Mitochondrial Genome of the Pocilloporid Scleractinian
Date Issued
2008
Date
2008
Author(s)
Chen, Chienhsun
Abstract
In this dissertation, I focus on the study of mitochondrial genome (mitogenome) of the scleractinian family Pocilloporidae to address two main evolutionary issues. Firsty, the slow-evolution hypothesis of anthozoan mitochondrial (mt) DNA was evaluated by comparing mitogenomes of 2 sibling (sister) coral species. Secondly, the evolutionary phylogeny of the Pocilloporidae was investigated by mitogenomic analyses.he complete mitochondrial genomes of 2 sibling (sister) Seriatopora species were first sequenced and determined in order to verify the slow evolution of anthozoan mtDNA (Chapter 3). Afterward different mtDNA regions were evaluated by analyzing variations and divergences within and between populations of the same species and by comparisons between 2 Seriatopora species. Gene arrangement of the Seriatopora mitogenomes is similar to the currently published scleractinian mitogenomes with the exception of three eclusive features, including gene atp8, a duplicated trnW (tRNATRP), and a putative control region located between atp6 and nad4. The significances of a highest value in between-species variation and a lowest one in within-population comparison showed several protein-coding genes and intergenic spacers could provide phylogenetic information in discerning among recently-diverged populations or boundaries of delineating species. Phylogenetic analyses of the hypervariable regions for the Indo-West Pacific populations also revealed a monophyly of the Andaman-Sea Seriatopora, which is suggested to be separated geographically since 3 million years ago. Evaluation of the molecular evolution of atp6 and the putative control region showed 2- to 7-fold higher divergence rates among populations or between species than those published for scleractinian mitogenomes. This study not only successfully reveals the phylogenies of Se. hystrix and Se. caliendrum from the West Pacific Ocean by mtDNA of the 9th intergenic spacer, putative control region, atp6, and the cox1 genes, but also highlights the potential utility of hypervariable regions of mt phylogenetic tree construction for Seriatopora below the species level. The hypothesis of slow evolution of anthozoan mtDNA should be treated with caution, since the evolutionary rate of the mitogenomes could be highly variable among different genes and intergenic spacers, and even in different scleractinian lineages.ince unique mt features were detected in Seriatopora corals, I extended the determination of complete mitogenomes to three confamilial genera in order to understand whether these mt characteristics are also present in other pocilloporid corals (Chapter 4). The mitogenomes of the Madracis formosa, Pocillopora damicornis, and Stylophora pistillata were amplified and determined. The entire mitogenomes of pocilloporid corals ranged from 16,951 to 17,426 bp with the A+T contents ranging from 68.3% to 70.1%. The gene order of protein-coding genes was identical to those of other scleractinian corals. The novel atp8 gene, first described in Seriatopora corals, was also confirmed using RT-PCR, Northern blot, and sequence analyses in other genera of the Pocilloporidae. The intergenic spacer between atp6 and nad4, containing distinct repeated elements, conserved sequence blocks and domains, and functional structures, possesses typical characteristics of a putative control region for the four coral genera. A duplicated trnW, detected in the region close to the cox1 which shares the highly conserved primary and secondary structures of its original counterpart, was discovered in both Seriatopora and Stylophora. These molecular characteristics are unique and provide phylogenetic information for future evaluation of the status of the family Pocilloporidae in the evolutionary history of scleractinian corals.he phylogenetic status of the pocilloporid corals were revised in various aspects according to the mt system (Chapter 5). Different approaches, such as differences in amino-acid usage and molecular phylogeny of 13 protein-coding genes, were utilized to clarify the unsolved discordance between traditional taxonomy and former molecular phylogeny. My results support the former phylogenetic evidence of rDNA sequence. Results of the amino-acid usage and the phylogenetic analyses indicated that the extant Scleractinia was polyphyletically distributed into 3 separate clades, including pocilloporid, complex- and robust-clade corals. The pocilloporid was jointed as a sister clade to robust-clade corals, indicating its most recent common ancestor with robust clade rather than the implicated relationship in conventional taxonomy.olecular-dating analysis of the phylogenetic trees was used to estimate the development of the pocilloporid lineage. The molecular-dating analysis showed a 330 million years (MY) divergence between the pocilloporid and the robust-clade corals, which is about 100 MY earlier than the oldest fossil Astrocoeniina (middle Triassic). After examining several possible key factors, I suggest that the discrepancy between the oldest fossil record and the molecular-dating estimate may be an evidence of the “naked-coral” hypothesis. The soft-bodied Pocilloporidae (Astrocoeniina) group might have diverged from the robust-clade scleractinian during in the Carboniferous (about 330 Ma), then evolved their skeleton later in the Triassic.omparisons of mitogenome size, nucleotide composition, and initiation/termination of protein-coding genes indicate that scleractinians could be separated into 3 groups which were concordant with previous studies (Chapter 6). Based on the results of mitogenomic analyses, the Pocilloporidae was deeply diverged from the robust clade and could be considered a distinct lineage of scleractinian corals, in addition to the 2 scleractinian clades by former molecular evidences. The taxonomic status within the Astrocoeniina was also discussed.
Subjects
Scleractinian
Pocilloporidae
Mitogenome
Type
thesis
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