Browsing by Subject "Systematics"
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Item A systematic study of select species complexes of Eleocharis subgenus Limnochloa (Cyperaceae)(2009-05-15) Rosen, David JonathanA systematic study of two complexes of closely related species within Eleocharis subg. Limnochloa was conducted to better define poorly understood species and to lay the foundation for a worldwide revision of this group. Research utilized scanning electron microscopy (SEM), study of more than 2300 herbarium specimens and types from 35 herbaria, multivariate analysis, and field studies in the southeast United States and Mexico. Examination of achene gross- and micromorphology using SEM indicated a relationship among the species of the Eleocharis mutata complex (comprising E. mutata, E. spiralis, and E. cellulosa), their distinctness from the E. acutangula complex (comprising E. acutangula s.l. and E. obtusetrigona) and support the placement of all taxa studied within subg. Limnochloa. All species examined shared micromorphological characters typical of subg. Limnochloa. A systematic study of the worldwide morphological variation of E. mutata suggests it is represented by a single taxon throughout its distribution and is native to the New World and probably introduced in tropical Africa. The taxonomic relationship of Eleocharis mutata and E. spiralis was explored using discriminant analysis, PCA and phyto-geography, supporting the recognition of the two taxa as distinct at the rank of species. A systematic study of E. cellulosa suggests it is represented by a single taxon throughout its distribution, with an apparent Caribbean genotype distinguished by the presence of perianth bristles with retrorse spinules. A systematic study of the worldwide variation of E. acutangula s.l. resulted in its segregation into two infraspecific taxa, E. acutangula subsp. acutangula and E. acutangula subsp. breviseta, and two new South American species, E. neotropica and E. steinbachii. Nomenclatural history and lectotypification of certain taxa studied are discussed, and two basyionyms and two synonyms of accepted taxa are lectotypified. A taxonomic treatment is provided that includes a key, detailed descriptions and complete synonymy of each species, line drawings prepared from select specimens examined, and notes on habitat and distribution. Future research goals and needs are discussed.Item Advances in diapriid (Hymenoptera: diapriidae) systematics, with contributions to cybertaxonomy and the analysis of rRNA sequence data(2009-05-15) Yoder, Matthew JonDiapriids (Hymenoptera: Diapriidae) are small parasitic wasps. Though found throughout the world they are relatively unknown. A framework for advancing diapriid systematics is developed by introducing a new web-based application/database capable of storing a broad range of systematic data, and the first molecular phylogeny specifically focused at examining intrafamilial relationships. In addition to these efforts, a description of a new taxon is provided. Several advantages of digital description, including linking descriptions to an ontology of morphological terms, are highlighted. The functionality of the database is further illustrated in the production of a catalog of diapriid host associations. The hosts database currently holds over 450 association records, for over 500 named taxa (parasitoids and hosts), and over 180 references. Diapriids are found to be primarily endoparasitoids of Diptera emerging from the host pupa. Phylogenetic inference for a molecular dataset of 28S and 18S rRNA sequence data, derived from a diverse selection of diapriids, is accomplished with a new suite of tools developed for handling complex rRNA datasets. Several parsimony-based methodologies, including an alignment-free method of analyzing multiple sequences, are reviewed and applied using the new software tools. Diapriid phylogenetic relationships are shown to be broadly congruent with existing morphology-based classifications. Methods for analyzing typically excluded sequence data are shown to recover phylogenetic signal that would otherwise be lost and the alignment-free method performed remarkably well in this regard. Empirically, phylogenetic approaches that incorporate structural data were not notably different than those that did not.Item The comparative osteology and phylogenetic relationships of lepidosirenid lungfishes(2011-05) Criswell, Katharine Elizabeth; Bell, Christopher J., 1966-; Rowe, Timothy B.; Daeschler, Edward B.Lepidosirenidae is a clade of freshwater lungfishes that comprise the South American Lepidosiren paradoxa and four African species of the genus Protopterus. These two genera have been geographically separated since the Early Cretaceous break-up of Gondwana, but they share similar biology and skeletal morphology. The lepidosirenid species traditionally were distinguished by a combination of features such as head-to-body ratios, the number of pairs of vertebral ribs, and the presence or absence of external gills, but there are no published discrete skeletal characteristics and no published comparative studies including all extant species. I used High Resolution X-Ray Computed Tomography (CT), X-Ray photography, and alcohol-preserved, cleared-and-stained, and dry skeletal specimens from museum collections to describe the skeletal morphology of all species of lepidosirenid lungfishes in a comparative context. I digitally disarticulated the bones in each CT scan to compile a comprehensive comparative atlas of the cranial and pectoral elements of all extant lungfish. I discovered that the anocleithrum in Lepidosiren paradoxa, which was previously thought to be lacking, is actually present. I also identified skeletal differences between species in the frontoparietal, parasphenoid, supraorbital, and suboperculum. I incorporated those characters into the first morphological phylogenetic analysis to determine the interrelationships of the lepidosirenids. I also used previously published molecular sequence data from the ribosomal RNA gene 16s to run combined morphological and molecular phylogenetic analyses. To generate phylogenetic hypotheses using different types of data and different methods of determining phylogeny, I employed the maximum parsimony, maximum likelihood, and Bayesian inference methods. Lepidosirenidae is monophyletic in almost all analyses, Protopterus is monophyletic in each analysis, and Protopterus annectens and Protopterus aethiopicus are sister taxa in every analysis. The phylogenetic positions of Protopterus dolloi and Protopterus amphibius are incongruent in many of the analyses, which indicates that further examination of the skeletal variation and addition of molecular sequences of different genes is needed. Based on the comparative morphological atlas and the phylogenetic analyses, questions of lepidosirenid biogeography, morphological variation within lungfish, and better identification of lungfish fossils can now be investigated in a more rigorous context.Item Molecular systematics of Meconopsis Vig. (Papaveraceae): taxonomy, polyploidy evolution, and historical biogeography from a phylogenetic insight(2013-12) Xiao, Wei, active 2013; Simpson, Beryl BrintnallKnown as the Himalayan poppies or the blue poppies, Meconopsis is a genus with approximately 50 species distributed through the high altitude of the Himalaya and the Hengduan Mountains (SW China). This dissertation is a study of the systematics of Meconopsis primarily using molecular phylogenetic methods. DNA sequences of chloroplast matK, ndhF, trnL-trnF, rbcL, and nuclear ITS were collected to reconstruct the phylogenies of the genus. Results showed that traditional Meconopsis is a polyphyletic group and revealed extensive mismatches between the nuclear ITS tree and the chloroplast tree. Based on the phylogenies, the taxonomy of Meconopsis was revised, making Meconopsis monophyletic. Four new sections (sect. Meconopsis, sect. Aculeatae, sect. Primulinae, and sect. Grandes) were proposed as well as a species complex (M. horridula). The chloroplast phylogeny and a likelihood method (chromEvol) were applied to ancestral chromosome number estimation to reconstruct the polyploidy evolution history of the genus. The analysis recovered an ancient triploid ancestor shared by sect. Primulinae and sect. Grandes. A low-copy nuclear gene (GAPDH) network of Meconopsis was further reconstructed, which indicated that the ancient triploid ancestor was formed by hybridization. A hypothesis of reticulate history of Meconopsis was also proposed based on the GAPDH network. Using a reconstructed rbcL phylogeny of Ranunculales, the stem group of Meconopsis was estimated at ca. 22 Mya by molecular dating, which coincided with the time of Asian interior desertification and the onset of Asian monsoon. These climatic changes could possibly have been the impetus for the split between Meconopsis and its sister clade. Ancestral area reconstruction was further conducted using likelihood-based methods. The result indicated that Meconopsis originated in the Himalaya, most likely in the west Himalaya, followed by migration to the Hengduan Mountains.Item Molecular systematics of the Mexican tussilaginioid genera (Asteraceae: Senecioneae)(2012-08) Quedensley, Taylor Sultan; Simpson, Beryl Brintnall; Jansen, Robert K., 1954-The Mexican tussilaginioid group consists of 13 diverse genera of sunflowers (Asteraceae: Senecioneae) distributed from the USA to Panama, with most species occurring in montane regions from Central Mexico to Guatemala. Presently, 140 species in 13 genera are recognized with many of these species considered to be endemic to threatened pine-oak forest or cloud forest ecosystems. Sixty-two species within the study group were included in a combined phylogenetic analysis of two regions of the nuclear ribosomal repeat, the internal and external transcribed spacers. Fifty-two of these taxa were analyzed in a phylogenetic framework for the first time. The results from the combined nrDNA analysis (62 species in 12 genera in the combined analysis) strongly support the monophyly of the Mexican tussilaginioid group, however, the topology and hypothesis testing using constraint models indicate that the genera Pittocaulon, Psacaliopsis, and Roldana are not monophyletic. Telanthophora s.s. is monophyletic, although this genus is nested within Roldana s.s. Endemism is abundant among the clade with over half of the species restricted to relatively small geographic areas. Moreover, most members of the group (ca. 120 species, or 87%) are present in montane regions under immense pressure from human land use practices at or above 1500 meters in Mexico and Guatemala. Two of the genera from my study group, Pippenalia and Psacaliopsis were taxonomically assessed based on their morphological characters and the nrDNA results. A single species, Psacaliopsis purpusii, remains in the genus, while Pippenalia delphinifolia, Psacaliopsis macdonaldii, and P. pudica are transferred to Psacalium. Funstonia gen. nov. is here erected a new genus encompassing a single species with two varieties. Chloroplast genomes of Arnoglossum atriplicifolium, Roldana aschenborniana, R. barba-johannis, and Telanthophora grandifolia were sequenced with next generation sequencing in order to identify regions of variation and to compare the assemblies produced via de novo and reference-based methods. The reference-based assemblies were more complete than the de novo assemblies, and therefore the former sequences were utilized for phylogenetic analyses.Item Systematics and evolution of extinct and extant Pan-Alcidae (Aves, Charadriiformes) : combined phylogenetic analyses, divergence estimation, and paleoclimatic interactions(2011-08) Smith, Neil Adam; Clarke, Julia A.; Bell, Christopher J.; Cannatella, David C.; Rowe, Timothy B.; Sprinkle, JamesAlthough the ecological interactions and ethology of the wing-propelled diving seabirds known as the Alcidae (Aves, Charadriiformes) have been intensively studied, systematic studies of the clade have been overwhelmingly limited to extant taxa. Pan-Alcidae have the richest fossil record among Charadriiformes, with specimens representing more than 35 million years of evolutionary history. Morphometric and apomorphy-based taxonomic revision of previously named extinct pan-alcids along with description of new species of extinct pan-alcids facilitated refined estimates of species richness. Combined phylogenetic analyses of morphological and molecular sequence data including pan-alcid fossils elucidated the poorly understood evolutionary history of the clade. Divergence estimation analysis for Charadriiformes placed previously hypothesized episodes of pan-alcid radiation and extinction in context with proposed paleoclimatic drivers of alcid evolution.Item Trends in evolutionary morphology : a case study in the relationships of angel sharks and batoid fishes(2010-05) Claeson, Kerin Michele; Bell, Christopher J., 1966-; Rowe, Timothy B.; Hendrickson, Dean; Sprinkle, James; McEachran, John D.Chondrichthyans are cartilaginous fishes that include the extant chimaeras, sharks, and batoids, and their extinct relatives. In this dissertation, I examined the growth, development, and relationships of extinct and extant chondrichthyans. I reexamined the skeleton of fossil and fetal specimens of the angel sharks (Squatiniformes) and reanalyzed the current morphologically based hypothesis of chondrichthyan evolution, which conflicts with the current molecular based hypothesis. I did this by including extinct taxa and new characters based on dentition, and the ethmoid, occipital, pectoral, and vertebral skeleton. My results supported the pre-existing morphological hypothesis that angel sharks, saw sharks, and batoids form a clade. However, some of my new characters, particularly those based on the vertebral morphology, indicate that fetal and juvenile angel sharks do not share as many apomorphies with batoids as previously hypothesized from the examination of adults. I also examine the relationships of major groups within batoids, beginning with the construction of a hypothesis of the evolutionary history of electric rays (Torpediniformes). My results are consistent with previous rank-based classifications. However, they deviate from previous classifications depending on the criteria used to generate the hypothesis and on which taxon, or combination of taxa, were used to root the ingroup phylogeny. Because pectoral and vertebral morphology are so critical to morphological hypotheses, I also examined the growth and development of the synarcual cartilage in batoid fishes, with particular emphasis on the synarcual of skates (Rajiformes). My results demonstrate that calcification and chondrification do not proceed in the same order, temporally and spatially. Finally, I redescribe the extinct batoid †Cyclobatis, known only from the Cretaceous, and evaluate its phylogenetic position. My results indicate that †Cyclobatis, the oldest known rajid, is also the sister taxon to a clade of all known extant members of Rajidae. Furthermore, the inclusion of new characters, mainly derived from the synarcual, help to resolve the interrelationships of Rajidae.