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Investigations Into Plant Genome Evolution Using Massive
INVESTIGATIONS INTO PLANT GENOME EVOLUTION USING MASSIVE PARALLEL SEQUENCING by Saemundur Sveinsson M.Sc., The University of Iceland, 2009 A THESIS SUBMITTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY in THE FACULTY OF GRADUATE AND POSTDOCTORAL STUDIES (Botany) THE UNIVERSITY OF BRITISH COLUMBIA (Vancouver) July 2014 © Saemundur Sveinsson, 2014 Abstract The advancements of various massively parallel sequencing (MPS) methods in the last five years have enabled researchers to tackle biological problems that until recently seemed intractable. One of the most widely used MPS methods comes from Illumina®, which combines short and accurate sequencing reads with high throughput. Data generated using Illumina sequencing is used in every chapter of this thesis to characterize patterns of genome evolution using phylogenetic approaches in various plant genera. The thesis is focused on three main aspects of plant genome evolution: transposable elements (chapter 2), polyploidy (chapters 3 and 4) and plastid genomes (chapters 5 and 6). In every chapter phylogenetic hypotheses are generated from sequences assembled from Illumina reads, which I use to frame my research questions. In chapter 2 I investigated intra- and interspecific patterns of transposable element (TE) abundance in Theobroma cacao and related species. I found that reference based mapping of short sequencing reads works well to characterize TEs within the same species but is not reliable for interspecific comparison. In chapter 3 I used Illumina sequenced transcriptomes of 11 flax species, to investigate the presence of paleopolyploidy event within the genus. I discovered a previously unknown paleopolyploidy event, occurring 23 – 42 million years ago. In chapter 4 I used low coverage Illumina whole genome sequencing to test a hypothesis regarding the allopolyploid origin of a North-American Lathyrus species, L. -
Useful Plants of Amazonian Ecuador
USEFUL PLANTS OF AMAZONIAN ECUADOR (U.S. Agency for International Development Grant No. LAC-0605-GSS-7037-00) Fourth Progress Report 15 October 1989 - 15 Apri 1 1990 Bradley C. Bennett, Ph.0 Institute of Economic Botany The New York Botanical Garden Bronx, New York 10458-5126 212-220-8763 TABLE OF CONTENTS FIELDWORK ....................................................1 SHUAR MANUSCRIPT ............................................. 2 MANUAL PREPARATION ...........................................2 CLASSIFICATION ...............................................3 RELATED PROJECT WORK ......................................... 4 RELATION WITH MUSE0 ECUATORIANO .............................. 4 FINANCES .....................................................5 FUTURE PROJECTS ..............................................5 APPENDICES ...................................................7 APPENDIX A .USEFUL PLANTS OF THE SHUAR MANUSCRIPT ...... 1 APPENDIX B .USEFUL PLANTS OF AMAZONIAN ECUADOR ....... 183 APPENDIX C .LETTER FROM DIOSCORIDES .................. 234 APPENDIX D .SAMPLE MANUSCRIPT TREATMENTS BIXACEAE ......................................... 236 MALVACEAE ........................................ 239 APPENDIX E .ILLUSTRATIONS ............................ 246 APPENDIX F .USEFUL PLANT CLASSIFICATION .............. 316 APPENDIX G .VARIATION IN COMMON PLANT NAMES AND THEIR USAGE AMONG THE SHUAR IN ECUADOR .............. 322 APPENDIX H .ECONOMIC AND SOCIOLOGICAL ASPECTS OF ETHNOBOTANY ................................... 340 APPENDIX I .FUTURE PROJECT -
Cacao and Its Allies
CACAO AND ITS ALLIES A TAXONOMIC REVISION OF THE GENUS THEOBROMA Jose Cuatrecasas Introduction "Celebrem etiam per universam Americam multique usua fructum Cacao appellatum." Clusius, 1605. "Cacao nomen barbarum, quo rejecto Theobroma dicta est arbor, cum fructus basin sternat potioni delicatissimae, Baluberrimae, maxime nutrienti, chocolate mexicanis, Euro- paeis quondam folis Magnatis propriae (ffpotfta rwf 8&av, Vos Deos feci dixit Deus de imperantibus), licet num vilior fact a." Linnaeus, Hort. Cliff. 379. 1737. Theobroma, a genus of the family Sterculiaceae, is particularly noteworthy because one of its members is the popular "cacao tree" or "cocoa tree." The uses and cultivation of this outstanding tropical plant were developed in the western hemisphere by the Mayas in Central America a long time before Europeans arrived on the con- tinent. The now universally used name cacao is derived directly from the Nahuatl "cacahuatl" or "cacahoatl," just as the name of the popular drink, chocolate, is derived from "xocoafcl" or "chocoatl." The economic importance of cacao has given rise to great activity in several fields of development and research, especially in agronomy. Historians and anthropologists have also been very much interested in learning the role played by cacao in the economy and social relations of the early American populations. There exists today an extensive literature devoted to the many problems related to cacao. I saw cacao for the first time in Colombia in 1932, but became actually interested in the genus in 1939 and the years following, when I found cacao trees growing wild in the rain forests of the Amazonian basin. I was fascinated by the unique structure of the flowers of the cocoa tree, and its extraordinary fruit. -
Useful Plants of Amazonian Ecuador Third Project
USEFUL PLANTS OF AMAZONIAN ECUADOR THIRD PROJECT REPORT (15 APRIL 1S89 - 15 OCTOBER 1989) BRADLEY C. BENNETT INSTITUTE OF ECONOMIC BOTANY THE NEW YORK BOTANICAL GARDEN BRONX, NEW YORK 10458-5126 TABLE OF CONTENTS FIELDWORK ................................................ 1 STUDENT FIELD PROJECTS ......................... o......... 2 RELATED PROJECT WORK ................................ 3 MANUAL PREPARATION ................................... o.... 4 SAMPLE DESCRIPTION OF BIXACEAE ............................. 5 SAMPLE DESCRIPTION OF MALVACEAE .......................... 8 ILLUSTRATIONS FOR MALVACEAE ............................. 15 OUTLINE OF MANUAL ....................................... 20 RELATIONSHIP WITH MUSEO ECUATORIANO ....................... 21 FINANCES ................................................ 21 APPENDIX A - LETTER FROM RICHARD ABEL, DIOSCORIDES ...... 23 APPENDIX B - USEFUL PLANTS FROM AMAZONIAN ECUADOR ....... 25 APPENDIX C - LIST OF USEFUL SHUAR PLANTS .................114 USEFUL PLANTS OF AMAZONIAN ECUADOR - 1 THIRD PROJECT REPORT (15 APRIL 1989 - 15 OCTOBER 1989) In this report we describe the third six months' progress of the "Useful plants of Amazonian Ecuador" project undertaken by New York Botanical Garden's Institute of Economic Botany (IEB) under an U.S. Agency for International Development contract. We are preparing a manual on Amazonian Ecuador's useful plants. This reference incorporates original fieldwork, herbarium data, and published ethnobotanical studies. FIELDWORK. Dr. Bradley C. Bennett (IEB) and Srta. Patricia Gomez Andrade (Museo Ecuatoriano de Ciencias Naturales) travelled to the Shuar Centro Yukutais for one week of fieldwork beginning 20 April 1989. They worked in previously uncollected swampy regions sol..th of Yukutais. Community members named almost 75% of the plants they collected and knew uses for at least half. Bennett went to the states for one month on 10 May. He returned to Ecuador on 10 June 1989. For the next two months he taught a School for Field Studies' ethnobotany course. -
Investigations Into Plant Genome Evolution Using Massive
INVESTIGATIONS INTO PLANT GENOME EVOLUTION USING MASSIVE PARALLEL SEQUENCING by Saemundur Sveinsson M.Sc., The University of Iceland, 2009 A THESIS SUBMITTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY in THE FACULTY OF GRADUATE AND POSTDOCTORAL STUDIES (Botany) THE UNIVERSITY OF BRITISH COLUMBIA (Vancouver) July 2014 © Saemundur Sveinsson, 2014 Abstract The advancements of various massively parallel sequencing (MPS) methods in the last five years have enabled researchers to tackle biological problems that until recently seemed intractable. One of the most widely used MPS methods comes from Illumina®, which combines short and accurate sequencing reads with high throughput. Data generated using Illumina sequencing is used in every chapter of this thesis to characterize patterns of genome evolution using phylogenetic approaches in various plant genera. The thesis is focused on three main aspects of plant genome evolution: transposable elements (chapter 2), polyploidy (chapters 3 and 4) and plastid genomes (chapters 5 and 6). In every chapter phylogenetic hypotheses are generated from sequences assembled from Illumina reads, which I use to frame my research questions. In chapter 2 I investigated intra- and interspecific patterns of transposable element (TE) abundance in Theobroma cacao and related species. I found that reference based mapping of short sequencing reads works well to characterize TEs within the same species but is not reliable for interspecific comparison. In chapter 3 I used Illumina sequenced transcriptomes of 11 flax species, to investigate the presence of paleopolyploidy event within the genus. I discovered a previously unknown paleopolyploidy event, occurring 23 – 42 million years ago. In chapter 4 I used low coverage Illumina whole genome sequencing to test a hypothesis regarding the allopolyploid origin of a North-American Lathyrus species, L. -
Contributions from the United States National Herbarium Volume 54: 1-180
^ SMITHSONIAN INSTITUTION «K Contributions of the United States National Herbarium c7U Volume 54: 1-180 Floristic Checklist of the Mache-Chindul Mountains of Northwestern Ecuador by John L. Clark David A. Neill and Mercedes Asanza Department of Botany National Museum of Natural History Washington, DC 2006 SMITHSONIAN INSTITUTION Contributions from the United States National Herbarium Volume 54: 1-180 Floristic Checklist of the Mache-Chindul Mountains of Northwestern Ecuador by John L. Clark, David A. Neill and Mercedes Asanza Department of Botany National Museum of Natural History Washington, DC 2006 ) ABSTRACT Clark, John L., David A. Neill, and Mercedes Asanza. Floristic Checklist of the Mache-Chindul Moun- tains of Northwestern Ecuador. Contributions from the United States National Herbarium, volume 54, 1 80 pages (including 23 figures). An inventory of the vascular plants of the Mache-Chindul Mountains is presented from collecting expeditions beginning in 1991 to present. The Mache-Chindul Mountains reach an elevation of 800 meters and are located in northwestern Ecuador in the southernmost part of the province of Esmeraldas (00°21'N 79°44'W) and the northern- most part of the province of Manabi (00°25'S 79°57'W). The Pacific Ocean lies 20-30 km due west and the equator transects the 2 middle of this mountain range. The Mache-Chindul range occupies about 400 km and harbors the last large tract of coastal wet forest in Ecuador, an area less than 4% of its original size. Important protected areas include the Reserva Ecologica Mache- Chindul, Bilsa Biological Station, Bosque Protector Cerro Pata de Pajaro, and the Reserva Lalo Loor. -
Ecuador's Choco Andean Corridor
ECUADOR’S CHOCO ANDEAN CORRIDOR: A LANDSCAPE APPROACH FOR CONSERVATION AND SUSTAINABLE DEVELOPMENT by REBECA MARIA JUSTICIA (Under the Direction of C. Ronald Carroll) ABSTRACT This dissertation describes the history of establishment of the Chocó Andean Corridor of Northwest Ecuador, elaborates on a systematic process of prioritization of conservation areas, illustrates how ambitious plans are being implemented on the ground and, along the way, addresses such difficult issues as integrating research, conservation, funding, development and political agendas. The general aim is to advance the understanding of the key elements essential for successful Neotropical forest conservation; the specific goal is to provide baseline studies that can be used to formulate conservation and land-use management policy related to the development of the Chocó Andean corridor. To encompass the geographic magnitude and thematic complexity of my object of study, I use an embedded case study methodology. An ecoregional approach reconciles the protection of biodiversity beyond the boundaries of the established National System of Protected Areas (SNAP) with the human needs of community development and economic alternatives to deforestation and may well present the best future conservation scenario. Protected areas alone do not serve well the two main objectives of biodiversity conservation—representation and permanency. Economic pressure drives deforestation, and viable alternatives to deforestation must be implemented. Reforestation with the native bamboo (Guadua