BOTANY 2019, AJB Reports for Associate Editors
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Conceptual Barriers to Progress Within Evolutionary Biology
Found Sci (2009) 14:195–216 DOI 10.1007/s10699-008-9153-8 Conceptual Barriers to Progress Within Evolutionary Biology Kevin N. Laland · John Odling-Smee · Marcus W. Feldman · Jeremy Kendal Published online: 26 November 2008 © Springer Science+Business Media B.V. 2008 Abstract In spite of its success, Neo-Darwinism is faced with major conceptual barriers to further progress, deriving directly from its metaphysical foundations. Most importantly, neo- Darwinism fails to recognize a fundamental cause of evolutionary change, “niche construc- tion”. This failure restricts the generality of evolutionary theory, and introduces inaccuracies. It also hinders the integration of evolutionary biology with neighbouring disciplines, includ- ing ecosystem ecology, developmental biology, and the human sciences. Ecology is forced to become a divided discipline, developmental biology is stubbornly difficult to reconcile with evolutionary theory, and the majority of biologists and social scientists are still unhappy with evolutionary accounts of human behaviour. The incorporation of niche construction as both a cause and a product of evolution removes these disciplinary boundaries while greatly generalizing the explanatory power of evolutionary theory. Keywords Niche construction · Evolutionary biology · Ecological inheritance · Ecosystem ecology · Developmental biology 1 Introduction On the face of it, evolutionary biology is a thriving discipline: It is built on the solid theoret- ical foundations of mathematical population biology; it has a rich and productive empirical K. N. Laland (B) School of Biology, University of St. Andrews, Bute Building, Queens Terrace, St. Andrews, Fife KY16 9TS, UK e-mail: [email protected] J. Odling-Smee Mansfield College, University of Oxford, Oxford OX1 3TF, UK M. -
Jesse D. Hollister
Ecology and Evolutionary Biology Stony Brook University [email protected] Jesse D. Hollister Education 2009 Ph.D. Biological Sciences, University of California, Irvine 2003 B.A. Biology, Sonoma State University Professional Experience Jan. 2015- Assistant Professor, Dept. of Ecology and Evolutionary Biology, Stony Brook University 2012-2014 Postdoctoral Fellow, Dept. of Ecology and Evolutionary Biology, University of Toronto. Advisors: Stephen Wright, Marc Johnson 2009-2011 Postdoctoral Fellow, Dept. of Organismic and Evolutionary Biology, Harvard University. Advisor: Kirsten Bomblies Publications 13. Hollister, J.D. 2014. Polyploidy: adaptation to the genomic environment. New Phytologist. DOI: 10.1111/nph.12942 12. Hough, J., J.D. Hollister, W. Wang, S.C.H. Barrett, and S.I Wright. 2014. Genetic degeneration of old and young Y chromosomes in the flowering plant Rumex hastatulus. PNAS. 111(21): 7713-7718. 11. Hollister, J.D. 2014. Genomic variation in Arabidopsis: tools and insights from next generation sequencing. Chromosome Research. 1-13. 10. Yant, L. *, J.D. Hollister*, K. Wright, B. Arnold, J. Higgins, F. C. Franklin, and K. Bomblies. 2013. Meiotic adaptation to a genome-doubled state in Arabidopsis arenosa. Curr. Biol. 23(21): R961-63 *Co-first Authors 9. Hollister, J.D., B. Arnold, E. Svedin, K. Xue, B. Dilkes, and K. Bomblies. 2012. Genetic adaptation associated with genome doubling in autotetraploid Arabidopsis arenosa. PLoS Genet. 8(12), e1003093 8. B.C. Hunter, J. D. Hollister, and K. Bomblies. 2012. Epigenetic inheritance: what news for evolution? Curr. Biol. 22(2): R54-55. 7. Hollister, J.D., L. Smith, Y. Guo, F. Ott, D. Weigel, and B. -
Economic Botany: General References James P
Humboldt State University Digital Commons @ Humboldt State University Botanical Studies Open Educational Resources and Data 2-2017 Economic Botany: General References James P. Smith Jr Humboldt State University, [email protected] Follow this and additional works at: http://digitalcommons.humboldt.edu/botany_jps Part of the Botany Commons Recommended Citation Smith, James P. Jr, "Economic Botany: General References" (2017). Botanical Studies. 23. http://digitalcommons.humboldt.edu/botany_jps/23 This Economic Botany - Ethnobotany is brought to you for free and open access by the Open Educational Resources and Data at Digital Commons @ Humboldt State University. It has been accepted for inclusion in Botanical Studies by an authorized administrator of Digital Commons @ Humboldt State University. For more information, please contact [email protected]. ECONOMIC BOTANY: GENERAL REFERENCES James P. Smith, Jr. Professor Emeritus of Botany Department of Biological Sciences Humboldt State University Arcata, California February 2017 Ford, R. I. (editor). 1978. The nature and status of THE SCOPE OF STUDY ethnobotany. Anthrop. Papers No. 67. Museum of Anthropology. Univ. of Michigan. Ann Arbor. 428 pp. Alcorn, J. B. 1995. Economic botany, conservation, and development: what's the connection? Ann. Fosberg, F. R. 1948. Economic botany -- a modern Missouri Bot. Gard. 82(1): 34-36. concept of its scope. Econ. Bot. 2(1): 3-14. Balick, M. J. 1996. Transforming ethnobotany for Gilmore, M. R. 1932. Importance of ethnobotanical the new millenium. Ann. Missouri Bot. Gard. 83(1): investigation. American Anthrop. 34: 320-327. 58-66. Gomez-Pompa, A. 1986. La botanica economica: un Barrau, J. 1971. L'ethnobotanique au carrefour des punto de vista. -
ALKALOID-BEARING PLANTS and THEIR CONTAINED ALKALOIDS by J
ALKALOID-BEARING PLANTS and Their Contained Alkaloids TT'TBUCK \ \ '■'. Technical Bulletin No. 1234 AGRICULTURAL RESEARCH SERVICE U.S. DEPARTMENT OF AGRICULTURE ACKNOWLEDGMENTS The authors are indebted to J. W. Schermerhorn and M. W. Quimby, Massachusetts College of Pharmacy, for access to the original files of the Lynn Index; to K. F. Rauiïauf, Smith, Kline & French Labora- tories, and to J. H. Hoch, Medical College of South Carolina, for extensive lists of alkaloid plants; to V. S. Sokolov, V. L. Komarova Academy of Science, Leningrad, for a copy of his book; to J. M. Fogg, Jr., and H. T. Li, Morris Arboretum, for botanical help and identification of Chinese drug names ; to Michael Dymicky, formerly of the Eastern Utilization Research and Development Division, for ex- tensive translations; and to colleagues in many countries for answering questions raised during the compilation of these lists. CONTENTS Page Codes used in table 1 2 Table 1.—Plants and their contained alkaloids 7 Table 2.—Alkaloids and the plants in which they occur 240 Washington, D.C. Issued August 1961 For sale by the Superintendent of Documents, Qovemment Printing OflSce. Washington 25, D.C. Price $1 ALKALOID-BEARING PLANTS AND THEIR CONTAINED ALKALOIDS By J. J. WiLLAMAN, chemist, Eastern Utilization Research and Development Division, and BERNICE G. SCHUBERT, taxonomist. Crops Research Division, Agricultural Research Service This compilation assembles in one place all the scattered information on the occurrence of alkaloids in the plant world. It consists of two lists: (1) The names of the plants and of their contained alkaloids; and (2) the names and empirical formulas of the alkaloids. -
Bio. Sci. 103 Study Questions From: “Economic Botany” 3Rd Ed. Simpson & Ogorzaly Chapter 1 1. About How Many of the E
Bio. Sci. 103 Study questions from: “Economic Botany” 3rd Ed. Simpson & Ogorzaly Chapter 1 1. About how many of the edible species of plants known have been eaten historically by humans? Of this total, about how many have been eaten with some regularity? And of this total, about how many are now of major economic importance? 2. What is the major difference between the primary and secondary compounds that plants produce? 3. What is an angiosperm? What is a gymnosperm? (Note that the text has a glossary on P. 486) 4. What are the 2 main functions of the roots of plants? 5. What is a root that emerges from a stem called? 6. What are the 3 different kinds of underground stems, which are used for food storage? 7. What is a bulb? 8. What is the meaning of the following terms? Endosperm, Perfect Flowers, Imperfect Flowers, Monoecious, Dioecious, “Double Fertilization,” Pollinators, Gametophytes, Sporophytes. 9. Be prepared to give the names and sequences in development, represented by the drawings you received in class. 10. What 3 features possessed by seeds make them good sources of food for humans? 11. What is the name of the system of breeding that most plants in nature use, even if they are self- compatible? What does this system ensure? 12. What is the meaning of the following terms: Clone, Grafting, Autopolyploid, and Allopolyploid. 13. Why do triploid organisms have trouble with seed production? 14. What is a major advantage to a farmer in growing a crop plant far from its native home? What is a possible hazard in doing this? 15. -
Economic Botany
ECONOMIC BOTANY MANOJ KUMAR SHARMA Ph.D., F.L.S. (London) J.V. College, Baraut An ISO 9001:2008 Certified Company 2/25, Ansari Road, Darya Ganj-110 002 ECONOMIC BOTANY Copyright © VAYU EDUCATION OF INDIA ISBN: 978-93-83137-46-6 First Edition: 2013 Rs. 300/- All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, electronic, mechanical, photocopying, recording or otherwise, without the prior permission of the Publishers. Laser Typesetting : Upasana Graphics, New Delhi Published by: VAYU EDUCATION OF INDIA 2/25, Ansari Road, Darya Ganj, New Delhi-110 002 Ph.: 91-11-43526600, 41564445 Fax: 91-11-41564440 E-mail: [email protected], [email protected] Web: www.veiindia.com PREFACE The field of applied science, dealing with the practical or economic aspects of a subject, lends itself much better to such treatment than does the field of pure science. This is particularly true of botany. From earliest time plants have been intimately bound up with human existence. Not only have they played an important part in the everyday life of mankind, but they have had a profound influence on the course of history and civilization. Aknowledge of the industrial, medicinal, and edible plants cannot fail to broaden one’s outlook. First of all I thank to almighty for giving me strength for this noble cause. My respectful thank to Dr. Y. S. Tomar, Dr. Sudhir Kumar, Dr. Baljeet Singh, Dr.S. P. Singh, Dr. A. K. Sharma, Dr. Rajeshwari Sharma, Dr. -
Tansley Insight Rapid Evolution in Plant–Microbe Interactions – an Evolutionary Genomics Perspective
Review Tansley insight Rapid evolution in plant–microbe interactions – an evolutionary genomics perspective Author for correspondence: Sophie de Vries1 , Eva H. Stukenbrock2,3 and Laura E. Rose1 Laura E. Rose 1 € € € Tel: +49 211 81 13406 Institute of Population Genetics, Heinrich Heine University Dusseldorf, Universitatsstraße 1 40225, Dusseldorf, Germany; Email: [email protected] 2Environmental Genomics, Max Planck Institute for Evolutionary Biology, Pl€on, Germany; 3The Botanical Institute, Christian- Received: 6 May 2019 Albrechts University of Kiel, Am Botanischen Garden 9-11 24118, Kiel, Germany Accepted: 13 January 2020 Contents Summary 1256 VI. The role of reticulate evolution 1258 I. Introduction 1256 VII. Concluding comments 1260 II. Signatures of selection 1257 Acknowledgements 1260 III. Convergent evolution 1257 References 1261 IV. Cryptic genetic variation 1258 V. Evidence of host jumps 1258 Summary New Phytologist (2020) 226: 1256–1262 Access to greater genomic resolution through new sequencing technologies is transforming the doi: 10.1111/nph.16458 field of plant pathology. As scientists embrace these new methods, some overarching patterns and observations come into focus. Evolutionary genomic studies are used to determine not only Key words: co-evolution, convergent the origins of pathogen lineages and geographic patterns of genetic diversity, but also to discern evolution, crop protection, genetic variation, how natural selection structures genetic variation across the genome. With greater and greater natural selection, phytopathogens. resolution, we can now pinpoint the targets of selection on a large scale. At multiple levels, crypsis and convergent evolution are evident. Host jumps and shifts may be more pervasive than once believed, and hybridization and horizontal gene transfer (HGT) likely play important roles in the emergence of genetic novelty. -
Using Phylogenetics to Detect Pollinatormediated Floral Evolution
New Review Phytologist Research review Using phylogenetics to detect pollinator-mediated floral evolution Author for correspondence: Stacey DeWitt Smith Stacey DeWitt Smith Department of Biology, Duke University, Durham, NC 27708, USA Tel: +1 919 684 3378 Email: [email protected] Received: 28 February 2010 Accepted: 6 April 2010 Summary New Phytologist (2010) 188: 354–363 The development of comparative phylogenetic methods has provided a powerful doi: 10.1111/j.1469-8137.2010.03292.x toolkit for addressing adaptive hypotheses, and researchers have begun to apply these methods to test the role of pollinators in floral evolution and diversification. Key words: ancestral state reconstruction, One approach is to reconstruct the history of both floral traits and pollination sys- diversification, floral evolution, phylogenetic tems to determine if floral trait change is spurred by shifts in pollinators. Looking generalized least squares, phylogenetics, across multiple shifts, it is also possible to test for significant correlations between pollination system, stochastic mapping, floral evolution and pollinators using parsimony, likelihood and Bayesian methods transition rate. for discrete characters or using statistical comparative methods for continuous characters. Evolutionary shifts in pollinators and floral traits may cause changes in diversification rates, and new methods are available for simultaneously studying character evolution and diversification rates. Relatively few studies have yet used formal comparative methods to elucidate how pollinators affect floral evolution across the phylogeny, and fruitful directions for future applications are discussed. consistent with the idea that these syndromes reflect floral Introduction adaptation (Stebbins, 1970; Fenster et al., 2004). These Comparative analysis has a long history in the study of comparative studies of floral morphology and pollination plant–pollinator interactions. -
Plant Domestication and the Origins of Agriculture - B.C
ECONOMIC BOTANY - Plant Domestication and the Origins of Agriculture - B.C. Bennett PLANT DOMESTICATION AND THE ORIGINS OF AGRICULTURE B.C. Bennett Department of Biological Sciences and Center for Ethnobiology and Natural Products, Florida International University, Miami, FL 33199 USA Keywords: agriculture, centers of domestication, cultivars, domesticates, domestication, foraging, strategies, origins of agricultures, selection Contents 1. Introduction 2. Domestication 2.1 Background 2.2 Characteristics of Domesticates 2.3. The First Farmers 3. Why Farm? 3.1. Agriculture and Religion 3.2. Cultural Evolutionism 3.3. Dump Heaps 3.4. Convenience 3.5. Population Increase 3.6. Environmental Change 3.7. Food Abundance 3.8. Co-evolution 3.9. Increased Familiarity 3.10. Broad Spectrum Revolution 4. Conclusions Appendix Glossary Bibliography Biographical Sketch Summary UNESCO – EOLSS Of the four primary subsistence strategies recognized by anthropologists, agriculture now dominates. In many societies, less than 1% of the population produces sufficient food supplies toSAMPLE support the whole population. CHAPTERS Horticulture remains important in some regions, especially the tropics. A few cultures rely entirely on pastoralism. Foraging, the dominant practice 10,000 years ago, is exceedingly rare today. Agriculture relies on a relatively small palette of domesticated plant resources to sustain the world’s human population. Of the more than nearly 2750,000 species of flowering plants, less than 1% has been domesticated. Three species (wheat, corn, and rice) provide more than 60% of the world’s calories. Domesticated species have been genetically altered through human selection to such an extent that they can not survive on their own. Common traits of cultivars include increased size of edible parts, increased palatability, decreased armament, absence of dormancy, decreased toxicity, abbreviated flowering, ©Encyclopedia of Life Support Systems(EOLSS) ECONOMIC BOTANY - Plant Domestication and the Origins of Agriculture - B.C. -
Phylogenetic Trends and Environmental Correlates of Nuclear Genome Size Variation in Helianthus Sunflowers
Research Phylogenetic trends and environmental correlates of nuclear genome size variation in Helianthus sunflowers Fan Qiu1, Eric J. Baack2 , Kenneth D. Whitney3 , Dan G. Bock4 , Hannah M. Tetreault1 , Loren H. Rieseberg4 and Mark C. Ungerer1 1Division of Biology, Kansas State University, Manhattan, KS 66506, USA; 2Department of Biology, Luther College, Decorah, IA 52101, USA; 3Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA; 4Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada Summary Author for correspondence: Flowering plants serve as a powerful model for studying the evolution of nuclear genome Fan Qiu size (GS) given the tremendous GS variation that exists both within and across angiosperm lin- Tel: +1 7855325574 eages. Email: [email protected] Helianthus sunflowers consist of c. 50 species native to North America that occupy diverse Received: 3 July 2018 habitats and vary in ploidy level. In the current study, we generated a comprehensive GS Accepted: 29 August 2018 database for 49 Helianthus species using flow cytometric approaches. We examined variabil- ity across the genus and present a comparative phylogenetic analysis of GS evolution in New Phytologist (2019) 221: 1609–1618 diploid Helianthus species. doi: 10.1111/nph.15465 Results demonstrated that different clades of diploid Helianthus species showed evolution- ary patterns of GS contraction, expansion and relative stasis, with annual diploid species Key words: genome size (GS) evolution, evolving smaller GS with the highest rate of evolution. Phylogenetic comparative analyses of growing season, Helianthus, phylogenetic diploids revealed significant negative associations of GS with temperature seasonality and cell comparative analysis, temperature seasonality. production rate, indicating that the evolution of larger GS in Helianthus diploids may be more permissible in habitats with longer growing seasons where selection for more rapid growth may be relaxed. -
Evolutionary Network Genomics of Wood Formation in a Phylogenetic Survey of Angiosperm Forest Trees
Research Evolutionary network genomics of wood formation in a phylogenetic survey of angiosperm forest trees Matthew Zinkgraf1,2* , Shu-Tang Zhao3*, Courtney Canning1, Suzanne Gerttula1, Meng-Zhu Lu3 , Vladimir Filkov4 and Andrew Groover1,5 1USDA Forest Service, Pacific Southwest Research Station, Davis, CA 95618, USA; 2College of Science and Engineering, Western Washington University, Bellingham, WA 98225-9063, USA; 3State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; 4Computer Science, University of California Davis, Davis, CA 95618, USA; 5Department of Plant Biology, University of California Davis, Davis, CA 95616, USA Summary Authors for correspondence: Wood formation was present in early angiosperms, but has been highly modified through Andrew Groover evolution to generate the anatomical diversity seen in extant angiosperm lineages. In this pro- Tel: +1 530 759 1738 ject, we modeled changes in gene coexpression relationships associated with the evolution of Email: [email protected] wood formation in a phylogenetic survey of 13 angiosperm tree species. Vladimir Filkov Gravitropic stimulation was used as an experimental treatment to alter wood formation and Tel: +1 530 752 8393 also perturb gene expression. Gene transcript abundances were determined using RNA Email: fi[email protected] sequencing of developing wood tissues from upright trees, and from the top (tension wood) and bottom (opposite wood) tissues of gravistimulated trees. Meng-Zhu Lu Tel: +86 571 6383 9132 A network-based approach was employed to align gene coexpression networks across Email: [email protected] species based on orthologous relationships. A large-scale, multilayer network was modeled Received: 20 May 2020 that identified both lineage-specific gene coexpression modules and modules conserved Accepted: 6 July 2020 across multiple species. -
Download Plant Biology Journals
Plant Specific Society (Yes or (Yes or Managing Journal Name Impact Factor (2019) Publisher No) Discipline Types of articles No) Name of the society Open Access or Not Editor/Associate Editor Journal Contact Editor in Chief Stella M. Hurtley, Julia Fahrenkamp-Uppenbrink, Phillip D. Dzuromi, Sacha Vignieri and Andrew M. Sr. 1 Science 41.845 AAAS No Multidisciplinary science Research, Review Yes AAAS No Sugden [email protected] Holden Thorp Sr. 2 Science Advances 11.5 AAAS No Multidisciplinary science Research, Review Yes AAAS Hybrid-open access Ali Shilatifard [email protected] Holden Thorp Proceedings of the National Sr. 3 PNAS 9.412 National Academy of Sciences No Multidisciplinary Science Research Yes Academy of Sciences Delayed open-access Emma P. Shumeyko [email protected] May R. Berenbaum Sr. 4 Plant Cell 8.63 ASPB Yes Plant cell and molecular biology Research, Review Yes ASPB Yes Jennifer A. Regala [email protected] Blake Meyers Sr. 5 Science Signaling 7.4 AAAS No "Signal transduction in physiology and disease" Research, Review Yes AAAS Yes Large editorial board [email protected] Michael B. Yaffe Society for Experimental Biology (SEB) and the "Molecular plant sciences and their applications through plant Association of Applied François Belzile, Xiao-Ya Chen Sr. 6 Plant Biotechnology Journal 6.305 Wiley-Blackwell Yes biotechnology" Research, Review Yes Biologists (AAB) Yes and co-workers [email protected] Henry Daniell Research, Advances, Society for experimental biology Federica Brandizzi, Alisdair R. [email protected] , tpj@wiley. Sr. 7 The Plant Journal 6.14 Wiley-Blackwell Yes All key areas of plant biology Resources Yes (SEB) Yes Fernie com Lee Sweetlove Julia Bailey-Serres, Alice Y.