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Research: Positive selective sweeps of epigenetic mutations regulating specialized metabolites in plants
- Kazumasa Shirai,
- Mitsuhiko P. Sato,
- Ranko Nishi,
- Masahide Seki,
- Yutaka Suzuki,
- and Kousuke Hanada
Genome Res. June 2021 31: 1060-1068; Published in Advance May 18, 2021, doi:10.1101/gr.271726.120
...regions of genes associated with specialized metabolites show a selective sweep signature in the A. thaliana population. Thus, naturally selected mCGs appear to be key mutations that cause the expressional diversity associated with specialized metabolites during plant evolution.All living organisms use...
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Research: Inference of selective forces on house mouse genomes during secondary contact in East Asia
- Kazumichi Fujiwara,
- Shunpei Kubo,
- Toshinori Endo,
- Toyoyuki Takada,
- Toshihiko Shiroishi,
- Hitoshi Suzuki,
- and Naoki Osada
Genome Res. March 2024 34: 366-375; Published in Advance March 20, 2024, doi:10.1101/gr.278828.123
...structure model for the population history of the Japanese. Japan Rev 2: 1–33. ↵Healy TM, Burton RS. 2020. Strong selective effects of mitochondrial DNA on the nuclear . Proc Natl Acad Sci 117: 6616–6621. doi:10.1073/pnas.1910141117 ↵Hermisson J, Pennings PS, Kelley J. 2017. Soft sweeps and beyond...
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Method: Rapid SARS-CoV-2 surveillance using clinical, pooled, or wastewater sequence as a sensor for population change
- Apurva Narechania,
- Dean Bobo,
- Kevin Deitz,
- Rob DeSalle,
- Paul J. Planet,
- and Barun Mathema
Genome Res. October 2024 34: 1651-1660; Published in Advance September 25, 2024, doi:10.1101/gr.278594.123
...accumulate s, the KHILL curve of a transitioning population will asymptote to a higher value than the simpler population left in the wake of a selective sweep (Fig. 2C).Since the KHILL approach operates on containers of unaligned strings our main computational challenge is to reduce the number of string...
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Research: Comparative genomics of Cryptosporidium parvum reveals the emergence of an outbreak-associated population in Europe and its spread to the United States
- Greta Bellinzona,
- Tiago Nardi,
- Michele Castelli,
- Gherard Batisti Biffignandi,
- Karim Adjou,
- Martha Betson,
- Yannick Blanchard,
- Ioana Bujila,
- Rachel Chalmers,
- Rebecca Davidson,
- Nicoletta D'Avino,
- Tuulia Enbom,
- Jacinto Gomes,
- Gregory Karadjian,
- Christian Klotz,
- Emma Östlund,
- Judith Plutzer,
- Ruska Rimhanen-Finne,
- Guy Robinson,
- Anna Rosa Sannella,
- Jacek Sroka,
- Christen Rune Stensvold,
- Karin Troell,
- Paolo Vatta,
- Barbora Zalewska,
- Claudio Bandi,
- Davide Sassera,
- and Simone M. Cacciò
Genome Res. June 2024 34: 877-887; Published in Advance July 8, 2024, doi:10.1101/gr.278830.123
...with a recent origin and expansion of population 3, which can be explained by various factors, such as genetic drift (e.g., population bottlenecks) or selective sweeps.We tested whether the presence of highly similar s in population 3 could have biased these results. We randomly selected a single isolate from...
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Method: Optimized sample selection for cost-efficient long-read population sequencing
- T. Rhyker Ranallo-Benavidez,
- Zachary Lemmon,
- Sebastian Soyk,
- Sergey Aganezov,
- William J. Salerno,
- Rajiv C. McCoy,
- Zachary B. Lippman,
- Michael C. Schatz,
- and Fritz J. Sedlazeck
Genome Res. May 2021 31: 910-918; Published in Advance April 2, 2021, doi:10.1101/gr.264879.120
...subpopulations (SNVs). The seven African subpopulations are the most diverse, and the five East Asian subpopulations are the least diverse according to their corresponding β values. (B) Selective sweep on Chromosome 6. For each 5-Mbp window on Chromosome 6, the β Z-scores for the 26 populations are plotted...
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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 describe the history of past divergence and admixture events among any number of populations. The method—called graph-aware retrieval of selective sweeps (GRoSS)—has good power to detect loci in the with strong evidence for past selective sweeps and can also identify which branch of the graph was most...
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Research: Genome-wide patterns of natural variation reveal strong selective sweeps and ongoing genomic conflict in Drosophila mauritiana
- Viola Nolte,
- Ram Vinay Pandey,
- Robert Kofler,
- and Christian Schlötterer
Genome Res. January 2013 23: 99-110; Published in Advance October 10, 2012, doi:10.1101/gr.139873.112
...regions (&gt;500 kb) showed the signature of almost complete selective sweeps. We propose that the absence of population structure and limited geographic distribution could explain why such pronounced sweep patterns are restricted to D. mauritiana . Further evidence for strong adaptive evolution...
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Method: Network-based hierarchical population structure analysis for large genomic data sets
- Gili Greenbaum,
- Amir Rubin,
- Alan R. Templeton,
- and Noah A. Rosenberg
Genome Res. December 2019 29: 2020-2033; Published in Advance November 6, 2019, doi:10.1101/gr.250092.119
...to adaptation of A. thaliana to specific local conditions (Li et al. 2010; Fournier-Level et al. 2011; Horton et al. 2012). For example, the branch corresponding to the coastal population in northeastern Spain has been suggested to be locally adapted to high salinity (Busoms et al. 2015). Selective sweeps...
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Research: Selective sweeps and parallel mutation in the adaptive recovery from deleterious mutation in Caenorhabditis elegans
- Dee R. Denver,
- Dana K. Howe,
- Larry J. Wilhelm,
- Catherine A. Palmer,
- Jennifer L. Anderson,
- Kevin C. Stein,
- Patrick C. Phillips,
- and Suzanne Estes
Genome Res. December 2010 20: 1663-1671; Published in Advance October 29, 2010, doi:10.1101/gr.108191.110
...of the fixation of new mutations under positive selection and complete self-fertilization. (A) Deterministic sweep of a new adaptive mutation in an infinitely large self-fertilizing population under different strengths of selection. There can be a significant lag before the mutation reaches a high enough...
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Resource: Genome variation and population structure among 1142 mosquitoes of the African malaria vector species Anopheles gambiae and Anopheles coluzzii
- The Anopheles gambiae 1000 Genomes Consortium
Genome Res. October 2020 30: 1533-1546; Published in Advance September 28, 2020, doi:10.1101/gr.262790.120
...evidence for isolation between island and mainland populations, as well as between individual islands (Bergey et al. 2020). However, some selective sweeps at insecticide-resistance loci had spread through both mainland and island populations; thus, isolation is not complete, and some contemporary gene flow...
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