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Phylogenetic Models Linking Speciation and Extinction to Chromosome and Mating System Evolution
Phylogenetic Models Linking Speciation and Extinction to Chromosome and Mating System Evolution by William Allen Freyman A dissertation submitted in partial satisfaction of the requirements for the degree of Doctor of Philosophy in Integrative Biology and the Designated Emphasis in Computational and Genomic Biology in the Graduate Division of the University of California, Berkeley Committee in charge: Dr. Bruce G. Baldwin, Chair Dr. John P. Huelsenbeck Dr. Brent D. Mishler Dr. Kipling W. Will Fall 2017 Phylogenetic Models Linking Speciation and Extinction to Chromosome and Mating System Evolution Copyright 2017 by William Allen Freyman Abstract Phylogenetic Models Linking Speciation and Extinction to Chromosome and Mating System Evolution by William Allen Freyman Doctor of Philosophy in Integrative Biology and the Designated Emphasis in Computational and Genomic Biology University of California, Berkeley Dr. Bruce G. Baldwin, Chair Key evolutionary transitions have shaped the tree of life by driving the processes of spe- ciation and extinction. This dissertation aims to advance statistical and computational ap- proaches that model the timing and nature of these transitions over evolutionary trees. These methodological developments in phylogenetic comparative biology enable formal, model- based, statistical examinations of the macroevolutionary consequences of trait evolution. Chapter 1 presents computational tools for data mining the large-scale molecular sequence datasets needed for comparative phylogenetic analyses. I describe a novel metric, the miss- ing sequence decisiveness score (MSDS), which assesses the phylogenetic decisiveness of a matrix given the pattern of missing sequence data. In Chapter 2, I introduce a class of phylogenetic models of chromosome number evolution that accommodate both anagenetic and cladogenetic change. -
Outline of Angiosperm Phylogeny
Outline of angiosperm phylogeny: orders, families, and representative genera with emphasis on Oregon native plants Priscilla Spears December 2013 The following listing gives an introduction to the phylogenetic classification of the flowering plants that has emerged in recent decades, and which is based on nucleic acid sequences as well as morphological and developmental data. This listing emphasizes temperate families of the Northern Hemisphere and is meant as an overview with examples of Oregon native plants. It includes many exotic genera that are grown in Oregon as ornamentals plus other plants of interest worldwide. The genera that are Oregon natives are printed in a blue font. Genera that are exotics are shown in black, however genera in blue may also contain non-native species. Names separated by a slash are alternatives or else the nomenclature is in flux. When several genera have the same common name, the names are separated by commas. The order of the family names is from the linear listing of families in the APG III report. For further information, see the references on the last page. Basal Angiosperms (ANITA grade) Amborellales Amborellaceae, sole family, the earliest branch of flowering plants, a shrub native to New Caledonia – Amborella Nymphaeales Hydatellaceae – aquatics from Australasia, previously classified as a grass Cabombaceae (water shield – Brasenia, fanwort – Cabomba) Nymphaeaceae (water lilies – Nymphaea; pond lilies – Nuphar) Austrobaileyales Schisandraceae (wild sarsaparilla, star vine – Schisandra; Japanese -
Conserving Europe's Threatened Plants
Conserving Europe’s threatened plants Progress towards Target 8 of the Global Strategy for Plant Conservation Conserving Europe’s threatened plants Progress towards Target 8 of the Global Strategy for Plant Conservation By Suzanne Sharrock and Meirion Jones May 2009 Recommended citation: Sharrock, S. and Jones, M., 2009. Conserving Europe’s threatened plants: Progress towards Target 8 of the Global Strategy for Plant Conservation Botanic Gardens Conservation International, Richmond, UK ISBN 978-1-905164-30-1 Published by Botanic Gardens Conservation International Descanso House, 199 Kew Road, Richmond, Surrey, TW9 3BW, UK Design: John Morgan, [email protected] Acknowledgements The work of establishing a consolidated list of threatened Photo credits European plants was first initiated by Hugh Synge who developed the original database on which this report is based. All images are credited to BGCI with the exceptions of: We are most grateful to Hugh for providing this database to page 5, Nikos Krigas; page 8. Christophe Libert; page 10, BGCI and advising on further development of the list. The Pawel Kos; page 12 (upper), Nikos Krigas; page 14: James exacting task of inputting data from national Red Lists was Hitchmough; page 16 (lower), Jože Bavcon; page 17 (upper), carried out by Chris Cockel and without his dedicated work, the Nkos Krigas; page 20 (upper), Anca Sarbu; page 21, Nikos list would not have been completed. Thank you for your efforts Krigas; page 22 (upper) Simon Williams; page 22 (lower), RBG Chris. We are grateful to all the members of the European Kew; page 23 (upper), Jo Packet; page 23 (lower), Sandrine Botanic Gardens Consortium and other colleagues from Europe Godefroid; page 24 (upper) Jože Bavcon; page 24 (lower), Frank who provided essential advice, guidance and supplementary Scumacher; page 25 (upper) Michael Burkart; page 25, (lower) information on the species included in the database. -
Price Genus Species Origine Cultivar Character Colour
Price Genus Species Origine Cultivar Character Colour Height Situation Rockgarden Alpine house Trough Soil €.3,- Acantholimon ulicinum Turkey cushion pink 10cm sunny x lime €.4,- Androsace akbaitalensis Tibet cushion pink 5cm semi-shade x x acid €.2,- Androsace barbulata Caucasus cushion white 5cm semi-shade x neutral €.12,- Androsace bryomorpha Pamir cushion white 1cm semi-shade x x neutral €.3,- Androsace bulleyana China tufted orange-yellow 5cm semi-shade x x acid €.2,- Androsace carnea Alps tufted pink 5cm semi-shade x x acid €.4,- Androsace delavayi China cushion white or pink 2cm semi-shade x x granite €.3,- Androsace elatior China tufted pink 10cm semi-shade x x neutral €.3,- Androsace globifera China cushion pink 3cm semi-shade x x acid €.2,- Androsace hausmannii Alps cushion white 3cm semi-shade x x neutral €.2,- Androsace jaquemontii Himalaya cushion pink 3cm semi-shade x x x acid €.2,- Androsace jaquemontii Himalaya cushion purple 3cm semi-shade x x x acid €.2,- Androsace kosopoljanskii Caucasus cushion white 5cm semi-shade x x x lime €.3,- Androsace laevigata Oregon cushion pink 5cm semi-shade x x neutral €.3,- Androsace mucronifolia Himalaya cushion pink 3cm semi-shade x x x acid €.3,- Androsace x marpensis Himalaya cushion pink 3cm semi-shade x x x acid €.2,- Androsace mucr. x sempervivoides Himalaya cushion pink 3cm semi-shade x x acid €.3,- Androsace nivalis British Columbia cushion pink 5cm semi-shade x x x neutral €.4,- Androsace nortonii China cushion pale pink 5cm semi-shade x x x acid €.3,- Androsace aff. pavlovskii Kyrgistan cushion pink 3cm semi-shade x x neutral €.3,- Androsace pavlovskii Kyrgistan cushion pink 3cm semi-shade x x neutral €.2,- Androsace pubescens Alps cushion white 3cm semi-shade x x x neutral €.4,- Androsace sarmentosa Himalaya cushion pink 3cm semi-shade x x neutral €.2,- Androsace sempervivoides Himalaya ' Susan Joan' cushion pink 5cm semi-shade x x neutral €.4,- Androsace sp. -
December 2012 Number 1
Calochortiana December 2012 Number 1 December 2012 Number 1 CONTENTS Proceedings of the Fifth South- western Rare and Endangered Plant Conference Calochortiana, a new publication of the Utah Native Plant Society . 3 The Fifth Southwestern Rare and En- dangered Plant Conference, Salt Lake City, Utah, March 2009 . 3 Abstracts of presentations and posters not submitted for the proceedings . 4 Southwestern cienegas: Rare habitats for endangered wetland plants. Robert Sivinski . 17 A new look at ranking plant rarity for conservation purposes, with an em- phasis on the flora of the American Southwest. John R. Spence . 25 The contribution of Cedar Breaks Na- tional Monument to the conservation of vascular plant diversity in Utah. Walter Fertig and Douglas N. Rey- nolds . 35 Studying the seed bank dynamics of rare plants. Susan Meyer . 46 East meets west: Rare desert Alliums in Arizona. John L. Anderson . 56 Calochortus nuttallii (Sego lily), Spatial patterns of endemic plant spe- state flower of Utah. By Kaye cies of the Colorado Plateau. Crystal Thorne. Krause . 63 Continued on page 2 Copyright 2012 Utah Native Plant Society. All Rights Reserved. Utah Native Plant Society Utah Native Plant Society, PO Box 520041, Salt Lake Copyright 2012 Utah Native Plant Society. All Rights City, Utah, 84152-0041. www.unps.org Reserved. Calochortiana is a publication of the Utah Native Plant Society, a 501(c)(3) not-for-profit organi- Editor: Walter Fertig ([email protected]), zation dedicated to conserving and promoting steward- Editorial Committee: Walter Fertig, Mindy Wheeler, ship of our native plants. Leila Shultz, and Susan Meyer CONTENTS, continued Biogeography of rare plants of the Ash Meadows National Wildlife Refuge, Nevada. -
Androsace Komovensis Sp. Nov., a Long Mistaken Local Endemic from the Southern Balkan Peninsula with Biogeographic Links to the Eastern Alps
Schönswetter & Schneeweiss • Androsace komovensis sp. nov. TAXON 58 (2) • May 2009: 544–549 Androsace komovensis sp. nov., a long mistaken local endemic from the southern Balkan Peninsula with biogeographic links to the Eastern Alps Peter Schönswetter & Gerald M. Schneeweiss Department of Biogeography and Botanical Garden, University of Vienna, 1030 Vienna, Austria. [email protected] (author for correspondence) In the course of molecular phylogeographical investigations in Androsace sect. Aretia a previously unrecog- nised entity from Crna Gora/Montenegro was identified as a genetically and morphologically clearly separated lineage and is described here as a new species, Androsace komovensis Schönswetter & Schneew. It is restricted to a single high-alpine rock-cliff in the Komovi mountain range in Montenegro. The new species morphologi- cally resembles A. mathildae Levier from the Abruzzo mountains (Italy), but differs in the persistent, dense and regular indumentum of the leaf margin. Molecular phylogenetic data indicate that A. komovensis Schöns- wetter & Schneew. is not closely related to A. mathildae Levier, but instead is sister species to the Eastern Alpine endemic A. hausmanni Leyb. KEYWORDS: Androsace komovensis, Crna Gora/Montenegro, Primulaceae, species nova Spanish mountains and the Carpathians, and one species INTRODUCTION in the French Massif Central. The genus Androsace L. (Primulaceae) comprises ca. In the course of molecular phylogeographical in- 150 species mainly distributed in extra-tropical mountain vestigations covering the European members of /Aretia ranges of the Northern Hemisphere (Mabberley, 2008). (e.g., Dixon & al., 2007, 2008), we investigated the single A phylogeny based on nuclear ribosomal ITS and chlo- Balkan population of A. mathildae Levier. -
(Dr. Sc. Nat.) Vorgelegt Der Mathematisch-Naturwissenschaftl
Zurich Open Repository and Archive University of Zurich Main Library Strickhofstrasse 39 CH-8057 Zurich www.zora.uzh.ch Year: 2012 Flowers, sex, and diversity: Reproductive-ecological and macro-evolutionary aspects of floral variation in the Primrose family, Primulaceae de Vos, Jurriaan Michiel Posted at the Zurich Open Repository and Archive, University of Zurich ZORA URL: https://doi.org/10.5167/uzh-88785 Dissertation Originally published at: de Vos, Jurriaan Michiel. Flowers, sex, and diversity: Reproductive-ecological and macro-evolutionary aspects of floral variation in the Primrose family, Primulaceae. 2012, University of Zurich, Facultyof Science. FLOWERS, SEX, AND DIVERSITY. REPRODUCTIVE-ECOLOGICAL AND MACRO-EVOLUTIONARY ASPECTS OF FLORAL VARIATION IN THE PRIMROSE FAMILY, PRIMULACEAE Dissertation zur Erlangung der naturwissenschaftlichen Doktorwürde (Dr. sc. nat.) vorgelegt der Mathematisch-naturwissenschaftliche Fakultät der Universität Zürich von Jurriaan Michiel de Vos aus den Niederlanden Promotionskomitee Prof. Dr. Elena Conti (Vorsitz) Prof. Dr. Antony B. Wilson Dr. Colin E. Hughes Zürich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s ist ein zentrales Ziel in der Evolutionsbiologie, die Muster der Vielfalt und die Prozesse, die sie erzeugen, zu verstehen. -
Springs and Springs-Dependent Taxa of the Colorado River Basin, Southwestern North America: Geography, Ecology and Human Impacts
water Article Springs and Springs-Dependent Taxa of the Colorado River Basin, Southwestern North America: Geography, Ecology and Human Impacts Lawrence E. Stevens * , Jeffrey Jenness and Jeri D. Ledbetter Springs Stewardship Institute, Museum of Northern Arizona, 3101 N. Ft. Valley Rd., Flagstaff, AZ 86001, USA; Jeff@SpringStewardship.org (J.J.); [email protected] (J.D.L.) * Correspondence: [email protected] Received: 27 April 2020; Accepted: 12 May 2020; Published: 24 May 2020 Abstract: The Colorado River basin (CRB), the primary water source for southwestern North America, is divided into the 283,384 km2, water-exporting Upper CRB (UCRB) in the Colorado Plateau geologic province, and the 344,440 km2, water-receiving Lower CRB (LCRB) in the Basin and Range geologic province. Long-regarded as a snowmelt-fed river system, approximately half of the river’s baseflow is derived from groundwater, much of it through springs. CRB springs are important for biota, culture, and the economy, but are highly threatened by a wide array of anthropogenic factors. We used existing literature, available databases, and field data to synthesize information on the distribution, ecohydrology, biodiversity, status, and potential socio-economic impacts of 20,872 reported CRB springs in relation to permanent stream distribution, human population growth, and climate change. CRB springs are patchily distributed, with highest density in montane and cliff-dominated landscapes. Mapping data quality is highly variable and many springs remain undocumented. Most CRB springs-influenced habitats are small, with a highly variable mean area of 2200 m2, generating an estimated total springs habitat area of 45.4 km2 (0.007% of the total CRB land area). -
Apomixis Is Not Prevalent in Subnival to Nival Plants of the European Alps
Annals of Botany 108: 381–390, 2011 doi:10.1093/aob/mcr142, available online at www.aob.oxfordjournals.org Apomixis is not prevalent in subnival to nival plants of the European Alps Elvira Ho¨randl1,*, Christoph Dobesˇ2, Jan Suda3,4, Petr Vı´t3,4, Toma´sˇ Urfus3,4, Eva M. Temsch1, Anne-Caroline Cosendai1, Johanna Wagner5 and Ursula Ladinig5 1Department of Systematic and Evolutionary Botany, Faculty of Life Sciences, University of Vienna, A-1030 Vienna, Austria, 2Department of Pharmacognosy, Faculty of Life Sciences, University of Vienna, A-1090 Vienna, Austria, 3Department of Botany, Faculty of Science, Charles University in Prague, CZ-128 01 Prague, Czech Republic, 4Institute of Botany, Academy of Sciences of the Czech Republic, CZ-252 43 Pru˚honice, Czech Republic and 5Institute of Botany, University of Innsbruck, A-6020 Innsbruck, Austria * For correspondence. E-mail [email protected] Received: 2 December 2010 Returned for revision: 14 January 2011 Accepted: 28 April 2011 Published electronically: 1 July 2011 † Background and Aims High alpine environments are characterized by short growing seasons, stochastic climatic conditions and fluctuating pollinator visits. These conditions are rather unfavourable for sexual reproduction of flowering plants. Apomixis, asexual reproduction via seed, provides reproductive assurance without the need of pollinators and potentially accelerates seed development. Therefore, apomixis is expected to provide selective advantages in high-alpine biota. Indeed, apomictic species occur frequently in the subalpine to alpine grassland zone of the European Alps, but the mode of reproduction of the subnival to nival flora was largely unknown. † Methods The mode of reproduction in 14 species belonging to seven families was investigated via flow cyto- metric seed screen. -
Disentangling Drivers of Plant Endemism and Diversification
Perspectives in Plant Ecology, Evolution and Systematics 28 (2017) 19–27 Contents lists available at ScienceDirect Perspectives in Plant Ecology, Evolution and Systematics journal homepage: www.elsevier.com/locate/ppees Disentangling drivers of plant endemism and diversification in the European MARK Alps – A phylogenetic and spatially explicit approach ⁎ Jan Smyčkaa, , Cristina Roqueta, Julien Renauda, Wilfried Thuillera, Niklaus E. Zimmermannb, Sébastien Lavergnea a Université Grenoble Alpes, CNRS, Laboratoire d’Ecologie Alpine (LECA), 2233 rue de la Piscine, FR-38000 Grenoble, France b Swiss Federal Research Institute WSL, Zürcherstrasse 111, CH-8903 Birmensdorf, Switzerland ARTICLE INFO ABSTRACT Keywords: Plant endemism in the European Alps is clustered into particular geographic areas. Two contrasted and non Glacial refugia exclusive hypotheses have been suggested to explain these hotspots of endemism: (i) those areas were glacial High elevation refugia, where endemism reflects survival-recolonisation dynamics since the onset of Pleistocene glaciations, (ii) Mountains those are high elevation mountain areas, where endemism was fostered by local speciation events due to geo- Speciation graphic isolation and harsh environmental niches, or by low dispersal ability of inhabiting species. Dispersal Here, we quantitatively compared these two hypotheses using data of species distribution in the European Phylogenetic uncertainty Alps (IntraBioDiv database), species phylogenetic relationships, and species ecological and biological char- acteristics. We developed a spatially and phylogenetically explicit modelling framework to analyze spatial patterns of endemism and the phylogenetic structure of species assemblages. Moreover, we analyzed inter- relations between species trait syndromes and endemism. We found that high endemism occurrs in potential glacial refugia, but only those on calcareous bedrock, and also in areas with high elevation. -
High-Elevation Limits and the Ecology of High-Elevation Vascular Plants: Legacies from Alexander Von Humboldt1
a Frontiers of Biogeography 2021, 13.3, e53226 Frontiers of Biogeography REVIEW the scientific journal of the International Biogeography Society High-elevation limits and the ecology of high-elevation vascular plants: legacies from Alexander von Humboldt1 H. John B. Birks1,2* 1 Department of Biological Sciences and Bjerknes Centre for Climate Research, University of Bergen, PO Box 7803, Bergen, Norway; 2 Ecological Change Research Centre, University College London, Gower Street, London, WC1 6BT, UK. *Correspondence: H.J.B. Birks, [email protected] 1 This paper is part of an Elevational Gradients and Mountain Biodiversity Special Issue Abstract Highlights Alexander von Humboldt and Aimé Bonpland in their • The known uppermost elevation limits of vascular ‘Essay on the Geography of Plants’ discuss what was plants in 22 regions from northernmost Greenland known in 1807 about the elevational limits of vascular to Antarctica through the European Alps, North plants in the Andes, North America, and the European American Rockies, Andes, East and southern Africa, Alps and suggest what factors might influence these upper and South Island, New Zealand are collated to provide elevational limits. Here, in light of current knowledge a global view of high-elevation limits. and techniques, I consider which species are thought to be the highest vascular plants in twenty mountain • The relationships between potential climatic treeline, areas and two polar regions on Earth. I review how one upper limit of closed vegetation in tropical (Andes, can try to -
On the Distribution of Utah's Hanging Gardens
Great Basin Naturalist Volume 49 Number 1 Article 1 1-31-1989 On the distribution of Utah's hanging gardens Stanley L. Welsh Brigham Young University Follow this and additional works at: https://scholarsarchive.byu.edu/gbn Recommended Citation Welsh, Stanley L. (1989) "On the distribution of Utah's hanging gardens," Great Basin Naturalist: Vol. 49 : No. 1 , Article 1. Available at: https://scholarsarchive.byu.edu/gbn/vol49/iss1/1 This Article is brought to you for free and open access by the Western North American Naturalist Publications at BYU ScholarsArchive. It has been accepted for inclusion in Great Basin Naturalist by an authorized editor of BYU ScholarsArchive. For more information, please contact [email protected], [email protected]. The Great Basin Naturalist Published at Provo, Utah, by Brigham Young University ISSN 0017-3614 Volume 49 31 January 1989 No. 1 ON THE DISTRIBUTION OF UTAH'S HANGING GARDENS Stanley L. Welsh 1 Abstract. —This is a summary monograph of the hanging gardens as they occur in the Colorado River and Virgin River portions of the Colorado Plateau in Utah. Discussed in this paper are the hanging gardens, their geography, geomorphology, aspects of distribution and diversity, and principal vascular and algal plant species. Animal trapping studies and plant productivity aspects are reviewed. The sea of aridity that overlies southern tively recent origin, geologically speaking Utah and vicinity is broken by seasonal influ- (Hintze 1972). ences and by the dendritic trenches of the The geological strata are remarkably evi- Colorado River and its tributaries. The effects dent in this arid setting, where vegetative of the river are restricted to its banks and cover is thin and where rate of soil develop- adjacent alluvial terraces; the riparian vegeta- ment is exceeded by processes of erosion.