Sterechinus neumayeri is an abundant regular sea urchin that lives in the shallow Antarctic waters. This organism has been used as a model system in many fields of the Antarctic biology. Yet, understanding of the evolutionary identity of the species, such as its phylogenetic relationships and divergence time, remains limited. Here, we reconstructed the molecular phylogenies of the species together with two sea urchin species in southernmost South America (Loxechinus albus and Pseudechinus magellanicus), a parechinid species (Paracentrotus lividus) and three strongylocentrotid species (Strongylocentrotus purpuratus, S. intermedius, and Hemicentrotus pulcherrimus) using mitochondrial DNA sequences of 12S rDNA-tRNA(gln) region (877nt) and cytochrome oxidase subunit I (COI, 1079nt). The rate of sequence evolution and the divergence time of the species were then estimated from the trees. The phylogenetic trees reveal that S. neumayeri is a sister group to the lineage of L. albus and P. lividus, and separated from the lineage 24–35 million years ago (m.y.a.). The divergence between S. neumayeri and L. albus coincides with the separation of Antarctica from South America, suggesting that the tectonic event must have provoked the cladogenesis of the species through vicariance.
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