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Ecol Evol
2017 May 17;713:4543-4551. doi: 10.1002/ece3.3042.
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Rates and relations of mitochondrial genome evolution across the Echinoidea, with special focus on the superfamily Odontophora.
Láruson ÁJ
.
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In order to better characterize the placement of genus Tripneustes, as a representative of the Toxopneustidae family within the broader sea urchin mitochondrial (MT) phylogeny, the complete MT genome of Tripneustes gratilla was generated and compared with all published echinoid MT genomes currently available on NCBI GenBank. The MT genome phylogeny supports the existence of the superfamily Odontophora (consisting of the families Strongylocentrotidae, Echinometridae, and Toxopneustidae). A relaxed molecular-clock time calibration suggests a split between the three key Odontophore MT lineages occurred during the late Eocene/Oligocene. Major global oceanographic changes have been inferred during this time frame, potentially driving species diversification through environmental selection pressures. To test for signatures of selection acting on the mitochondria, the historical rate of gene evolution of individual MT genes was assessed through a branch-site comparison of nonsynonymous to synonymous substitution ratios (ω). Models of positive selection and neutral evolution, as compared via a likelihood ratio test, show no evidence of strong historical positive selection on mitochondrial genes at the genesis of the Odontophora. However, while pairwise ω comparison revealed signatures of strong negative selection, relatively elevated ω values were observed within the Strongylocentrotus genus.
Figure 1. Bayesian tree showing mitochondrial genome relationships among the Echinoids. Posterior probabilities at all bifurcating nodes were 100%. Species are displayed to the right of the branch tips and color coded to their representative families. Blue error bars represent the 95% CI of the node height
Figure 2. A heatmap depicting ω averaged across all 13 CDS, for each pairwise comparison. Lower values are depicted as cooler colors (blue), and higher values are presented as warmer colors (red). The largest values were consistently observed within genus Strongylocentrotus, specifically when S. purpuratus was compared to its congenerics S. pallidus and S. intermedius
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