Darwin, Evolution, Evolutionisms
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Stable and Widespread Structural Heteroplasmy in Chloroplast Genomes Revealed by a New Long-Read Quantification Method
bioRxiv preprint doi: https://doi.org/10.1101/692798; this version posted July 11, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Classification: Biological Sciences, Evolution Title: Stable and widespread structural heteroplasmy in chloroplast genomes revealed by a new long-read quantification method Weiwen Wang a, Robert Lanfear a a Research School of Biology, Australian National University, Canberra, ACT, Australia, 2601 Corresponding Author: Weiwen Wang, [email protected] Robert Lanfear, [email protected], +61 2 6125 2536 Keywords: Single copy inversion, flip-flop recombination, chloroplast genome structural heteroplasmy 1 bioRxiv preprint doi: https://doi.org/10.1101/692798; this version posted July 11, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 1 Abstract 2 The chloroplast genome usually has a quadripartite structure consisting of a large 3 single copy region and a small single copy region separated by two long inverted 4 repeats. It has been known for some time that a single cell may contain at least two 5 structural haplotypes of this structure, which differ in the relative orientation of the 6 single copy regions. However, the methods required to detect and measure the 7 abundance of the structural haplotypes are labour-intensive, and this phenomenon 8 remains understudied. -
Proceedings Amurga Co
PROCEEDINGS OF THE AMURGA INTERNATIONAL CONFERENCES ON ISLAND BIODIVERSITY 2011 PROCEEDINGS OF THE AMURGA INTERNATIONAL CONFERENCES ON ISLAND BIODIVERSITY 2011 Coordination: Juli Caujapé-Castells Funded and edited by: Fundación Canaria Amurga Maspalomas Colaboration: Faro Media Cover design & layout: Estudio Creativo Javier Ojeda © Fundación Canaria Amurga Maspalomas Gran Canaria, December 2013 ISBN: 978-84-616-7394-0 How to cite this volume: Caujapé-Castells J, Nieto Feliner G, Fernández Palacios JM (eds.) (2013) Proceedings of the Amurga international conferences on island biodiversity 2011. Fundación Canaria Amurga-Maspalomas, Las Palmas de Gran Canaria, Spain. All rights reserved. Any unauthorized reprint or use of this material is prohibited. No part of this book may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, recording, or by any information storage and retrieval system without express written permission from the author / publisher. SCIENTIFIC EDITORS Juli Caujapé-Castells Jardín Botánico Canario “Viera y Clavijo” - Unidad Asociada CSIC Consejería de Medio Ambiente y Emergencias, Cabildo de Gran Canaria Gonzalo Nieto Feliner Real Jardín Botánico de Madrid-CSIC José María Fernández Palacios Universidad de La Laguna SCIENTIFIC COMMITTEE Juli Caujapé-Castells, Gonzalo Nieto Feliner, David Bramwell, Águedo Marrero Rodríguez, Julia Pérez de Paz, Bernardo Navarro-Valdivielso, Ruth Jaén-Molina, Rosa Febles Hernández, Pablo Vargas. Isabel Sanmartín. ORGANIZING COMMITTEE Pedro -
Ecuador & the Galapagos Islands
Ecuador & the Galapagos Islands - including Sacha Lodge Extension Naturetrek Tour Report 29 January – 20 February 2018 Medium Ground-finch Blue-footed Booby Wire-tailed Manakin Galapagos Penguin Green Sea Turtle Report kindly compiled by Tour participants Sally Wearing, Rowena Tye, Debbie Hardie and Sue Swift Images courtesy of David Griffiths, Sue Swift, Debbie Hardie, Jenny Tynan, Rowena Tye, Nick Blake and Sally Wearing Naturetrek Mingledown Barn Wolf’s Lane Chawton Alton Hampshire GU34 3HJ UK T: +44 (0)1962 733051 E: [email protected] W: www.naturetrek.co.uk Tour Report Ecuador & the Galapagos Islands - including Sacha Lodge Extension Tour Leader in the Galapagos: Juan Tapia with 13 Naturetrek Clients This report has kindly been compiled by tour participants Sally Wearing, Rowena Tye, Debbie Hardie and Sue Swift. Day 1 Monday 29th January UK to Quito People arrived in Quito via Amsterdam with KLM or via Madrid with Iberia, while Tony came separately from the USA. Everyone was met at the airport and taken to the Hotel Vieja Cuba; those who were awake enough went out to eat before a good night’s rest. Day 2 Tuesday 30th January Quito. Weather: Hot and mostly sunny. The early risers saw the first few birds of the trip outside the hotel: Rufous- collared Sparrow, Great Thrush and Eared Doves. After breakfast, an excellent guide took us on a bus and walking tour of Quito’s old town. This started with the Basilica del Voto Nacional, where everyone marvelled at the “grotesques” of native Ecuadorian animals such as frigatebirds, iguanas and tortoises. -
Polyploidy and the Evolutionary History of Cotton
POLYPLOIDY AND THE EVOLUTIONARY HISTORY OF COTTON Jonathan F. Wendel1 and Richard C. Cronn2 1Department of Botany, Iowa State University, Ames, Iowa 50011, USA 2Pacific Northwest Research Station, USDA Forest Service, 3200 SW Jefferson Way, Corvallis, Oregon 97331, USA I. Introduction II. Taxonomic, Cytogenetic, and Phylogenetic Framework A. Origin and Diversification of the Gossypieae, the Cotton Tribe B. Emergence and Diversification of the Genus Gossypium C. Chromosomal Evolution and the Origin of the Polyploids D. Phylogenetic Relationships and the Temporal Scale of Divergence III. Speciation Mechanisms A. A Fondness for Trans-oceanic Voyages B. A Propensity for Interspecific Gene Exchange IV. Origin of the Allopolyploids A. Time of Formation B. Parentage of the Allopolyploids V. Polyploid Evolution A. Repeated Cycles of Genome Duplication B. Chromosomal Stabilization C. Increased Recombination in Polyploid Gossypium D. A Diverse Array of Genic and Genomic Interactions E. Differential Evolution of Cohabiting Genomes VI. Ecological Consequences of Polyploidization VII. Polyploidy and Fiber VIII. Concluding Remarks References The cotton genus (Gossypium ) includes approximately 50 species distributed in arid to semi-arid regions of the tropic and subtropics. Included are four species that have independently been domesticated for their fiber, two each in Africa–Asia and the Americas. Gossypium species exhibit extraordinary morphological variation, ranging from herbaceous perennials to small trees with a diverse array of reproductive and vegetative -
Long-Reads Reveal That the Chloroplast Genome Exists in Two Distinct Versions in Most Plants
GBE Long-Reads Reveal That the Chloroplast Genome Exists in Two Distinct Versions in Most Plants Weiwen Wang* and Robert Lanfear* Division of Ecology and Evolution, Research School of Biology, Australian National University, Acton, Australian Capital Territory, Australia *Corresponding authors: E-mails: [email protected]; [email protected]. Accepted: November 15, 2019 Downloaded from https://academic.oup.com/gbe/article/11/12/3372/5637229 by guest on 02 October 2021 Data deposition: The Herrania umbratica and Siraitia grosvenorii chloroplast genomes in this project have been deposited at NCBI under the accession MN163033 and MK279915. Abstract The chloroplast genome usually has a quadripartite structure consisting of a large single copy region and a small single copy region separated by two long inverted repeats. It has been known for some time that a single cell may contain at least two structural haplotypes of this structure, which differ in the relative orientation of the single copy regions. However, the methods required to detect and measure the abundance of the structural haplotypes are labor-intensive, and this phenomenon remains understudied. Here, we develop a new method, Cp-hap, to detect all possible structural haplotypes of chloroplast genomes of quadripartite structure using long-read sequencing data. We use this method to conduct a systematic analysis and quantification of chloroplast structural haplotypes in 61 land plant species across 19 orders of Angiosperms, Gymnosperms, and Pteridophytes. Our results show that there are two chloroplast structural haplotypes which occur with equal frequency in most land plant individuals. Nevertheless, species whose chloroplast genomes lack inverted repeats or have short inverted repeats have just a single structural haplotype. -
Variation Than Mainland Populations?
Heredity 78 (1997) 311—327 Received 30Apr11 1996 Do island populations have less genetic variation than mainland populations? R. FRANKHAM* Key Centre for Biodiversity and Bioresources, Macquarie University, Sydney, NSW2109, Australia Islandpopulations are much more prone to extinction than mainland populations. The reasons for this remain controversial. If inbreeding and loss of genetic variation are involved, then genetic variation must be lower on average in island than mainland populations. Published data on levels of genetic variation for allozymes, nuclear DNA markers, mitochondrial DNA, inversions and quantitative characters in island and mainland populations were analysed. A large and highly significant majority of island populations have less allozyme genetic variation than their mainland counterparts (165 of 202 comparisons), the average reduction being 29 per cent. The magnitude of differences was related to dispersal ability. There were related differ- ences for all the other measures. Island endemic species showed lower genetic variation than related mainland species in 34 of 38 cases. The proportionate reduction in genetic variation was significantly greater in island endemic than in nonendemic island populations in mammals and birds, but not in insects. Genetic factors cannot be discounted as a cause of higher extinction rates of island than mainland populations. Keywords:allozymes,conservation, endemic species, extinction, genetic variation, islands. of endemic plant species as threatened on 15 islands. Introduction Human activities have been the major cause of Islandpopulations have a much higher risk of species extinctions on islands in the past 50000 years extinction than mainland populations (Diamond, (Olson, 1989) through over-exploitation, habitat loss 1984; Vitousek, 1988; Flesness, 1989; Case et al., and introduced species. -
Compositae Giseke (1792)
Multequina ISSN: 0327-9375 [email protected] Instituto Argentino de Investigaciones de las Zonas Áridas Argentina VITTO, LUIS A. DEL; PETENATTI, E. M. ASTERÁCEAS DE IMPORTANCIA ECONÓMICA Y AMBIENTAL. PRIMERA PARTE. SINOPSIS MORFOLÓGICA Y TAXONÓMICA, IMPORTANCIA ECOLÓGICA Y PLANTAS DE INTERÉS INDUSTRIAL Multequina, núm. 18, 2009, pp. 87-115 Instituto Argentino de Investigaciones de las Zonas Áridas Mendoza, Argentina Disponible en: http://www.redalyc.org/articulo.oa?id=42812317008 Cómo citar el artículo Número completo Sistema de Información Científica Más información del artículo Red de Revistas Científicas de América Latina, el Caribe, España y Portugal Página de la revista en redalyc.org Proyecto académico sin fines de lucro, desarrollado bajo la iniciativa de acceso abierto ISSN 0327-9375 ASTERÁCEAS DE IMPORTANCIA ECONÓMICA Y AMBIENTAL. PRIMERA PARTE. SINOPSIS MORFOLÓGICA Y TAXONÓMICA, IMPORTANCIA ECOLÓGICA Y PLANTAS DE INTERÉS INDUSTRIAL ASTERACEAE OF ECONOMIC AND ENVIRONMENTAL IMPORTANCE. FIRST PART. MORPHOLOGICAL AND TAXONOMIC SYNOPSIS, ENVIRONMENTAL IMPORTANCE AND PLANTS OF INDUSTRIAL VALUE LUIS A. DEL VITTO Y E. M. PETENATTI Herbario y Jardín Botánico UNSL, Cátedras Farmacobotánica y Famacognosia, Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Ej. de los Andes 950, D5700HHW San Luis, Argentina. [email protected]. RESUMEN Las Asteráceas incluyen gran cantidad de especies útiles (medicinales, agrícolas, industriales, etc.). Algunas han sido domesticadas y cultivadas desde la Antigüedad y otras conforman vastas extensiones de vegetación natural, determinando la fisonomía de numerosos paisajes. Su uso etnobotánico ha ayudado a sustentar numerosos pueblos. Hoy, unos 40 géneros de Asteráceas son relevantes en alimentación humana y animal, fuentes de aceites fijos, aceites esenciales, forraje, miel y polen, edulcorantes, especias, colorantes, insecticidas, caucho, madera, leña o celulosa. -
Hunter-Central Rivers, New South Wales
Biodiversity Summary for NRM Regions Guide to Users Background What is the summary for and where does it come from? This summary has been produced by the Department of Sustainability, Environment, Water, Population and Communities (SEWPC) for the Natural Resource Management Spatial Information System. It highlights important elements of the biodiversity of the region in two ways: • Listing species which may be significant for management because they are found only in the region, mainly in the region, or they have a conservation status such as endangered or vulnerable. • Comparing the region to other parts of Australia in terms of the composition and distribution of its species, to suggest components of its biodiversity which may be nationally significant. The summary was produced using the Australian Natural Natural Heritage Heritage Assessment Assessment Tool Tool (ANHAT), which analyses data from a range of plant and animal surveys and collections from across Australia to automatically generate a report for each NRM region. Data sources (Appendix 2) include national and state herbaria, museums, state governments, CSIRO, Birds Australia and a range of surveys conducted by or for DEWHA. Limitations • ANHAT currently contains information on the distribution of over 30,000 Australian taxa. This includes all mammals, birds, reptiles, frogs and fish, 137 families of vascular plants (over 15,000 species) and a range of invertebrate groups. The list of families covered in ANHAT is shown in Appendix 1. Groups notnot yet yet covered covered in inANHAT ANHAT are are not not included included in the in the summary. • The data used for this summary come from authoritative sources, but they are not perfect. -
Darwin, Plants and Portugal Autor(Es): Paiva, Jorge Publicado
Darwin, plants and Portugal Autor(es): Paiva, Jorge Publicado por: Imprensa da Universidade de Coimbra URL persistente: URI:http://hdl.handle.net/10316.2/31257 DOI: DOI:http://dx.doi.org/10.14195/978-989-26-0342-1_4 Accessed : 30-Sep-2021 22:17:11 A navegação consulta e descarregamento dos títulos inseridos nas Bibliotecas Digitais UC Digitalis, UC Pombalina e UC Impactum, pressupõem a aceitação plena e sem reservas dos Termos e Condições de Uso destas Bibliotecas Digitais, disponíveis em https://digitalis.uc.pt/pt-pt/termos. Conforme exposto nos referidos Termos e Condições de Uso, o descarregamento de títulos de acesso restrito requer uma licença válida de autorização devendo o utilizador aceder ao(s) documento(s) a partir de um endereço de IP da instituição detentora da supramencionada licença. Ao utilizador é apenas permitido o descarregamento para uso pessoal, pelo que o emprego do(s) título(s) descarregado(s) para outro fim, designadamente comercial, carece de autorização do respetivo autor ou editor da obra. Na medida em que todas as obras da UC Digitalis se encontram protegidas pelo Código do Direito de Autor e Direitos Conexos e demais legislação aplicável, toda a cópia, parcial ou total, deste documento, nos casos em que é legalmente admitida, deverá conter ou fazer-se acompanhar por este aviso. pombalina.uc.pt digitalis.uc.pt A presente colecção reúne originais de cultura científica resultantes da investigação no Ana Leonor Pereira | João Rui Pita Pedro Ricardo Fonseca Ana Leonor Pereira One hundred and fifty years ago, more precisely on the 24th of November of 1859, Darwin âmbito da história das ciências e das técnicas, da história da farmácia, da história da Darwin, introduced a new paradigm in natural history with the publication of On the origin of species medicina e de outras dimensões das práticas científicas nas diferentes interfaces com a João Rui Pita by means of natural selection, or the preservation of favoured races in the struggle for life. -
QTL Mapping for Flowering-Time and Photoperiod Insensitivity of Cotton Gossypium Darwinii Watt
RESEARCH ARTICLE QTL mapping for flowering-time and photoperiod insensitivity of cotton Gossypium darwinii Watt Fakhriddin N. Kushanov1☯, Zabardast T. Buriev1, Shukhrat E. Shermatov1, Ozod S. Turaev1, Tokhir M. Norov1, Alan E. Pepper2, Sukumar Saha3, Mauricio Ulloa4, John Z. Yu5, Johnie N. Jenkins3, Abdusattor Abdukarimov1, Ibrokhim Y. Abdurakhmonov1☯* 1 Laboratory of Structural and Functional Genomics, Center of Genomics and Bioinformatics, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan, 2 Department of Biology, Texas A&M a1111111111 University, Colleges Station, Texas, United States of America, 3 Crop Science Research Laboratory, United a1111111111 States Department of Agriculture-Agricultural Research Services, Starkville, Mississippi, United States of a1111111111 America, 4 Plant Stress and Germplasm Development Research, United States Department of Agriculture- a1111111111 Agricultural Research Services, Lubbock, Texas, United States of America, 5 Southern Plains Agricultural a1111111111 Research Center, United States Department of Agriculture-Agricultural Research Services, College Station, Texas, United States of America ☯ These authors contributed equally to this work. * [email protected] OPEN ACCESS Citation: Kushanov FN, Buriev ZT, Shermatov SE, Abstract Turaev OS, Norov TM, Pepper AE, et al. (2017) QTL mapping for flowering-time and photoperiod Most wild and semi-wild species of the genus Gossypium are exhibit photoperiod-sensitive insensitivity of cotton Gossypium darwinii Watt. PLoS ONE 12(10): e0186240. https://doi.org/ flowering. The wild germplasm cotton is a valuable source of genes for genetic improvement 10.1371/journal.pone.0186240 of modern cotton cultivars. A bi-parental cotton population segregating for photoperiodic Editor: Turgay Unver, Dokuz Eylul Universitesi, flowering was developed by crossing a photoperiod insensitive irradiation mutant line with TURKEY its pre-mutagenesis photoperiodic wild-type G. -
Cotton Genetic Resources. a Review Mehboob-Ur-Rahman, Shaheen, Tabbasam, Muhammad Iqbal, Ashraf, Zafar, Andrew Paterson
Cotton genetic resources. A review Mehboob-Ur-Rahman, Shaheen, Tabbasam, Muhammad Iqbal, Ashraf, Zafar, Andrew Paterson To cite this version: Mehboob-Ur-Rahman, Shaheen, Tabbasam, Muhammad Iqbal, Ashraf, et al.. Cotton genetic re- sources. A review. Agronomy for Sustainable Development, Springer Verlag/EDP Sciences/INRA, 2012, 32 (2), pp.419-432. 10.1007/s13593-011-0051-z. hal-00930526 HAL Id: hal-00930526 https://hal.archives-ouvertes.fr/hal-00930526 Submitted on 1 Jan 2012 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Agron. Sustain. Dev. (2012) 32:419–432 DOI 10.1007/s13593-011-0051-z REVIEW ARTICLE Cotton genetic resources. A review Mehboob-ur-Rahman & Tayyaba Shaheen & Nabila Tabbasam & Muhammad Atif Iqbal & Muhammad Ashraf & Yusuf Zafar & Andrew H. Paterson Accepted: 29 July 2011 /Published online: 13 October 2011 # INRA and Springer-Verlag, France 2011 Abstract Since 6000 BC, cotton has been cultivated for lint Much of the genetic diversity among G. barbadense cultivars fiber, which now dominates the natural textile industry is attributed to the introgression of G. hirsutum alleles. This worldwide. Common resources such as an integrated web process highlights the importance of introgression of new database, a microsatellite database, and comparative quantita- alleles from accessions of all the Gossypium species into tive trait loci (QTL) resources for Gossypium have accelerated cultivated cotton species. -
Phylogeny of Hinterhubera, Novenia and Related
Louisiana State University LSU Digital Commons LSU Doctoral Dissertations Graduate School 2006 Phylogeny of Hinterhubera, Novenia and related genera based on the nuclear ribosomal (nr) DNA sequence data (Asteraceae: Astereae) Vesna Karaman Louisiana State University and Agricultural and Mechanical College, [email protected] Follow this and additional works at: https://digitalcommons.lsu.edu/gradschool_dissertations Recommended Citation Karaman, Vesna, "Phylogeny of Hinterhubera, Novenia and related genera based on the nuclear ribosomal (nr) DNA sequence data (Asteraceae: Astereae)" (2006). LSU Doctoral Dissertations. 2200. https://digitalcommons.lsu.edu/gradschool_dissertations/2200 This Dissertation is brought to you for free and open access by the Graduate School at LSU Digital Commons. It has been accepted for inclusion in LSU Doctoral Dissertations by an authorized graduate school editor of LSU Digital Commons. For more information, please [email protected]. PHYLOGENY OF HINTERHUBERA, NOVENIA AND RELATED GENERA BASED ON THE NUCLEAR RIBOSOMAL (nr) DNA SEQUENCE DATA (ASTERACEAE: ASTEREAE) A Dissertation Submitted to the Graduate Faculty of the Louisiana State University and Agricultural and Mechanical College in partial fulfillment of the requirements for the degree of Doctor of Philosophy in The Department of Biological Sciences by Vesna Karaman B.S., University of Kiril and Metodij, 1992 M.S., University of Belgrade, 1997 May 2006 "Treat the earth well: it was not given to you by your parents, it was loaned to you by your children. We do not inherit the Earth from our Ancestors, we borrow it from our Children." Ancient Indian Proverb ii ACKNOWLEDGMENTS I am indebted to many people who have contributed to the work of this dissertation.