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  • About
  • The Global ETD Search service is a free service for researchers to find electronic theses and dissertations. This service is provided by the Networked Digital Library of Theses and Dissertations.
    Our metadata is collected from universities around the world. If you manage a university/consortium/country archive and want to be added, details can be found on the NDLTD website.
221

Taxonomy and Phylogeny of Lycodinae (Teleostei: Zoarcidae) from the Southern Ocean and Magellan Province

Corbella i Felip, Cecília 06 March 2013 (has links)
La família zoarcidae, és una de les més diverses del subordre Zoarcoidei (Perciformes), comprèn 4 subfamílies (Lycozoarcinae, Zoarcinae, Gymnelinae i Lycodinae) i inclou més de 240 espècies en 54 gèneres. Aquesta família té una distribució molt àmplia ja que es troba a quasi tots els mars i oceans del món, la majoria de les espècies habiten a les zones litorals, a la plataforma continental i a la meitat superior del talús continental però algunes habiten a la zona abissal. Les espècies de la família Zoarcidae són molt abundants al Pacífic Nord i a l’Atlàntic Nord tot hi que també hi ha gèneres que es distribueixen pel sud de l’oceà Atlàntic, l’Àrtic, l’oceà Pacífic i per l’oceà Antàrctic. Probablement, l’origen dels zoàrcids va ser al nord-oest de l’oceà Pacífic, concretament al mar de Okhotsk. En aquesta zona, hi habiten representants de les 4 subfamílies, hi ha una gran diversitat d’espècies i un gran nombre d’endemismes. Aquesta tesi, està centrada en l’estudi de la subfamília Lycodinae. Aquesta subfamília és la més diversa dintre dels Zoarcidae i presenta 38 gèneres i més de 190 espècies. És un grup de peixos força desconegut com queda palès en el fet que en els últims anys s’han descrit 5 gèneres nous (Leucogrammolycus, Gosztonyia, Bellingshausenia, Santelmoa i Bentartia) i de ben segur que en queden molts més per descriure. La sistemàtica d’aquesta subfamília ha estat discutida per molts autors, i tot hi que recentment s’hi han incorporat les dades moleculars, encara hi ha alguns punts de la seva sistemàtica que no han quedat resolts. El principal objectiu d’aquesta tesi és contribuir en el coneixement de la diversitat i de la filogènia de la subfamília Lycodinae. Per tal d’assolir aquest objectiu, s’han realitzat quatre estudis. S’han estudiat exemplars de la subfamília Lycodinae procedents de la província de Magallanes, de l’oceà Antàrtic i del mar de Solomon (sud-oest de l’oceà Pacífic). Com a resultat d’aquest treball, s’han descrit 2 gèneres nous (Patagolycus i Argentinolycus) i un tercer gènere, el gènere Iluocoetes s’ha descrit de nou. Per altra banda, s’han descrit dues espècies noves del gènere Santelmoa (S. fusca i S. antarctica) de l’oceà Antàrtic i una nova espècie (Pachycara matallanasi) del mar de Solomon. L’últim treball, és una anàlisi filogenètica d’alguns gèneres de la subfamília Lycodinae realitzat mitjançant dades moleculars (Citocrom Oxidasa I i Regió Control) i dades anatòmiques. L’arbre filogenètic ens mostra que el gènere Lycodapus es troba a la base de l’arbre clarament separat de tots els altres gèneres. Els gèneres restants es troben dividits principalment en dos grups, per una banda els gèneres Antàrtics i per l’altra els gèneres Magallànics. Pachycara brachycephalum apareix clarament separat de les altres espècies de Pachycara (P. priedei i P. matallanasi ). El mateix resultat el trobem a les espècies del gènere Lycenchelys (L. bachmanni i L. wilkesi) que també es troben separades. Aquests dos casos mostren la necessitat de realitzar una revisió completa d’alguns gèneres de la subfamília Lycodinae mitjançant dades anatòmiques i moleculars. / Family Zoarcidae (eelpouts) is the largest family of the suborder Zoarcoidei (Perciformes), including 4 subfamilies (Lycozoarcinae, Zoarcinae, Gymnelinae and Lycodinae) and about 240 species in 54 genera. This family has a wide distribution and it is found in all oceans and seas of the world; it primarily inhabits mud bottoms of the continental shelves and the slopes of boreal seas, but some species are known from the abyssal zone. Species of Lycodinae are abundant in the North Pacific and North Atlantic seas but there has been some radiation into the Arctic, South America and Antarctic waters. The origin of eelpouts was probably in the North Pacific (Okhotsk Sea); this is evidenced by a very high diversity and a higher number of endemisms, and by the fact that there are representatives of all the 4 subfamilies of Zoarcidae. This thesis is focused on the taxonomic and phylogeny of Lycodinae. Subfamily Lycodinae is the largest subfamily within Zoarcidae and it includes 38 genera and about 190 species. It is a fish group little known; in the last few years, 5 new genera have been described (Leucogrammolycus, Gosztonyia, Bellingshausenia, Santelmoa and Bentartia) and there are probably still many species and genera which remain undescribed. The systematic of Lycodinae has been widely discussed by many authors, and although molecular data has been added in the last few years, there are some points that are still unclear. The aim of this thesis is to contribute to the knowledge of the diversity and the phylogeny of subfamily Lycodinae. To achieve the objectives, four studies have been carried out. Specimens from Magellan province, the Southern Ocean and the Solomon Sea (Western South Pacific) have been studied. As a result, 2 new genera, Patagolycus and Argentinolycus, have been described and a third genus (Iluocoetes) has been redescribed. Two new species of Santelmoa (S. fusca and S. antarctica) have been described from the Southern Ocean and a new species (Pachycara matallanasi) from the Solomon Sea has been described. The last study is a phylogenetic analysis of some genera of Lycodinae. It has been carried out using molecular data (Cytochrome Oxidase I and Control Region) and anatomical data. Resulting trees show that, Lycodapus is separated from all other genera and that the remaining genera are divided into Antarctic and Magellanic genera. Pachycara brachycephalum appeared in a separated clade of Pachycara priedei and Pachycara matallanasi. The same result is found in species of Lycenchelys (L.bachmanni and L. wilkesi) which are separated. These two cases show that a complete review using anatomic and molecular data is required in some genera of Lycodinae.
222

Phylogenetic characterization of equine influenza viruses from Swedish outbreaks from 1979 to 2001

Acar, Binnaz January 2011 (has links)
Introduction: Equine influenza virus, an influenza type A virus, belongs to the family of Orthomyxoviridae. Equine influenza is a major cause of respiratory disease in horses and outbreaks have severe economical repercussions for the horse industry. It is considered to be endemic in Sweden and between 1997 and 2006 there have been around 10 to 40 outbreaks every year. The objective of this study was to do a phylogenetic characterization of equine influenza outbreaks that occurred in Sweden during a twenty year period. Methods: The haemagglutinin and neuraminidase gene of 14 samples and the complete genome of three samples collected over the span of 20 years were sequenced. The viral RNA were extracted, amplified with OneStep RT-PCR and sequenced. Results & Discussion: The phylogenetic tree and deduced amino acid sequence of HA1 illustrated that different lineages of equine influenza virus has circulated simultaneously in the Swedish horse population. The isolates mainly belonged to pre-divergence-, Eurasian- and American lineages. To characterize equine influenza viruses is important for vaccine strain selection, to fully understand the disease and how the virus evolves.
223

Molecular phylogenetic studies in nyctaginaceae: patterns of diversification in arid North America

Douglas, Norman Alan 04 May 2007 (has links)
The Four O'clock Family (Nyctaginaceae) has a number of genera with unusual morphological and ecological characters, several of which appear to have a "tendency" to evolve repeatedly in Nyctaginaceae. I present a molecular phylogeny for the Nyctaginaceae, consider taxonomic implications, biogeographic patterns, and the evolution of cleistogamy and gypsophily. These characters have each evolved multiple times in the xeric-adapted genera of the family. Further progress towards understanding these phenomena requires specific investigation of the ecology of pollination and gypsum tolerance. In the genus Boerhavia, an intensively sampled phylogeny based on internal transcribed spacer (ITS) and nitrate reductase (NIA) sequences provides new insights into relationships among species in the genus, and identifies a clade of annual species centered in the Sonoran Desert. Phylogeographic patterns are present in the genus that may reflect both relatively ancient vicariant events as well as the post-Pleistocene expansion of the Sonoran Desert. Many species in this group are found to be genetically cohesive, however two annual species complexes are found which species were nonmonophyletic. Since several mechanisms can potentially lead to the finding of nonmonophyletic species, Amplified Fragment Length Polymorphisms (AFLPs) were used to examine the structure of genetic variation in the two complexes. These data show that in these two groups, different evolutionary mechanisms are needed to explain the distribution of genetic diversity within and among populations. A complex comprised of Boerhavia spicata and B. xanti shows little evidence of genetic divergence between the species in Sonora, a pattern which may indicate recent contact between two very closely related forms. In contrast, high genetic structure between populations is found in the other complex, which contains the species with umbellate inflorescences. This complex includes several nominal species with highly restricted distributions, whose evolution may have been facilitated by low gene flow among populations. Little evidence was found for associations of inbreeding within populations, and floral traits which might be expected to influence outcrossing rates. / Dissertation
224

Sound Characteristics of the Large Yellow Croaker, Larimichthys crocea and Phylogeny of the Western Pacific Sciaenid Genera Inferred by Molecular Evidence

Lo, Pei-chun 13 July 2011 (has links)
The fishes of the family Sciaenidae have been known to vocalize during the reproductive season, and it is known that in most species only the male calls. Sounds are produced by vibration of the sonic muscles, which set the swim bladder into resonance. In addition, they also emit sounds by the same mechanism while being disturbed. The large yellow croaker, Larimichthys crocea (Perciformes, Sciaenidae) is one of the important commercial fish species distributed in South China Sea, East China Sea and southern Yellow Sea. In the past years, they have been overfished because of their high fishery value. Many aquatic farms started to culture economically important sciaenids because of the established artificial propagation technique. Now large yellow croakers have been successfully cultured in Fuchien Province, China. Unlike most sciaenids, the sonic muscles are only possessed by male, both male and female large yellow croakers have sonic muscles. This species provides the best opportunity to investigate the characteristics of sounds produced by different genders. The aims of this study were 1) to describe the hand-held disturbance sounds in large yellow croakers, 2) to describe the sounds produced during courtship and spawning in large yellow croakers being injected hormone (LHRH-A3), 3) to investigate the phylogenetic position of large yellow croaker in relation to other sciaenid fishes, and 4) to understand the evolutionary path of swim bladder morphology in the family Sciaenidae. The results show that 1) the pulse numbers of hand-held disturbance sounds in large yellow croaker can reach 23; 2) The reproductive sounds consisted of 1 to 7 pulses which started at about 1400 hr, and both vocal activity (no. sounds/min) and pulse numbers per call would increase with time. However, spawning occupied at the time slot when pulse numbers per call reached 7 in the unisex pond. The sounds in the ponds with only males or females can only recorded the sounds with 1 to 2 pulses; 3) The genus Collichthys was the sister taxon of large yellow croaker. Morphology of the swim bladder in Collichthys is similar to large yellow croaker; 4) Morphology of swim bladder evolved from simple to complex forms. Finally, Larimichthys, Collichthys, and other sciaenid genera distributed in the Indo-western Pacific Ocean including Miichthys, Boesemania, Bahaba, Panna, Atrobucca, Otolithes, Pterotolithus, Chrysochir, Paranebris, Protonibea, Pennahia, Nibea, Dendrophysa and Johnius form a monophyletic group with a bootstrap value of 100. Most of the members have the complex swim bladders with many appendages except Boesemania, Bahaba and Paranebris. Presence of simple form of the swim bladder in these three genera is inferred as a result of morphological reversal.
225

Molecular Phylogeny, Biogeography, and Evolutionary Trends of the genus Phalaenopsis (Orchidaceae)

Tsai, Chi-Chu 14 February 2004 (has links)
Species of Phalaenopsis Blume (Orchidaceae) are found throughout tropical Asia, namely South China, Indochina, India, Southeast Asia, and Australia. This genus is comprised of approximately 66 species according to the latest classification. Most of them possess commercial value. Thousands of Phalaenopsis cultivars have been grown for commercial goals. Although this orchid is very beautiful and popular throughout the world, studies on the molecular systematics and phylogenetic relationships among these orchids are still deficient. Phylogenetic trees inferred from the internal transcribed spacers 1 and 2 (ITS1+ITS2) region of nuclear ribosomal DNA (nrDNA) and chloroplast DNAs (cpDNAs), including the intron of trnL, the IGS of trnL-trnF, and the IGS of atpB-rbcL, were used to clarify the phylogenetics and evolutionary trends of the genus Phalaenopsis (Orchidaceae). Molecular data are provided to clarify the latest systematics of the genus Phalaenopsis as suggested by Christenson (2001). He treated the genera of Doritis and Kingidium as synonyms of the genus Phalaenopsis and divided it into the five subgenera of Proboscidioides, Aphyllae, Parishianae, Polychilos, and Phalaenopsis. The results concurred that the genera Doritis and Kingidium should be treated as synonyms of the genus Phalaenopsis as suggested by Christenson (2001). The subgenera of Aphyllae and Parishianae were both shown to be monophyletic groups, and to be highly clustered with the subgenus Proboscidioides and two sections (including sections Esmeralda and Deliciosae) of the subgenus Phalaenopsis, which have the same morphological characters of four pollinia as well as similar biogeographies. Furthermore, neither the subgenus Phalaenopsis nor Polychilos was found to be a monophyletic group in this study. In addition, the phylogenetic tree indicates that Phalaenopsis is monophyletic and does not support the existing subgeneric and sectional classification. The phylogenetic tree of the genus Phalaenopsis is basically congruent with the geographical distributions of this genus. Based on the tree, two major clades were separated within the genus Phalaenopsis. The first clade, having four pollinia, included sections Proboscidiodes, Parishianae, and Esmeralda, of which are distributed in South China, India, and Indochina. The second clade, bearing two pollinia, included the sections Phalaenopsis, Polychilos, and Fuscatae, of which are distributed in Malaysia, Indonesia, and the Philippines. In addition, the biogeography of the genus Phalaenopsis is congruent with the historical geology of the distribution regions of this genus as well. According to molecular evidences, biogeography, historical geology, and the evolutionary trend of pollinia number of orchid, evolutionary trends of the genus Phalaenopsis were deduced. The subgenus Aphyllae was suggested to be the origin of Phalaenopsis and South China was suggested to be the origin center of Phalaenopsis. In addition, there were two dispersal pathways of Phalaenopsis from the origin center to Southeast Asia. In one pathway, Phalaenopsis species dispersed from South China to Southeast Asia, in particular the Philippines, using Indochina, older lands of the Philippines (Mindoro, Palawan, Zamboanga, etc.) as steppingstones, from which the subgenus Phalaenopsis developed. In the other pathway, Phalaenopsis species dispersed from South China to Southeast Asia, in particular Indonesia and Malaysia, using the Malay Peninsula as a steppingstone, from which the subgenus Polychilos developed. Furthermore, molecular data and geological dating were used to estimate the substitution rates of DNA from the genus Phalaenopsis based on the hypothesis of the molecular clock. The substitution rates of both ITS and cpDNA data from the genus Phalaenopsis were 2.4~4.7 x 10-9 and 3.9~7.8 x 10¡V10 substitutions/site/year, respectively. The substitution rates of ITS data of the genus Phalaenopsis are approximately six times those of cpDNA. Based on the substitution rates, the divergence time among most of the P. lueddemanniana complex was estimated to have been during the Pleistocene. The section Deliciosae separated from the section Stauroglottis at 21~10.5 Mya. Furthermore, the phylogenetics of the close species of Phalaenopsis will be evaluated based on molecular data, involving three groups of close Phalaenopsis species, namely the P. amabilis complex, P. sumatrana complex, and P. violacea complex. For the first complex, the internal transcribed spacer 1 and 2 (ITS1+ITS2) regions of nuclear ribosomal DNA (nrDNA) were applied to evaluate the phylogenetics of the P. amabilis complex, namely P. amabilis, P. amabilis subsp. moluccana, P. amabilis subsp. rosenstromii, P. aphrodite, P. aphrodite subsp. formosana, and P. sanderiana. Based on molecular data, each of species/subspecies from the P. amabilis complex with the exception of P. aphrodite and its subspecies could be separated from each other. Phalaenopsis aphrodite from different locations and its subspecies could not be separated from each other, but all of them were separable from different populations/subspecies of P. amabilis. In addition, P. sanderiana was nested within both P. amabilis and its subspecies. These results do not support P. sanderiana being treated as a separate species from P. amabilis. In addition, I suggest that P. aphrodite is the origin of the P. amabilis complex and originated in the Philippines. Phalaenopsis amabilis and P. sanderiana descended from P. aphrodite (or its ancestor). Based on the phylogenetic tree, evolutionary trends of the P. amabilis complex were suggested. Within evolutionary trends of P. amabilis complex, two different lineages with different dispersal pathways were suggested. First, P. aphrodite, dispersed into Palawan and evolved to be P. amabilis, thereafter further dispersing into Borneo and Sumatra. Second, P. aphrodite dispersed into southern Mindanao and evolved into P. sanderiana, thereafter further dispersing into Sulawesi and New Guinea, from which P. amabilis subsp. moluccana and P. amabilis subsp. rosenstromii developed, respectively. For the second complex, the phylogenetic relationship of the P. sumatrana complex, namely P. sumatrana, P. corningiana, and P. zebrina, was detected based on the ITS1 and ITS2 regions of nrDNA, the intron of trnL, and the IGS of atpB-rbcL of cpDNA. The P. sumatrana complex includes the two species of P. sumatrana and P. corningiana, as well as a problem species, P. zebrina, according to the concepts of Sweet (1980) and Christenson (2001). Based on the phylogenetic tree inferred from the ITS sequence, accessions of P. sumatrana cannot be separated from those of P. corningiana. Furthermore, accessions of P. zebrina can be separated from those of both P. sumatrana and P. corningiana. In addition, analyses of both sequences of the trnL intron and atpB-rbcL IGS of cpDNA apparently cannot discriminate among these three species of the P. sumatrana complex. Based on the molecular data of this study, plants of P. zebrina might be treated as a separate species from both P. sumatrana and P. corningiana. In the evolutionary trend of the P. sumatrana complex, plants of P. zebrina were deduced to be the relative origin group of the P. sumatrana complex based on the phylogenetic tree and biogeography. In addition, plants of both P. sumatrana and P. corningiana might have descended from plants of P. zebrina. For the third complex, the phylogenetic trees inferred from the internal transcribed spacer 1 and 2 (ITS1+ITS2) regions of nuclear ribosomal DNA (nrDNA), the intron of trnL, and the intergenic spacer of atpB-rbcL of chloroplast DNA (cpDNA) were used to clarify the phylogenetic relationships of the P. violacea complex. The complex includes the two species of P. violacea and P. bellina, according to the concept of Christenson (2001). Based on the phylogenetic tree inferred from the ITS sequence, P. bellina could not be separated from most populations from P. violacea with the exception of the population distributed on Mentawai Is., Indonesia. In addition, analyses of both the intron of trnL and the IGS of atpB-rbcL of cpDNA apparently could not discriminate among the three species of the P. sumatrana complex. Based on the morphological characters, P. violacea from Mentawai Is. bears a long floral rachis and was separable from the other groups of the P. violacea complex. Therefore, the results in this study have a trend to treat the population of Mentawai Is. of the P. violacea complex as a separate species from P. violacea. In the evolutionary trend of the P. violacea complex, Mentawai plants of this complex might be descended from those of Sumatra/the Malay Peninsula according to the phylogenetic analysis and biogeography.
226

Revision of the mole genus Mogera (Mammalia: Lipotyphla: Talpidae) from Taiwan

Kawada, Shin-ichiro, Shinohara, Akio, Kobayashi, Shuji, Harada, Masashi, Oda, Sen-ichi, Lin, Liang-Kong 05 1900 (has links)
No description available.
227

Phylogeny and Biogeography of the Capricornis swinhoei Based on Mitochondrial DNA Sequences

Shiu, Shiou-Min 23 August 2002 (has links)
Abstracts Capricornis swinhoei is one of the indangered wild animals in Taiwan. The objective of this study is using molecular biology and morphology methods to analyze the genetic diversity, observed population structure, differentiation and biogeographic relationships among the population of Capricornis swinhoei. Samples used in this study were collected from the Central Mountains located in Taiwan. DNA sequences (1099 bp) from the mitochondrial DNA (mtDNA) control region, D-loop, were used to test the phylogeographic relationships among the Capricornis swinhoei. A phylogenetic tree was constructed on the basis of GCG-Seq Web and MEGA softwares. In addition, distance analyses, neighbor-join, and maximum parsimony to resolve these phylogenetic relationships were performed. The C. sumatraensis and C. crispus sequence were also determined and used as the outgroups. Our findings clearly demonstrate that Capricornis swinhoei can be clustered into two groups, north and south groups, and consistent with the truth of geographic isolation. The data obtained from this study may facilitate the program of wildlife conservation in Taiwan.
228

Taxonomy, distribution and reproduction of deep-sea eels in Taiwan waters and the phylogeny of Anguilliformes and Congroidei (Elopomorpha: Teleostei)

Chen, Yu-Yun 16 December 2002 (has links)
Abstract There are 43 species of deep-sea eels of 8 families, which including 1 species of Chlopsidae, 2 species of Muraenidae, 3 species of Ophichthide, 14 species of Congridae, 2 species of Muraenesocidae, 2 species of Nemichthyidae, 2 species of Nettastomidae, and 15 species of Synaphobranchidae, which its depth from 150 to 1200 meters and distribution from NE coast to the coast of Taitong and SW coast in Taiwan waters. Meanwhile, there are 3 new species (i.e., Dysomma longirostrum, Ophichthus aphotistos, Synaphobranchus sinensis) and 11 new records (i.e., Chilorhinchus platyrhynchus, Ophisurus macrorhynchus, Rhechias retrotincta, Macroceohenchelys brachialis, M. soela, Japonoconger sivicolus, nettastoma solitarium, Meadia abyssale, Dysommina rugosa, Ilyophis brunneus, Synaphobranchus kaupi) are described. The study in this part also recognize vertebral formulae is useful of elucidating the difference among the species. Morphology of swimbladder, stomatch, gonads of the deep-sea eels and the melanin layer of diaphragm are able to be as a distinctive character to find out the relationship among the species and the families. Most eels¡¦ reproductive season concentrate on September to November, whatever, the synaphobranchids have two reproductive seasons, which are on May and September to October. And it should become important to make further research on the above phenomenon. True eels (anguilliforms) form a monophyletic taxon from 16 apomorphic characters, e.g., Well-developed olfactory bulbs, lateral-protruded telencephalon, large-sized tectum, a distinct gap between telencephalon and tectum, reduced neural arch, hamel arch, and uroneural, triangled urostyle, epural absent, convergent hypural, fused hypural 1-2 and hypural 3-4-5, gap between hypural 1-2 and parhypural, and a gap between hypural 1-2 and hypural 3-4-5. The present study also find (1) Muraenoidei and angulloidei are a sister ¡Vgroup by sharing a slit between telencephalon and tectum, smaller olfactory bulb and lobe, and slit on area posttrema; (2)Congroidei is a monophyletic group by sharing an oval tectum, large cerebellum, and ungrooved area postrema, fusion of hypural 3, 4, and 5; (3) Congroidea and Synaphobranchoidea share a fusion of parhypural with hypural 1 and a concave present between uroneural and hypural, which should be treated as a sister group; (4) most eels of Congridae share a FS-caudal-fin and should be treated as a clade; (5) Most eels of Ophichthidae share a reduced and degraded caudal-fin, which should be monoplyletic; (6) Synaphobranchinae¡BSimenchelyinae and Ilyophinae, uniquely sharing well¡Vdeveloped olfactory bulb, small telencephalon, lateral protrusion of telencephalon well developed, and cerebellum folded posteriorly, a CLC- caudal-fin and elevated hypural 3-4-5, and fusion of hypural 4 and 5, are belong to a monophyletic group; (7) a gap between parhypural and hypural 1 indicate Simenchelyinae and Ilyophinae should be treated as a sister group; (8) Eurypharynx, Cyema, and Monognathus sharing a reduced caudal fin and brain, which need further research to elucidate their relationship; (9) Dark-red saccus vasculosus appears to recommend a close relationship between Gavialiceps taeniola and duckbill eels. (10) A disc-like hypophysis suggests the eels, Albula, Pterothrissus, Notacanthus, Megalops, and Elops are closely related groups; (11) Albula, Pterothrissus, Megalops, and Elops share a distinct morphological type of tectum and cerebellum and they should be treated as closely related groups; (12) The brains¡¦ gross morphology of Albula, Pterothrissus, Megalops, and Elops are well developed, a correlation distinctly similar to that of the Clupea which need further study on the relationship among the taxa mentioned above and the Clupeiformes.
229

Structure-based methods for the phylogenetic analysis of ribosomal RNA molecules

Gillespie, Joseph James 01 November 2005 (has links)
Ribosomal RNA (rRNA) molecules form highly conserved secondary and tertiary structures via rRNA-rRNA and rRNA-protein interactions that collectively comprise the macromolecule that is the ribosome. Because of their cellular universality, rRNA molecules are commonly used for phylogeny estimations spanning all divergences of life. In this dissertation, I elucidate the structure of several rRNAs by analyzing multiply aligned sequences for basepair covariation and conserved higher order structural motifs. Specifically, I predict novel structures for expansion segments D2 and D3 of the nuclear large subunit rRNA (28S) and variable regions V4-V9 of the nuclear small subunit rRNA (18S) from from 249 galerucine leaf beetles (Coleoptera: Chrysomelidae). I describe a novel means for characterizing regions of alignment ambiguity that improves methods for retaining phylogenetic information without violating nucleotide positional homology. In the program PHASE, I explore a variety of RNA maximum likelihood models using the 28S rRNA dataset and discuss the utitilty of these models in light of their performance under Bayesian analysis. I conclude that seven-state models are likely the best models to use for phylogenetic estimation, although I cannot determine with confidence which of the two seven-state models (7A or 7D) is better. Evaluation of the unpaired sites within both rRNAs in Modeltest provided a similar model of evolution for these non-pairing regions (TrN+ I+G). In addition, a sequenced region of the mitochondrial cytochrome oxidase I gene (COI) from the galerucines was evaluated in Modeltest, with each codon position modeled separately (GTR+I+G for positions 1 and 2, GTR+G for position 3). The combined galerucine dataset (28S+18S rRNA helices, 28S+18S rRNA unpaired sites, COI 1st, 2nd and 3rd positions) provided for two mixedmodel Bayesian analysis of five discretely-modeled partitions (using 7A and 7D). The results of these analyses are compared with those obtained from equally weighted parsimony to provide a robust phylogenetic estimate of the Galerucinae and related leaf beetle taxa. Finally, the odd characteristics of strepsipteran 18S rRNA are evaluated through comparison of 12 strepsipterans with 163 structurally-aligned arthropod sequences. Among other interesting results, I identify errors in previously published strepsipteran sequences and predict structures not previously known from metazoan rRNA.
230

Phylogenetic analysis of tribe habrolepidini and revision of Homalopoda and Ceraptroceroideus (Hymenoptera: Encyrtidae)

Rodriguez Velez, Beatriz 12 April 2006 (has links)
A taxonomic and phylogenetic study of the tribe Habrolepidini is described. A cladistic analysis was carried out in order to establish the phylogenetic relationships of the supraspecific taxa of the tribe. An illustrated key for the identification at the level of genera is included. Based on the results of the phylogenetic analysis, the diagnosis and taxonomic descriptions of the recognized taxa are presented. A single most parsimonius parsimony tree was obtained from the cladistic analysis based on 67 morphological characters, generated by a two-step procedure using PAUP. Initially, heuristic searches considering all characters with equal weights resulted in three equally parsimonious trees. Then the method of successive approximation weighting was applied to the three trees. The values of statistic parameters of the most parsimonious tree are: length = 582 steps; consistency index = 0.4966, retention index = 0.5850. The results support the hypothesis that the tribe Habrolepidini is monophyletic. It is defined by the presence of a specialized ventral mandibular tooth that is formed through modification of a seta into a stout socketed spine and three more unambiguous characters, clava length from 2.57 to 3.28, small hexagonal sculpture of scutellum and sensilla in three circles in a straight line. The inclusion of the genera Anthemus, Arrenophagoidea, Arrenophagus, Thomsonisca and Zaomma into Habrolepidini is supported by the presence of the mandibular tooth or by sister group relationships to other taxa with the mandibular tooth. The revision of the genera Ceraptroceroideus and Homalopoda is included; the taxonomic revision of each genus includes a key, diagnosis, descriptions and illustrations for all the species.

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