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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
..., instead showed strong evidence for admixture with the Northwest and Harz Mountains regions (Figs. 4, 5).Recent demographic history inferred from the site-frequency spectrumTo infer recent demographic histories and Ne for each individual population, we used coalescent simulations and compared three models...
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Method: Efficient inference of population size histories and locus-specific mutation rates from large-sample genomic variation data
- Anand Bhaskar,
- Y.X. Rachel Wang,
- and Yun S. Song
Genome Res. February 2015 25: 268-279; Published in Advance January 6, 2015, doi:10.1101/gr.178756.114
...Efficient inference of population size histories and locus-specific mutation rates from large-sample genomic variation data Anand Bhaskar 1 , 2 , Y.X. Rachel Wang 3 and Yun S. Song 1 , 2 , 3 , 4 1 Simons Institute...
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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
...Population genetic inference from genomic sequence variation John E. Pool 1 , 2 , Ines Hellmann 3 , Jeffrey D. Jensen 1 , 5 and Rasmus Nielsen 1 , 4 , 6 1 Department of Integrative Biology, University of California, Berkeley...
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RESOURCE: Fast and flexible simulation of DNA sequence data
- Gary K. Chen,
- Paul Marjoram,
- and Jeffrey D. Wall
Genome Res. January 2009 19: 136-142; Published in Advance November 24, 2008, doi:10.1101/gr.083634.108
...– 204 . ↵ Schaffner, S.F. , Foo, C. , Gabriel, S. , Reich, D. , Daly, M.J. , Altshuler, D. ( 2005 ) Calibrating a coalescent simulation of human sequence variation . Genome Res. 15 : 1576 – 1583 . ↵ Scheet, P. , Stephens, M. ( 2006 ) A fast and flexible statistical model for large-scale population...
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Research: Whole-genome sequence analyses of Western Central African Pygmy hunter-gatherers reveal a complex demographic history and identify candidate genes under positive natural selection
- PingHsun Hsieh,
- Krishna R. Veeramah,
- Joseph Lachance,
- Sarah A. Tishkoff,
- Jeffrey D. Wall,
- Michael F. Hammer,
- and Ryan N. Gutenkunst
Genome Res. March 2016 26: 279-290; Published in Advance February 17, 2016, doi:10.1101/gr.192971.115
...and polygenic selection. We found that conventional statistical outlier approaches were biased toward identifying candidates in regions of high mutation or low recombination rate. To avoid this bias, we assigned P -values for candidates using whole-genome simulations incorporating demography and variation...
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Research: Genome sequencing reveals complex speciation in the Drosophila simulans clade
- Daniel Garrigan,
- Sarah B. Kingan,
- Anthony J. Geneva,
- Peter Andolfatto,
- Andrew G. Clark,
- Kevin R. Thornton,
- and Daven C. Presgraves
Genome Res. August 2012 22: 1499-1511; Published in Advance April 13, 2012, doi:10.1101/gr.130922.111
...as sites that are variable only within the D. simulans clade. Patterns of genomic variation and phylogeny The 2.25Mbp of sites that vary within theD. simulans clade can be classified into six mutually exclusive site types. We define three types of site for which the derived nucleotide change appears...
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Methods: Evidence for large inversion polymorphisms in the human genome from HapMap data
- Vikas Bansal,
- Ali Bashir,
- and Vineet Bafna
Genome Res. February 2007 17: 219-230; Published in Advance December 21, 2006, doi:10.1101/gr.5774507
...inversions on haplotype data with “no inversions.” To incorporate the heterogeneity in recombination rates in the simulated data, we used a recently developed coalescent simulation program ( Schaffner et al. 2005 ) that can generate population data incorporating variation in recombination rates and a wide...
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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
...of human variation, although the effects may be subtle over the majority of the human genome. A significant relationship was found between background-selection predictions and measures of skew in the allele frequency distribution. The genome-wide action of selection (positive and/or negative) is required...
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Method: Genealogy-based trait association with LOCATER boosts power at loci with allelic heterogeneity
- Xinxin Wang,
- Ryan Christ,
- Erica Young,
- Chul Joo Kang,
- Indraniel Das,
- Edward A. Belter, Jr.,
- Markku Laakso,
- Louis J.M. Aslett,
- David Steinsaltz,
- Nathan O. Stitziel,
- and Ira M. Hall
Genome Res. April 16, 2026 ; Published in Advance April 16, 2026, doi:10.1101/gr.280372.124
...to the SD signal (Fig. 2B). To highlight the coalescent path of significant haplotypes, we plotted a Genealogy-based method boosts association power Genome Research 7 www..org dendrogram of haplotypes based on hierarchical clustering of the similarity matrix at the lead marker, which showed that different...
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ARTICLE: A Recent Polyploidy Superimposed on Older Large-Scale Duplications in the Arabidopsis Genome
- Guillaume Blanc,
- Karsten Hokamp,
- and Kenneth H. Wolfe
Genome Res. February 1, 2003 13: 137-144; doi:10.1101/gr.751803
...of overlap that would be expected if all of the discovered blocks had been formed by random independent duplications. Simulation of random independent duplications was done by sequentially allocating each block pair to a random genomic location, except that overlaps between sister regions were not permitted...

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