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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 4. — Increasing the number of columns allows us to quantify how much information is retained in amino acid sequences (M5) relative to codon sequences (M0). The median standard errors of A) and B) decrease for both models as codons are added. The dashed horizontal line in a) indicates the observed median standard error of for 100 codons under M0, and illustrates that M5 requires a substantially longer alignment to reach a comparable standard error. Fitting functions of the form to the median standard errors, with equaling the number of alignment columns, allows us to quantify the difference in information content. Equating with indicates equivalent information content for codons in M0 and codons in M5: hence M5 recovers a fraction of the information available to M0. Alternatively, M5 has lost 100(1 )% of the information available to M0.

Inline graphic — Increasing the number of columns allows us to quantify how much information is retained in amino acid sequences (M5) relative to codon sequences (M0). The median standard errors of A) and B) decrease for both models as codons are added. The dashed horizontal line in a) indicates the observed median standard error of for 100 codons under M0, and illustrates that M5 requires a substantially longer alignment to reach a comparable standard error. Fitting functions of the form to the median standard errors, with equaling the number of alignment columns, allows us to quantify the difference in information content. Equating with indicates equivalent information content for codons in M0 and codons in M5: hence M5 recovers a fraction of the information available to M0. Alternatively, M5 has lost 100(1 )% of the information available to M0.