Molecular phylogeny and divergence time estimates for native giant clams (Cardiidae: Tridacninae) in the Asia-Pacific: Evidence from mitochondrial genomes and nuclear 18S rRNA genes

Abstract

Giant clams are conspicuous bivalves that inhabit in coral reefs. Among the giant clams, eight species of subfamily Tridacninae are the most common in the Asia-Pacific. However, very little is known about their evolutionary history. Here, we determined the complete mitochondria genome of Hippopus porcellanus, which was 29,434 bp in size and contained 13 protein-coding genes, 2 rRNAs and 23 tRNAs. The A+T composition of protein-coding regions was 57.99%, and the AT composition of the 3rd codon position was 59.33%, of which in agreement with the invertebrate bias favoring codons ending in A or T. Analysis of phylogenetic relationships according to the concatenated nucleotide data set containing 18S rRNA gene and 13 protein-coding genes, the phylogenetic relationship was analyzed by Maximum likelihood and Bayesian inference methods. The results showed that T. maxima was placed with the clade comprising T. noae, T. squamosa, and T. crocea, in which T. squamosa was highly similar to T. crocea and is consistent with the results of the previous studies using15 mitochondrial markers and nuclear 18S rRNA. Moreover, the inferred divergence time of Tridacnidae species is generally consistent with the fossil record of Tridacnidae. The divergence time of H. porcellanus and H. hippopus was about 10.64 Mya, this result is in agreement with the speculation that H. porcellanus also originated in Miocene. The availability of molecular phylogeny and divergence time estimation provides information genetic relationship of Tridacninae, which could be helpful to the ecological research and conservation of giant clams.