mbs: modifying Hudson's ms software to generate samples of DNA sequences with a biallelic site under selection - PubMed (original) (raw)

mbs: modifying Hudson's ms software to generate samples of DNA sequences with a biallelic site under selection

Kosuke M Teshima et al. BMC Bioinformatics. 2009.

Abstract

Background: The pattern of single nucleotide polymorphisms, or SNPs, contains a tremendous amount of information with respect to the mechanisms of the micro-evolutionary process of a species. The inference of the roles of these mechanisms, including natural selection, relies heavily on computer simulations. A coalescent simulation is extremely powerful in generating a large number of samples of DNA sequences from a population (species) when all mutations are neutral, and Hudson's ms software is frequently used for this purpose.However, it has been difficult to incorporate natural selection into the coalescent framework.

Results: We herein present a software application to generate samples of DNA sequences when there is a biallelic site targeted by selection. This software application, referred to as mbs, is developed by modifying Hudson's ms. The mbs software is so flexible that it can incorporate any arbitrary histories of population size changes and any mode of selection as long as selection is operating on a biallelic site.

Conclusion: mbs provides opportunities to investigate the effect of any mode of selection on the pattern of SNPs under various demography.

PubMed Disclaimer

Figures

Figure 1

An example of the allele frequency and demographic change. Illustration of an example of the allele frequency and demographic changes (left), and their input format (right).

Similar articles

• msABC: a modification of Hudson's ms to facilitate multi-locus ABC analysis.
  Pavlidis P, Laurent S, Stephan W. Pavlidis P, et al. Mol Ecol Resour. 2010 Jul;10(4):723-7. doi: 10.1111/j.1755-0998.2010.02832.x. Epub 2010 Feb 2. Mol Ecol Resour. 2010. PMID: 21565078
• GENOMEPOP: a program to simulate genomes in populations.
  Carvajal-Rodríguez A. Carvajal-Rodríguez A. BMC Bioinformatics. 2008 Apr 30;9:223. doi: 10.1186/1471-2105-9-223. BMC Bioinformatics. 2008. PMID: 18447924 Free PMC article.
• msHOT: modifying Hudson's ms simulator to incorporate crossover and gene conversion hotspots.
  Hellenthal G, Stephens M. Hellenthal G, et al. Bioinformatics. 2007 Feb 15;23(4):520-1. doi: 10.1093/bioinformatics/btl622. Epub 2006 Dec 6. Bioinformatics. 2007. PMID: 17150995
• PopGenome: an efficient Swiss army knife for population genomic analyses in R.
  Pfeifer B, Wittelsbürger U, Ramos-Onsins SE, Lercher MJ. Pfeifer B, et al. Mol Biol Evol. 2014 Jul;31(7):1929-36. doi: 10.1093/molbev/msu136. Epub 2014 Apr 16. Mol Biol Evol. 2014. PMID: 24739305 Free PMC article.
• Coalescence 2.0: a multiple branching of recent theoretical developments and their applications.
  Tellier A, Lemaire C. Tellier A, et al. Mol Ecol. 2014 Jun;23(11):2637-52. doi: 10.1111/mec.12755. Epub 2014 May 20. Mol Ecol. 2014. PMID: 24750385 Review.

Cited by

• Scalable CNN-based classification of selective sweeps using derived allele frequencies.
  van den Belt S, Zhao H, Alachiotis N. van den Belt S, et al. Bioinformatics. 2024 Sep 1;40(Suppl 2):ii29-ii36. doi: 10.1093/bioinformatics/btae385. Bioinformatics. 2024. PMID: 39230693 Free PMC article.
• Power of neutrality tests for detecting natural selection.
  Tanaka T, Hayakawa T, Teshima KM. Tanaka T, et al. G3 (Bethesda). 2023 Sep 30;13(10):jkad161. doi: 10.1093/g3journal/jkad161. G3 (Bethesda). 2023. PMID: 37481468 Free PMC article.
• Genome-wide scans for selective sweeps using convolutional neural networks.
  Zhao H, Souilljee M, Pavlidis P, Alachiotis N. Zhao H, et al. Bioinformatics. 2023 Jun 30;39(39 Suppl 1):i194-i203. doi: 10.1093/bioinformatics/btad265. Bioinformatics. 2023. PMID: 37387128 Free PMC article.
• Efficient ancestry and mutation simulation with msprime 1.0.
  Baumdicker F, Bisschop G, Goldstein D, Gower G, Ragsdale AP, Tsambos G, Zhu S, Eldon B, Ellerman EC, Galloway JG, Gladstein AL, Gorjanc G, Guo B, Jeffery B, Kretzschumar WW, Lohse K, Matschiner M, Nelson D, Pope NS, Quinto-Cortés CD, Rodrigues MF, Saunack K, Sellinger T, Thornton K, van Kemenade H, Wohns AW, Wong Y, Gravel S, Kern AD, Koskela J, Ralph PL, Kelleher J. Baumdicker F, et al. Genetics. 2022 Mar 3;220(3):iyab229. doi: 10.1093/genetics/iyab229. Genetics. 2022. PMID: 34897427 Free PMC article.
• Studying models of balancing selection using phase-type theory.
  Zeng K, Charlesworth B, Hobolth A. Zeng K, et al. Genetics. 2021 Jun 24;218(2):iyab055. doi: 10.1093/genetics/iyab055. Genetics. 2021. PMID: 33871627 Free PMC article.

References

1. 1. Hudson RR. Gene genealogies and the coalescent process. In: Futuyma D, Antonovics J, editor. Oxford Surveys in Evolutionary Biology. Vol. 7. New York: Oxford University Press; 1990. pp. 1–44.
2. 1. Hudson RR. Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics. 2002;18:337–338. doi: 10.1093/bioinformatics/18.2.337. - DOI - PubMed
3. 1. Nielsen R, Hellmann I, Hubisz M, Bustamante C, Clark AG. Recent and ongoing selection in the human genome. Nat Rev Genet. 2007;8:857–868. doi: 10.1038/nrg2187. - DOI - PMC - PubMed
4. 1. Hudson RR, Kaplan NL. The coalescent process in models with selection and recombination. Genetics. 1988;120:831–840. - PMC - PubMed
5. 1. Bravermann JM, Hudson RR, Kaplan NL, Langley CH, Stephan W. The hitchhiking effect on the site frequency spectrum of DNA polymorphisms. Genetics. 1995;140:783–796. - PMC - PubMed

Publication types

MeSH terms

Substances

LinkOut - more resources

• Full Text Sources

  • BioMed Central
  • Europe PubMed Central
  • PubMed Central