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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
...02912, USA Corresponding author: emilia_huerta-sanchez@brown.eduAbstractThe exchange and subsequent incorporation of genetic material between distinct lineages, known as introgression, has emerged as a crucial concept in understanding human evolutionary history. With the advent of high...
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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
...also emerge from alternative genomic processes, such as incomplete lineage sorting, population structure, or selection (Eriksson and Manica 2012; Smith and Kronforst 2013; Zheng and Janke 2018). However, only introgression should lead to exceptionally high levels of sequence identity between the donor...
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Research: Positive selection in noncoding genomic regions of vocal learning birds is associated with genes implicated in vocal learning and speech functions in humans
- James A. Cahill,
- Joel Armstrong,
- Alden Deran,
- Carolyn J. Khoury,
- Benedict Paten,
- David Haussler,
- and Erich D. Jarvis
Genome Res. November 2021 31: 2035-2049; Published in Advance October 19, 2021, doi:10.1101/gr.275989.121
...in a lineage was positively correlated with branch length and the number of species in the clade being assessed. The branch length finding is consistent with a relatively stable rate of positive selection events within each lineage. It is broadly consistent with the finding that most human ARs are shared...
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Research: Evolutionary rewiring of the wheat transcriptional regulatory network by lineage-specific transposable elements
- Yuyun Zhang,
- Zijuan Li,
- Yu'e Zhang,
- Kande Lin,
- Yuan Peng,
- Luhuan Ye,
- Yili Zhuang,
- Meiyue Wang,
- Yilin Xie,
- Jingyu Guo,
- Wan Teng,
- Yiping Tong,
- Wenli Zhang,
- Yongbiao Xue,
- Zhaobo Lang,
- and Yijing Zhang
Genome Res. December 2021 31: 2276-2289; Published in Advance September 9, 2021, doi:10.1101/gr.275658.121
...of transcription factor binding motifsFor de novo motif discovery, the peaks were sorted by Q-value and then by fold enrichment. The 600-bp sequence centered on the top 3000 peak summits was used to detect motifs by MEME-ChIP (Machanick and Bailey 2011) of the MEME software toolkit (version 5.1.1). All peaks were...
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Method: Identifying loci under positive selection in complex population histories
- Alba Refoyo-Martínez,
- Rute R. da Fonseca,
- Katrín Halldórsdóttir,
- Einar Árnason,
- Thomas Mailund,
- and Fernando Racimo
Genome Res. September 2019 29: 1506-1520; Published in Advance July 30, 2019, doi:10.1101/gr.246777.118
...to detect positive selection along sequenced s, however, use simplified representations of past histories as models of genetic drift. Here, we present the first method that can detect signatures of strong local adaptation across the using arbitrarily complex admixture graphs, which are typically used...
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Research: Convergent origination of a Drosophila-like dosage compensation mechanism in a reptile lineage
- Ray Marin,
- Diego Cortez,
- Francesco Lamanna,
- Madapura M. Pradeepa,
- Evgeny Leushkin,
- Philippe Julien,
- Angélica Liechti,
- Jean Halbert,
- Thoomke Brüning,
- Katharina Mössinger,
- Timo Trefzer,
- Christian Conrad,
- Halie N. Kerver,
- Juli Wade,
- Patrick Tschopp,
- and Henrik Kaessmann
Genome Res. December 2017 27: 1974-1987; Published in Advance November 13, 2017, doi:10.1101/gr.223727.117
...represent an ancient XY system that originated at least ≈160 million years ago in the ancestor of Iguania lizards, shortly after the separation from the snake lineage. The age of this system approximately coincides with the ages of the avian and two mammalian sex chromosomes systems. To compensate...
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Research: Phylogenomic evidence for ancient hybridization in the genomes of living cats (Felidae)
- Gang Li,
- Brian W. Davis,
- Eduardo Eizirik,
- and William J. Murphy
Genome Res. January 2016 26: 1-11; Published in Advance October 30, 2015, doi:10.1101/gr.186668.114
...) but also contained nuclear signatures of ancient hybridization with the Geoffroy’s cat (Table 1; Fig. 3A), suggesting an extended history of admixture between the three species lineages. A Central American tigrina (Fig. 1; Supplemental Fig. S8) showed large mitochondrial and nuclear divergence (11...
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Research: Full-genome evolutionary histories of selfing, splitting, and selection in Caenorhabditis
- Cristel G. Thomas,
- Wei Wang,
- Richard Jovelin,
- Rajarshi Ghosh,
- Tatiana Lomasko,
- Quang Trinh,
- Leonid Kruglyak,
- Lincoln D. Stein,
- and Asher D. Cutter
Genome Res. May 2015 25: 667-678; Published in Advance March 17, 2015, doi:10.1101/gr.187237.114
...), the topological positions of highest-weight migration events suggest the possibility that this method detects incomplete sorting of ancestral polymorphism from ancient population subdivision (Fig. 3; Supplemental Fig. 7). These diverse -wide analyses all are consistent and extend the findings from phylogeographic...
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Research: Comparative analysis of mammalian Y chromosomes illuminates ancestral structure and lineage-specific evolution
- Gang Li,
- Brian W. Davis,
- Terje Raudsepp,
- Alison J. Pearks Wilkerson,
- Victor C. Mason,
- Malcolm Ferguson-Smith,
- Patricia C. O'Brien,
- Paul D. Waters,
- and William J. Murphy
Genome Res. September 2013 23: 1486-1495; Published in Advance June 20, 2013, doi:10.1101/gr.154286.112
...of 17 MSY genes, most being constrained by negative selection for nearly 100 million years. The X-degenerate and ampliconic gene classes are partitioned into distinct chromosomal domains in most mammals, but were radically restructured on the human lineage. We identified multiple conserved noncoding...
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Research: Phylogeny-wide analysis of social amoeba genomes highlights ancient origins for complex intercellular communication
- Andrew J. Heidel,
- Hajara M. Lawal,
- Marius Felder,
- Christina Schilde,
- Nicholas R. Helps,
- Budi Tunggal,
- Francisco Rivero,
- Uwe John,
- Michael Schleicher,
- Ludwig Eichinger,
- Matthias Platzer,
- Angelika A. Noegel,
- Pauline Schaap,
- and Gernot Glöckner
Genome Res. November 2011 21: 1882-1891; Published in Advance July 14, 2011, doi:10.1101/gr.121137.111
...-Nd)/(Sd+Nd) values). Estimates for the timing of divergence from a LCA can be derived from phylogenetic analysis of protein sequences. To avoid errors associated with specific proteins being under selection in some lineages, we randomly selected a total of 33 genes that are well conserved between fungi...
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