Abstract
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.
Highlights
There are presently over 1,000 described species of sea urchins that collectively make up the class Echinoidea, the sea urchins, within the Phylum Echinodermata (WoRMS, 2017)
Previous attempts at placement of the Toxopneustidae family within the greater sea urchin phylogenetic tree using morphology have suggested that the Toxopneustidae, Echinometridae, and the Strongylocentrotidae together form the superfamily Odontophora (Kroh & Smith, 2010)
A-t ail hybridization and cDNA generation were accomplished with an Illumina TruSeq kit and sequencing was performed on an Illumina MiSeq (300 cycle, single end) at the Hawaii Institute of Marine Biology (HIMB) Core Genetics facility, Oahu, Hawaii
Summary
There are presently over 1,000 described species of sea urchins that collectively make up the class Echinoidea, the sea urchins, within the Phylum Echinodermata (WoRMS, 2017). LÁRUSON the much-studied Caribbean “green sea urchin,” Lytechinus variegatus (Watts, McClintock, & Lawrence, 2013), and the Indo-Pacific “collector urchin,” Tripneustes gratilla (Lawrence & Agatsuma, 2013), along with eight other recognized species (WoRMS, 2017) Though these species are well recognized and studied, their familial phylogeny is not as well established. Values of ω close to 1 suggest neutrality, values much less than 1 suggest the action of purifying selection in removing amino acid substitutions, and values much greater than 1 pointing to positive selection on amino acid change (Kryazhimskiy & Plotkin, 2008; Nielsen & Yang, 2003) Extending this approach to inferred historical sequences of shared ancestors allows for an estimation of past instances of selection-driven divergence. Two branch-site tests of positive selection, a “strict” and “relaxed” variety, were performed on the branch giving rise to the Odontophora, in order to assess the influence of climate shifts driving lineage divergence through positive natural selection
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