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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
...aligned to a reference assembly, informative markers such as -wide single-nucleotide polymorphisms (SNPs) generated via high-throughput genomic data can contribute to the understanding of past and contemporary population demographics (Campana et al. 2016; Gautier et al. 2016; du Plessis et al. 2023; Luo...
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Research: Comparative genomics of Cryptosporidium parvum reveals the emergence of an outbreak-associated population in Europe and its spread to the United States
- Greta Bellinzona,
- Tiago Nardi,
- Michele Castelli,
- Gherard Batisti Biffignandi,
- Karim Adjou,
- Martha Betson,
- Yannick Blanchard,
- Ioana Bujila,
- Rachel Chalmers,
- Rebecca Davidson,
- Nicoletta D'Avino,
- Tuulia Enbom,
- Jacinto Gomes,
- Gregory Karadjian,
- Christian Klotz,
- Emma Östlund,
- Judith Plutzer,
- Ruska Rimhanen-Finne,
- Guy Robinson,
- Anna Rosa Sannella,
- Jacek Sroka,
- Christen Rune Stensvold,
- Karin Troell,
- Paolo Vatta,
- Barbora Zalewska,
- Claudio Bandi,
- Davide Sassera,
- and Simone M. Cacciò
Genome Res. June 2024 34: 877-887; Published in Advance July 8, 2024, doi:10.1101/gr.278830.123
....Within-population genetic indicesTo gain further insight into the genetic differentiation of the two populations in the “Western” lineage (i.e., populations 2 and 3), we calculated linkage disequilibrium (LD) decay, Tajima's D values, and nucleotide diversity (π).We found that population 3 had a slower...
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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
....R. , Stoneking, M. ( 1993 ) The genetic structure of ancient human populations . Curr. Anthropol. 34 : 483 – 496 . ↵ Hayes, B.J. , Visscher, P.M. , McPartlan, H.C. , Goddard, M.E. ( 2003 ) Novel multilocus measure of linkage disequilibrium to estimate past effective population size . Genome Res. 13 : 635 – 643...
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Research: Human population dispersal “Out of Africa” estimated from linkage disequilibrium and allele frequencies of SNPs
- Brian P. McEvoy,
- Joseph E. Powell,
- Michael E. Goddard,
- and Peter M. Visscher
Genome Res. June 2011 21: 821-829; Published in Advance April 25, 2011, doi:10.1101/gr.119636.110
...of population genetics, 4th ed. Sinauer Associates, Sunderland, MA. Hayes BJ, Visscher PM,McPartlan HC, GoddardME. 2003. Novel multilocus measure of linkage disequilibrium to estimate past effective population size. Genome Res 13: 635–643. Hill WG. 1975. Linkage disequilibrium among multiple neutral alleles...
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Method: Network-based hierarchical population structure analysis for large genomic data sets
- Gili Greenbaum,
- Amir Rubin,
- Alan R. Templeton,
- and Noah A. Rosenberg
Genome Res. December 2019 29: 2020-2033; Published in Advance November 6, 2019, doi:10.1101/gr.250092.119
...differentiation, across hierarchical scales, in the European branch accords with past studies of this geographic region (Sharbel et al. 2000; Nordborg et al. 2005; François et al. 2008; The 1001 Genomes Consortium 2016).Structure can also be ascertained at a very fine scale by examining branches close to the tips...
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LETTER: Haplotype Information and Linkage Disequilibrium Mapping for Single Nucleotide Polymorphisms
- Xin Lu,
- Tianhua Niu,
- and Jun S. Liu
Genome Res. September 2003 13: 2112-2117; doi:10.1101/gr.586803
...-8057. Accepted July 7, 2003. Received July 3, 2002. Cold Spring Harbor Laboratory Press References ↵ Abecasis, G.R. and Cookson, W.O. 2000 . GOLD—graphical overview of linkage disequilibrium. Bioinformatics 16 : 182 –183. ↵ Akey, J.M., Zhang, K., Xiong, M., Doris, P., and Jin, L. 2001 . The effect...
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METHODS: Bayesian Analysis of Haplotypes for Linkage Disequilibrium Mapping
- Jun S. Liu,
- Chiara Sabatti,
- Jun Teng,
- Bronya J.B. Keats,
- and Neil Risch
Genome Res. October 1, 2001 11: 1716-1724; doi:10.1101/gr.194801
...to the location of the disease gene(s). The reason is that the allele frequencies of these markers in the disease population still reflect those originally carried by the founder chromosome(s), with modifications introduced by recombinations and mutations. This phenomenon, known as linkage disequilibrium (LD...
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REVIEW: Linkage Disequilibrium and the Search for Complex Disease Genes
- L.B. Jorde
Genome Res. October 1, 2000 10: 1435-1444; doi:10.1101/gr.144500
..., University of Utah Health Sciences Center, Salt Lake City, Utah 84112, USA During the past two decades, linkage analysis has been phenomenally successful in localizing Mendelian disease genes. Linkage disequilibrium (LD) analysis, which effectively incorporates the effects of many past generations...
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Review: Population genetic inference from genomic sequence variation
- John E. Pool,
- Ines Hellmann,
- Jeffrey D. Jensen,
- and Rasmus Nielsen
Genome Res. March 2010 20: 291-300; Published in Advance January 12, 2010, doi:10.1101/gr.079509.108
...; Braverman et al. 1995; Fu 1997), to an excess of high-frequency derived alleles in flanking regions (Fay and Wu 2000), to effects on linkage disequilibrium (e.g., Przeworski 2002; Kim andNielsen 2004;McVean 2007). These signals have been incorporated into methods that scan population genomic data for loci...
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Methods: Population differentiation as a test for selective sweeps
- Hua Chen,
- Nick Patterson,
- and David Reich
Genome Res. March 2010 20: 393-402; Published in Advance January 19, 2010, doi:10.1101/gr.100545.109
...). However, since this method relies on linkage disequilibrium (LD), which breaks down quickly over time, it provides weak power to detect historical sweeps that are ‘‘ancient’’ and ended up to several thousand generations ago. Selection has also been identified using methods that model the allele frequency...

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