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EvolSeq

Author(s): Tony Weisstein1, John R Jungck2

1. Truman State University 2. Interdisciplinary Science Learning Center at the University of Delaware

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Summary:
An Excel worksheet that simulates the molecular evolution of DNA sequences.

Licensed under these terms

Version 1.0 - published on 11 Sep 2018 doi:10.25334/Q44B01 - cite this

Keywords

  1. molecular evolution
  2. DNA

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  2. Subdiscipline
  3. Audience Level
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Contents:
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Overview

This worksheet simulates the molecular evolution of DNA sequences. The program begins with a single (random) sequence, then follows that sequence through time as it reproduces and mutates. Eventually, up to 20 evolutionary related sequences are generated. EvolSeq then calculates the genetic distances between each pair of DNA sequences, and also between the associated amino acid sequences.

Popular Text Citations

Mount D.W. 2001. Bioinformatics: Sequence and Genome Analysis, pp. 237-280. Cold Spring Harbor Laboratory Press: Cold Spring Harbor, New York.

Kimura, M. 1983. The Neutral Theory of Molecular Evolution. Cambridge University Press, Cambridge

Kimura, M. 1994. Population Genetics, Molecular Evolution, and the Neutral Theory: Selected Papers, University of Chicago Press.

Lewontin, R. 1974. The Genetic Basis of Evolutionary Change. Columbia University Press.

Research Articles

Ohta, T. 1992. "The nearly neutral theory of molecular evolution". Annual Review of Ecology and Systematics 23: 263-286.

Ohta, T. 1973. "Slightly deleterious mutant substitutions in evolution". Nature 246: 96-98.

Ohta, T. 2002. "Near-neutrality in evolution of genes and gene regulation". Proceedings of the National Academy of Sciences 99: 16134-16137

Sueoka, N. 1962. "On the genetic basis of variation and heterogeneity of DNA base composition". PNAS USA 48: 582–592

Ohta, T. and Gillespie, J.H. 1996. "Development of Neutral and Nearly Neutral Theories". Theoretical Population Biology 49: 128-142.

Kimura, M. 1991. The neutral theory of molecular evolution: a review of recent evidence. Jpn J Genet 66:367-86.

Doyle J.J. and Gaut B.S. 2000. Evolution of genes and taxa: a primer. Plant Molecular Biology 42: 1-23.

Data Sources

Smith, C.M. 2004. CMS Molecular Biology Resource

Tutorial & Background Materials

Holsinger, K. E. The Neutral Theory of Molecular Evolution (broken link - http://darwin.eeb.uconn.edu/eeb348/lecture-notes/molevol-neutral.pdf)

Bioinformatics Web 2003.

Golding B. and Morton D. 2003. Elementary Sequence Analysis, chapter 9.

Guttman D.S. 2004. Bio472H1S Computational Genomics and Bioinformatics Course Notes, Feb 4. (broken link - http://www.botany.utoronto.ca/courses/bio472/Bio472-Phylogenetics1-4spp.pdf)

Joyce D.E. 1996. Phylogeny and Reconstructing Phylogenetic Trees.

Weston P.H. and Crisp M.D. 1998. Introduction to Phylogenetic Systematics.

Citation

Researchers should cite this work as follows:

Fundamental Mathematical Concepts

Fundamental Mathematical Concepts
Neutral Theory of Molecular Evolution

Developed By

Developed by
Motoo Kimura

Primary Reference

Kimura, M. 1968. "Evolutionary rate at the molecular level". Nature 217: 624-626