rosaria Scozzari,
- Andrea Massaia,
- Beniamino Trombetta,
- Giovanna Bellusci,
- Natalie M. Myres,
- Andrea Novelletto,
- and Fulvio Cruciani
Genome Res. March 2014 24: 535-544; Published in Advance January 6, 2014, doi:10.1101/gr.160788.113
..., Utah 84604, USA; 4Sorenson Molecular Genealogy Foundation, Salt Lake City, Utah 84115, USA Sequence diversity and the ages of the deepest nodes of the MSY phylogeny remain largely unexplored due to the severely biased collection of SNPs available for study. We characterized 68 worldwide Y chromosomes...
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Research: A recent bottleneck of Y chromosome diversity coincides with a global change in culture
- Monika Karmin,
- Lauri Saag,
- Mário Vicente,
- Melissa A. Wilson Sayres,
- Mari Järve,
- Ulvi Gerst Talas,
- Siiri Rootsi,
- Anne-Mai Ilumäe,
- Reedik Mägi,
- Mario Mitt,
- Luca Pagani,
- Tarmo Puurand,
- Zuzana Faltyskova,
- Florian Clemente,
- Alexia Cardona,
- Ene Metspalu,
- Hovhannes Sahakyan,
- Bayazit Yunusbayev,
- Georgi Hudjashov,
- Michael DeGiorgio,
- Eva-Liis Loogväli,
- Christina Eichstaedt,
- Mikk Eelmets,
- Gyaneshwer Chaubey,
- Kristiina Tambets,
- Sergei Litvinov,
- Maru Mormina,
- Yali Xue,
- Qasim Ayub,
- Grigor Zoraqi,
- Thorfinn Sand Korneliussen,
- Farida Akhatova,
- Joseph Lachance,
- Sarah Tishkoff,
- Kuvat Momynaliev,
- François-Xavier Ricaut,
- Pradiptajati Kusuma,
- Harilanto Razafindrazaka,
- Denis Pierron,
- Murray P. Cox,
- Gazi Nurun Nahar Sultana,
- Rane Willerslev,
- Craig Muller,
- Michael Westaway,
- David Lambert,
- Vedrana Skaro,
- Lejla Kovačevic´,
- Shahlo Turdikulova,
- Dilbar Dalimova,
- Rita Khusainova,
- Natalya Trofimova,
- Vita Akhmetova,
- Irina Khidiyatova,
- Daria V. Lichman,
- Jainagul Isakova,
- Elvira Pocheshkhova,
- Zhaxylyk Sabitov,
- Nikolay A. Barashkov,
- Pagbajabyn Nymadawa,
- Evelin Mihailov,
- Joseph Wee Tien Seng,
- Irina Evseeva,
- Andrea Bamberg Migliano,
- Syafiq Abdullah,
- George Andriadze,
- Dragan Primorac,
- Lubov Atramentova,
- Olga Utevska,
- Levon Yepiskoposyan,
- Damir Marjanovic´,
- Alena Kushniarevich,
- Doron M. Behar,
- Christian Gilissen,
- Lisenka Vissers,
- Joris A. Veltman,
- Elena Balanovska,
- Miroslava Derenko,
- Boris Malyarchuk,
- Andres Metspalu,
- Sardana Fedorova,
- Anders Eriksson,
- Andrea Manica,
- Fernando L. Mendez,
- Tatiana M. Karafet,
- Krishna R. Veeramah,
- Neil Bradman,
- Michael F. Hammer,
- Ludmila P. Osipova,
- Oleg Balanovsky,
- Elza K. Khusnutdinova,
- Knut Johnsen,
- Maido Remm,
- Mark G. Thomas,
- Chris Tyler-Smith,
- Peter A. Underhill,
- Eske Willerslev,
- Rasmus Nielsen,
- Mait Metspalu,
- Richard Villems,
- and Toomas Kivisild
Genome Res. April 2015 25: 459-466; Published in Advance March 13, 2015, doi:10.1101/gr.186684.114
...-recombining loci in the human. Previous studies have established a standard Y chromosome haplogroup nomenclature based on resequencing of limited tracts of the locus in small numbers of geographically diverse samples (The Y Chromosome Consortium 2002; Karafet et al. 2008; van Oven et al. 2013). As a result...
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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
...assemblies (Fig. 1A,B; Supplemental Table S1). Scaffold N50 values are 108.1 and 107.5 Mb. Haplotype 1 contains the X Chromosome, which was assembled as a chromosome-level scaffold. The Y Chromosome could not be assembled well. We identified 24 autosomes, implying that the sequenced individual has...
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Research: Genomic analyses of wild argali, domestic sheep, and their hybrids provide insights into chromosome evolution, phenotypic variation, and germplasm innovation
- Xin Li,
- San-Gang He,
- Wen-Rong Li,
- Ling-Yun Luo,
- Ze Yan,
- Dong-Xin Mo,
- Xing Wan,
- Feng-Hua Lv,
- Ji Yang,
- Ya-Xi Xu,
- Juan Deng,
- Qiang-Hui Zhu,
- Xing-Long Xie,
- Song-Song Xu,
- Chen-Xi Liu,
- Xin-Rong Peng,
- Bin Han,
- Zhong-Hui Li,
- Lei Chen,
- Jian-Lin Han,
- Xue-Zhi Ding,
- Renqing Dingkao,
- Yue-Feng Chu,
- Jin-Yan Wu,
- Li-Min Wang,
- Ping Zhou,
- Ming-Jun Liu,
- and Meng-Hua Li
Genome Res. September 2022 32: 1669-1684; Published in Advance August 10, 2022, doi:10.1101/gr.276769.122
...assembly of argali ram had a total length of 2.66 Gb across 29 chromosomes (i.e., 27 autosomes, X Chromosome, and Y Chromosome) with variable sizes of 45.10–280.78 Mb (Supplemental Fig. S2; Supplemental Table S2). For the F1-hybrid assay, we first assembled a of ∼5.21 Gb consisting of 458 contigs...
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LETTER: Fitting background-selection predictions to levels of nucleotide variation and divergence along the human autosomes
- Floyd A. Reed,
- Joshua M. Akey,
- and Charles F. Aquadro
Genome Res. September 2005 15: 1211-1221; doi:10.1101/gr.3413205
...- and Y-chromosomes and focus on the autosomes in the present report because (1) more multilocus data from a common set of DNA samples are available for the autosomes; (2) the autosomes make up the majority of the ; and (3) selection, mutation, and effective population size parameters are expected...

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