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Method: A formal perturbation equation between genotype and phenotype determines the Evolutionary Action of protein-coding variations on fitness
- Panagiotis Katsonis and
- Olivier Lichtarge
Genome Res. December 2014 24: 2050-2058; Published in Advance September 12, 2014, doi:10.1101/gr.176214.114
...of genotype perturbations on fitness. At the molecular level, the action estimates the deleterious impact of substitutions in proteins from viruses, bacteria, and eukaryotes. In individuals, this deleterious impact measured by the Evolutionary Action correlates with the pathogenicity and clinical course...
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Research: GC-biased gene conversion drives accelerated evolution of ultraconserved elements in mammalian and avian genomes
- Anguo Liu,
- Nini Wang,
- Guoxiang Xie,
- Yang Li,
- Xixi Yan,
- Xinmei Li,
- Zhenliang Zhu,
- Zhuohui Li,
- Jing Yang,
- Fanxin Meng,
- Mingle Dou,
- Weihuang Chen,
- Nange Ma,
- Yu Jiang,
- Yuanpeng Gao,
- and Yu Wang
Genome Res. October 2023 33: 1673-1689; Published in Advance October 26, 2023, doi:10.1101/gr.277784.123
...and chimpanzee s (Capra et al. 2013), most studies mainly focused on protein-coding genes or the general impact of gBGC in humans and a few other lineages of interest (Kostka et al. 2012; Mugal et al. 2013; Figuet et al. 2014; Rousselle et al. 2019). However, the functional consequences of identified...
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Research: Using genome-wide measures of coancestry to maintain diversity and fitness in endangered and domestic pig populations
- Mirte Bosse,
- Hendrik-Jan Megens,
- Ole Madsen,
- Richard P.M.A. Crooijmans,
- Oliver A. Ryder,
- Frédéric Austerlitz,
- Martien A.M. Groenen,
- and M. Angeles R. de Cara
Genome Res. July 2015 25: 970-981; Published in Advance June 10, 2015, doi:10.1101/gr.187039.114
.... Which variants are maintained can be essential for the success of the breeding program. Actively changing the genetic composition in a population through management may, as a side effect, reduce the frequency of advantageous variants or increase the number of deleterious alleles. Therefore, the impact...
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Research: Pedigree-based estimation of human mobile element retrotransposition rates
- Julie Feusier,
- W. Scott Watkins,
- Jainy Thomas,
- Andrew Farrell,
- David J. Witherspoon,
- Lisa Baird,
- Hongseok Ha,
- Jinchuan Xing,
- and Lynn B. Jorde
Genome Res. October 2019 29: 1567-1577; doi:10.1101/gr.247965.118
....089789.108 ↵Cordaux R, Batzer MA. 2009. The impact of retrotransposons on human evolution. Nat Rev Genet 10: 691–703. doi:10.1038/nrg2640 ↵Cordaux R, Hedges DJ, Herke SW, Batzer MA. 2006. Estimating the retrotransposition rate of human Alu elements. Gene 373: 134–137. doi:10.1016/j.gene.2006...
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Methods: Detecting heterozygosity in shotgun genome assemblies: Lessons from obligately outcrossing nematodes
- Antoine Barrière,
- Shiaw-Pyng Yang,
- Elizabeth Pekarek,
- Cristel G. Thomas,
- Eric S. Haag,
- and Ilya Ruvinsky
Genome Res. March 2009 19: 470-480; Published in Advance February 9, 2009, doi:10.1101/gr.081851.108
...and not merely by chance. Both the overall amount and chromosomal distribution of heterozygous DNA is highly variable between assemblies of close relatives produced by identical methodologies, and allele frequencies have continued to change after strains were sequenced. Our results highlight the impact of mating...
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Methods: Identification of deleterious mutations within three human genomes
- Sung Chun and
- Justin C. Fay
Genome Res. September 2009 19: 1553-1561; Published in Advance July 14, 2009, doi:10.1101/gr.092619.109
...their effects are largely masked in the heterozygous state (Simmons and Crow 1977). The presence of deleterious mutations within the human population has a significant impact on human health. Inbreeding causes an increase in child morbidity and mortality and suggests that each human carries a sufficient number...
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Research: Analysis of canine gene constraint identifies new variants for orofacial clefts and stature
- Reuben M. Buckley,
- Nüket Bilgen,
- Alexander C. Harris,
- Peter Savolainen,
- Cafer Tepeli,
- Metin Erdoğan,
- Aitor Serres Armero,
- Dayna L. Dreger,
- Frank G. van Steenbeek,
- Marjo K. Hytönen,
- Heidi G. Parker,
- Jessica Hale,
- Hannes Lohi,
- Bengi Çınar Kul,
- Adam R. Boyko,
- and Elaine A. Ostrander
Genome Res. May 2025 35: 1080-1093; Published in Advance March 24, 2025, doi:10.1101/gr.280092.124
...to no deleterious impact in a heterozygous state remains unobservable, as do variants that produce no phenotype until after a dog's reproductive years have elapsed. This is relevant to canines, where a high degree of inbreeding makes dogs especially susceptible to genetic load and recessive disease allele burden...
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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
...). Notably, previous studies have suggested that hybridization was already evident during the Chalcolithic in Iberia (Catagnano 2016). Abrupt climatic events documented for this period in the Iberian Peninsula (Bernal-Wormull et al. 2023) may have also impacted wolf population dynamics, potentially...
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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
...lines indicate uncertainty of inferred Ne based on 100 bootstrap replicates. Blue and green bars show the timing of the last glacial maximum and last interglacial, respectively. The most recent Ne estimate with reduced accuracy is displayed by a dotted line on the left.Genotyping and variant calling...
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Resource: A harmonized public resource of deeply sequenced diverse human genomes
- Zan Koenig,
- Mary T. Yohannes,
- Lethukuthula L. Nkambule,
- Xuefang Zhao,
- Julia K. Goodrich,
- Heesu Ally Kim,
- Michael W. Wilson,
- Grace Tiao,
- Stephanie P. Hao,
- Nareh Sahakian,
- Katherine R. Chao,
- Mark A. Walker,
- Yunfei Lyu,
- gnomAD Project Consortium,
- Heidi L. Rehm,
- Benjamin M. Neale,
- Michael E. Talkowski,
- Mark J. Daly,
- Harrison Brand,
- Konrad J. Karczewski,
- Elizabeth G. Atkinson,
- and Alicia R. Martin
Genome Res. May 2024 34: 796-809; Published in Advance May 15, 2024, doi:10.1101/gr.278378.123
...of minor allele frequency (MAF) for AFR in gnomAD v3.1 data using TOPMed, HGDP + 1kGP, and 1kGP reference panels in SNP array (B) and low-coverage sequencing data (C). Aggregate r2, which is the correlation between the imputed dosages and high-coverage “truth” genotype calls, was computed in MAF bins...

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