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Research: Evolutionary conservation of Y Chromosome ampliconic gene families despite extensive structural variation
- Wesley A. Brashear,
- Terje Raudsepp,
- and William J. Murphy
Genome Res. December 2018 28: 1841-1851; Published in Advance October 31, 2018, doi:10.1101/gr.237586.118
...radiation of modern Felidae: a genetic assessment. Science 311: 73–77. doi:10.1126/science.1122277 ↵Karmin M, Saag L, Vicente M, Wilson Sayres MA, Järve M, Talas UG, Rootsi S, Ilumäe AM, Mägi R, Mitt M, et al. 2015. A recent bottleneck of Y chromosome diversity coincides with a global change in culture...
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Research: Origin and domestication of papaya Y^h chromosome
- Robert VanBuren,
- Fanchang Zeng,
- Cuixia Chen,
- Jisen Zhang,
- Ching Man Wai,
- Jennifer Han,
- Rishi Aryal,
- Andrea R. Gschwend,
- Jianping Wang,
- Jong-Kuk Na,
- Lixian Huang,
- Lingmao Zhang,
- Wenjing Miao,
- Jiqing Gou,
- Jie Arro,
- Romain Guyot,
- Richard C. Moore,
- Ming-Li Wang,
- Francis Zee,
- Deborah Charlesworth,
- Paul H. Moore,
- Qingyi Yu,
- and Ray Ming
Genome Res. April 2015 25: 524-533; Published in Advance March 11, 2015, doi:10.1101/gr.183905.114
...divergence supports the hypothesis that hermaphrodite papaya is a product of human domestication. We estimate that Y h arose only ∼4000 yr ago, well after crop plant domestication in Mesoamerica &gt;6200 yr ago but coinciding with the rise of the Maya civilization. The Y h chromosome has lower nucleotide...
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Research: Great ape Y Chromosome and mitochondrial DNA phylogenies reflect subspecies structure and patterns of mating and dispersal
- Pille Hallast,
- Pierpaolo Maisano Delser,
- Chiara Batini,
- Daniel Zadik,
- Mariano Rocchi,
- Werner Schempp,
- Chris Tyler-Smith,
- and Mark A. Jobling
Genome Res. April 2016 26: 427-439; Published in Advance February 16, 2016, doi:10.1101/gr.198754.115
...Great ape Y Chromosome and mitochondrial DNA phylogenies reflect subspecies structure and patterns of mating and dispersal Pille Hallast 1 , 2 , Pierpaolo Maisano Delser 1 , 6 , Chiara Batini 1 , Daniel Zadik 1 , Mariano Rocchi 3...
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Research: Ancient dog introgression into the Iberian wolf genome may have facilitated adaptation to human-dominated landscapes
- Diana Lobo,
- Hernán E. Morales,
- Cock Van Oosterhout,
- José Vicente López-Bao,
- Pedro Silva,
- Luis Llaneza,
- Carolina Pacheco,
- Diana Castro,
- Germán Hernández-Alonso,
- George Pacheco,
- John Archer,
- M. Thomas P. Gilbert,
- Nuno Ferrand,
- and Raquel Godinho
Genome Res. March 2025 35: 432-445; Published in Advance February 14, 2025, doi:10.1101/gr.279093.124
...samples to investigate whether hybridization with domestic dogs resulted in genetic introgression. We identified a dog-derived block on Chromosome 2 in Iberian wolves, displaying signatures consistent with introgression and high nucleotide similarity among introgressed individuals. Additionally, our...
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Method: BINDER achieves accurate identification of hierarchical TADs by comprehensively characterizing consensus TAD boundaries
- Yangyang Liu,
- Bingqiang Liu,
- and Juntao Liu
Genome Res. May 2025 35: 1194-1208; Published in Advance March 17, 2025, doi:10.1101/gr.279647.124
...structures, hierarchical TADs play important roles in epigenetic organization, transcriptional activity, gene regulation, and cell differentiation. Currently, it remains a highly challenging task to accurately identify hierarchical TADs in a computational manner. The key bottleneck for existing TAD callers...
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Review: Recent advances in methods to characterize archaic introgression in modern humans
- David Peede,
- Mayra M. Bañuelos,
- Jazeps Medina Tretmanis,
- Miriam Miyagi,
- and Emilia Huerta-Sánchez
Genome Res. February 2026 36: 239-256; Published in Advance January 16, 2026, doi:10.1101/gr.278993.124
...harbor 1%–4% Neanderthal ancestry (Green et al. 2010). Later that year, a finger bone from Siberia revealed a new archaic human group, the Denisovans, who also interbred with early modern humans (Reich et al. 2010). In contrast to the global distribution of Neanderthal ancestry, Denisovan ancestry occurs...
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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
...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 1 , Andrea Massaia 1 , Beniamino Trombetta 1 , Giovanna Bellusci 2 , Natalie M...
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Research: Independent expansion, selection, and hypervariability of the TBC1D3 gene family in humans
- Xavi Guitart,
- David Porubsky,
- DongAhn Yoo,
- Max L. Dougherty,
- Philip C. Dishuck,
- Katherine M. Munson,
- Alexandra P. Lewis,
- Kendra Hoekzema,
- Jordan Knuth,
- Stephen Chang,
- Tomi Pastinen,
- and Evan E. Eichler
Genome Res. November 2024 34: 1798-1810; Published in Advance August 6, 2024, doi:10.1101/gr.279299.124
...Chromosome 17q12 (Fig. 1A). Expression data in humans from the Genome-Tissue Expression (GTEx) project reveal TBC1D3 is modestly expressed globally, with increased expression in testis and brain tissue (The GTEx Consortium 2020). TBC1D3 expression and function were initially observed in prostate tumor...
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Method: A high-throughput screening method for selecting feature SNPs to evaluate breed diversity and infer ancestry
- Meilin Zhang,
- Heng Du,
- Yu Zhang,
- Yue Zhuo,
- Zhen Liu,
- Yahui Xue,
- Lei Zhou,
- Sixuan Zhou,
- Wanying Li,
- and Jian-Feng Liu
Genome Res. August 2025 35: 1875-1886; Published in Advance July 15, 2025, doi:10.1101/gr.280176.124
...data in population stratification analysis, ancestry prediction, and breed diversity assessments leads to overfitting issues in computational models and creates computational bottlenecks. Therefore, selecting genetic variants that express high amounts of information for use in population diversity...
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LETTER: Common inheritance of chromosome Ia associated with clonal expansion of Toxoplasma gondii
- Asis Khan,
- Ulrike Böhme,
- Krystyna A. Kelly,
- Ellen Adlem,
- Karen Brooks,
- Mark Simmonds,
- Karen Mungall,
- Michael A. Quail,
- Claire Arrowsmith,
- Tracey Chillingworth,
- Carol Churcher,
- David Harris,
- Matthew Collins,
- Nigel Fosker,
- Audrey Fraser,
- Zahra Hance,
- Kay Jagels,
- Sharon Moule,
- Lee Murphy,
- Susan O'Neil,
- Marie-Adele Rajandream,
- David Saunders,
- Kathy Seeger,
- Sally Whitehead,
- Thomas Mayr,
- Xuenan Xuan,
- Junichi Watanabe,
- Yutaka Suzuki,
- Hiroyuki Wakaguri,
- Sumio Sugano,
- Chihiro Sugimoto,
- Ian Paulsen,
- Aaron J. Mackey,
- David S. Roos,
- Neil Hall,
- Matthew Berriman,
- Bart Barrell,
- L. David Sibley,
- and James W. Ajioka
Genome Res. September 2006 16: 1119-1125; Published in Advance August 10, 2006, doi:10.1101/gr.5318106
...of alleles on chromosome Ia in the recent origin and widespread success of the clonal lineages of T. gondii. Toxoplasma gondii is a globally distributed protozoan parasite that infects ~25% of the human population and a similar proportion of birds and mammals ( Dubey and Beattie 1988 ; Hall et al. 2001...

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