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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
..., such as Neanderthals and Denisovans, into the s of modern humans due to historical gene flow events is known as archaic introgression. As new methods and data sets uncover a more complex intermingling between our ancestors and archaic humans than previously thought, the relevance of archaic introgression has only...
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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
...noncoding sequence 1 (HACNS1) is another example; it is thought to serve as a human-specific enhancer that contributed to the evolution of human limb features (Prabhakar et al. 2008; Dutrow et al. 2022).Recently, researchers also found that several UCEs have changed in some mammalian lineages despite...
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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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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
...Stéphane Peyrégne, Michael James Boyle, Michael Dannemann, and Kay Prüfer Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany Natural selection that affected modern humans early in their evolution has likely shaped some of the traits...
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Perspective: Comparative genomics as a tool to understand evolution and disease
- Jessica Alföldi and
- Kerstin Lindblad-Toh
Genome Res. July 2013 23: 1063-1068; doi:10.1101/gr.157503.113
...protein Much has been learned about recent human evolution by the comparison of the modern human with those of extinct human species and the chimpanzee. Comparison of the Neanderthal to our own revealed several examples of recent fixation in the human , and showed that 91% of HARs lost their mammalian...
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Resource: Systematic detection of brain protein-coding genes under positive selection during primate evolution and their roles in cognition
- Guillaume Dumas,
- Simon Malesys,
- and Thomas Bourgeron
Genome Res. March 2021 31: 484-496; Published in Advance January 13, 2021, doi:10.1101/gr.262113.120
...multiple alignments) (Paten et al. 2008) to extract a measurement of evolution for 11,667 of the 1:1 orthologs across primates, selected from the 17,808 protein-coding genes in the modern human (available online from https://genevo.pasteur.fr/) (Fig. 1A; see also Supplemental Figs. S1, S2; Kapheim et al...
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Research: The population genomics of rhesus macaques (Macaca mulatta) based on whole-genome sequences
- Cheng Xue,
- Muthuswamy Raveendran,
- R. Alan Harris,
- Gloria L. Fawcett,
- Xiaoming Liu,
- Simon White,
- Mahmoud Dahdouli,
- David Rio Deiros,
- Jennifer E. Below,
- William Salerno,
- Laura Cox,
- Guoping Fan,
- Betsy Ferguson,
- Julie Horvath,
- Zach Johnson,
- Sree Kanthaswamy,
- H. Michael Kubisch,
- Dahai Liu,
- Michael Platt,
- David G. Smith,
- Binghua Sun,
- Eric J. Vallender,
- Feng Wang,
- Roger W. Wiseman,
- Rui Chen,
- Donna M. Muzny,
- Richard A. Gibbs,
- Fuli Yu,
- and Jeffrey Rogers
Genome Res. December 2016 26: 1651-1662; Published in Advance October 17, 2016, doi:10.1101/gr.204255.116
...Rogers1,2 1Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA; 2Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA; 3University of Texas Health Science Center, Houston, Texas 77030, USA; 4Southwest National Primate Research...
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Methods: Recovering the geographic origin of early modern humans by realistic and spatially explicit simulations
- Nicolas Ray,
- Mathias Currat,
- Pierre Berthier,
- and Laurent Excoffier
Genome Res. August 2005 15: 1161-1167; doi:10.1101/gr.3708505
...is the most likely place of origin for modern humans. Footnotes [Supplemental material is available online at www.genome.org.] Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.3708505. ↵ 1 Corresponding author. E-mail nicolas.ray@zoo.unibe.ch ; fax...
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Research: Clustered mutations in hominid genome evolution are consistent with APOBEC3G enzymatic activity
- Yishay Pinto,
- Orshay Gabay,
- Leonardo Arbiza,
- Aaron J. Sams,
- Alon Keinan,
- and Erez Y. Levanon
Genome Res. May 2016 26: 579-587; Published in Advance April 7, 2016, doi:10.1101/gr.199240.115
...-induced genome evolution, which played a role in the evolution of both modern and archaic humans. This novel mutational mechanism exhibits several unique features, such as its higher tendency to mutate transcribed regions and regulatory elements and its ability to generate clusters of concurrent point mutations...
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Research: Extension of cortical synaptic development distinguishes humans from chimpanzees and macaques
- Xiling Liu,
- Mehmet Somel,
- Lin Tang,
- Zheng Yan,
- Xi Jiang,
- Song Guo,
- Yuan Yuan,
- Liu He,
- Anna Oleksiak,
- Yan Zhang,
- Na Li,
- Yuhui Hu,
- Wei Chen,
- Zilong Qiu,
- Svante Pääbo,
- and Philipp Khaitovich
Genome Res. April 2012 22: 611-622; Published in Advance February 2, 2012, doi:10.1101/gr.127324.111
...development involves the MEF2A-mediated activity-dependent regulatory pathway. Evolutionarily, this change may have taken place after the split of the human and the Neanderthal lineages. Footnotes ↵ 9 Corresponding authors. E-mail zqiu@ion.ac.cn . E-mail paabo@eva.mpg.de . E...
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