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. 2021 Sep 2;7(2):veab073. doi: 10.1093/ve/veab073

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© The Author(s) 2021. Published by Oxford University Press.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 7. — SARS-CoV-2 phylogeny with lineages colored by their transmission fitness (R_e). The annotation block provides each sampled tip’s PANGO lineage assignment and genotype for several ‘landmark’ genetic features in Spike. Fitness is predicted based on each lineage’s ancestral features using the fitted fitness mapping function with spatial, genetic and random effects. For the purposes of visualization, the full ML tree was thinned to include only 1000 randomly sampled tips and the fitness color scale was capped at a $Inline graphic$ to emphasize variation in fitness surrounding the mean rather than the full range of fitness values.

Inline graphic — SARS-CoV-2 phylogeny with lineages colored by their transmission fitness (R_e). The annotation block provides each sampled tip’s PANGO lineage assignment and genotype for several ‘landmark’ genetic features in Spike. Fitness is predicted based on each lineage’s ancestral features using the fitted fitness mapping function with spatial, genetic and random effects. For the purposes of visualization, the full ML tree was thinned to include only 1000 randomly sampled tips and the fitness color scale was capped at a $Inline graphic$ to emphasize variation in fitness surrounding the mean rather than the full range of fitness values.