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Research: Widespread natural selection on metabolite levels in humans
- Yanina Timasheva,
- Kaido Lepik,
- Orsolya Liska,
- Balázs Papp,
- and Zoltán Kutalik
Genome Res. August 2024 34: 1121-1129; Published in Advance August 16, 2024, doi:10.1101/gr.278756.123
...successfully applied to high-level traits, the prevalence and mode of selection acting on molecular traits remain poorly understood. Here, we estimate the action of natural selection on genetic variants associated with metabolite levels, an important layer of molecular traits. By leveraging summary statistics...
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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
...the ongoing evolution of human phenotypes, with beneficial mutations being fixed by positive selection, and detrimental ones being eliminated through purifying selection. In medical terminology, this spectrum is categorized as “case and control” or “disease and health,” representing two ends of the phenotypic...
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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
...from the farmers is ∼68% (C.I.: 67.9%–68.2%). Model selection and validation of demographic inference We used three approaches to validate our demographic inference (Methods). First, to remove the effects of linkage, we refit ourmodels to a subset of the data in which variant sites were at least 0...
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Letter: Complex selection on 5′ splice sites in intron-rich organisms
- Manuel Irimia,
- Scott William Roy,
- Daniel E. Neafsey,
- Josep F. Abril,
- Jordi Garcia-Fernandez,
- and Eugene V. Koonin
Genome Res. November 2009 19: 2021-2027; Published in Advance September 10, 2009, doi:10.1101/gr.089276.108
...of nucleotide change at intron boundaries in three groups of closely related intron-rich species. We find evidence for qualitatively different modes of selection acting across sites: Mutations from observed consensus nucleotides to variant nucleotides are efficiently opposed by selection, but mutations from...
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Perspective: Constructing genomic maps of positive selection in humans: Where do we go from here?
- Joshua M. Akey
Genome Res. May 2009 19: 711-722; doi:10.1101/gr.086652.108
...of African populations are studied, inferences about the relative frequency of positive selection between African and non-African populations and patterns of shared selective events will remain speculative. Regulatory versus protein adaptive evolution An ongoing debate, now over three decades old and still...
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LETTER: Fitting background-selection predictions to levels of nucleotide variation and divergence along the human autosomes
- Floyd A. Reed,
- Joshua M. Akey,
- and Charles F. Aquadro
Genome Res. September 2005 15: 1211-1221; doi:10.1101/gr.3413205
...the effects of widespread diversity reducing selection (for reviews, see Andolfatto 2001 ; Aquadro et al. 2001 ). The primary selective processes hypothesized to explain the apparent reduction of variation in regions of low recombination are (2a) background selection associated with the ongoing selective...
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Research: Complete genomes of Asgard archaea reveal diverse integrated and mobile genetic elements
- Luis E. Valentin-Alvarado,
- Ling-Dong Shi,
- Kathryn E. Appler,
- Alexander Crits-Christoph,
- Valerie De Anda,
- Benjamin A. Adler,
- Michael L. Cui,
- Lynn Ly,
- Pedro Leão,
- Richard J. Roberts,
- Rohan Sachdeva,
- Brett J. Baker,
- David F. Savage,
- and Jillian F. Banfield
Genome Res. October 2024 34: 1595-1609; Published in Advance October 15, 2024, doi:10.1101/gr.279480.124
...@berkeley.eduAbstractAsgard archaea are of great interest as the progenitors of Eukaryotes, but little is known about the mobile genetic elements (MGEs) that may shape their ongoing evolution. Here, we describe MGEs that replicate in Atabeyarchaeia, a wetland Asgard archaea lineage represented by two complete s. We used soil depth...
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Research: Large-scale investigation of species-specific orphan genes in the human gut microbiome elucidates their evolutionary origins
- Nikolaos Vakirlis and
- Anne Kupczok
Genome Res. June 2024 34: 888-903; Published in Advance July 8, 2024, doi:10.1101/gr.278977.124
...intriguing, as each newly sequenced is adding novel genes to the pan. This suggests that there is an ongoing appearance of genes in pans, which has been mainly attributed to horizontal gene transfer (HGT). Bacteria are constantly under selection pressure to adapt to changing conditions or to colonize new...
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Research: Extensive sampling of Saccharomyces cerevisiae in Taiwan reveals ecology and evolution of predomesticated lineages
- Tracy Jiaye Lee,
- Yu-Ching Liu,
- Wei-An Liu,
- Yu-Fei Lin,
- Hsin-Han Lee,
- Huei-Mien Ke,
- Jen-Pan Huang,
- Mei-Yeh Jade Lu,
- Chia-Lun Hsieh,
- Kuo-Fang Chung,
- Gianni Liti,
- and Isheng Jason Tsai
Genome Res. May 2022 32: 864-877; Published in Advance March 31, 2022, doi:10.1101/gr.276286.121
...) (Supplemental Fig. S16), which supported genetic differentiation as a result of geographical isolation (Liti et al. 2006).Population genomics across lineagesPatterns of segregating sites can be used to infer the relative contributions and frequencies of reproduction modes in nature (Tsai et al. 2008). Wild S...
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Resource: An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesis
- Guanjue Xiang,
- Cheryl A. Keller,
- Elisabeth Heuston,
- Belinda M. Giardine,
- Lin An,
- Alexander Q. Wixom,
- Amber Miller,
- April Cockburn,
- Michael E.G. Sauria,
- Kathryn Weaver,
- Jens Lichtenberg,
- Berthold Göttgens,
- Qunhua Li,
- David Bodine,
- Shaun Mahony,
- James Taylor,
- Gerd A. Blobel,
- Mitchell J. Weiss,
- Yong Cheng,
- Feng Yue,
- Jim Hughes,
- Douglas R. Higgs,
- Yu Zhang,
- and Ross C. Hardison
Genome Res. March 2020 30: 472-484; Published in Advance March 4, 2020, doi:10.1101/gr.255760.119
...CREs and gene expression produced a versatile resource to improve selection of cCREs potentially regulating target genes. These resources are available from our VISION website to aid research in genomics and hematopoiesis.Individual laboratories and major consortia (e.g., The ENCODE Project Consortium 2012...
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