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Review: Recent advances in methods to characterize archaic introgression in modern humans
- David Peede,
- Mayra M. Bañuelos,
- Jazeps Medina Tretmanis,
- Miriam Miyagi,
- and Emilia Huerta-Sánchez
Genome Res. February 2026 36: 239-256; Published in Advance January 16, 2026, doi:10.1101/gr.278993.124
...demographic history for the control, target, and source populations, ArchIE has been used to identify introgressed segments in West African s, which are believed to have been inherited from an unsampled archaic population (Durvasula and Sankararaman 2020). hmmix (Table 2; Skov et al. 2018; Macià et al. 2025...
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Research: Model-based analyses of whole-genome data reveal a complex evolutionary history involving archaic introgression in Central African Pygmies
- PingHsun Hsieh,
- August E. Woerner,
- Jeffrey D. Wall,
- Joseph Lachance,
- Sarah A. Tishkoff,
- Ryan N. Gutenkunst,
- and Michael F. Hammer
Genome Res. March 2016 26: 291-300; Published in Advance February 17, 2016, doi:10.1101/gr.196634.115
...Model-based analyses of whole-genome data reveal a complex evolutionary history involving archaic introgression in Central African Pygmies PingHsun Hsieh 1 , August E. Woerner 2 , 3 , Jeffrey D. Wall 4 , Joseph Lachance 5 , 6 , Sarah A...
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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
...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 1 , Krishna R. Veeramah 2 , 3 , Joseph Lachance 4 , 5...
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Research: Evidence for selfing in a vertebrate from whole-genome sequencing
- Astrid Böhne,
- Zeynep Oğuzhan,
- Ioannis Chrysostomakis,
- Simon Vitt,
- Denis Meuthen,
- Sebastian Martin,
- Sandra Kukowka,
- and Timo Thünken
Genome Res. December 2023 33: 2133-2142; Published in Advance December 7, 2023, doi:10.1101/gr.277368.122
...disentangled the underlying meiotic processes and provided insight into the 's trajectory under the particular type of reproduction (Booth et al. 2012; Card et al. 2021).We here set out to elucidate possible facultative selfing in the West African cichlid fish Benitochromis nigrodorsalis, which has been...
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Research: The role of transposon activity in shaping cis-regulatory element evolution after whole-genome duplication
- Øystein Monsen,
- Lars Grønvold,
- Alex Datsomor,
- Thomas Harvey,
- James Kijas,
- Alexander Suh,
- Torgeir R. Hvidsten,
- and Simen Rød Sandve
Genome Res. March 2025 35: 475-488; Published in Advance February 12, 2025, doi:10.1101/gr.278931.124
...prior to the WGD. Analysis of individual TE insertions, however, revealed enrichment of TE-CREs originating from WGD-associated TE activity, particularly for the DTT (Tc1-Mariner) DNA elements. Furthermore, coexpression analyses supported the presence of TE-driven gene regulatory network evolution...
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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
...Iberia, revealed that all wolves with the dog Δblock clustered together and closer to dogs (Fig. 2C). This clustering suggests a common origin for the Δblock through the same introgression event.Evidence that the dog block is an introgressed variant using whole- dataTo enhance the resolution provided...
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Research: An atlas of fish genome evolution reveals delayed rediploidization following the teleost whole-genome duplication
- Elise Parey,
- Alexandra Louis,
- Jérôme Montfort,
- Yann Guiguen,
- Hugues Roest Crollius,
- and Camille Berthelot
Genome Res. September 2022 32: 1685-1697; Published in Advance August 12, 2022, doi:10.1101/gr.276953.122
...atlas to investigate how the postduplication rediploidization process has shaped extant teleost s and reveals the early history of tetraploid fishes. We find evidence for prolonged recombination between entire duplicated chromosomes after the TGD, thus strongly suggesting that the ancestor of teleosts...
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Method: Haplotype and population structure inference using neural networks in whole-genome sequencing data
- Jonas Meisner and
- Anders Albrechtsen
Genome Res. August 2022 32: 1542-1552; Published in Advance July 6, 2022, doi:10.1101/gr.276813.122
..., the method performed slightly better with LD-pruned data (Supplemental Table S1, S2).1000 Genomes ProjectWe applied HaploNet to the entire 1000 Genomes Project and separately to each of its five superpopulations (African [AFR], American [AMR], East Asian [EAS], European [EUR], and South Asian [SAS]). Each...
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Research: Whole-genome resequencing of temporally stratified samples reveals substantial loss of haplotype diversity in the highly inbred Scandinavian wolf population
- Agnese Viluma,
- Øystein Flagstad,
- Mikael Åkesson,
- Camilla Wikenros,
- Håkan Sand,
- Petter Wabakken,
- and Hans Ellegren
Genome Res. March 2022 32: 449-458; Published in Advance February 8, 2022, doi:10.1101/gr.276070.121
...legacy of the African cheetah, Acinonyx jubatus. Genome Biol 16: 277. doi:10.1186/s13059-015-0837-4 ↵Dufresnes C, Miquel C, Remollino N, Biollaz F, Salamin N, Taberlet P, Fumagalli L. 2018. Howling from the past: historical phylogeography and diversity losses in European grey wolves. Proc Biol Sci 285...
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Method: Accelerated somatic mutation calling for whole-genome and whole-exome sequencing data from heterogenous tumor samples
- Shuangxi Ji,
- Tong Zhu,
- Ankit Sethia,
- and Wenyi Wang
Genome Res. April 2024 34: 633-641; Published in Advance April 8, 2024, doi:10.1101/gr.278456.123
...as a major contributing caller to reach final consensus calls by The Cancer Genome Atlas (TCGA) PanCanAtlas project (Ellrott et al. 2018), across approximately 13,000 tumor samples, and the International Cancer Genome Consortium Pan-Cancer Analysis of Whole Genomes (ICGC-PCAWG) initiative (The ICGC/TCGA Pan...
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