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Annelids and Mollusks from Chemosynthetic Environments of the Pacific Ocean
Get PDFThis 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
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An integrative reassessment of Hesionidae (Annelida, Phyllodocida) phylogeny, with revision of Hesiospina (Annelida, Hesionidae), new deep-sea genus and species, and new mitochondrial genomes
No full textMost 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
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From syngnathid systematics to seadragon siblings - Investigating nested scales of divergence using novel molecular tools
Get PDFThis 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
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A Reevaluation of the Phylogenetic Position of Antonbruunia (Annelida: Phyllodocida) and New Species Description
Get PDFThe 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
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Get PDFWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
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