DOCSLIB.ORG

BM CC EB What Can We Learn from a Tree? Leaf N Ca

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

Introduction to Comparative Methods BM CC EB What can we learn from a tree? Leaf N Ca Co r y SLA op r nales h yllales Max height icales r Berbe oliales f Leaf size E Santalales r Aqui idopsidales Escalloniaceae ales Seed mass r Aste runiales B yphiaceae Apiales r rac Malpighiales a Eric. P ales Dipsacalesry Icacinaceaeaginaceae Gar r Bo Cary. Gentianales Oxalidales Solanales Celast Ast. rales Cucurbitales Ast2. Fagales Lamiales Rosales Fab. Fabales Monilophyte yllales Bras. Zygoph Gymn. Rosid. Cycadales Brassicales Gnetales Magn. Pinales Nymphaeales Arec. Austrobail Chlo vales Mono. Canellalesranthaceaeey Mal Pipe ales rales rteales Lau r Hue Myrt. ales Magnoliales P andanales Sapindales Dioscoreales Commelinales Prot. Zingibe Arecacales rales rtales Crossosomatales My P oales aniales r Vitales Ge agales r ales r Aspa s Saxif e l Buxaceae Proteales a r Dilleniaceae i Gunne agales aceae l i r Sabiaceae L unculales n Aco Ra Alismatales Cornwell et al. 2014 J Ecology making trees is hard.... because trees are information-rich the coming age of the megaphylogeny* * trees that are too big for your brain ensembl Why do you want to make or use trees? What do you hope to learn? What can you do? • Diversification (speciation and extinction) • Character evolution • Characters and diversification • Biogeography • Testing complex evolutionary models Diversification (speciation and extinction) Sharks Polypteriformes Chondrostei Amiiformes Elopomorpha Osteoglossomorpha Ostariophysi Clupeomorpha Esociformes Salmoniformes Galaxiiformes Stomiiformes Osmeriformes Argentiniformes Aulopiformes Myctophiformes Beryciformes+Stephanoberyciformes Ophidiiformes Percomorpha Scombridae Polymixiiformes Lampriformes Percopsiformes Zeiforms Latimeridae Dipnoi Gymnophiona Anura Caudata Monotremes Marsupials Boreoeutheria Afrotheria+Xenarthra Sphenodon NongekkoSquamates Taxa Gekkos 1 Pleurodira 5 Cryptodira Crocodylinae 10 Gavialidae 50 Camininae 100 Alligatorinae 500 Tinamiformes 1000 Struthioniformes 5000 Neoaves 10000 Galliformes 20000 Anseriformes 500 400 300 200 100 0 MYA Character evolution ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● Siren intermedia Siren lacertina Pseudobranchus striatus Pseudobranchus axanthus Onychodactylus fischeri Ranodon sibiricus Paradactylodon mustersi Paradactylodon gorganensis shift direction Pachyhynobius shangchengensis Hynobius formosanus Hynobius sonani Hynobius retardatus Hynobius boulengeri Hynobius kimurae Hynobius abei Hynobius lichenatus Hynobius tokyoensis 1.00 Hynobius nigrescens Hynobius takedai Hynobius stejnegeri Hynobius katoi Hynobius chinensis Hynobius yiwuensis Hynobius amjiensis Hynobius guabangshanensis Hynobius leechii 0.80 Hynobius okiensis Hynobius tsuensis Hynobius dunni Hynobius nebulosus Hynobius hidamontanus Salamandrella keyserlingii Liua tsinpaensis Liua shihi 0.50 Batrachuperus yenyuanensis Batrachuperus tibetanus Batrachuperus pinchonii Batrachuperus londongensis Cryptobranchus alleganiensis Andrias japonicus Andrias davidianus Necturus punctatus Necturus maculosus 0.20 Necturus lewisi Necturus beyeri Necturus alabamensis Proteus anguinus Rhyacotriton variegatus Rhyacotriton cascadae Rhyacotriton kezeri Rhyacotriton olympicus 0.00 Amphiuma tridactylum Amphiuma means Amphiuma pholeter Desmognathus auriculatus Desmognathus brimleyorum Desmognathus monticola Desmognathus fuscus Desmognathus welteri Desmognathus ochrophaeus point.seq -0.20 Desmognathus imitator Desmognathus marmoratus Desmognathus quadramaculatus Desmognathus aeneus Desmognathus wrighti Phaeognathus hubrichti Aneides flavipunctatus Aneides ferreus -0.50 Aneides lugubris Aneides hardii Aneides aeneus Ensatina eschscholtzii Hydromantes platycephalus Hydromantes italicus Karsenia koreana Plethodon albagula Plethodon glutinosus -0.80 Plethodon cylindraceus Plethodon teyahalee Plethodon cheoah Plethodon shermani Plethodon meridianus Plethodon amplus Plethodon montanus Plethodon ouachitae -1.00 Plethodon caddoensis Plethodon jordani Plethodon metcalfi Plethodon kentucki Plethodon yonahlossee Plethodon dorsalis Plethodon ventralis Plethodon angusticlavius Plethodon welleri Plethodon punctatus Plethodon wehrlei Plethodon hubrichti Plethodon nettingi Plethodon richmondi Plethodon shenandoah Plethodon cinereus Plethodon hoffmani Plethodon serratus Plethodon idahoensis Plethodon vandykei Plethodon neomexicanus Plethodon dunni Plethodon vehiculum Plethodon elongatus Eurycea tridentifera Eurycea neotenes Eurycea sosorum Eurycea nana Eurycea rathbuni Eurycea wilderae Bolitoglossinae Eurycea junaluska Eurycea bislineata Eurycea cirrigera Eurycea longicauda Eurycea lucifuga Eurycea quadridigitata Eurycea spelaea Eurycea tynerensis Eurycea multiplicata Pseudotriton ruber Pseudotriton montanus Gyrinophilus porphyriticus Stereochilus marginatus Batrachoseps major Batrachoseps attenuatus posterior rates Batrachoseps wrightorum Cryptotriton nasalis Cryptotriton alvarezdeltoroi Nyctanolis pernix Dendrotriton rabbi Dendrotriton cuchumatanus rep(-0.5, length(point.seq)) Nototriton barbouri Nototriton richardi Nototriton guanacaste 3.011 Nototriton picadoi Nototriton abscondens Oedipina uniformis Oedipina pacificensis Oedipina poelzi Oedipina pseudouniformis Oedipina cyclocauda Oedipina gephyra Oedipina elongata 0.519 Oedipina parvipes Oedipina complex Oedipina savagei Bradytriton silus Thorius troglodytes Thorius dubitus Chiropterotriton magnipes Chiropterotriton chondrostega 0.090 Chiropterotriton multidentatus Chiropterotriton priscus Chiropterotriton lavae Chiropterotriton dimidiatus Chiropterotriton arboreus Pseudoeurycea scandens Pseudoeurycea galeanae Pseudoeurycea cephalica Pseudoeurycea naucampatepetl 0.015 Pseudoeurycea gigantea Pseudoeurycea boneti Pseudoeurycea bellii Pseudoeurycea goebeli Pseudoeurycea brunnata Pseudoeurycea exspectata Pseudoeurycea rex Pseudoeurycea smithi 0.003 Pseudoeurycea anitae Pseudoeurycea cochranae Pseudoeurycea gadovii Pseudoeurycea melanomolga Pseudoeurycea longicauda Pseudoeurycea robertsi Pseudoeurycea altamontana Pseudoeurycea unguidentis Pseudoeurycea saltator point.seq 0.000 Pseudoeurycea juarezi Pseudoeurycea werleri Pseudoeurycea mystax Pseudoeurycea nigromaculata Pseudoeurycea lynchi Pseudoeurycea leprosa Pseudoeurycea firscheini Lineatriton lineolus 0.000 Parvimolge townsendi Ixalotriton parvus Ixalotriton niger Bolitoglossa hartwegi Bolitoglossa rufescens Bolitoglossa occidentalis Bolitoglossa odonnelli Bolitoglossa lignicolor Bolitoglossa yucatana 0.000 Bolitoglossa striatula Bolitoglossa mexicana Bolitoglossa platydactyla Bolitoglossa flaviventris Bolitoglossa macrinii Bolitoglossa riletti Bolitoglossa hermosa Bolitoglossa rostrata 0.000 Bolitoglossa helmrichi Bolitoglossa engelhardti Bolitoglossa lincolni Bolitoglossa franklini Bolitoglossa porrasorum Bolitoglossa longissima Bolitoglossa decora Bolitoglossa synoria Bolitoglossa celaque Bolitoglossa morio Bolitoglossa dunni Bolitoglossa diaphora Bolitoglossa conanti Bolitoglossa carri Bolitoglossa dofleini Bolitoglossa subpalmata Bolitoglossa pesrubra Bolitoglossa gracilis Bolitoglossa marmorea Bolitoglossa minutula Bolitoglossa cerroensis Bolitoglossa schizodactyla Bolitoglossa colonnea Bolitoglossa sima Bolitoglossa biseriata Bolitoglossa palmata Bolitoglossa peruviana Bolitoglossa altamazonica Bolitoglossa medemi Bolitoglossa adspersa Hemidactylium scutatum Pleurodeles waltl Pleurodeles poireti Tylototriton vietnamensis Tylototriton hainanensis Tylototriton asperrimus Tylototriton wenxianensis Tylototriton kweichowensis Tylototriton verrucosus Tylototriton taliangensis Echinotriton andersoni Echinotriton chinhaiensis Pachytriton brevipes Pachytriton labiatus Paramesotriton deloustali shift probability Paramesotriton fuzhongensis Paramesotriton guangxiensis Paramesotriton hongkongensis Paramesotriton chinensis Paramesotriton caudopunctatus Paramesotriton laoensis rep(-0.5, length(point.seq)) Cynops ensicauda Cynops pyrrhogaster Cynops cyanurus 1.000 Cynops chenggongensis Cynops orphicus Cynops orientalis Neurergus strauchii Neurergus microspilotus Neurergus kaiseri Neurergus crocatus Ommatotriton vittatus Ommatotriton ophryticus 0.875 Calotriton asper Calotriton arnoldi Triturus carnifex Triturus dobrogicus Triturus karelinii Triturus cristatus Triturus marmoratus Triturus pygmaeus 0.750 Lissotriton boscai Lissotriton italicus Lissotriton helveticus Lissotriton montandoni Lissotriton vulgaris Mesotriton alpestris Euproctus platycephalus Euproctus montanus Notophthalmus viridescens 0.625 Notophthalmus perstriatus Notophthalmus meridionalis Taricha rivularis Taricha sierrae Taricha torosa Taricha granulosa Mertensiella caucasica Chioglossa lusitanica 0.500 Lyciasalamandra atifi Lyciasalamandra helverseni Lyciasalamandra antalyana Lyciasalamandra billae Lyciasalamandra fazilae Lyciasalamandra luschani Lyciasalamandra flavimembris Salamandra salamandra Salamandra atra point.seq 0.375 Salamandra corsica Salamandra lanzai Salamandra infraimmaculata Salamandra algira Salamandrina perspicillata Salamandrina terdigitata Ambystoma gracile Ambystoma maculatum 0.250 Ambystoma macrodactylum Ambystoma californiense Ambystoma rosaceum Ambystoma dumerilii Ambystoma rivulare Ambystoma lermaense Ambystoma granulosum Ambystoma altamirani Ambystoma velasci 0.125 Ambystoma taylori Ambystoma tigrinum Ambystoma ordinarium Ambystoma andersoni Ambystoma flavipiperatum Ambystoma mexicanum Ambystoma amblycephalum Ambystoma jeffersonianum 0.000 Ambystoma laterale Ambystoma annulatum Ambystoma cingulatum Ambystoma bishopi Ambystoma opacum Ambystoma barbouri Ambystoma texanum Dicamptodon aterrimus Dicamptodon ensatus Dicamptodon tenebrosus Dicamptodon copei photos from wiki commons Characters and diversification Silvestro et al. 2013 Evolution Biogeography Ree and Smith 2008 Sys Biol Testing Complex Evolutionary Models Price et al. 2014 Nature.
Recommended publications
  • Toward a Resolution of Campanulid Phylogeny, with Special Reference to the Placement of Dipsacales

    Toward a Resolution of Campanulid Phylogeny, with Special Reference to the Placement of Dipsacales

    TAXON 57 (1) • February 2008: 53–65 Winkworth & al. • Campanulid phylogeny MOLECULAR PHYLOGENETICS Toward a resolution of Campanulid phylogeny, with special reference to the placement of Dipsacales Richard C. Winkworth1,2, Johannes Lundberg3 & Michael J. Donoghue4 1 Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Caixa Postal 11461–CEP 05422-970, São Paulo, SP, Brazil. [email protected] (author for correspondence) 2 Current address: School of Biology, Chemistry, and Environmental Sciences, University of the South Pacific, Private Bag, Laucala Campus, Suva, Fiji 3 Department of Phanerogamic Botany, The Swedish Museum of Natural History, Box 50007, 104 05 Stockholm, Sweden 4 Department of Ecology & Evolutionary Biology and Peabody Museum of Natural History, Yale University, P.O. Box 208106, New Haven, Connecticut 06520-8106, U.S.A. Broad-scale phylogenetic analyses of the angiosperms and of the Asteridae have failed to confidently resolve relationships among the major lineages of the campanulid Asteridae (i.e., the euasterid II of APG II, 2003). To address this problem we assembled presently available sequences for a core set of 50 taxa, representing the diver- sity of the four largest lineages (Apiales, Aquifoliales, Asterales, Dipsacales) as well as the smaller “unplaced” groups (e.g., Bruniaceae, Paracryphiaceae, Columelliaceae). We constructed four data matrices for phylogenetic analysis: a chloroplast coding matrix (atpB, matK, ndhF, rbcL), a chloroplast non-coding matrix (rps16 intron, trnT-F region, trnV-atpE IGS), a combined chloroplast dataset (all seven chloroplast regions), and a combined genome matrix (seven chloroplast regions plus 18S and 26S rDNA). Bayesian analyses of these datasets using mixed substitution models produced often well-resolved and supported trees.
  • Apiales, Aquifoliales, Boraginales, , Brassicales, Canellales

    Apiales, Aquifoliales, Boraginales, , Brassicales, Canellales

    Kingdom: Plantae Phylum: Tracheophyta Class: Magnoliopsida Order: Apiales, Aquifoliales, Boraginales, , Brassicales, Canellales, Caryophyllales, Celastrales, Ericales, Fabales, Garryales, Gentianales, Lamiales, Laurales, Magnoliales, Malpighiales, Malvales, Myrtales, Oxalidales, Picramniales, Piperales, Proteales, Rosales, Santalales, Sapindales, Solanales Family: Achariaceae, Anacardiaceae, Annonaceae, Apocynaceae, Aquifoliaceae, Araliaceae, Bignoniaceae, Bixaceae, Boraginaceae, Burseraceae, Calophyllaceae, Canellaceae, Cannabaceae, Capparaceae, Cardiopteridaceae, Caricaceae, Caryocaraceae, Celastraceae, Chrysobalanaceae, Clusiaceae, Combretaceae, Dichapetalaceae, Ebenaceae, Elaeocarpaceae, Emmotaceae, Erythroxylaceae, Euphorbiaceae, Fabaceae, Goupiaceae, Hernandiaceae, Humiriaceae, Hypericaceae, Icacinaceae, Ixonanthaceae, Lacistemataceae, Lamiaceae, Lauraceae, Lecythidaceae, Lepidobotryaceae, Linaceae, Loganiaceae, Lythraceae, Malpighiaceae, Malvaceae, Melastomataceae, Meliaceae, Monimiaceae, Moraceae, Myristicaceae, Myrtaceae, Nyctaginaceae, Ochnaceae, Olacaceae, Oleaceae, Opiliaceae, Pentaphylacaceae, Phyllanthaceae, Picramniaceae, Piperaceae, Polygonaceae, Primulaceae, Proteaceae, Putranjivaceae, Rhabdodendraceae, Rhamnaceae, Rhizophoraceae, Rosaceae, Rubiaceae, Rutaceae, Sabiaceae, Salicaceae, Sapindaceae, Sapotaceae, Simaroubaceae, Siparunaceae, Solanaceae, Stemonuraceae, Styracaceae, Symplocaceae, Ulmaceae, Urticaceae, Verbenaceae, Violaceae, Vochysiaceae Genus: Abarema, Acioa, Acosmium, Agonandra, Aiouea, Albizia, Alchornea,
  • Outline of Angiosperm Phylogeny

    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
  • Lessons from 20 Years of Plant Genome Sequencing: an Unprecedented Resource in Need of More Diverse Representation

    Lessons from 20 Years of Plant Genome Sequencing: an Unprecedented Resource in Need of More Diverse Representation

    bioRxiv preprint doi: https://doi.org/10.1101/2021.05.31.446451; this version posted May 31, 2021. 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-NC-ND 4.0 International license. Lessons from 20 years of plant genome sequencing: an unprecedented resource in need of more diverse representation Authors: Rose A. Marks1,2,3, Scott Hotaling4, Paul B. Frandsen5,6, and Robert VanBuren1,2 1. Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA 2. Plant Resilience Institute, Michigan State University, East Lansing, MI 48824, USA 3. Department of Molecular and Cell Biology, University of Cape Town, Rondebosch 7701, South Africa 4. School of Biological Sciences, Washington State University, Pullman, WA, USA 5. Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, USA 6. Data Science Lab, Smithsonian Institution, Washington, DC, USA Keywords: plants, embryophytes, genomics, colonialism, broadening participation Correspondence: Rose A. Marks, Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA; Email: [email protected]; Phone: (603) 852-3190; ORCID iD: https://orcid.org/0000-0001-7102-5959 Abstract The field of plant genomics has grown rapidly in the past 20 years, leading to dramatic increases in both the quantity and quality of publicly available genomic resources. With an ever- expanding wealth of genomic data from an increasingly diverse set of taxa, unprecedented potential exists to better understand the evolution and genome biology of plants.
  • A Visual Guide to Collecting Plant Tissues for DNA

    A Visual Guide to Collecting Plant Tissues for DNA

    A visual guide to collecting plant tissues for DNA Collecting kit checklist Silica gel1 Permanent marker and pencil Resealable bags, airtight plastic container Razor blade / Surgical scissors Empty tea bags or coffee filters Ethanol and paper tissue or ethanol wipes Tags or jewellers tags Plant press and collecting book 1. Selection and preparation of fresh plant tissue: Sampling avoided. Breaking up leaf material will bruise the plant tissue, which will result in enzymes being released From a single plant, harvest 3 – 5 mature leaves, or that cause DNA degradation. Ideally, leaf material sample a piece of a leaf, if large (Picture A). Ideally should be cut into smaller fragments with thick a leaf area of 5 – 10 cm2 should be enough, but this midribs being removed (Picture C). If sampling robust amount should be adjusted if the plant material is leaf tissue (e.g. cycads, palms), use a razor blade or rich in water (e.g. a succulent plant). If leaves are surgical scissors (Picture D). small (e.g. ericoid leaves), sample enough material to equate a leaf area of 5 – 10 cm2. If no leaves are Succulent plants available, other parts can be sampled such as leaf buds, flowers, bracts, seeds or even fresh bark. If the If the leaves are succulent, use a razor blade to plant is small, select the biggest specimen, but never remove epidermal slices or scoop out parenchyma combine tissues from different individuals. tissue (Picture E). Cleaning Ideally, collect clean fresh tissues, however if the leaf or plant material is dirty or shows potential contamination (e.g.
  • Winter 2004.Pmd

    Winter 2004.Pmd

    The Lady-Slipper, 19:4 / Winter 2004 1 The Lady-Slipper Kentucky Native Plant Society Number 19:4 Winter 2004 A Message from the President: It’s Membership Winter is upon us. I hope everyone had some opportunity to experience the colors of Fall and now some of us will turn our attention to winter botany. While I was unable to Renewal Time! attend, I understand that our Fall meeting at Shakertown Kentucky Native Plant Society with Dr. Bill Bryant from Thomas More College as the guest EMBERSHIP ORM speaker was a great success. M F Our Native Plant Certification program was relatively successful this Fall. Plant taxonomy failed to meet Name(s) ____________________________________ because the NKU’s Community Education Bulletin was Address ____________________________________ mailed too late for anyone to sign up for the course. The woody plants course did, however, have a successful run. City, State, Zip ______________________________ This coming Spring, we will be offering Basic Plant Taxonomy, Plant Communities and Spring Wildflowers of KY County __________________________________ Central Kentucky. Tel.: (home) ______________________________ You will see in this issue that we are promoting “Chinquapin” the newsletter of the Southern Appalachian (work) ______________________________ Botanical Society (SABS). SABS is an organization E-mail _______________________________ largely made up of professional botanists and produces a quarterly scholarly journal. The newsletter “Chinquapin” o Add me to the e-mail list for time-critical native plant news has more of a general interest approach much like our o Include my contact info in any future KNPS Member Directory newsletter but on a regional scale. In this issue we have Membership Categories: provided subscription information on page 7.
  • Evolutionary History of Floral Key Innovations in Angiosperms Elisabeth Reyes

    Evolutionary History of Floral Key Innovations in Angiosperms Elisabeth Reyes

    Evolutionary history of floral key innovations in angiosperms Elisabeth Reyes To cite this version: Elisabeth Reyes. Evolutionary history of floral key innovations in angiosperms. Botanics. Université Paris Saclay (COmUE), 2016. English. NNT : 2016SACLS489. tel-01443353 HAL Id: tel-01443353 https://tel.archives-ouvertes.fr/tel-01443353 Submitted on 23 Jan 2017 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. NNT : 2016SACLS489 THESE DE DOCTORAT DE L’UNIVERSITE PARIS-SACLAY, préparée à l’Université Paris-Sud ÉCOLE DOCTORALE N° 567 Sciences du Végétal : du Gène à l’Ecosystème Spécialité de Doctorat : Biologie Par Mme Elisabeth Reyes Evolutionary history of floral key innovations in angiosperms Thèse présentée et soutenue à Orsay, le 13 décembre 2016 : Composition du Jury : M. Ronse de Craene, Louis Directeur de recherche aux Jardins Rapporteur Botaniques Royaux d’Édimbourg M. Forest, Félix Directeur de recherche aux Jardins Rapporteur Botaniques Royaux de Kew Mme. Damerval, Catherine Directrice de recherche au Moulon Président du jury M. Lowry, Porter Curateur en chef aux Jardins Examinateur Botaniques du Missouri M. Haevermans, Thomas Maître de conférences au MNHN Examinateur Mme. Nadot, Sophie Professeur à l’Université Paris-Sud Directeur de thèse M.
  • GENOME EVOLUTION in MONOCOTS a Dissertation

    GENOME EVOLUTION in MONOCOTS a Dissertation

    GENOME EVOLUTION IN MONOCOTS A Dissertation Presented to The Faculty of the Graduate School At the University of Missouri In Partial Fulfillment Of the Requirements for the Degree Doctor of Philosophy By Kate L. Hertweck Dr. J. Chris Pires, Dissertation Advisor JULY 2011 The undersigned, appointed by the dean of the Graduate School, have examined the dissertation entitled GENOME EVOLUTION IN MONOCOTS Presented by Kate L. Hertweck A candidate for the degree of Doctor of Philosophy And hereby certify that, in their opinion, it is worthy of acceptance. Dr. J. Chris Pires Dr. Lori Eggert Dr. Candace Galen Dr. Rose‐Marie Muzika ACKNOWLEDGEMENTS I am indebted to many people for their assistance during the course of my graduate education. I would not have derived such a keen understanding of the learning process without the tutelage of Dr. Sandi Abell. Members of the Pires lab provided prolific support in improving lab techniques, computational analysis, greenhouse maintenance, and writing support. Team Monocot, including Dr. Mike Kinney, Dr. Roxi Steele, and Erica Wheeler were particularly helpful, but other lab members working on Brassicaceae (Dr. Zhiyong Xiong, Dr. Maqsood Rehman, Pat Edger, Tatiana Arias, Dustin Mayfield) all provided vital support as well. I am also grateful for the support of a high school student, Cady Anderson, and an undergraduate, Tori Docktor, for their assistance in laboratory procedures. Many people, scientist and otherwise, helped with field collections: Dr. Travis Columbus, Hester Bell, Doug and Judy McGoon, Julie Ketner, Katy Klymus, and William Alexander. Many thanks to Barb Sonderman for taking care of my greenhouse collection of many odd plants brought back from the field.
  • Phylogenomic Approach

    Phylogenomic Approach

    Toward the ultimate phylogeny of Magnoliaceae: phylogenomic approach Sangtae Kim*1, Suhyeon Park1, and Jongsun Park2 1 Sungshin University, Korea 2 InfoBoss Co., Korea Mr. Carl Ferris Miller Founder of Chollipo Arboretum in Korea Chollipo Arboretum Famous for its magnolia collection 2020. Annual Meeting of Magnolia Society International Cholliop Arboretum in Korea. April 13th~22th, 2020 http://WWW.Chollipo.org Sungshin University, Seoul, Korea Dr. Hans Nooteboom Dr. Liu Yu-Hu Twenty-one years ago... in 1998 The 1st International Symposium on the Family Magnoliaceae, Gwangzhow Dr. Hiroshi Azuma Mr. Richard Figlar Dr. Hans Nooteboom Dr. Qing-wen Zeng Dr. Weibang Sun Handsome young boy Dr. Yong-kang Sima Dr. Yu-wu Law Presented ITS study on Magnoliaceae - never published Ten years ago... in 2009 Presented nine cp genome region study (9.2 kbp) on Magnoliaceae – published in 2013 2015 1st International Sympodium on Neotropical Magnoliaceae Gadalajara, 2019 3rd International Sympodium and Workshop on Neotropical Magnoliaceae Asterales Dipsacales Apiales Why magnolia study is Aquifoliales Campanulids (Euasterids II) Garryales Gentianales Laminales Solanales Lamiids important in botany? Ericales Asterids (Euasterids I) Cornales Sapindales Malvales Brassicales Malvids Fagales (Eurosids II) • As a member of early-diverging Cucurbitales Rosales Fabales Zygophyllales Celestrales Fabids (Eurosid I) angiosperms, reconstruction of the Oxalidales Malpighiales Vitales Geraniales Myrtales Rosids phylogeny of Magnoliaceae will Saxifragales Caryphyllales
  • Rich Zingiberales

    Rich Zingiberales

    RESEARCH ARTICLE INVITED SPECIAL ARTICLE For the Special Issue: The Tree of Death: The Role of Fossils in Resolving the Overall Pattern of Plant Phylogeny Building the monocot tree of death: Progress and challenges emerging from the macrofossil- rich Zingiberales Selena Y. Smith1,2,4,6 , William J. D. Iles1,3 , John C. Benedict1,4, and Chelsea D. Specht5 Manuscript received 1 November 2017; revision accepted 2 May PREMISE OF THE STUDY: Inclusion of fossils in phylogenetic analyses is necessary in order 2018. to construct a comprehensive “tree of death” and elucidate evolutionary history of taxa; 1 Department of Earth & Environmental Sciences, University of however, such incorporation of fossils in phylogenetic reconstruction is dependent on the Michigan, Ann Arbor, MI 48109, USA availability and interpretation of extensive morphological data. Here, the Zingiberales, whose 2 Museum of Paleontology, University of Michigan, Ann Arbor, familial relationships have been difficult to resolve with high support, are used as a case study MI 48109, USA to illustrate the importance of including fossil taxa in systematic studies. 3 Department of Integrative Biology and the University and Jepson Herbaria, University of California, Berkeley, CA 94720, USA METHODS: Eight fossil taxa and 43 extant Zingiberales were coded for 39 morphological seed 4 Program in the Environment, University of Michigan, Ann characters, and these data were concatenated with previously published molecular sequence Arbor, MI 48109, USA data for analysis in the program MrBayes. 5 School of Integrative Plant Sciences, Section of Plant Biology and the Bailey Hortorium, Cornell University, Ithaca, NY 14853, USA KEY RESULTS: Ensete oregonense is confirmed to be part of Musaceae, and the other 6 Author for correspondence (e-mail: [email protected]) seven fossils group with Zingiberaceae.
  • Phylogeny of Rosids! ! Rosids! !

    Phylogeny of Rosids! ! Rosids! !

    Phylogeny of Rosids! Rosids! ! ! ! ! Eurosids I Eurosids II Vitaceae Saxifragales Eurosids I:! Eurosids II:! Zygophyllales! Brassicales! Celastrales! Malvales! Malpighiales! Sapindales! Oxalidales! Myrtales! Fabales! Geraniales! Rosales! Cucurbitales! Fagales! After Jansen et al., 2007, Proc. Natl. Acad. Sci. USA 104: 19369-19374! Phylogeny of Rosids! Rosids! ! ! ! ! Eurosids I Eurosids II Vitaceae Saxifragales Eurosids I:! Eurosids II:! Zygophyllales! Brassicales! Celastrales! Malvales! Malpighiales! Sapindales! Oxalidales! Myrtales! Fabales! Geraniales! Rosales! Cucurbitales! Fagales! After Jansen et al., 2007, Proc. Natl. Acad. Sci. USA 104: 19369-19374! Alnus - alders A. rubra A. rhombifolia A. incana ssp. tenuifolia Alnus - alders Nitrogen fixation - symbiotic with the nitrogen fixing bacteria Frankia Alnus rubra - red alder Alnus rhombifolia - white alder Alnus incana ssp. tenuifolia - thinleaf alder Corylus cornuta - beaked hazel Carpinus caroliniana - American hornbeam Ostrya virginiana - eastern hophornbeam Phylogeny of Rosids! Rosids! ! ! ! ! Eurosids I Eurosids II Vitaceae Saxifragales Eurosids I:! Eurosids II:! Zygophyllales! Brassicales! Celastrales! Malvales! Malpighiales! Sapindales! Oxalidales! Myrtales! Fabales! Geraniales! Rosales! Cucurbitales! Fagales! After Jansen et al., 2007, Proc. Natl. Acad. Sci. USA 104: 19369-19374! Fagaceae (Beech or Oak family) ! Fagaceae - 9 genera/900 species.! Trees or shrubs, mostly northern hemisphere, temperate region ! Leaves simple, alternate; often lobed, entire or serrate, deciduous
  • ABSTRACTS 117 Systematics Section, BSA / ASPT / IOPB

    ABSTRACTS 117 Systematics Section, BSA / ASPT / IOPB

    Systematics Section, BSA / ASPT / IOPB 466 HARDY, CHRISTOPHER R.1,2*, JERROLD I DAVIS1, breeding system. This effectively reproductively isolates the species. ROBERT B. FADEN3, AND DENNIS W. STEVENSON1,2 Previous studies have provided extensive genetic, phylogenetic and 1Bailey Hortorium, Cornell University, Ithaca, NY 14853; 2New York natural selection data which allow for a rare opportunity to now Botanical Garden, Bronx, NY 10458; 3Dept. of Botany, National study and interpret ontogenetic changes as sources of evolutionary Museum of Natural History, Smithsonian Institution, Washington, novelties in floral form. Three populations of M. cardinalis and four DC 20560 populations of M. lewisii (representing both described races) were studied from initiation of floral apex to anthesis using SEM and light Phylogenetics of Cochliostema, Geogenanthus, and microscopy. Allometric analyses were conducted on data derived an undescribed genus (Commelinaceae) using from floral organs. Sympatric populations of the species from morphology and DNA sequence data from 26S, 5S- Yosemite National Park were compared. Calyces of M. lewisii initi- NTS, rbcL, and trnL-F loci ate later than those of M. cardinalis relative to the inner whorls, and sepals are taller and more acute. Relative times of initiation of phylogenetic study was conducted on a group of three small petals, sepals and pistil are similar in both species. Petal shapes dif- genera of neotropical Commelinaceae that exhibit a variety fer between species throughout development. Corolla aperture of unusual floral morphologies and habits. Morphological A shape becomes dorso-ventrally narrow during development of M. characters and DNA sequence data from plastid (rbcL, trnL-F) and lewisii, and laterally narrow in M.