Population Genetics of Vascular Epiphytes; Optimization of DNA Extraction and Cross Species Transference in Tillandsia usneoides

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dc.contributor.author Brown, Joshua Isaiah
dc.coverage.spatial United States en_US
dc.date.accessioned 2020-12-09T20:51:22Z
dc.date.available 2020-12-09T20:51:22Z
dc.date.issued 2020-10
dc.identifier.other 5EDE107A-0EAB-4B53-8352-0B2F8399D282 en_US
dc.identifier.uri https://hdl.handle.net/10428/4604
dc.description.abstract Vascular epiphytes are found in more than 70 different families and make up 9-10% of the 290,000 described species of vascular plants. Despite their significant contribution to vascular flora diversity, they have received far less attention in population genetic studies than their terrestrial counterparts. This study had three goals: (I) Provide a comprehensive literature review on the population genetics of vascular epiphytes to answer questions such as, which taxa have been surveyed and where did these studies take place? What types of molecular markers have been used? What types of population genetic measures have been reported? What are the general findings across different taxa? And what journals have published these sorts of studies? (II) Develop a DNA extraction technique for an ecologically and culturally important epiphytic plant, Tillandsia usneoides (Spanish moss) that produces high yields of DNA while also minimizing possible contaminants that could affect downstream processes. (III) Asses the utility of cross-species transference as a method to develop usable microsatellite DNA primers for T. usneoides. In the literature review, I found 25 published studies in 13 journals that studied population genetics of vascular epiphytes, representing three taxonomic families in seven countries and four continents. To date, seven types of molecular markers have been used. Interestingly, these markers do not follow typical usage trends that has been observed in other groups, with allozymes being used more frequently than microsatellite DNA, and with no published studies to date that have used SNPs. Taxonomic and geographic biases in the population genetic literature reflect general patterns observed in the ecological literature, with most studies conducted in North America and focused on Orchidaceae (41%), Polypodiaceae (36%) and Bromeliaceae (23%). Due to the diversity of life history strategies observed in epiphytes, it is difficult to generalize population genetic results across taxa; nevertheless, in ferns, there was evidence of high gene diversity and genotype frequencies that conformed to Hardy-Weinberg expectations, whereas results were more variable for orchids and bromeliads. It is difficult to generalize results across the different taxa studied, this is believed to be reflect the diversity of life history strategies observed in epiphytes. For the DNA extraction study, we found that a modified CTAB extraction produced the highest yield and highest quality DNA. Utilizing extracted DNA from T. usneoides, cross-species transference of microsatellite primers from seven different taxa in the family Bromeliaceae was assessed. Of the 36 primer sets that were screened, we identified 15 loci that produced fragments that were close in size to what was reported in the primer notes, but only 7 of the 15 loci produced polymorphic loci without other apparent abnormalities. For the seven loci, the number of alleles ranged from 2 to 12. Although limited in number, the primer sets that we identified should be sufficient for assessing broad scale population genetic patterns in T. usneoides. Keyword 1: Epiphytes Keyword 2: Cross-species transference Keyword 3: Tillandsia usneoides en_US
dc.description.tableofcontents I BACKGROUND 1 -- II POPULATION GENETICS OF VASCULAR EPIPHYTES 3 -- Introduction 3 -- Materials and Methods 5 -- Definition of an Epiphyte 5 -- Literature Search 6 -- Results 6 -- Geographic and Taxonomic Trends 6 -- Usage of molecular markers over time 7 -- Population Genetic Measures and Findings 7 -- Journal Type 9 -- Discussion 9 -- Conclusion 15 -- III OPTIMIZATION OF DNA EXTRACTION IN TILLANDSIA USNEOIDES 17 -- Introduction 17 -- Materials and Methods 19 -- CTAB and Viogene extraction methods Comparison 19 -- CTAB extraction 19 -- Results 21 -- CTAB and Viogene comparison 21 -- Discussion 21 -- IV CROSS SPECIES TRANSFERNCE OF MICROSATELLITE PRIMERS 23 -- Introduction 23 -- iv -- Materials and Methods 25 -- Preliminary Work 25 -- Sample Collection for Current Study and Mixed Profile Analysis 26 -- Microsatellite Selection and Amplification 27 -- Fragment Analysis 28 -- Genetic Analysis 28 -- Results 29 -- Genetic Variation and Marker Identification 29 -- Discussion 30 -- Conclusion 33 -- REFERENCES 36 -- APPENDIX A: Figures 45 -- APPENDIX B: Tables 52 en_US
dc.format.extent 1 electronic document, 72 pages en_US
dc.format.mimetype application/pdf en_US
dc.language.iso en_US en_US
dc.rights This dissertation is protected by the Copyright Laws of the United States (Public Law 94-553, revised in 1976). Consistent with fair use as defined in the Copyright Laws, brief quotations from this material are allowed with proper acknowledgement. Use of the materials for financial gain with the author's expressed written permissions is not allowed. en_US
dc.subject Academic theses en_US
dc.subject Ecology en_US
dc.subject Epiphytes en_US
dc.subject Genetic transformation en_US
dc.subject Spanish moss en_US
dc.title Population Genetics of Vascular Epiphytes; Optimization of DNA Extraction and Cross Species Transference in Tillandsia usneoides en_US
dc.type Thesis en_US
dc.contributor.department Department of Biology of the College of Science & Mathematics en_US
dc.description.advisor Anderson, Corey D.
dc.description.committee Calestani, Cristina
dc.description.committee Chambers, Eric
dc.description.degree M.S. en_US
dc.description.major Biology en_US

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