Supplementary_Table_1

Supplementary Table 1. Material examined and GenBank Accession numbers

SUBSET_18_GENES

Nexus alignment file for the subset (37 taxa and 18 gene fragments; 17616 sites; no missing data). The alignment file is fully annotated for gene partitions, including the batch command in PAUP* to export individual gene files

Supplementary_Table_2

Supplementary Table 2. Primers used and optimized PCR conditions

Supplementary Table4

Likelihood (ln) scores for gene trees and AU test P values comparing gene tree topologies estimated with RAxML against the concatenation topology (from Fig. 3, pruned to only include taxa in the subset), calculated under homogeneous (RAxML) and non-homogeneous (nhPhyML) optimization. The nhPhyML model used unlimited base equilibrium frequencies. Values in bold highlight cases in which the concatenation topology resulted in either better or non-significantly worse likelihood scores

Supplementary_Table_3

Supplementary Table 3. Characterization of molecular markers, variation, distribution of present/missing sequences and taxa, and GenBank accession numbers (see also Supplementary Table 1)

FIG_SUP_2_Subset_trees

Supplementary Figure 2. Four representative multi-locus phylogenies based on the subset. Color branches represent flatfish lineages (cyan, Pleuronectoidei; orange, Psettodoidei)

Concerted Evolution of Duplicate Control Regions in the Mitochondria of Species of the Flatfish Family Bothidae (Teleostei: Pleuronectiformes)

<div><p>Mitogenomes of flatfishes (Pleuronectiformes) exhibit the greatest diversity of gene rear-rangements in teleostean fishes. Duplicate control regions (CRs) have been found in the mito-genomes of two flatfishes, <i>Samariscus latus</i> (Samaridae) and <i>Laeops lanceolata</i> (Bothidae), which is rare in teleosts. It has been reported that duplicate CRs have evolved in a concerted fashion in fishes and other animals, however, whether concerted evo-lution exists in flatfishes remains unknown. In this study, based on five newly sequenced and six previously reported mitogenomes of lefteye flounders in the Bothidae, we explored whether duplicate CRs and concerted evolution exist in these species. Results based on the present study and previous reports show that four out of eleven bothid species examined have duplicate CRs of their mitogenomes. The core regions of the duplicate CRs of mitogenomes in the same species have identical, or nearly identical, sequences when compared to each other. This pattern fits the typical characteristics of concerted evolution. Additionally, phylogenetic and ancestral state reconstruction analysis also provided evidence to support the hypothesis that duplicate CRs evolved concertedly. The core region of concerted evolution is situated at the conserved domains of the CR of the mitogenome from the termination associated sequences (TASs) to the conserved sequence blocks (CSBs). Commonly, this region is con-sidered to regulate mitochondrial replication and transcription. Thus, we hypothesize that the cause of concerted evolution of the duplicate CRs in the mtDNAs of these four bothids may be related to some function of the conserved sequences of the CRs during mitochondrial rep-lication and transcription. We hope our results will provide fresh insight into the molecular mechanisms related to replication and evolution of mitogenomes.</p></div

Phylogenetic tree for 11 bothids with two other flatfishes as outgroup using the core region of CRs.

<p>The first number beside the internal branch indicates Bayesian posterior probability (values below 0.9 not shown); the second number represents the bootstrap value (values below 50% not shown).</p

ALL_TAXA_20_GENES

Nexus dataset with the complete alignment (214 taxa and 20 gene fragments; 19461 sites). The alignment file is fully annotated for gene partitions, including the batch command in PAUP* to export individual gene files

The hypothesized evolutionary mode of duplicate CRs of 11 bothids with two flatfishes as outgroup.

<p>The mode was hypothesized based on the highest likelihood values of the ASR result. Number and CRs status beside the nodes are based on the highest likelihood value of the ASR result. The two close likelihood values of 40.6% and 42.5% for the node including <i>B</i>. <i>pantherinus</i> and <i>B</i>. <i>myriaster</i> are shown.</p