The new species Antonbruunia milenae sp. nov. found off the coast of San Diego, CA, USA at a depth of 845 m inside the Calyptogena pacifica Dall, 1891 clam is described. It is used to reevaluate the phylogenetic position of Antonbruunia Hartman & Boss, 1966 with analyses using 20 Pilargidae Saint-Joseph, 1899 species and three Nephtyidae Grube, 1850 species as an outgroup. The three gene and sixteen gene concatenated maximum likelihood phylogenies show that Antonbruunia is a pilargid, making Antonbruunidae Fauchald, 1977 a junior synonym of Pilargidae. In addition, Hermundurinae subfam. nov. is erected, Glyphohesione Friedrich, 1970 is moved out of Pilarginae Saint-Joseph, 1899, and Synelminae Salazar-Vallejo 1987 is emended to include Antonbruunia, Glyphohesione, and Otopsis Ditlevsen, 1917.

This dissertation examined various scales of nested genetic divergences in a group of marine fishes, the Syngnathidae (seahorses, pipefishes and seadragons). At the broadest scale, it investigated the phylogenetic relationships among syngnathids with comprehensive sampling of the global diversity of the group. High-throughput sequence data from $>$1000 Ultraconserved Elements (UCEs) was integrated with fossil and biogeographic information to obtain a highly resolved phylogeny. The dense sampling allowed for reconstructions of the likely ancestral form of brood care and biogeographic range. At shallower levels of divergence, molecular tools were used to gain insights into the biology of the elusive leafy and common seadragons, which are considered of conservation concern in Australia. A third species of seadragon, the ruby seadragon, was described after its discovery through DNA sequencing. Traditional genetic methods showed that both the leafy and the common seadragon species were significantly structured across their range and large regional variation in levels of genetic diversity existed. Following up on these results, we collected additional samples in low diversity regions of the leafy seadragon and increased the coverage across the genome. The chosen approach was to explore the utility of UCEs - loci that have been largely used at deeper scales - at intraspecific divergences. We found that UCEs harbored several thousand single nucleotide polymorphisms (SNPs) in each species and allowed for fine-scale resolution of population structure. We integrated paleooceanographic information on historical sea-levels and ocean temperature to gain a better understanding on the historical drivers of seadragon diversity. At the shallowest scale, UCEs were used to evaluate potential relatedness among leafy seadragons displayed in aquaria. We found that the genetic estimates of relatedness often align well with the relatedness predicted from aquarium records. The results suggest that a large number of close relatives are present in aquaria, which has implications for the selection of suitable breeding pairs.

This dissertation utilized molecular methods to reveal new species of annelids and mollusks from chemosynthetic environments in the Pacific Ocean and examined their biogeography and evolutionary history. Sanger sequencing revealed three new species of Bathymodiolus mussels that are partially restricted by depth at seeps along the Costa Rica Margin, and confirmed the presence of B. thermophilus at a seep with molecular data for the first time. New species of the iphionid Thermiphione and vestimentiferan tube worm Lamellibrachia are also described using a combination of Sanger-sequenced molecular data and morphological data. The close relationship of the new Lamellibrachia species with relatives across the Panama Isthmus suggests a vicariant event post-radiation of Lamellibrachia into the Atlantic. Sanger-sequencing also revealed two putative new species of the vestimentiferan tube worm Alaysia. High-throughput sequencing and mitochondrial genome skimming provided the data necessary to place these new species, as well as the vestimentiferan genera Alaysia and Arcovestia into the phylogeny of Vestimentifera for the first time. Additional sequencing of whole mitochondrial genomes in this group provided the data necessary to generate the most complete mitogenomic phylogeny of Vestimentifera to date. The resulting topology suggests the most recent common ancestor of Vestimentifera was a vent-inhabitant of the Pacific Ocean.

Most phylogenetic relationships within Hesionidae remain unresolved to this day. The integrative study herein reassessed the phylogeny of Hesionidae by combining molecular data from Sanger sequencing, morphology, and mitogenomic data from whole genome sequencing. In Chapter 1, we presented the most comprehensive phylogenetic analysis combining molecular and morphological data of Hesionidae to date. Results from our concatenated maximum likelihood analysis of four genes (COI, 16S, 18S, and 28S) recovered Hesiospina—a genus known for their emergent notopodial spines not found in any other hesionids—as non-monophyletic, and the generic diagnosis was emended to include only the shallow water taxa H. aurantiaca and H. similis. To retain monophyly in Hesiospina, we introduced Psamathispina gen. nov. to represent another hesionid group with emergent notopodial spines exclusive to the deep-sea. Psamathispina gen. nov. includes two previously described species transferred from Hesiospina—P. legendrei comb. nov. and P. vestimentifera comb. nov.—and four new species described herein—P. nathani sp. nov., P. raymondi sp. nov., P. tustisonorum sp. nov., and P. yingyiae sp. nov. In Chapter 2, we constructed the first six complete mitochondrial genomes for Amphiduros pacificus, Gyptis cf. robertscrippsi, Hesiolyra bergi, Hesiospina cf. similis 2, Leocrates rousei, and Micropodarke dubia, and also the first three partial mitochondrial genomes for Hesiospina aurantiaca, Psamathe fusca, and Psamathispina raymondi. Our phylogenomic analyses, which used a multi-loci dataset of dataset of 13 protein-coding genes (PCGs) and four ribosomal RNA genes (12S, 16S, 18S, and 28S) yielded strong support for the erection of Psamathispina in Chapter 1.