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Method: A spectral component approach leveraging identity-by-descent graphs to address recent population structure in genomic analysis
- Ruhollah Shemirani,
- Gillian M. Belbin,
- Sinead Cullina,
- Christa Caggiano,
- Christopher R. Gignoux,
- Noah Zaitlen,
- and Eimear E. Kenny
Genome Res. March 2026 36: 534-546; Published in Advance December 23, 2025, doi:10.1101/gr.280659.125
.... 2013), genetic drift (Nei and Tajima 1981), selection (Berg et al. 2019; Sohail et al. 2019; Mathieson et al. 2023), and assortative mating (Border et al. 2022). These processes create systematic differences in variant frequencies within and between populations that can violate key statistical...
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Research: Genotype imputation from low-coverage data for medical and population genetic analyses
- Simone Andrea Biagini,
- Sara Becelaere,
- Mio Aerden,
- Tatjana Jatsenko,
- Laurens Hannes,
- Philip Van Damme,
- Jeroen Breckpot,
- Koenraad Devriendt,
- Bernard Thienpont,
- Joris Robert Vermeesch,
- Isabelle Cleynen,
- and Toomas Kivisild
Genome Res. September 2025 35: 1929-1941; Published in Advance July 22, 2025, doi:10.1101/gr.280175.124
...et al. 2019; Zhen et al. 2024). Similarly, a GWAS approach applied on imputed LPS data of 140,000 NIPS profiles from the Netherlands has been successful in identifying loci that affect the concentration and fragmentation properties of cell-free DNA in plasma (Linthorst et al. 2024). However, the full...
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Research: Transposon accumulation at xenobiotic gene family loci in aphids
- Tobias Baril,
- Adam Pym,
- Chris Bass,
- and Alex Hayward
Genome Res. October 2023 33: 1718-1733; Published in Advance October 18, 2023, doi:10.1101/gr.277820.123
...in the aphid M. persicae nicotianae (Puinean et al. 2010; de Little et al. 2017). More widely, there is evidence that the selective accumulation of TEs at rapidly evolving host loci under strong selection may represent a general evolutionary process. For example, studies have reported the enrichment of TEs...
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Method: Identifying chromosomal subpopulations based on their recombination histories advances the study of the genetic basis of phenotypic traits
- Carlos Ruiz-Arenas,
- Alejandro Cáceres,
- Marcos López,
- Dolors Pelegrí-Sisó,
- Josefa González,
- and Juan R. González
Genome Res. December 2020 30: 1802-1814; Published in Advance November 17, 2020, doi:10.1101/gr.258301.119
...in recombination histories within a genomic region.Recombination produces offspring chromosomes with new combinations of maternal and paternal DNA material at each side of a recombination event (Thacker and Keeney 2016). As such, recombination is a main source of novel genetic diversity. At the population level...
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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
...the TBC1D3 loci (Liao et al. 2023; Makova et al. 2024; Mao et al. 2024). The goals of this study were to reconstruct the evolutionary history of this gene family, to assess the extent of human genetic diversity, and to determine how this variation relates to changes in selection and expression of the gene...
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Research: Evolutionarily new genes in humans with disease phenotypes reveal functional enrichment patterns shaped by adaptive innovation and sexual selection
- Jian-Hai Chen,
- Patrick Landback,
- Deanna Arsala,
- Alexander Guzzetta,
- Shengqian Xia,
- Jared Atlas,
- Dylan Sosa,
- Yong E. Zhang,
- Jingqiu Cheng,
- Bairong Shen,
- and Manyuan Long
Genome Res. March 2025 35: 379-392; Published in Advance February 14, 2025, doi:10.1101/gr.279498.124
..., phenotypic enrichment, pleiotropy, and selective constraints. First, are older genes more likely to be disease genes, and if so, why? Second, does the rate of disease gene emergence (per million years) differ across macroevolutionary history? Third, do young genes show a phenotypic preference for certain...
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Method: Optimized sample selection for cost-efficient long-read population sequencing
- T. Rhyker Ranallo-Benavidez,
- Zachary Lemmon,
- Sebastian Soyk,
- Sergey Aganezov,
- William J. Salerno,
- Rajiv C. McCoy,
- Zachary B. Lippman,
- Michael C. Schatz,
- and Fritz J. Sedlazeck
Genome Res. May 2021 31: 910-918; Published in Advance April 2, 2021, doi:10.1101/gr.264879.120
...5030561 ↵Hughes AL, Yeager M. 1998. Natural selection and the evolutionary history of major histocompatibility complex loci. Front Biosci 3: d509–d516. doi:10.2741/A298 ↵Lupski JR. 2015. Structural variation mutagenesis of the human : impact on disease and evolution. Environ Mol Mutagen 56: 419–436. doi...
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Research: Purifying selection on noncoding deletions of human regulatory loci detected using their cellular pleiotropy
- David W. Radke,
- Jae Hoon Sul,
- Daniel J. Balick,
- Sebastian Akle,
- Alzheimer's Disease Neuroimaging Initiative,
- Robert C. Green,
- and Shamil R. Sunyaev
Genome Res. June 2021 31: 935-946; Published in Advance May 7, 2021, doi:10.1101/gr.275263.121
...identifying feature. The classic example is the analysis of selective constraints on protein-coding genes evident from the depletion of missense or nonsense genetic variants. These advances, however, are not directly translatable to the analysis of noncoding DNA, which has increasingly become a focus of human...
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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
...dormouse, and combine comprehensive short and long-read transcriptomics data sets with homology-based methods to generate a highly complete gene annotation. Demographic history analysis of the reveal a sharp population decline since the last interglacial, indicating an association between colder climates...
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Research: Genome-wide relaxation of selection and the evolution of the island syndrome in Orkney voles
- Xuejing Wang and
- Gerald Heckel
Genome Res. June 2024 34: 851-862; Published in Advance July 2, 2024, doi:10.1101/gr.278487.123
...the accuracy of the detection of positive selection (Grossman et al. 2010).In this study, we investigated the genomic interplay between selection and genetic drift leading to the island syndrome in a system with an exceptionally long and clear history of population isolation. Common voles (Microtus arvalis...

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