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. 2020 Apr 30;70(1):21–32. doi: 10.1093/sysbio/syaa036

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© The Author(s) 2020. Published by Oxford University Press, on behalf of the Society of Systematic Biologists.

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 1. — The path of a sequence through amino acid space contains information about which codons may have been visited. We illustrate a W (tryptophan) L (leucine) H (histidine) trajectory that requires multiple synonymous substitutions. Amino acid states representing the trajectory are shown in dark font. Compatible corresponding (unobserved) codons are shown in lighter font. Faded out boxes represent neighboring states in the genetic code. Solid arrows indicate changes required for the trajectory with the minimum number of steps, while dashed arrows indicate substitutions associated with multiple compatible paths. Black arrows denote nonsynonymous substitutions, and lighter arrows indicate synonymous substitutions.

Inline graphic — The path of a sequence through amino acid space contains information about which codons may have been visited. We illustrate a W (tryptophan) L (leucine) H (histidine) trajectory that requires multiple synonymous substitutions. Amino acid states representing the trajectory are shown in dark font. Compatible corresponding (unobserved) codons are shown in lighter font. Faded out boxes represent neighboring states in the genetic code. Solid arrows indicate changes required for the trajectory with the minimum number of steps, while dashed arrows indicate substitutions associated with multiple compatible paths. Black arrows denote nonsynonymous substitutions, and lighter arrows indicate synonymous substitutions.