DOI: 10.5281/zenodo.14869225
title: The COX1 Mutation Drives Structural Innovation Despite Silent tRNA Variation in Semiaquatic Bugs

description: Supplementary Figure 1 Phylogenetic relationships of Gerromorpha are presented based on optimal tree of AA dataset. The species followed by an asterisk (*) are sequenced in this study. The topology is based on the maximum likelihood results with full partition. Species followed by an asterisk (*) were sequenced in this study. Numbers on the nodes represent the bootstrap support.

Supplementary Figure 2 Phylogenetic relationships of Gerromorpha are presented based on optimal tree of P12R dataset. The species followed by an asterisk (*) are sequenced in this study. The topology is based on the maximum likelihood results with full partition. Species followed by an asterisk (*) were sequenced in this study. Numbers on the nodes represent the bootstrap support.

Supplementary Figure 3 Phylogenetic relationships of Gerromorpha are presented based on optimal tree of P123R dataset. The species followed by an asterisk (*) are sequenced in this study. The topology is based on the maximum likelihood results with full partition. Species followed by an asterisk (*) were sequenced in this study. Numbers on the nodes represent the bootstrap support.

Supplementary Figure 4 Phylogenetic relationships of Gerromorpha are presented based on optimal tree of AA dataset. The species followed by an asterisk (*) are sequenced in this study. The topology is based on the maximum likelihood results with merged partition. Species followed by an asterisk (*) were sequenced in this study. Numbers on the nodes represent the bootstrap support.

Supplementary Figure 5 Phylogenetic relationships of Gerromorpha are presented based on optimal tree of P12R dataset. The species followed by an asterisk (*) are sequenced in this study. The topology is based on the maximum likelihood results with merged partition. Species followed by an asterisk (*) were sequenced in this study. Numbers on the nodes represent the bootstrap support.

Supplementary Figure 6 Phylogenetic relationships of Gerromorpha are presented based on optimal tree of P123R dataset. The species followed by an asterisk (*) are sequenced in this study. The topology is based on the maximum likelihood results with merged partition. Species followed by an asterisk (*) were sequenced in this study. Numbers on the nodes represent the bootstrap support.

Supplementary Figure 7 Phylogenetic relationships of Gerromorpha are presented based on optimal tree of AA dataset. The species followed by an asterisk (*) are sequenced in this study. The topology is based on the maximum likelihood results with no partition. Species followed by an asterisk (*) were sequenced in this study. Numbers on the nodes represent the bootstrap support.

Supplementary Figure 8 Phylogenetic relationships of Gerromorpha are presented based on optimal tree of P12R dataset. The species followed by an asterisk (*) are sequenced in this study. The topology is based on the maximum likelihood results with no partition. Species followed by an asterisk (*) were sequenced in this study. Numbers on the nodes represent the bootstrap support.

Supplementary Figure 9 Phylogenetic relationships of Gerromorpha are presented based on optimal tree of P123R dataset. The species followed by an asterisk (*) are sequenced in this study. The topology is based on the maximum likelihood results with no partition. Species followed by an asterisk (*) were sequenced in this study. Numbers on the nodes represent the bootstrap support.

Supplementary Figure 10 Bayesian phylogenetic reconstruction of Gerromorpha using P123R dataset. The topology is based on the CAT-GTR model by PhyloBayes. Species followed by an asterisk (*) were sequenced in this study. Numbers on the nodes represent the posterior probability support.

Supplementary Figure 11 Phylogenetic relationships of Gerromorpha are presented based on optimal tree of P123R dataset containing the mitochondrial data of Potamometra zhengi generated in this study. The species followed by an asterisk (*) are sequenced in this study. The topology is based on the maximum likelihood results with no partition. Species followed by an asterisk (*) were sequenced in this study. Numbers on the nodes represent the bootstrap support. 

Supplementary Figure 12 The proposed transcriptional model for mitochondrial protein-coding genes (PCGs) in Potamometra zhengi. Polycistronic primary transcripts are highlighted with red boxes, while monocistronic processed mRNAs are shown in grey.

Supplementary Figure 13 Selection pressure, CAI and amino acid statistics for 13 PCGs in Gerromorpha. The phylogenetic relationships of Gerromorpha are depicted based on the optimal tree derived from the P123R dataset. Species marked with an asterisk (*) indicate those sequenced in this study. The pie chart below the node represents the proportion of selected pressure sites based on the aBSREL results. The first heat map block illustrates the CAI values of the 13 PCGs. The second dot chart block shows the amino acid composition statistics of PCGs.

Supplementary Figure 14 Divergence phylogenetic tree of Gerromorpha based on P123R dataset. Green horizontal bars represent 95% credibility intervals. The fossil calibrations employed in this study are depicted as orange nails. The scale axis of the tree is expressed in millions of years. The Quaternary is represented by purple rectangles, the Neogene is denoted by ‘Neo.’, and other periods are not abbreviated. Key nodes were annotated with the estimated divergence times and their confidence intervals. The time unit is Mya. Species marked with an asterisk (*) indicate those sequenced in this study.

Supplementary Figure 15 Multiple sequence alignment of mitochondrial COX1 codons in Gerromorpha. Visualization produced with TranslatorX.

The GFF file within the Potamometra zhengi full-length transcript archive can be imported into Geneious for visualization of full-length transcripts.