Browsing by Subject "Systematics"
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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 Phylogeny and biogeography of Paepalanthus subg. Platycaulon (Poales: Eriocaulaceae) in the high-Andean páramos of South America : a story of long-distance migration and rapid diversification(2016-08) Diaz Peña, Carmen Amalia; Simpson, Beryl Brintnall; Cannatella, David; Jansen, Robert; Mauseth, James; León, BlancaTropical Andes are located in northern South America and run from northern Chile and Argentina through Bolivia, Peru, Ecuador, Colombia and Venezuela. They are classified as a biodiversity hotspot and harbor more than 20,000 endemic species of plants. Páramos are ecosystems located above 2600 meters of altitude located on the northern portion of the tropical Andes starting in northern Ecuador through Venezuela. Páramos have been available for colonization since the Quaternary, ca. 4 mya, and currently have ca. 3,300 species of plants. The páramo flora is a mixture of tropical and temperate elements and only by studying them we are able to understand the evolutionary history behind the current páramo plant diversity. Erioculaceae is a pantropical family present in the páramos and other highland formations of South America such as campos de altitude in the Brazilian shield and the tepuis in the Guiana shield. The most speciose genus in the family is Paepalanthus, which is divided into six subgenera; P. subg. Platycaulon is the only subgenus with a disjunct distribution in the páramos and the campos rupestres in the Brazilian shield. Previous studies have reconstructed the evolutionary history of Erioculaceae, but their results about P. subg. Platycaulon are not conclusive because they did not include páramo species in their analyses. The main goal of the present study is to evaluate the monophyly of páramo species of Erioculaceae, as well as to investigate their age, origin and possible forces that could be driving their evolution in the páramos. In order to answer these questions, we used plastid and nuclear molecular markers as well as genome sequences to reconstruct the phylogenetic and biogeographical history of P. subg. Platycaulon. Our results show that páramos species of P. subg. Platycaulon are not monophyletic and most of them come from Brazilian ancestors and are 2 my old or less. Incongruence between plastid and nuclear genome data supports the hypothesis of gene flow between páramo species of P. subg. Platycaulon.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.