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Updated Angiosperm Family Tree for Analyzing Phylogenetic Diversity and Community Structure
Acta Botanica Brasilica - 31(2): 191-198. April-June 2017. doi: 10.1590/0102-33062016abb0306 Updated angiosperm family tree for analyzing phylogenetic diversity and community structure Markus Gastauer1,2* and João Augusto Alves Meira-Neto2 Received: August 19, 2016 Accepted: March 3, 2017 . ABSTRACT Th e computation of phylogenetic diversity and phylogenetic community structure demands an accurately calibrated, high-resolution phylogeny, which refl ects current knowledge regarding diversifi cation within the group of interest. Herein we present the angiosperm phylogeny R20160415.new, which is based on the topology proposed by the Angiosperm Phylogeny Group IV, a recently released compilation of angiosperm diversifi cation. R20160415.new is calibratable by diff erent sets of recently published estimates of mean node ages. Its application for the computation of phylogenetic diversity and/or phylogenetic community structure is straightforward and ensures the inclusion of up-to-date information in user specifi c applications, as long as users are familiar with the pitfalls of such hand- made supertrees. Keywords: angiosperm diversifi cation, APG IV, community tree calibration, megatrees, phylogenetic topology phylogeny comprising the entire taxonomic group under Introduction study (Gastauer & Meira-Neto 2013). Th e constant increase in knowledge about the phylogenetic The phylogenetic structure of a biological community relationships among taxa (e.g., Cox et al. 2014) requires regular determines whether species that coexist within a given revision of applied phylogenies in order to incorporate novel data community are more closely related than expected by chance, and is essential information for investigating and avoid out-dated information in analyses of phylogenetic community assembly rules (Kembel & Hubbell 2006; diversity and community structure. -
Baseline Biodiversity Report
FINAL Baseline Biodiversity Survey for Potrero Mason Property Prepared for: County of San Diego Department of Parks and Recreation 5500 Overland Avenue Drive, Suite 410 San Diego, California 92123 Contact: Jennifer Price Prepared by: 605 Third Street Encinitas, California 92024 Contact: Brock Ortega DECEMBER 2012 Printed on 30% post-consumer recycled material. Final Baseline Biodiversity Survey Potrero Mason Property TABLE OF CONTENTS Section Page No. LIST OF ACRONYMS ................................................................................................................ V EXECUTIVE SUMMARY .......................................................................................................VII 1.0 INTRODUCTION..............................................................................................................1 1.1 Purpose of the Report.............................................................................................. 1 1.2 MSCP Context ........................................................................................................ 1 2.0 PROPERTY DESCRIPTION ...........................................................................................9 2.1 Project Location ...................................................................................................... 9 2.2 Geographical Setting ............................................................................................... 9 2.3 Geology and Soils .................................................................................................. -
RNA-Seq Highlights Parallel and Contrasting Patterns in the Evolution of the Nuclear Genome of Fully Mycoheterotrophic Plants Mikhail I
Schelkunov et al. BMC Genomics (2018) 19:602 https://doi.org/10.1186/s12864-018-4968-3 RESEARCH ARTICLE Open Access RNA-seq highlights parallel and contrasting patterns in the evolution of the nuclear genome of fully mycoheterotrophic plants Mikhail I. Schelkunov1* , Aleksey A. Penin1,2,3 and Maria D. Logacheva1,4,5* Abstract Background: While photosynthesis is the most notable trait of plants, several lineages of plants (so-called full heterotrophs) have adapted to obtain organic compounds from other sources. The switch to heterotrophy leads to profound changes at the morphological, physiological and genomic levels. Results: Here, we characterize the transcriptomes of three species representing two lineages of mycoheterotrophic plants: orchids (Epipogium aphyllum and Epipogium roseum) and Ericaceae (Hypopitys monotropa). Comparative analysis is used to highlight the parallelism between distantly related fully heterotrophic plants. In both lineages, we observed genome-wide elimination of nuclear genes that encode proteins related to photosynthesis, while systems associated with protein import to plastids as well as plastid transcription and translation remain active. Genes encoding components of plastid ribosomes that have been lost from the plastid genomes have not been transferred to the nuclear genomes; instead, some of the encoded proteins have been substituted by homologs. The nuclear genes of both Epipogium species accumulated nucleotide substitutions twice as rapidly as their photosynthetic relatives; in contrast, no increase in the substitution rate was observed in H. monotropa. Conclusions: Full heterotrophy leads to profound changes in nuclear gene content. The observed increase in the rate of nucleotide substitutions is lineage specific, rather than a universal phenomenon among non-photosynthetic plants. -
The Plastomes of Two Species in the Endoparasite Genus Pilostyles (Apodanthaceae) Each Retain Just Five Or Six Possibly Functional Genes
GBE The Plastomes of Two Species in the Endoparasite Genus Pilostyles (Apodanthaceae) Each Retain Just Five or Six Possibly Functional Genes Sidonie Bellot1,* and Susanne S. Renner1 1Department of Biology, Ludwig Maximilian University, Munich, Germany *Corresponding author: E-mail: [email protected]. Accepted: December 6, 2015 Data deposition: The plastomes of Pilostyles aethiopica and Pilostyles hamiltonii have been deposited at GenBank under the accessions KT981955 and KT981956. Abstract Downloaded from The 23 species of mycoheterotrophic or exoparasitic land plants (from 15 genera and 6 families) studied so far all retain a minimal set of 17 of the normally 116 plastome genes. Only Rafflesia lagascae, an endoparasite concealed in its host except when flowering, has been reported as perhaps lacking a plastome, although it still possesses plastid-like compartments. We analyzed two other endo- parasites, the African Apodanthaceae Pilostyles aethiopica and the Australian Pilostyles hamiltonii, both living inside Fabaceae. http://gbe.oxfordjournals.org/ Illumina and 454 data and Sanger resequencing yielded circularized plastomes of 11,348 and 15,167 bp length, with both species containing five possibly functional genes (accD, rps3, rps4, rrn16, rrn23) and two/three pseudogenes (rpoC2 in P. aethiopica and rpl2 and rps12 in both species; rps12 may be functional in P. hamiltonii). Previously known smallest land plant plastomes contain 27–29 genes, making these Apodanthaceae plastomes the most reduced in size and gene content. A similar extent of divergence might have caused the plastome of Rafflesia to escape detection. The higher plastome degeneration in both these families of endoparasites, Rafflesiaceae and Apodanthaceae, of similar high age, compared with exoparasites points to a difference of plastome function between those two modes of parasitic life. -
First Reports and Generic Descriptions of the Achlorophyllous Holoparasites Apodanthaceae (Cucurbitales) of Colombia
González y Pabón-Mora Actual Biol Volumen 36 / Número 101, 2014 First reports and generic descriptions of the achlorophyllous holoparasites Apodanthaceae (Cucurbitales) of Colombia Primeros registros y descripciones genéricas de la familia de holoparásitos aclorófilos Apodanthaceae (Cucurbitales) de Colombia Favio González1, 3, Natalia Pabón-Mora2, 4 Abstract The Apodanthaceae (Cucurbitales) are one of the 12 parasitic clades of flowering plants and the only holoparasitic family with a vegetative phase entirely endophytic, growing primarily on Fabaceae and Salicaceae stems. The two genera of the family, Apodanthes and Pilostyles, are broadly distributed in Colombia, although they remain extremely under-collected and poorly known. Based on field and herbarium work, and a review of the literature, we provide detailed generic-level descriptions of the family. We also update the records of the family in Colombia and discuss the homology and taxonomic implications of floral characters such as perianth scales, pollen sacs, and the central column. Finally, we provide photographic records of Colombian Apodanthaceae, and some guidelines for properly collecting these plants. Key words: Apodanthaceae, Apodanthes, Cucurbitales, Colombian flora, parasitic flowering plants,Pilostyles Resumen Apodanthaceae (Cucurbitales) es uno de los doce clados de angiospermas parasíticas, y la única familia de especies holoparasíticas con la fase vegetativa completamente endofítica en tallos principalmente de especies de Fabaceae y Salicaceae. Los dos géneros de la familia, Apodanthes y Pilostyles están ampliamente distribuidos en Colombia, aunque han sido muy poco recolectados y permanecen poco conocidos. Con base en trabajo de campo y de herbario, y una extensa revisión bibliográfica, se describen en detalle los caracteres genéricos de la familia. -
Seed Shape Quantification in the Order Cucurbitales
ISSN 2226-3063 e-ISSN 2227-9555 Modern Phytomorphology 12: 1–13, 2018 https://doi.org/10.5281/zenodo.1174871 RESEARCH ARTICLE Seed shape quantification in the order Cucurbitales Emilio Cervantes 1, 2*, José Javier Martín Gómez 1 1 Instituto de Recursos Naturales y Agrobiología de Salamanca-Consejo Superior de Investigaciones Científicas (IRNASA–CSIC), Cordel de Merinas 40, 37008 Salamanca, Spain; * [email protected] 2 Grupo de Investigación Reconocido Bases Moleculares del Desarrollo, Universidad de Salamanca (GIR BMD-USAL), Edificio Departamental, Campus Miguel de Unamuno, 37007 Salamanca, Spain Received: 03.10.2017 | Accepted: 23.01.2018 | Published: 17.02.2018 Abstract Seed shape quantification in diverse species of the families belonging to the order Cucurbitales is done based on the comparison of seed images with geometric figures. Quantification of seed shape is a useful tool in plant description for phenotypic characterization and taxonomic analysis. J index gives the percent of similarity of the image of a seed with a geometric figure and it is useful in taxonomy for the study of relationships between plant groups. Geometric figures used as models in the Cucurbitales are the ovoid, two ellipses with different x/y ratios and the outline of the Fibonacci spiral. The images of seeds have been compared with these figures and values of J index obtained. The results obtained for 29 species in the family Cucurbitaceae support a relationship between seed shape and species ecology. Simple seed shape, with images resembling simple geometric figures like the ovoid, ellipse or the Fibonacci spiral, may be a feature in the basal clades of taxonomic groups. -
Holoparasitic Rafflesiaceae Possess the Most Reduced Endophytes And
Annals of Botany 114: 233–242, 2014 doi:10.1093/aob/mcu114, available online at www.aob.oxfordjournals.org Holoparasitic Rafflesiaceae possess the most reduced endophytes and yet give rise to the world’s largest flowers Downloaded from https://academic.oup.com/aob/article-abstract/114/2/233/2769112 by Harvard University user on 28 September 2018 Lachezar A. Nikolov1, P. B. Tomlinson2, Sugumaran Manickam3, Peter K. Endress4, Elena M. Kramer1 and Charles C. Davis1,* 1Department of Organismic and Evolutionary Biology, Harvard University Herbaria, Cambridge, MA 02138, USA, 2The Kampong, National Tropical Botanical Garden, 4013 Douglas Road, Miami, FL 33133, USA, 3Rimba Ilmu Botanic Garden, Institute of Biological Sciences, University of Malaya, 50603 Kuala Lumpur, Malaysia and and 4Institute of Systematic Botany, University of Zurich, Zollikerstrasse 107, CH-8008 Zurich, Switzerland * For correspondence. E-mail [email protected] Received: 21 January 2014 Returned for revision: 10 March 2014 Accepted: 2 May 2014 Published electronically: 18 June 2014 † Background and Aims Species in the holoparasitic plant family Rafflesiaceae exhibit one of the most highly modi- fied vegetative bodies in flowering plants. Apart from the flower shoot and associated bracts, the parasite is a myce- lium-like endophyte living inside their grapevine hosts. This study provides a comprehensive treatment of the endophytic vegetative body for all three genera of Rafflesiaceae (Rafflesia, Rhizanthes and Sapria), and reports on the cytology and development of the endophyte, including its structural connection to the host, shedding light on the poorly understood nature of this symbiosis. † Methods Serial sectioning and staining with non-specific dyes, periodic–Schiff’s reagent and aniline blue were employed in order to characterize the structure of the endophyte across a phylogenetically diverse sampling. -
Checklist of the Vascular Plants of San Diego County 5Th Edition
cHeckliSt of tHe vaScUlaR PlaNtS of SaN DieGo coUNty 5th edition Pinus torreyana subsp. torreyana Downingia concolor var. brevior Thermopsis californica var. semota Pogogyne abramsii Hulsea californica Cylindropuntia fosbergii Dudleya brevifolia Chorizanthe orcuttiana Astragalus deanei by Jon P. Rebman and Michael G. Simpson San Diego Natural History Museum and San Diego State University examples of checklist taxa: SPecieS SPecieS iNfRaSPecieS iNfRaSPecieS NaMe aUtHoR RaNk & NaMe aUtHoR Eriodictyon trichocalyx A. Heller var. lanatum (Brand) Jepson {SD 135251} [E. t. subsp. l. (Brand) Munz] Hairy yerba Santa SyNoNyM SyMBol foR NoN-NATIVE, NATURaliZeD PlaNt *Erodium cicutarium (L.) Aiton {SD 122398} red-Stem Filaree/StorkSbill HeRBaRiUM SPeciMeN coMMoN DocUMeNTATION NaMe SyMBol foR PlaNt Not liSteD iN THE JEPSON MANUAL †Rhus aromatica Aiton var. simplicifolia (Greene) Conquist {SD 118139} Single-leaF SkunkbruSH SyMBol foR StRict eNDeMic TO SaN DieGo coUNty §§Dudleya brevifolia (Moran) Moran {SD 130030} SHort-leaF dudleya [D. blochmaniae (Eastw.) Moran subsp. brevifolia Moran] 1B.1 S1.1 G2t1 ce SyMBol foR NeaR eNDeMic TO SaN DieGo coUNty §Nolina interrata Gentry {SD 79876} deHeSa nolina 1B.1 S2 G2 ce eNviRoNMeNTAL liStiNG SyMBol foR MiSiDeNtifieD PlaNt, Not occURRiNG iN coUNty (Note: this symbol used in appendix 1 only.) ?Cirsium brevistylum Cronq. indian tHiStle i checklist of the vascular plants of san Diego county 5th edition by Jon p. rebman and Michael g. simpson san Diego natural history Museum and san Diego state university publication of: san Diego natural history Museum san Diego, california ii Copyright © 2014 by Jon P. Rebman and Michael G. Simpson Fifth edition 2014. isBn 0-918969-08-5 Copyright © 2006 by Jon P. -
Phylogenetic Origins of Parasitic Plants Daniel L. Nickrent Chapter 3, Pp. 29-56 In: J. A. López-Sáez, P. Catalán and L
Phylogenetic Origins of Parasitic Plants Daniel L. Nickrent Chapter 3, pp. 29-56 in: J. A. López-Sáez, P. Catalán and L. Sáez [eds.], Parasitic Plants of the Iberian Peninsula and Balearic Islands This text first written in English (as appears here) was translated into Spanish and appeared in the book whose Spanish citation is: Nickrent, D. L. 2002. Orígenes filogenéticos de las plantas parásitas. Capitulo 3, pp. 29-56 In J. A. López-Sáez, P. Catalán and L. Sáez [eds.], Plantas Parásitas de la Península Ibérica e Islas Baleares. Mundi-Prensa Libros, S. A., Madrid. Throughout its history, the field of plant systematics has undergone changes in response to the advent of new philosophical ideas, types of data, and methods of analysis. It is no exaggeration to say that the past decade has witnessed a virtual revolution in phylogenetic investigation, owing mainly to the application of molecular methodologies and advancements in data analysis techniques. These powerful approaches have provided a source of data, independent of morphology, that can be used to address long-standing questions in angiosperm evolution. These new methods have been applied to systematic and phylogenetic questions among parasitic plants (Nickrent et al. 1998), but have often raised as many new questions as they have solved, in part due to the amazingly complex nature of the genetic systems present in these organisms. The goal of this chapter is to provide a general synopsis of the current state of understanding of parasitic plant phylogeny. To place in context results concerning the parasites, it is necessary to first examine general features of angiosperm phylogeny. -
The Biology of Non-Weedy Parasitic Plants: the Third Symposium
Plant Ecology and Evolution 14x (x): xx–xx, 2016 http://dx.doi.org/10.5091/plecevo.201x.xxx EDITORIAL The biology of non-weedy parasitic plants: the third symposium Renate A. Wesselingh Editor and symposium organiser Third symposium on the biology of non-weedy parasitic plants: excursion at the Montagne de Sosoye (Namur Province), a protected Site of Biological Importance. This was one of the two sites that were visited on 14 September 2013, both with calcareous grasslands, which are excellent places to observe high biodiversity in Belgium, even in early autumn. Photograph by Agata Klimkowska. Proofs In September 2013, the third symposium on the biology of parasitic plants, hemiparasitic or holoparasitic, that are not non-weedy parasitic plants was held in Belgium. The meet- considered to be agricultural weeds. ing followed in the footsteps of the two previous editions of The third symposium on the biology of non-weedy para- the symposium held in 2004 in Wageningen, the Netherlands sitic plants was held in Namur in Belgium on 12–15 Sep- (Wesselingh & Borg 2005, Wesselingh & van Groenendael tember 2013 and attracted 26 participants from eight coun- 2005) and in 2008 in České Budĕjovice in the Czech Repub- tries. Two invited talks, ten contributed talks and ten posters lic (Štech & Wesselingh 2010). The aim of these symposia is were presented. Although the scope of the meeting had been to focus on the ecology, ecophysiology and evolution of non- enlarged to other parasitic plant families, many of the par- weedy parasitic plants, thereby consolidating its own niche ticipants presented work on the commonly studied Oroban- compared to the larger meetings on parasitic plants that often chaceae, ranging from Rhinanthus, Pedicularis and Mela- focus mostly on the parasites that pose problems in agricul- mpyrum to Euphrasia and Odontites. -
Holoparasitic Rafflesiaceae Possess the Most Reduced
Annals of Botany 114: 233–242, 2014 doi:10.1093/aob/mcu114, available online at www.aob.oxfordjournals.org Holoparasitic Rafflesiaceae possess the most reduced endophytes and yet give rise to the world’s largest flowers Lachezar A. Nikolov1, P. B. Tomlinson2, Sugumaran Manickam3, Peter K. Endress4, Elena M. Kramer1 and Charles C. Davis1,* 1Department of Organismic and Evolutionary Biology, Harvard University Herbaria, Cambridge, MA 02138, USA, 2The Kampong, National Tropical Botanical Garden, 4013 Douglas Road, Miami, FL 33133, USA, 3Rimba Ilmu Botanic Garden, Institute of Biological Sciences, University of Malaya, 50603 Kuala Lumpur, Malaysia and and 4Institute of Systematic Botany, University of Zurich, Zollikerstrasse 107, CH-8008 Zurich, Switzerland * For correspondence. E-mail [email protected] Received: 21 January 2014 Returned for revision: 10 March 2014 Accepted: 2 May 2014 Published electronically: 18 June 2014 † Background and Aims Species in the holoparasitic plant family Rafflesiaceae exhibit one of the most highly modi- fied vegetative bodies in flowering plants. Apart from the flower shoot and associated bracts, the parasite is a myce- lium-like endophyte living inside their grapevine hosts. This study provides a comprehensive treatment of the endophytic vegetative body for all three genera of Rafflesiaceae (Rafflesia, Rhizanthes and Sapria), and reports on the cytology and development of the endophyte, including its structural connection to the host, shedding light on the poorly understood nature of this symbiosis. † Methods Serial sectioning and staining with non-specific dyes, periodic–Schiff’s reagent and aniline blue were employed in order to characterize the structure of the endophyte across a phylogenetically diverse sampling. -
2 ANGIOSPERM PHYLOGENY GROUP (APG) SYSTEM History Of
ANGIOSPERM PHYLOGENY GROUP (APG) SYSTEM The Angiosperm Phylogeny Group, or APG, refers to an informal international group of systematic botanists who came together to try to establish a consensus view of the taxonomy of flowering plants (angiosperms) that would reflect new knowledge about their relationships based upon phylogenetic studies. As of 2010, three incremental versions of a classification system have resulted from this collaboration (published in 1998, 2003 and 2009). An important motivation for the group was what they viewed as deficiencies in prior angiosperm classifications, which were not based on monophyletic groups (i.e. groups consisting of all the descendants of a common ancestor). APG publications are increasingly influential, with a number of major herbaria changing the arrangement of their collections to match the latest APG system. Angiosperm classification and the APG Until detailed genetic evidence became available, the classification of flowering plants (also known as angiosperms, Angiospermae, Anthophyta or Magnoliophyta) was based on their morphology (particularly that of the flower) and their biochemistry (what kinds of chemical compound they contained or produced). Classification systems were typically produced by an individual botanist or by a small group. The result was a large number of such systems (see List of systems of plant taxonomy). Different systems and their updates tended to be favoured in different countries; e.g. the Engler system in continental Europe; the Bentham & Hooker system in Britain (particularly influential because it was used by Kew); the Takhtajan system in the former Soviet Union and countries within its sphere of influence; and the Cronquist system in the United States.