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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. -
Adaptive Radiations: from Field to Genomic Studies
Adaptive radiations: From field to genomic studies Scott A. Hodges and Nathan J. Derieg1 Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, CA 93106 Adaptive radiations were central to Darwin’s formation of his phenotype–environment correlation, (iii) trait utility, and (iv) theory of natural selection, and today they are still the centerpiece rapid speciation. Monophyly and rapid speciation for many of for many studies of adaptation and speciation. Here, we review the the classic examples of adaptive radiation have been established advantages of adaptive radiations, especially recent ones, for by using molecular techniques [e.g., cichlids (4), Galapagos detecting evolutionary trends and the genetic dissection of adap- finches (5, 6), and Hawaiian silverswords (7)]. Ecological and tive traits. We focus on Aquilegia as a primary example of these manipulative experiments are used to identify and test pheno- advantages and highlight progress in understanding the genetic type–environmental correlations and trait utility. Ultimately, basis of flower color. Phylogenetic analysis of Aquilegia indicates such studies have pointed to the link between divergent natural that flower color transitions proceed by changes in the types of selection and reproductive isolation and, thus, speciation (3). anthocyanin pigments produced or their complete loss. Biochem- Studies of adaptive radiations have exploded during the last 20 ical, crossing, and gene expression studies have provided a wealth years. In a search of the ISI Web of Science with ‘‘adaptive of information about the genetic basis of these transitions in radiation’’ (limited to the subject area of evolutionary biology) Aquilegia. To obtain both enzymatic and regulatory candidate we found 80 articles published in 2008 compared with only 1 in genes for the entire flavonoid pathway, which produces antho- 1990. -
Mcclinton Unr 0139M 13052.Pdf
University of Nevada, Reno Habitat preferences, intraspecific variation, and restoration of a rare soil specialist in northern Nevada A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science in Natural Resources and Environmental Science by Jamey D. McClinton Dr. Elizabeth A. Leger/Thesis Advisor December, 2019 Copyright by Jamey D. McClinton 2019 All Rights Reserved We recommend that the thesis prepared under our supervision by Jamey D. McClinton Entitled Habitat preferences, intraspecific variation, and restoration of a rare soil specialist in northern Nevada be accepted in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE Elizabeth Leger, Ph.D., Advisor Paul Verburg, Ph.D., Committee member Thomas Parchman, Ph.D., Graduate School Representative David W. Zeh, Ph.D., Dean, Graduate School December-2019 i Abstract Edaphic specialization in plants is associated with the development of novel adaptations that frequently lead to speciation, causing unique edaphic environments to be associated with rare and endemic plant species worldwide. These species contribute significantly to global biodiversity, but are especially vulnerable to disturbance and climate change because of their inherently patchy distributions and locally adapted populations. Successful conservation of these species depends upon understanding their habitat requirements and the amounts and distributions of genetic and phenotypic diversity among populations. Little is known about the habitat requirements or -
Yerba Buena Chapter – CNPS
PROGRAMS Everyone is welcome to attend membership meetings in the Recreation Room of the San Francisco YERBA County Fair Building (SFCFB) at 9 th Avenue and Lincoln Way in Golden Gate Park. The #71 and #44 buses stop at the building. The N-Judah, #6, #43, and #66 lines stop within 2 blocks. Before our BUENA programs, we take our speakers to dinner at Chang’s Kitchen, 1030 Irving Street, between 11 th and 12 th Avenues. Join us for good Chinese food and interesting conversation. Meet at the restaurant at 5:30 pm. RSVP appreciated but not required - call Jake Sigg at 415-731-3028 if you wish to notify. September 5, THURSDAY, 7:30 pm The Ecology and Plants of the Farallon Islands Speaker: Peter Pyle The Farallon Islands, part of the City and County of San Francisco, is a National Wildlife Refuge located NEW S 27 miles west of the Golden Gate Bridge. Cold ocean currents and other environmental factors there lead to high ocean productivity and a thriving marine wildlife ecology. Biologists working for PRBO/Point THE YERBA BUENA Blue Conservation Science and the U.S. Fish and Wildlife Service have resided on Southeast Farallon Island since April 1968, studying all aspects of the island's environment and ecology. Peter Pyle spent CHAPTER OF THE over 2,100 nights at the island's biological station in 1980-2003, primarily focused on birds, marine CALIFORNIA mammals, and white sharks, but also dabbling in everything else including bats, dragonflies, salamanders, NATIVE PLANT butterflies, crickets, mushrooms, and, yes, even the island's unique fog-whipped flora. -
Literature Cited
Literature Cited Robert W. Kiger, Editor This is a consolidated list of all works cited in volumes 19, 20, and 21, whether as selected references, in text, or in nomenclatural contexts. In citations of articles, both here and in the taxonomic treatments, and also in nomenclatural citations, the titles of serials are rendered in the forms recommended in G. D. R. Bridson and E. R. Smith (1991). When those forms are abbre- viated, as most are, cross references to the corresponding full serial titles are interpolated here alphabetically by abbreviated form. In nomenclatural citations (only), book titles are rendered in the abbreviated forms recommended in F. A. Stafleu and R. S. Cowan (1976–1988) and F. A. Stafleu and E. A. Mennega (1992+). Here, those abbreviated forms are indicated parenthetically following the full citations of the corresponding works, and cross references to the full citations are interpolated in the list alphabetically by abbreviated form. Two or more works published in the same year by the same author or group of coauthors will be distinguished uniquely and consistently throughout all volumes of Flora of North America by lower-case letters (b, c, d, ...) suffixed to the date for the second and subsequent works in the set. The suffixes are assigned in order of editorial encounter and do not reflect chronological sequence of publication. The first work by any particular author or group from any given year carries the implicit date suffix “a”; thus, the sequence of explicit suffixes begins with “b”. Works missing from any suffixed sequence here are ones cited elsewhere in the Flora that are not pertinent in these volumes. -
Extended Phylogeny of Aquilegia: the Biogeographical and Ecological Patterns of Two Simultaneous but Contrasting Radiations
Plant Syst Evol (2010) 284:171–185 DOI 10.1007/s00606-009-0243-z ORIGINAL ARTICLE Extended phylogeny of Aquilegia: the biogeographical and ecological patterns of two simultaneous but contrasting radiations Jesu´s M. Bastida • Julio M. Alca´ntara • Pedro J. Rey • Pablo Vargas • Carlos M. Herrera Received: 29 April 2009 / Accepted: 25 October 2009 / Published online: 4 December 2009 Ó Springer-Verlag 2009 Abstract Studies of the North American columbines respective lineages. The genus originated between 6.18 (Aquilegia, Ranunculaceae) have supported the view that and 6.57 million years (Myr) ago, with the main pulses of adaptive radiations in animal-pollinated plants proceed diversification starting around 3 Myr ago both in Europe through pollinator specialisation and floral differentiation. (1.25–3.96 Myr ago) and North America (1.42–5.01 Myr However, although the diversity of pollinators and floral ago). The type of habitat occupied shifted more often in morphology is much lower in Europe and Asia than in the Euroasiatic lineage, while pollination vectors shifted North America, the number of columbine species is more often in the Asiatic-North American lineage. similar in the three continents. This supports the Moreover, while allopatric speciation predominated in the hypothesis that habitat and pollinator specialisation have European lineage, sympatric speciation acted in the North contributed differently to the radiation of columbines in American one. In conclusion, the radiation of columbines different continents. To establish the basic background to in Europe and North America involved similar rates of test this hypothesis, we expanded the molecular phylog- diversification and took place simultaneously and inde- eny of the genus to include a representative set of species pendently. -
APPENDIX D Biological Technical Report
APPENDIX D Biological Technical Report CarMax Auto Superstore EIR BIOLOGICAL TECHNICAL REPORT PROPOSED CARMAX AUTO SUPERSTORE PROJECT CITY OF OCEANSIDE, SAN DIEGO COUNTY, CALIFORNIA Prepared for: EnviroApplications, Inc. 2831 Camino del Rio South, Suite 214 San Diego, California 92108 Contact: Megan Hill 619-291-3636 Prepared by: 4629 Cass Street, #192 San Diego, California 92109 Contact: Melissa Busby 858-334-9507 September 29, 2020 Revised March 23, 2021 Biological Technical Report CarMax Auto Superstore TABLE OF CONTENTS EXECUTIVE SUMMARY ................................................................................................ 3 SECTION 1.0 – INTRODUCTION ................................................................................... 6 1.1 Proposed Project Location .................................................................................... 6 1.2 Proposed Project Description ............................................................................... 6 SECTION 2.0 – METHODS AND SURVEY LIMITATIONS ............................................ 8 2.1 Background Research .......................................................................................... 8 2.2 General Biological Resources Survey .................................................................. 8 2.3 Jurisdictional Delineation ...................................................................................... 9 2.3.1 U.S. Army Corps of Engineers Jurisdiction .................................................... 9 2.3.2 Regional Water Quality -
Serpentine Geoecology of Eastern North America: a Review
RHODORA, Vol. 111, No. 945, pp. 21–108, 2009 E Copyright 2009 by the New England Botanical Club SERPENTINE GEOECOLOGY OF EASTERN NORTH AMERICA: A REVIEW NISHANTA RAJAKARUNA College of the Atlantic, 105 Eden Street, Bar Harbor, ME 04609 Current Address: Department of Biological Sciences, One Washington Square, San Jose´ State University, San Jose´, CA 95192-0100 e-mail: [email protected] TANNER B. HARRIS University of Massachusetts, Fernald Hall, 270 Stockbridge Road, Amherst, MA 01003 EARL B. ALEXANDER 1714 Kasba Street, Concord, CA 94518 ABSTRACT. Serpentine outcrops are model habitats for geoecological studies. While much attention has been paid to serpentine outcrops worldwide, the literature on eastern North American serpentine and associated biota is scant. This review examines the available literature, published and unpublished, on geoecological studies conducted on serpentine in eastern North America, from Newfoundland through Que´bec and New England south to Alabama. Most serpentine outcrops in the region have been mapped, but there have been few intensive mineralogical and pedological investigations. The limited soil analyses available suggest elevated levels of heavy metals such as Ni, near-neutralpH values, and Ca:Mg ratios , 1, characteristic of serpentine soils worldwide. Botanical studies to date have largely focused on floristic surveys and the influence of fire exclusion and grazing on indigenous vegetation. To date, 751 taxa of vascular plants belonging to 92 families have been reported from serpentine outcrops in the region. Two taxa, Agalinis acuta and Schwalbea americana, are federally endangered in the United States while many others are listed as rare, endangered, or imperiled in one or more states or provinces. -
Southwestern Rare and Endangered Plants: Proceedings of the Fourth
Conservation Implications of Spur Length Variation in Long-Spur Columbines (Aquilegia longissima) CHRISTOPHER J. STUBBEN AND BROOK G. MILLIGAN Department of Biology, New Mexico State University, Las Cruces, New Mexico 88003 ABSTRACT: Populations of long-spur columbine (Aquilegia longissima) with spurs 10-16 cm long are known only from a few populations in Texas, a historical collection near Baboquivari Peak, Arizona, and scattered populations in Coahuila, Chihuahua, and Nuevo Leon, Mexico. Populations of yellow columbine with spurs 7-10 cm long are also found in Arizona, Texas, and Mexico, and are now classified as A. longissima in the recent Flora of North America. In a multivariate analysis of floral characters from 11 yellow columbine populations representing a continuous range of spur lengths, populations with spurs 10-16 cm long are clearly separate from other populations based on increasing spur length and decreasing petal and sepal width. The longer-spurred columbines generally flower after monsoon rains in late summer or fall, and occur in intermittently wet canyons and steep slopes in pine-oak forests. Also, longer-spurred flowers can be pollinated by large hawkmoths with tongues 9-15 cm long. Populations with spurs 7-10 cm long cluster with the common golden columbine (A. chrysantha), and may be the result of hybridization between A. chrysantha and A. longissima. Uncertainty about the taxonomic status of intermediates has contributed to a lack of conservation efforts for declining populations of the long-spur columbine. The genus Aquilegia is characterized are difficult to identify accurately in by a wide diversity of floral plant keys. For example, floral spurs morphologies and colors that play a lengths are a key character used to major role in isolating two species via differentiate yellow columbine species in differences in pollinator visitation or the Southwest. -
Vascular Plants of Vina Plains Preserve Wurlitzer Unit
DO r:r:i :;:i·,iOVE Ff.'f)l,1 . ,- . - . "'I":; Vascular Plants of Vina Plains Preserve, Wurlitzer Unit Vernon H. Oswald Vaseular Plants of Vina Plains Preserve, Wurlitzer Unit Vernon H . Oswald Department of Biological Sciences California State University, C h ico Ch ico, California 95929-0515 1997 Revision RED BLUFF •CORN ING TEHAMA CO. -------------B1JITECO. ORLAND HWY 32 FIGURE I. Location of Vina P la.ins Preserve, Main Unit on the north, Wurlitzer Unit on the south. CONTENTS Figure 1. Location of Vina Plains Preserve ...... ................................. facing contents Figure 2. Wurlitzer Unit, Vina Plains Preserve ..... ............................... facing page I Introduction .. ... ..................................... ................................ ....... ....... ... ................ I References .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. ... ... .. .. .. .. .. .. .. .. .. .. 4 The Plant List: Ferns and fem allies .......... ................................................... ........... ................. 5 Di cot flowering plants ............... ...................................................... ................. 5 Monocot flowering plants .......... ..................................................................... 25 / ... n\ a: t, i. FIGURE 2. Wurlitzer Unit, Vina Plains Preserve (in yellow), with a small comer of the Main Unit showing on the north. Modified from USGS 7.5' topographic maps, Richardson Springs NW & Nord quadrangles. - - INTRODUCTION 1 A survey of the vascular flora of the Wurl itzer -
Baja California, Mexico, and a Vegetation Map of Colonet Mesa Alan B
Aliso: A Journal of Systematic and Evolutionary Botany Volume 29 | Issue 1 Article 4 2011 Plants of the Colonet Region, Baja California, Mexico, and a Vegetation Map of Colonet Mesa Alan B. Harper Terra Peninsular, Coronado, California Sula Vanderplank Rancho Santa Ana Botanic Garden, Claremont, California Mark Dodero Recon Environmental Inc., San Diego, California Sergio Mata Terra Peninsular, Coronado, California Jorge Ochoa Long Beach City College, Long Beach, California Follow this and additional works at: http://scholarship.claremont.edu/aliso Part of the Biodiversity Commons, Botany Commons, and the Ecology and Evolutionary Biology Commons Recommended Citation Harper, Alan B.; Vanderplank, Sula; Dodero, Mark; Mata, Sergio; and Ochoa, Jorge (2011) "Plants of the Colonet Region, Baja California, Mexico, and a Vegetation Map of Colonet Mesa," Aliso: A Journal of Systematic and Evolutionary Botany: Vol. 29: Iss. 1, Article 4. Available at: http://scholarship.claremont.edu/aliso/vol29/iss1/4 Aliso, 29(1), pp. 25–42 ’ 2011, Rancho Santa Ana Botanic Garden PLANTS OF THE COLONET REGION, BAJA CALIFORNIA, MEXICO, AND A VEGETATION MAPOF COLONET MESA ALAN B. HARPER,1 SULA VANDERPLANK,2 MARK DODERO,3 SERGIO MATA,1 AND JORGE OCHOA4 1Terra Peninsular, A.C., PMB 189003, Suite 88, Coronado, California 92178, USA ([email protected]); 2Rancho Santa Ana Botanic Garden, 1500 North College Avenue, Claremont, California 91711, USA; 3Recon Environmental Inc., 1927 Fifth Avenue, San Diego, California 92101, USA; 4Long Beach City College, 1305 East Pacific Coast Highway, Long Beach, California 90806, USA ABSTRACT The Colonet region is located at the southern end of the California Floristic Province, in an area known to have the highest plant diversity in Baja California. -
Draft Environmental Impact Statement
DOE/EIS–0458D DRAFT ENVIRONMENTAL IMPACT STATEMENT VOLUME I DEPARTMENT OF ENERGY LOAN GUARANTEE TO ROYAL BANK OF SCOTLAND FOR CONSTRUCTION AND STARTUP OF THE TOPAZ SOLAR FARM SAN LUIS OBISPO COUNTY, CALIFORNIA US Department of Energy, Lead Agency Loan Guarantee Program Office Washington, DC 20585 In Cooperation with US Army Corps of Engineers San Francisco District March 2011 COVER SHEET Lead Federal Agency: US Department of Energy Cooperating Agency: US Army Corps of Engineers Title: Draft Environmental Impact Statement for the US Department of Energy Loan Guarantee to Royal Bank of Scotland for Construction and Startup of the Topaz Solar Farm, San Luis Obispo County, California Contact: For additional copies or more information on this Draft Environmental Impact Statement (EIS), please contact: Ms. Angela Colamaria US Department of Energy Loan Programs Office (LP-10) 1000 Independence Avenue, SW Washington, DC 20585 Phone: 202-287-5387 Electronic mail: [email protected] Abstract: The US Department of Energy is proposing to issue a loan guarantee to Royal Bank of Scotland to provide funding to Topaz Solar Farms, Limited Liability Corporation (LLC) to construct and start up the Topaz Solar Farm, a nominal 550-megawatt photovoltaic solar energy generating facility. The facility would be located in unincorporated eastern San Luis Obispo County, California, approximately one mile north of the community of California Valley and six miles northwest of the Carrizo Plain National Monument. The proposed facility would consist of a solar field of ground-mounted PV modules, an electrical collection system that converts generated power from direct current to alternating current and delivers it to a Project substation for collection and conversion from 34.5 to 230 kV for delivery via a new on-site Pacific Gas and Electric (PG&E) switching station, and the PG&E switching station that interconnects the Project to PG&E’s existing Morro Bay to Midway 230-kV transmission line.