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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.
11

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.
12

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.
13

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.
14

Molecular phylogenetics and taxonomic issues in dragonfly systematics (Insecta: Odonata)

Hovmöller, Rasmus January 2006 (has links)
Dragonflies (Odonata) are one of the ancestral groups of extant insects. They represent one of the three most basal branches in the phylogeny of winged insects. The other two groups are the Ephemeroptera, mayflies, and Neoptera, the latter which covers the remaining winged insects. The first paper is about the phylogenetic position of Odonata in relation to the other basal insect clades using 18S and 28S rDNA sequences. It was demonstrated that there are under certain parameters a strong statistical support for a sister-group relationship between Odonata and Neoptera forming the group Palaeoptera. The second paper is about the phylogeny of the Holarctic dragonfly Leucorrhinia. Dragonfly larvae are frequently equipped with spines on the abdomen, with great variation in spinyness between species. From an analysis of sequences of ITS and 5.8S rDNA it was found that spines have been lost at least twice in Leucorrhinia, in the European L. rubicunda and again in a clade of North American species. The third paper is on the subfamily Ischnurinae (Odonata: Coenagrionidae), a group dominated by the two larger genera Ischnura and Enallagma along with several mono- or oligotypic genera. From the presented molecular study, using mitochondrial 16S rDNA and COII sequences, it is demonstrated that Ischnurinae, and Ischnura are monophyletic. Enallagma is not monophyletic, and the genus name Enallagma should be restricted to the E. cyathigerum clade. he fourth paper is a catalog of the genus Coenagrion, with full information on synonymy, type material and bibliographical data. The fifth paper is an appeal to the International Commission on Zoological Nomenclature to suppress the genus group name Agrion. The letter of appeal elucidates the priority of Agrion, and demonstrates why it has fallen out of use. A case if made for why Agrion should be placed on the list of unavailable names, and Calopteryx given full validity.
15

Combinatorial Aspects of Leaf-Labelled Trees

Humphries, Peter John January 2008 (has links)
Leaf-labelled trees are used commonly in computational biology and in other disciplines, to depict the ancestral relationships and present-day similarities between both extant and extinct species. Studying these trees from a mathematical perspective provides a foundation for developing tools and techniques that have practical applications. We begin by examining some quartet problems, namely determining the number of quartets that are required to infer the structure of a particular supertree. The quartet graph is introduced as a tool for tackling quartet problems, and is subsequently used to give new characterisations of compatible, definitive and identifying quartet sets. We then turn to investigating some properties of the subtrees induced by a collection of trees. This is motivated in part by the problem of reconstructing two or more trees simultaneously from their combined collection of subtrees. We also use some ideas drawn from Ramsey theory to show the existence of arbitrarily large common subtrees. Finally, we explore some extremal properties of the metric that is induced by the tree bisection and reconnection operation. This includes finding new (asymptotically) tight upper and lower bounds on both the size of the neighbourhoods in the metric space and on the diameter of the corresponding adjacency graph.
16

Evolutionary analysis of the relaxin peptide family and their receptors

Wilkinson, Tracey Nicole January 2006 (has links) (PDF)
The relaxin-like peptide family consists of relaxin-1, 2 and 3, and the insulin-like peptides (INSL)-3, 4, 5 and 6. The evolution of this family has been controversial; points of contention include the existence of an invertebrate relaxin and the absence of a ruminant relaxin. Using the known members of the relaxin peptide family, all available vertebrate and invertebrate genomes were searched for relaxin peptide sequences. Contrary to previous reports an invertebrate relaxin was not found; sequence similarity searches indicate the family emerged during early vertebrate evolution. Phylogenetic analyses revealed the presence of potential relaxin-3, relaxin and INSL5 homologs in fish; dating their emergence far earlier than previously believed. Furthermore, estimates of mutation rates suggested that the expansion of the family (i.e. the emergence of INSL6, INSL4 and relaxin-1) during mammalia was driven by positive Darwinian selection. In contrast, relaxin-3 is constrained by strong purifying selection, implying a highly conserved function. (For complete abstract open document)
17

PHYLOGENY OF PLANIGALE (MARSUPILIA: DASYURIDAE), A MULTIGENE APPROACH

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.
18

Phylogenetic revision of the genus Cherokia (Chamberlin, 1949) (Polydesmida: Xystodesmidae)

Vasquez Valverde, Luisa Fernanda 02 June 2021 (has links)
The family Xystodesmidae (Polydesmida) includes 521 species with a center of diversity concentrated in the Appalachian Mountains. Within this family, the genus Cherokia, a monotypic taxon with the type species Cherokia georgiana, is divided into three subspecies. The last revision of this genus was made by Richard Hoffman in 1960. Here, I used morphological and molecular data sets to review the genus, and evaluate whether it is a monophyletic group. I included material from literature records and three natural history collections. Newly collected samples were obtained through a citizen science project. Morphological characters such as the shape of the paranota, body size, and coloration were evaluated. Seven gene loci were used to estimate a molecular phylogeny of the genus, and a species delimitation analysis was used to evaluate the status of the subspecies. The geographical range of Cherokia was expanded to include a newly reported state (Virginia) and ca. 160 new localities compared to the previously known range. Morphological characters such as the shape of the paranota and body size that were historically used to establish subspecies, showed a direct relation with geographical distribution and elevation (clinal variation), but not with the phylogeny. Coloration was variable and did not accord with geography or phylogeny. The phylogeny recovered a monophyletic lineage, and the species delimitation test supports a single species. The molecular and morphological evidence showed that Cherokia is a monotypic genus with the sole species Cherokia georgiana being geographically widespread and highly variable in its morphology / Master of Science in Life Sciences / Millipedes are a mega-diverse group of soil dwelling animals that feed on leaf litter. The Appalachian Mountains has a huge diversity of millipedes, in particular those in the family Xystodesmidae. Within this family, I studied the genus Cherokia, commonly known as "Georgia flat-backed millipedes". The single species in this group, Cherokia georgiana, is divided into three subspecies. The last thorough study of this genus was done by Richard Hoffman in 1960, so a modern analysis with DNA sequencing was needed to test subspecies boundaries. Here, I used hundreds of specimens from three natural history museums, and fresh specimens obtained for DNA sequencing with the help of citizen scientists. I measured the shape and size of the body and coloration patterns to determine if they were related to the geographical distribution of Cherokia. I used DNA sequencing to make an evolutionary tree of the genus. I found Cherokia individuals in Virginia for the first time and found ca. 160 new sites or locations not reported previously. The shape and size of the body was related to millipede location and elevation. Coloration was not related to geography or phylogeny, and in some localities, multiple color patterns co-existed. The genetic information from DNA sequencing indicated that all Cherokia were more closely related to each other than to any other millipede genus. In conclusion, I found that the genus Cherokia is a single species, Cherokia georgiana, that has a wide geographical distribution and a considerable diversity of body shape and color. Diversity of shape and color does not reflect subspecies boundaries but instead reflects intra-population and geographic variation.
19

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
20

GEOGRAPHIC DISTRIBUTION AND MOLECULAR PHYLOGENETICS OF SEXUAL AND PARTHENOGENETIC POPULATIONS OF CAMPELOMA DECISUM (GASTROPODA, VIVIPARIDAE), A NORTH AMERICAN FRESHWATER SNAIL

Bower, Aaron Mikkael 01 May 2022 (has links)
The Red Queen hypothesis posits that, despite its costs, sexual reproduction is ubiquitous because it yields genotypic variation that can be adaptive in spatially or temporally heterogenous environments. Despite this, some metazoan species engage in facultative and even obligate cloning; investigation of these species can shed light on the conditions in which cloning might be an adaptive strategy. Freshwater snails are excellent study species for exploration of these questions due to their variable reproductive modes, relative ease of collection, and low vagility, leading to the ability to gather genetically distinct groups within a small geographic area. Campeloma decisum is a North American freshwater snail comprising both sexual populations, containing males and females, and parthenogenetic populations, containing only females. These two reproductive modes have been observed to be geographically grouped, with the parthenogens found in northern, formerly glaciated regions, and the sexuals living further south. The goal of this study was to obtain representatives from both sexual and parthenogenetic populations and perform phylogenetic analyses to gain insight into the origin of parthenogenesis within this group and elucidate any cryptic genetic diversity. Eleven populations of C. decisum were sampled and 46 cox1 sequences were obtained from them. These data were combined with Campeloma cox1 sequences from GenBank and maximum-likelihood trees were obtained using IQ-TREE. The resulting trees supported distinct sexual and parthenogenetic clusters, separated by relatively long internal branches. However, the outgroup branch was long, and SOWH tests 1) suggest that the position of the root of Campeloma cannot be determined with these data and 2) reject a clade comprising all C. decisum sequences. C. decisum harbors cryptic genetic diversity to the extent that it seems to comprise at least two genetically distinct lineages.

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