Concordant Phylogenetic Patterns Inferred from Mitochondrial and Microsatellite DNA in the Giant Clam Tridacna Crocea

The boring giant clam, Tridacna crocea Lamarck, 1819, is a CITES-listed bivalve that is declining due to overharvest and environmental degradation. Previous molecular studies in the Coral Triangle using mitochondrial DNA indicated the presence of deep phylogenetic divergence and strong phylogeographic structure across this region, suggesting the possibility of multiple cryptic species. In the present study, we compare data from non-recombining mitochondrial (mtDNA; cytochrome oxidase subunit 1, COI) and eight microsatellite loci to better understand patterns of genetic structure and species boundaries in T. crocea populations across Indonesia and the Philippines. Microsatellite loci and mtDNA data from 618 individuals representing 27 populations revealed highly concordant phylogeographic patterns and identified three genetically distinct regions: (1) Western Indonesia, (2) Philippines and Central Indonesia, and (3) Eastern Indonesia. Both marker types also showed evidence of isolation by distance. These results build on previous studies and confirm the presence of only three genetic partitions and the genetic isolation of Western Indonesia and Eastern Indonesia. However, individual admixture analyses based on microsatellite data show that the mtDNA clade that defines a phylogeographic province spanning the Philippines and Central Indonesia is a mixture of unique genetic clusters from the Philippines/Central Indonesia and Eastern Indonesia. The admixture of nuclear loci from individuals with regionally distinct mtDNA genomes suggests that despite deep genetic divisions, the three mitochondrial lineages are likely not distinct species and that some populations in Central Indonesia may be a sink for genetic diversity accumulated from populations to the north and east. While microsatellite data refined our understanding of the biology and evolutionary history of T. crocea, the broad concordance between these markers highlights the continued utility of mtDNA, particularly in developing biodiversity-rich countries where resources to support biodiversity science are limited

Seventy-four universal primers for characterizing the complete mitochondrial genomes of scleractinian corals (Cnidaria; Anthozoa)

Use of universal primers designed from a public DNA database can accelerate characterization of mitochondrial (mt) genomes for targeted taxa by polymerase chain reaction (PCR) amplification and direct DNA sequencing. This approach can obtain large amounts of mt information for phylogenetic inferences at lower costs and in less time. In this study, 88 primers were designed from 13 published scleractinian mt genomes, and these were tested on Euphyllia ancora, Galaxea fascicularis, Fungiacyathus stephanus, Porites okinawensis, Goniopora columna, Tubastraea coccinea, Pavona venosa, Oulastrea crispata, and Polycyathus sp., representing 7 families of complex and robust corals. Seventy-four of the 88 primers (84.1%) successfully amplified completed mt genomes of these 9 corals. Several unique features were identified, including a group I intron insertion in the cytochrome oxidase subunit I (COI) genes of Por. okinawensis, Gon. columna, T. coccinea, and F. stephanus and an extended length of the 3'-end of the COI gene of E. ancora. Preliminary tests using a subset of primers successfully obtained the COI 3'-end of Euphyllia representatives, and the resulting species phylogeny is in agreement with corallite characters and tentacle shapes. The universal primers provided herein effectively decoded scleractinian mt genomes, and can be used to reveal different levels of molecular phylogenetic inferences in scleractinian corals