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Research: Hierarchical architecture of neo-sex chromosomes and accelerated adaptive evolution in tortricid moths
- Fangyuan Yang,
- Li-Jun Cao,
- Petr Nguyen,
- Zhong-Zheng Ma,
- Jin-Cui Chen,
- Wei Song,
- and Shu-Jun Wei
Genome Res. January 2025 35: 66-77; Published in Advance January 6, 2025, doi:10.1101/gr.279569.124
..., and the demographic history inferred by SMC++ (Supplemental Fig. S10). The neo-Z Chromosome was evaluated individually from 24 male samples. The output in crossover rate per base (c/bp) was converted to the units of centimeters per million-base (cM/Mb) by multiplying by 108. The result was then mapped to 100 kb...
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Resource: The fine-scale recombination rate variation and associations with genomic features in a butterfly
- Aleix Palahí i Torres,
- Lars Höök,
- Karin Näsvall,
- Daria Shipilina,
- Christer Wiklund,
- Roger Vila,
- Peter Pruisscher,
- and Niclas Backström
Genome Res. May 2023 33: 810-823; Published in Advance June 12, 2023, doi:10.1101/gr.277414.122
...system for studying regional recombination rate variation and its potential molecular underpinnings. Here, we developed a large whole- resequencing data set from a population of wood whites to obtain high-resolution recombination maps using linkage disequilibrium information. The analyses revealed...
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Research: Pronounced inter- and intrachromosomal variation in linkage disequilibrium across the zebra finch genome
- Jessica Stapley,
- Tim R. Birkhead,
- Terry Burke,
- and Jon Slate
Genome Res. April 2010 20: 496-502; Published in Advance March 31, 2010, doi:10.1101/gr.102095.109
...maps of three human chromosomes across four populations reflect their demographic history and a common underlying recombination pattern. Genome Res 15: 454–462. de Massy B. 2003. Distribution of meiotic recombination sites. Trends Genet 19: 514–522. Gabriel SB, Schaffner SF, NguyenH,Moore JM, Roy J...
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Resource: Assembly of a pangenome for global cattle reveals missing sequences and novel structural variations, providing new insights into their diversity and evolutionary history
- Yang Zhou,
- Lv Yang,
- Xiaotao Han,
- Jiazheng Han,
- Yan Hu,
- Fan Li,
- Han Xia,
- Lingwei Peng,
- Clarissa Boschiero,
- Benjamin D. Rosen,
- Derek M. Bickhart,
- Shujun Zhang,
- Aizhen Guo,
- Curtis P. Van Tassell,
- Timothy P.L. Smith,
- Liguo Yang,
- and George E. Liu
Genome Res. August 2022 32: 1585-1601; Published in Advance August 17, 2022, doi:10.1101/gr.276550.122
...on Chromosome X (Rosen et al. 2020). The reference has been widely used for cattle genetic studies and for -enabled selection across major breeds of cattle in both subspecies, although it does not fully capture the genetic diversity of global cattle breeds as shown by assemblies of Scottish Highland (ARS...
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Resource: Exploration of fine-scale recombination rate variation in the domestic horse
- Samantha K. Beeson,
- James R. Mickelson,
- and Molly E. McCue
Genome Res. October 2019 29: 1744-1752; Published in Advance August 21, 2019, doi:10.1101/gr.243311.118
...format and VCFtools. Bioinformatics 27: 2156–2158. doi:10.1093/bioinformatics/btr330 ↵Dapper AL, Payseur BA. 2018. Effects of demographic history on the detection of recombination hotspots from linkage disequilibrium. Mol Biol Evol 35: 335–353. doi:10.1093/molbev/msx272 ↵Doan R, Cohen N, Harrington J...
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Research: Linked selection and recombination rate variation drive the evolution of the genomic landscape of differentiation across the speciation continuum of Ficedula flycatchers
- Reto Burri,
- Alexander Nater,
- Takeshi Kawakami,
- Carina F. Mugal,
- Pall I. Olason,
- Linnea Smeds,
- Alexander Suh,
- Ludovic Dutoit,
- Stanislav Bureš,
- Laszlo Z. Garamszegi,
- Silje Hogner,
- Juan Moreno,
- Anna Qvarnström,
- Milan Ružić,
- Stein-Are Sæther,
- Glenn-Peter Sætre,
- Janos Török,
- and Hans Ellegren
Genome Res. November 2015 25: 1656-1665; Published in Advance September 9, 2015, doi:10.1101/gr.196485.115
...populations and, owing to the conservation of the recombination landscape among species, evolves recurrently in independent lineages across the speciation continuum due to effects of linked selection. This supports models according to which the genomic landscape of differentiation does not primarily reflect...
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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
...( Sinauer Associates , Sunderland, MA ). ↵ McVean, G.A.T. ( 2002 ) A genealogical interpretation of linkage disequilibrium . Genetics 162 : 987 – 991 . ↵ Myers, S. , Bottolo, L. , Freeman, C. , McVean, G. , Donnelly, P. ( 2005 ) A fine-scale map of recombination rates and hotspots across the human . Science...
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LETTER: Extended Intermarker Linkage Disequilibrium in the Afrikaners
- Diana Hall,
- Ellen M. Wijsman,
- J. Louw Roos,
- Joseph A. Gogos,
- and Maria Karayiorgou
Genome Res. June 1, 2002 12: 956-961; doi:10.1101/gr.136202
...and feasibility. Am. J. Hum. Genet. 63 : 1871 – 1885 . ↵ Eaves I.A. , Merriman T.R. , Barber R.A. , Nutland S. , Tuomilehto-Wolf E. , Tuomilehto J. , Cucca F. , Todd J.A. ( 2000 ) The genetically isolated populations of Finland and Sardinia may not be a panacea for linkage disequilibrium mapping of common disease...
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ARTICLE: Extensive Genome-wide Linkage Disequilibrium in Cattle
- Frédéric Farnir,
- Wouter Coppieters,
- Juan-José Arranz,
- Paulette Berzi,
- Nadine Cambisano,
- Bernard Grisart,
- Latifa Karim,
- Fabienne Marcq,
- Laurence Moreau,
- Myriam Mni,
- Carine Nezer,
- Patricia Simon,
- Pascal Vanmanshoven,
- Danny Wagenaar,
- and Michel Georges
Genome Res. February 1, 2000 10: 220-227; doi:10.1101/gr.10.2.220
...disequilibrium mapping of common disease genes. Nature Genet. 22 : 139 – 144 . ↵ Laan M. , Pääbo S. ( 1997 ) Demographic history and linkage disequilibrium in human populations. Nature Genet. 17 : 435 – 438 . ↵ Lewontin R.C. ( 1964 ) The interaction of selection and linkage. I. General considerations; heterotic...
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RESOURCE: A novel DNA sequence database for analyzing human demographic history
- Jeffrey D. Wall,
- Murray P. Cox,
- Fernando L. Mendez,
- August Woerner,
- Tesa Severson,
- and Michael F. Hammer
Genome Res. August 2008 18: 1354-1361; Published in Advance May 20, 2008, doi:10.1101/gr.075630.107
...( Akey et al. 2004 ; Livingston et al. 2004 ; The ENCODE Project Consortium 2004 ; Crawford et al. 2005 ; Hinds et al. 2005 ; The International HapMap Consortium 2005 ). This is problematic for inferring demographic history as sampling strategies that pool individuals from many diverse populations and...

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