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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
...).Researchers have historically identified adaptively introgressed regions using outlier-based approaches (Racimo et al. 2015; Edelman and Mallet 2021), conducting -wide scans for positive selection and introgression, and then intersecting outlier regions to identify candidates. However, the genomic signature...
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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
...at this locus, differing by as many as 20 copies and ∼1 Mbp in length depending on haplotypes. We also show evidence of positive selection, as well as a significant change in the predicted human TBC1D3 protein sequence. Last, we find that, despite multiple duplications, human TBC1D3 expression is limited...
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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
...valuable candidates for such screenings.Genomic markers of positive selection can be a powerful guide to elucidating the molecular pathways underlying traits relevant to human phenotypes and diseases as demonstrated by recent studies of longevity (Keane et al. 2015), immunity (Zhang et al. 2013...
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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
...al. 2018). Combining tests for multiple signatures of selection in different categories which are nearly uncorrelated in the way they are affected by variation of recombination rate and genetic drift in neutral genomic regions, for example LD based XP-EHH and derived allele frequency, allows to boost...
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Research: Genome-wide patterns of selection–drift variation strongly associate with organismal traits across the green plant lineage
- Kavitha Uthanumallian,
- Andrea Del Cortona,
- Susana M. Coelho,
- Olivier De Clerck,
- Sebastian Duchene,
- and Heroen Verbruggen
Genome Res. August 2024 34: 1130-1139; Published in Advance August 29, 2024, doi:10.1101/gr.279002.124
...Genome-wide patterns of selection–drift variation strongly associate with organismal traits across the green plant lineage Kavitha Uthanumallian1, Andrea Del Cortona2, Susana M. Coelho3, Olivier De Clerck2, Sebastian Duchene4,5 and Heroen Verbruggen1,6 1Melbourne Integrative Genomics, School of Bio...
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Mini-Review: Large-scale genomic analysis of the domestic dog informs biological discovery
- Reuben M. Buckley and
- Elaine A. Ostrander
Genome Res. June 2024 34: 811-821; Published in Advance July 2, 2024, doi:10.1101/gr.278569.123
...Reuben M. Buckley and Elaine A. Ostrander National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA Corresponding author: eostrand@mail.nih.govAbstractRecent advances in genomics, coupled with a unique population structure and remarkable levels...
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Resource: Genome-wide identification of tandem repeats associated with splicing variation across 49 tissues in humans
- Kohei Hamanaka,
- Daisuke Yamauchi,
- Eriko Koshimizu,
- Kei Watase,
- Kaoru Mogushi,
- Kinya Ishikawa,
- Hidehiro Mizusawa,
- Naomi Tsuchida,
- Yuri Uchiyama,
- Atsushi Fujita,
- Kazuharu Misawa,
- Takeshi Mizuguchi,
- Satoko Miyatake,
- and Naomichi Matsumoto
Genome Res. March 2023 33: 435-447; Published in Advance March 27, 2023, doi:10.1101/gr.277335.122
..., Chr 19: 16,065,776–16,066,086; CACNA1A, Chr 19: 13,207,811–13,208,253) were amplified from genomic DNA using primers containing recognition sites for BamHI or EcoRV restriction enzymes (New England Biolabs). The samples were selected from our genomic DNA and WGS data collection, based on repeat...
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Research: Genomic origin, fragmentomics, and transcriptional properties of long cell-free DNA molecules in human plasma
- Huiwen Che,
- Peiyong Jiang,
- L.Y. Lois Choy,
- Suk Hang Cheng,
- Wenlei Peng,
- Rebecca W.Y. Chan,
- Jing Liu,
- Qing Zhou,
- W.K. Jacky Lam,
- Stephanie C.Y. Yu,
- So Ling Lau,
- Tak Y. Leung,
- John Wong,
- Vincent Wai-Sun Wong,
- Grace L.H. Wong,
- Stephen L. Chan,
- K.C. Allen Chan,
- and Y.M. Dennis Lo
Genome Res. February 2024 34: 189-200; Published in Advance February 26, 2024, doi:10.1101/gr.278556.123
...line. P-values by Wilcoxon rank-sum test. (E) Data from SMRT sequencing. (F) Data from ONT sequencing.As the abundance of long cfDNA molecules in human plasma showed a relationship with gene expression, we explored whether such a signature could be used to distinguish patients with hepatocellular...
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Method: Detecting ancient positive selection in humans using extended lineage sorting
- Stéphane Peyrégne,
- Michael James Boyle,
- Michael Dannemann,
- and Kay Prüfer
Genome Res. September 2017 27: 1563-1572; Published in Advance July 18, 2017, doi:10.1101/gr.219493.116
...; Pybus and Shapiro 2009), current methods have limited power to detect positive selection on the human lineage that acted during this older timeframe (see Sabeti et al. 2006 for a review on detectionmethods and their timeframes): an unusually high ratio of functional changes to nonfunctional changes...
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Method: Direct detection of natural selection in Bronze Age Britain
- Iain Mathieson and
- Jonathan Terhorst
Genome Res. November/December 2022 32: 2057-2067; Published in Advance October 31, 2022, doi:10.1101/gr.276862.122
...of ancient and present-day human s from Britain and identified seven loci with -wide significant evidence of selection in the past 4500 yr. Almost all of them can be related to increased vitamin D or calcium levels, suggesting strong selective pressure on these or related phenotypes. However, the strength...

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