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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.

Phylogenomics of Oceanic Bacteria

Viklund, Johan January 2013 (has links)
The focus of this thesis has been the phylogenomics and evolution of the Alphaproteobacteria. This is a very diverse group which encompasses bacteria from intraceullar parasites, such as the Rickettsiales, to freeliving bacteria such as the most abundant bacteria on earth, the SAR11. The genome sizes of the Alphaproteobacteria range between 1 Mb and 10 Mb. This group is also connected to the origin of the mitochondria. Several studies have placed the SAR11 clade together with the Rickettsiales and mitochon- dria. Here I have shown that this placement is an artifact of compositional heterogeneity. When choosing genes or sites less affected by heterogeneity we find that the SAR11-clade instead groups with free-living alphaproteobacteria. Gene-content analysis showed that SAR11 was missing several genes for recombination and DNA-repair. The relationships within the SAR11- clade has also been examined and questioned. Specifically, we found no support for placing the taxon referred to as HIMB59 within the SAR11. Ocean metagenomes have been investigated to determine whether the SAR11-clade is a potential relative of the mitochondria. No such relationship was found. Further I have shown how important it is to take the phylogenetic relationships into account when doing statistical analyzes of genomes. The evolution of LD12, the freshwater representative of SAR11, was investigated. Phyloge- nies and synonymous substitution frequencies showed the presence of three distinct subclades within LD12. The recombination to mutation rate was found to be extremely low. This is re- markable in light of the very high rate in the oceanic SAR11. This is may be due to adaptation to a more specialized niche. Finally we have compared structure-based and sequence-based methods for orthology pre- diction. A high fraction of the orfan proteins were predicted to code for intrinsically disordered proteins. Many phylogenetic methods are sensitive to heterogeneity and this needs to be taken into ac- count when doing phylogenies. There have been at least three independent genome reductions in the Alphaproteobacteria. The frequency of recombination differ greatly between freshwater and oceanic SAR11. Forces affecting the size of bacterial genomes and mechanisms of evolu- tionary change depend on the environmental context.

The study of genetic variation in trees using the random amplified polymorphic DNA (RAPD) technique

Allnutt, Theodore Richard January 1996 (has links)
No description available.

Molecular systematics of the galliformes, with particular reference to the endemic Vietnamese Gallopheasants (Lophura) and the Green Peafowl (Pavo muticus)

Scott, Euan Andrew January 1999 (has links)
No description available.

Exploring the Evolutionary History of North American Prairie Grouse (Genus: Tympanuchus) Using Multi-locus Coalescent Analyses

Galla, Stephanie J. 05 1900 (has links)
Conservation biologists are increasingly using phylogenetics as a tool to understand evolutionary relationships and taxonomic classification. The taxonomy of North American prairie grouse (sharp-tailed grouse, T. phasianellus; lesser prairie-chicken, T. pallidicinctus; greater prairie-chicken, T. cupido; including multiple subspecies) has been designated based on physical characteristics, geography, and behavior. However, previous studies have been inconclusive in determining the evolutionary history of prairie grouse based on genetic data. Therefore, additional research investigating the evolutionary history of prairie grouse is warranted. In this study, ten loci (including mitochondrial, autosomal, and Z-linked markers) were sequenced across multiple populations of prairie grouse, and both traditional and coalescent-based phylogenetic analyses were used to address the evolutionary history of this genus. Results from this study indicate that North American prairie grouse diverged in the last 200,000 years, with species-level taxa forming well-supported monophyletic clades in species tree analyses. With these results, managers of the critically endangered Attwater's prairie-chicken (T. c. attwateri) can better evaluate whether outcrossing Attwater's with greater prairie-chickens would be a viable management tool for Attwater's conservation.


Hintz, Ashley 01 May 2016 (has links)
Relationships within Planigalini have not been fully resolved in previous studies that employed only a few (1-3) genes. I employ a mutligene approach that has shown to be robust for other dasyurid tribes. An analysis was undertaken to assess relationships among the currently recognized Planigale species and two potentially new species from the Pilbara and Mount Tom Price regions of Western Australia. This study uses seven genes for phylogenetic estimation. An expanded dataset of mitochondrial 16S DNA sequences from across Australia was also analyzed to assess phylogeographic patterns in Planigale species. Internal nodes from concatenated and species tree analyses are not well supported. This group may be subject to ILS or past introgression; however more data are needed to differentiate between these phenomena. Results from individual genes do not agree on a single topology of relationships. The results from nuclear genes include strong support for internal nodes from protamine P1, but not beta fibrinogen intron 7 and inter-photoreceptor retinoid-binding protein. The mitochondrial gene analyses show few nodes as well supported, but agree that P. maculata and P. novaeguineae are sisters. The expanded 16S dataset agrees with previous work in that there are regional groupings of P. maculata haplotypes. Current ranges for planigale species are poorly documented and the entire genus warrants further investigation to determine whether there are more species than current taxonomy recognizes.

Systematic studies in the Boea group

Puglisi, Carmen January 2014 (has links)
Since it was first published, many additional species have been ascribed to the genus Boea Comm. ex Lam. As the genus grew in size, it also grew in morphological diversity until it was recircumscribed and became the source of a number of new segregate genera. Today, the Boea group (i.e. Boea, the segregate genera and other close relatives) comprises over 200 species in some 15 genera, found from China to Australia and throughout Malesia from Sumatra to the Solomon Islands. Previous molecular studies suggested a much more complex structure to the clade than previously thought. Here the most up to date phylogeny, covering all the genera known to belong to the Boea group, is presented. Parsimony and Bayesian Inference were the chosen approaches to the phylogenetic analysis of nine matrices generated using DNA data from 277 accessions. The markers used were the nuclear ITS and the chloroplast regions trnL-trnF (intron and spacer) and ndhF-rpl32-trnLUAG. The results show important discrepancies between the current taxonomy of the group and the clades delineated by the phylogeny. In an attempt to establish a natural classification of Boea and its allies, taxonomic and nomenclatural work was carried out on most of the genera found to be non-monophyletic. Boea Comm. ex Lam. is divided into two genera. The recircumscribed Boea is restricted to the group of taxa found in New Guinea, Solomon Islands and Australia. The genus is fully revised and contains 11 species, including the newly described Boea morobensis C.Puglisi. The Southeast Asian group of species formerly attributed to Boea, centred in Thailand, is given the resurrected name Dorcoceras Bunge. To the four species traditionally known to belong to this group, three new ones are added. These are Dorcoceras brunneum C.Puglisi, D. glabrum C.Puglisi and D. petiolatum C.Puglisi. Damrongia is deeply transformed with the synonymisation of D. cyanantha Triboun in D. trisepala (Barnett) D.J.Middleton & A.Weber, and the inclusion of Boea clarkeana Hemsl. and the three Asian species of Streptocarpus Lindl., S. orientalis Craib, S. burmanicus Craib and S. sumatranus B.L.Burtt. As a result of the phylogenetic study, a new genus, Middletonia C.Puglisi, is segregated from Paraboea. Middletonia consists of five species, including the newly described Middletonia glebosa C.Puglisi, and has its centre of distribution in Thailand. Finally, Paraboea (C.B.Clarke) Ridl. is recircumscribed with the inclusion of the genera Trisepalum C.B.Clarke and Phylloboea Benth. In order to limit the number of new combinations needed and maintain clarity, the name Paraboea was conserved against both Phylloboea and Trisepalum. In addition to the 15 new combinations in Paraboea, a new species from the Philippines, P. zamboangana C.Puglisi, is described.

Phylogenetic Analysis of Iliamna (Malvaceae) Using the Internal Transcribed Spacer Region

Bodo Slotta, Tracey A. 26 May 2000 (has links)
The genus Iliamna Greene has a taxonomically complex history. Since its desciption in 1906, the genus was not recognized for some time, several species were initially placed into other genera, and the species status of a few was questioned. Today, eight species of Iliamna are recognized. Six species are located in western North America and two are found isolated to the east. Species in Iliamna are very similar morphologically with only a few characters distinguishing several as separate entities. The need for systematic study became apparent since all but one species are considered rare or endangered. Also, the differentiation between two endangered species, I. corei and I. remota, was unclear in a previous study using random amplified polymorphic DNA fragments. Of the western species, four overlap in distribution (I. crandallii, I grandi ora, I. longisepala, and I. rivularis) and their recognition as separate species has been questioned. The focus of this study was to develop a phylogeny for Iliamna using sequences from the internal transcribed spacer region (ITS) of the nuclear ribosomal RNA genes in order to determine its biogeographical and evolutionary history. Cladistic analysis was performed and the resulting phylogeny is presented. The ITS data provide new insights in the origination of the genus and its distribution. In Iliamna, the ITS region is 677 base pairs long with 120 sites providing information in the formation of phylogenetic trees. Iliamna forms a well-supported clade distinct from related genera and is monophyletic. Three well-supported groups are formed. One contains representatives from the Pacific Northwest. Another contains all of the remaining species with the third clade nested therein. This last clade contains the two eastern species, I. corei and I. remota, but there is not enough variability to support the divergence of these taxa as distinct species. There is also not sufficient variability in the ITS region to identify the western species I. crandallii, I. grandi ora, I. longisepala and I. rivularis as distinct entities. / Master of Science

Description and phylogenetic analysis of a new alligatoroid from the Eocene of Laredo, Texas

Guest, Rachel L. 01 May 2014 (has links)
No description available.

Development of Molecular and Morphological Resources for Identification and Monitoring of Freshwater Mussel Species in the Genera Fusconaia and Pleurobema in the Green River, Kentucky

Hyde, Miluska Olivera 11 January 2021 (has links)
Freshwater mussel species in the genera Fusconaia and Pleurobema are particularly challenging to identify in the field. In this study, mussels from these genera were collected from the Green River, Kentucky for genetic and morphological analyses. I used molecular markers to detect any cryptic species within these genera and to test for genetic differentiation between two closely related nominal taxa P. rubrum and P. sintoxia using both mitochondrial (ND1, COI, 16S rRNA) and nuclear (ITS1) DNA sequences. After species identification, I used microsatellite DNA markers to estimate genetic diversity and effective population sizes (Ne) of species of Pleurobema. I used microsatellite primers that were developed for P. clava and P. pyriforme in previous studies, as well as microsatellites that I developed for P. plenum. Finally, I assessed morphological variation in my study species and developed dichotomous keys for the identification of both live mussels and shells. My results suggest that P. rubrum and P. sintoxia are the same species based on the mitochondrial DNA analyses, as there were few genetic differences between them. My results showed phylogenetically distinct lineages for F. flava, F. subrotunda, P. cordatum and P. plenum but no cryptic species were detected in the Green River. Current and contemporary Ne showed that these species have large population sizes that should allow for avoiding inbreeding and maintaining their evolutionary potential. Large genetic diversity as well as long-term effective population size could be the result of these species historically occurring as much larger assemblages that extended into the Ohio River and its numerous tributaries. The last objective was to assess morphometrical differences among these species. Using Canonical Variate Analysis, I found discernable morphological differences between the investigated species of Fusconaia and Pleurobema. The two Fusconaia species were morphologically different from the Pleurobema species. However, the Canonical Variate Analysis did not show differences among the Pleurobema species. I used decision tree analysis to develop a dichotomous tree, and random forest analysis was used to aid in the development of a dichotomous key by finding the most important diagnostic characters to distinguish these mussels. I then used the less subjective and easier to identify characters for the development of my dichotomous keys for live mussels and shells. However, both keys need to be tested in the field to determine their effectiveness. I could not separate P. rubrum and P. sintoxia mussels for morphometric analysis due to the lack of genetic differentiation and the inconsistent identification by the experts. However, I did describe a few individuals that look like P. rubrum and P. sintoxia to the eye of the experts. The description of these individuals matched previous descriptions of these mussels. Future studies need to assess taxonomic relationships among these species using genomics approaches, which might result in better node resolution. High genetic diversity and large effective population numbers for Pleurobema species suggest that these species' populations are genetically healthy. However, these results need to be interpreted carefully, and I therefore recommend additional studies to assess life history, habitat, host-fish availability, and current reproduction of these mussels in the Green River. / Doctor of Philosophy / Freshwater mussels offer important ecosystem services for humans to include water purification, nutrient storage and recycling, and mussels are part of the aquatic food web. In addition, freshwater mussels are indicators of ecosystem health. Because they rely on fish hosts to complete their complex life cycle, conservation of freshwater mussel species is particularly challenging. In this study, I focused my attention on freshwater mussel species commonly known as "pigtoes" which belong to the genera Fusconaia and Pleurobema. These species are difficult to distinguish morphologically even by experts. Hence, my study used molecular genetic markers to first identify these species. To assess the size and genetic health of these populations, I estimated genetic diversity and effective population number (Ne). Finally, I developed dichotomous keys to identify live mussel specimens and shells of molecularly identified mussels. My genetic results showed that there are five species of pigtoes in the Green River, which include Rough Pigtoe (Pleurobema plenum), Ohio Pigtoe (P. cordatum), Pink Pigtoe/Round Pigtoe (P. sintoxia/rubrum), Long-Solid (Fusconaia subrotunda), and Wabash Pigtoe (F. flava). A sixth pigtoe species, the endangered clubshell (Pleurobema clava), also is extant in the upper Green River but was not included in the analyses due to its rarity in the river. My results suggest that these mussel populations are large and healthy enough to survive and to adapt over time. The morphometric analysis using Canonical Variate Analysis (CVA) resulted in differentiation between F. flava and F. subrotunda. These two Fusconaia species also were morphologically different from the investigated species of Pleurobema. Results of this analysis suggest that species in the Genus Pleurobema remain difficult to differentiate from each other. The lack of genetic differentiation and the inconsistency in the experts' identification of P. rubrum and P. sintoxia, did not provide enough information to separate these two putative species for morphometric analysis. However, I was able to describe a few individuals that looked like typical examples of these two species to the eyes of the experts. Future taxonomic studies should use next-generation sequencing, which would likely result in a better resolution of evolutionary relationships. Large Ne values for each species suggest that these populations are genetically healthy. However, these results need to be considered together with results of future studies on life history, habitats, abundance, and reproduction of these species in the wild. Finally, the dichotomous mussel identification keys are intended to support more accurate identification of these species in the Green River, KY but need to be field-tested by mussel biologists

Morphological and molecular determination of Fucus (Fucales, Heterokontophyta) biogeography across North American shores

Young, Robert George January 2009 (has links)
The genus Fucus (Phaeophyceae) has nine commonly accepted species, six of which inhabit North American shores: F. gardneri, F. serratus, F. distichus, F. evanescens, F. vesiculosus, and F. spiralis. Fucus inhabit the intertidal zones of the Atlantic, Pacific and Arctic Oceans and due to their highly plastic and morphologically simple phenotypes, are valuable candidates for molecular phylogenetic research. Furthermore, Fucus species are valuable for biogeographic investigations due to their relatively slow migration, limited dispersal range, and easily collected distribution. The closest ancestral species to the genus is a Pacific endemic Hesperophycus californicus supporting a North Pacific origin of the species (Serrão et al. 1999). However, a closer relationship between Atlantic and Arctic Fucus has been described casting doubt on the Pacific origins of the genus (Lindstrom 2001, Dunton 1992). The investigation of Fucus across this area is necessary to elucidate the apparent contradiction in the origin of the genus. Samples were collected from 79 locations across North American waters. The amplification of the divergent mtDNA spacer region was performed to assess taxonomic placement of 55 collected species and reconstruct the biogeography of North American Fucus species. Morphological analysis was also completed based on 21 measured characteristics in an attempt to support molecular analysis. Results of the study indicate two distinct lineages among collected samples. One lineage (F. spiralis and F. vesiculosus) with a distinct Atlantic origin and the second lineage (F. distichus and F. serratus) with a widely distributed F. distichus, and the Atlantic F. serratus. Morphological analysis and statistical support for these lineages was determined through discriminant analysis of the collected samples. Overall results determined biogeographic influences in the F. distichus species complex across Arctic, Pacific, and Atlantic regions with little apparent biogeographical influence within F. vesiculosus, F. serratus and F. spiralis. Closer phylogenetic relationships between Arctic and Atlantic samples were apparent as suggested by Lindstrom (2001) and Dunton (1992).

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