Title

DNA barcoding the Medusozoa and Ctenophora

Date of Completion

January 2008

Keywords

Biology, Oceanography

Degree

Ph.D.

Abstract

DNA barcoding (i.e. a short genetic sequence for species identification) can be a valuable asset to the scientific community. DNA barcoding addresses the issues of identification of species, connection of life-history stages, delimiting species boundaries, and potentially population structure and phylogenetics. For most metazoans the mitochondrial cytochrome c oxidase subunit I (mtCOI) is used for barcoding. A barcode must lower levels of intra-specific variation compared to inter-specific variation. The feasibility of barcoding these groups was unknown. 95 species of Medusozoa were sequenced for mtCOI; patterns of variation within and between species were analyzed. Intra-specific variation ranged from 0-.061 (mean .012) and inter-specific variation ranged from .055-.369 (mean .161). In no case was there an overlap between intra- and inter-specific variation between congeneric species. A cluster diagram generated using the Neighbor Joining algorithm reliably coalesced all barcodes to their correct species. These data suggest that mtCOI is an appropriate barcoding tool for the Medusozoa.^ The phylogenetic signal encoded within the mtCOI barcoding gene was tested by sequencing both mtCOI and the 28S rDNA gene from 76 species of the Hydrozoa order Siphonophora. MtCOI contributed to phylogenetic reconstructions for some groups, normally those most recently diverged. Gene saturation occurred in mtCOI at ∼.112 genetic distance between species. Most of the gene saturation occurred in the third and, to a lesser extent, second codon positions. The Cystonectae and Calycophora were monophyletic clades, while the Physonectae were polyphyletic. Within the Physonectae families, the Apolemiidae, Forskalidae and Athorybiidae were monophyletic, while the Agalmidae were polyphyletic. Within the Calycophorae, only the Hippopoididae and possibly the Sphaeronectidae were monophyletic; the remaining families were polyphyletic.^ Some members of the phylum Ctenophora displayed insufficient levels of mtCOI variation for it to be used as a barcode. 20 species of Ctenophores were then sequenced for both the ITS-1 and 28S rDNA gene to test their utility as a barcode. 28S rDNA had too low variability (e.g. .05 between Pleurobrachia spp.). However, ITS-1 showed no intra-specific variation and sufficient inter-specific variation to be used as a barcode for this group, as demonstrated by haplotypes reliably clustering with the correct species. ^