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. 2021 Jun 16;13(8):evab142. doi: 10.1093/gbe/evab142

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© The Author(s) 2021. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

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. For commercial re-use, please contact journals.permissions@oup.com

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Fig. 3 — Gene function explains more variation in mobile gene sequence evolution than human host attributes. (a) Adjusted R² values for the categorical regressions between population genetic metrics (color-coded) and human host attributes. We only considered genes with at least 10X coverage in a sample, and we also required that mobile gene should have less than 30% missing values across samples, for a total of 1,333 genes included in this analysis. The five strongest and most prevalent correlations between population genetics metrics and human host factors are shown (FDR-adjusted P < 0.05). Not shown are village significantly correlated with Tajima’s D (0.75%) and dN/dS (0%), and household significantly correlated with $θ_{w}$ (0.38%). Human host age and sex did not show any significant effects on mobile gene sequence evolution. Each black point represents a mobile gene for which the categorical regression is significant. The percentage of significant genes out of the total number of genes tested is indicated in parentheses along the x-axis. For dN/dS, the sample size was reduced to n = 255 genes because an additional filter requiring mutations to be seen in the least five metagenomic reads was applied before computing dN/dS, which can other be sensitive to sequencing errors (Materials and Methods). (b) Adjusted R² values of the categorical regressions between a population genetic metric and the gene family. Each black point represents a sample for which the categorical regression is significant. The percentage of significant samples out of the total number of samples tested is indicated in parenthesis along the x-axis. Only 172 out of 175 samples for which metadata were available are included in this analysis. We only considered genes with at least 10X coverage in a sample. We only included genes with a gene family annotation and required that each gene family be represented by at least two genes. Finally, we only included genes present in 70% or more of the samples (less than 30% missing values), for a total of 512 genes.