Extended Data Fig. 9: Estimation of protein-coding gene selection with MKT-DoS tests across 11,651 orthologs between Ae. aegypti and Ae. albopictus. | Nature Ecology & Evolution

Extended Data Fig. 9: Estimation of protein-coding gene selection with MKT-DoS tests across 11,651 orthologs between Ae. aegypti and Ae. albopictus.

From: Adaptive genomic signatures of globally invasive populations of the yellow fever mosquito Aedes aegypti

Extended Data Fig. 9: Estimation of protein-coding gene selection with MKT-DoS tests across 11,651 orthologs between Ae. aegypti and Ae. albopictus.The alternative text for this image may have been generated using AI.

(a) Heatmaps show the clustering of 11,402 out of 11,651 orthologous protein-coding genes estimated to be under positive selection (Y-axis), according to DoS > 0 scores (left) and to MKT test: Dn/Ds > Pn/Ps (right), across Ae. aegypti populations (X-axis). Genes and populations were clustered using a binary matrix depicting the presence (red) or absence (grey) of positive selection in a gene; an analysis of distance and a clustering procedure were carried out with the method ‘war.D’. Only 356 positively selected genes, as estimated with the MKT and DoS tests, were detected in out-of-Africa populations exclusively. The genomic location of 354 of these adaptive protein-coding genes is widely distributed across the three chromosomes, and only two protein-coding genes were located in contigs (Supplementary Tables 22-23). (b) Top: the histogram shows the frequency distribution of MKT values (X-axis) for all orthologous protein-coding genes (Y-axis) included in the selection analyses, according to significant MKT values for positive selection in out-of-Africa populations (Dn/Ds > Pn/Ps; Fisher’s exact test, p-values adjusted for multiple testing with the Benjamini-Hochberg method and an FDR of 5%; Supplementary Table 22, Supplementary Data 7). Bottom: the histogram shows the frequency distribution of DoS values (X-axis) for all orthologous protein-coding genes (Y-axis) included in the selection analyses, according to DoS scores for positive (DoS > 0) and weak negative (DoS < 0) selection and also for neutral evolution (DoS = 0) (see Eq. (2) under Methods, Supplementary Table 23, Supplementary Data 6 and 8). (c) Overview of the DoS scores estimates for 11,402 out of 11,651 orthologous protein-coding genes across the 40 populations analyzed (see Methods, Supplementary Data 6 and 8). Note the proteome-wide presence of weak selection and (nearly) neutral evolution across protein-coding genes and Ae. aegypti populations (Supplementary Table 24).

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