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Mitochondrial Genome Architecture in Sponges, With MITOCHONDRIAL GENOME ARCHITECTURE IN SPONGES, WITH DESCRIPTIONS OF TWO NEW SPECIES FROM THE ABYSSAL NORTHEAST PACIFIC A Thesis Presented to the Faculty of the Moss Landing Marine Laboratories California State University Monterey Bay In Partial Fulfillment of the Requirements for the Degree Master of Science m Marine Science by Amanda Suzanne Kahn Fal12010 111 Copyright © 2010 by Amanda Suzanne Kahn All Rights Reserved IV For those who patiently support me while I pursue my dreams. v ABSTRACT Mitochondrial Genome Architecture in Sponges, with Descriptions of Two New Species from the Abyssal Northeast Pacific by Amanda Suzanne Kahn Master of Science in Marine Science California State University Monterey Bay, 2010 Mitochondrial genomics is an emerging field that aims to characterize evolution of the mitochondrion, an organelle found in nearly all eukaryotes. Such a ubiquitous feature presents a platform on which to address questions about phylogenetics, evolution, and molecular mechanisms across taxa. Porifera is a diverse phylum containing animals believed to be the first true multicellular organisms, yet few mitochondrial genomes have been sequenced across groups within the phylum. Classes within Porifera have parallel structures to those found in animals but not found in other sponge groups; therefore, relationships among and within classes are important for our understanding of the evolution of the phylum. Here I present two nearly complete mitochondrial genomes of two hexactinellid sponges, bringing the total number up to five. The five genomes provide coverage at various taxonomic levels within Hexactinellida, allowing a large range of comparisons of features such as gene loss, changes in gene order, and transcriptional and translational mechanisms. I also evaluate the phylogenetic value of mitochondrial gene sequences at different taxonomic levels. Finally, the two species, Bathydorus laniger and Docosaccus maculatus, are new to science and are formally described. Both are found in the same region and have similar gross morphology, but are from two different families within the order Lyssacinosida. Vl TABLE OF CONTENTS PAGE ABSTRACT .............................................................................................................................. V LIST OF TABLES ................................................................................................................ VIII LIST OF FIGURES ................................................................................................................ IX ACKNOWLEDGEMENTS .................................................................................................... XI INTRODUCTION ..................................................................................................................... 1 References ................................................................................................................ 3 1 MITOCHONDRIAL GENOME EVOLUTION IN GLASS SPONGES ...................... 5 Abstract .............................................................................................................. 5 Introduction ........................................................................................................ 6 Methods ............................................................................................................. 8 Phylogenetic analysis ................................................................................... 9 Results .............................................................................................................. 10 Genome structure and composition ........................................................... 10 Protein-coding genes .................................................................................. 12 Frameshifting insertions ............................................................................ 12 Gene arrangement ...................................................................................... 13 Phylogenetic analysis ................................................................................. 13 Discussion ........................................................................................................ 15 Genome structure and composition ........................................................... 15 Testing for linearity of the genome .................................. .......................... 16 Protein-coding genes .................................................................................. 18 Translational frameshifts ........................................................................... 18 Gene arrangement ...................................................................................... 19 Phylogenetic analysis ................................................................................. 20 Conclusions ...................................................................................................... 21 References .............................................................................................................. 22 2 BATHYDORUS LANIGER AND DOCOSACCUS MACULATUS (L YSSACINOSIDA; HEXACTINELLIDA): TWO NEW SPECIES OF GLASS SPONGES FROM THE ABYSSAL EASTERN NORTH PACIFIC OCEAN ........................................................................................................................ 26 Abstract ............................................................................................................ 26 Vll Introduction ......................................................................................................27 Material and Methods .. ........................... .........................................................28 Results .............................................................................................................. 30 Bathydorus laniger sp. n ............................................................................ 30 Material examined ...................... ......................... ................................ 30 Diagnosis ......... ............ .. ................................................... .......... ......... 30 L yssacine framework ........................................................................... 31 Spicules ................................... .... ......................................................... 33 Etymology. ........................................................................................... 34 Remarks ......................... ............. ......................................................... 34 Docosaccus maculatus sp. n ...................................................................... 36 Material examined ............................................................................... 36 Diagnosis . ............................................................................................ 36 Description ............................................. ............................................ .. 36 Lyssacine framework ........................................................................... 37 Spicules ................................................................................................ 39 Etymology.... ........................................................................................ 42 Remarks . ............. ...................... .. ..................................................... .... 42 Discussion ........................................................................................................ 42 References ........................................................................................................... ... 44 A GENBANK ACCESSION ENTRIES FOR BATHYDORUS LANIGER AND DOCOSACCUS MACULATUS ............. ........ .............................................................. 46 B GLOSSARY OF TERMS USED IN HEXACTINELLID TAXONOMY .................. 64 C MEASUREMENTS OF SPICULES FOUND IN BATHYDORUS LANIGER ........... 68 D MEASUREMENTS OF SPICULES FOUND IN DOCOSACCUS MACULATUS ............................. ................................................................................. 70 Vlll LIST OF TABLES PAGE Table 1-1. Comparison of protein-coding genes found in five species of glass sponges, and the pairwise similarities of their nucleotide and amino acid sequences ..................................................................................................................... 11 Table 1-2. Variations in the trnY(gua) repeats found in the otherwise non-coding region between nadl and cob of Docosaccus maculatus. All copies were 65 bp long. The first copy was at the 5' end of the repetitive region, the third copy at the farthest 3' end; the bold, second sequence is used as a reference sequence since it was predicted to be the functional trnY gene by tRNAscan- SE (Lowe and Eddy 1997) .............................. .................................................. .. ......... 12 Table 2-1. Spicule dimensions of Bathydorus laniger sp. n., from Station M, California, USA (dimensions in ~J.m, except for the choanosomal and pros tal diactin lengths, which are in mm) ....................... ........................ .... ............................. 35 Table 2-2. Spicule dimensions of Docosaccus maculatus sp. n., from Station M, California, USA (dimensions in ~J.m) .......................................................................... .40 IX LIST OF FIGURES PAGE Figure 1-1. The largest non-coding region (1,439 base pairs) in Docosaccus maculatus was a repetitive
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