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Why We Study Phylogeny? Mobil! a Tree Is Like a Mobil! “Tree of Life” (Klimt, Austria) “Tree of Life” Project PHYLOGENETICS

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Why we study phylogeny? Mobil! A tree is like a mobil! “Tree of Life” (Klimt, Austria) “Tree of Life” project http://tolweb.org/tree/ PHYLOGENETICS In biology, phylogenetics is the study of evolutionary relatedness among various groups of organisms (for example, species or populations), which is discovered through molecular sequencing data and morphological data matrices. The term phylogenetics is of Greek origin from the terms phyle/phylon (φυλή/φῦλον), meaning "tribe, race," and genetikos (γενετικός), meaning "relative to birth" from genesis (γένεσις, "birth"). Taxonomy, the classification, identification, and naming of organisms, has been richly informed by phylogenetics but remains methodologically and logically distinct.[1] The fields overlap however in the science of phylogenetic systematics –often called "cladism" or "cladistics" –, where only phylogenetic trees are used to delimit taxa, which represent groups of lineage-connected individuals.[2] In biological systematics as a whole, phylogenetic analyses have become essential in researching the evolutionary tree of life. • It is a genome world! - The first genome data: Haemophilus influenzae (1995) about 1.8M bp. - Homo sapiens (begun in 1990 and completed in 2001) about 3.3G bp. <$400,000,000 - in 2011, more than 30 plant genomes are determined. • Two examples for the effect of phylogeny in the text book: 1) the phylogeny transformed to systematics (classifications) 16S rDNA phylogeny: suggested three domains in the life. 2) the phylogeny showed evolutionary information HIV gene (env) phylogeny: gave evidence of infection pathway. HIV genome stored evolutionary information recount the very recent history of its spread. ► Not only just pure application to the systematics but also the tracing evolutionary history. Other examples of interesting phylogenetic studies giving great impacts to the classification • Soltis et al. (1999): Amborella is the basal-most angiosperm • Manatee: a sister to elephant • Whale: a sister to hippo • white stork (황새): a sister to condor • Birds: originated from dinosaurs And minor impact my studies on Magnoliaceae ;-) Summarized angiosperm phylogeny Asterales 국화, 초롱꽃 Dipsacales 인동, 산토끼꽃 Apiales 당귀, 인삼 Aquifoliales 감탕나무 Campanulids Garryales 두충 Asterids Gentianales 용담, 꼭두서니 Laminales 꿀풀, 금어초 Solanales 토마토, 메꽃 Lamiids Ericales 진달래, 앵초 Cornales 층층나무, 수국 Sapindales 귤, 단풍나무 Malvales 무궁화 Core- Brassicales 애기장대, 무우 Malvids Fagales 자작나무, 참나무 eudicots Cucurbitales 박, 베고니아 Rosales 장미, 느릅나무 Rosids Fabales 콩, 자귀나무 Zygophyllales 남가새 Celestrales 노박덩굴 Fabids Oxalidales 굉이밥 ⑧ Malpighiales 버드나무, 제비꽃 Geraniales 쥐손이풀 Myrtales 바늘꽃 Saxifragales 범의귀, 돌나물 Caryphyllales 카네이션, 선인장 Santalales 단향, 겨우살이 Beberidopsidales 매발톱나무 Gunnerales ⑥ Buxaceae 회양목 Trochodendraceae Proteales 연꽃, 버즘나무 Sabiaceae 나도밤나무 Basal EUDICOTS ⑤ eudicots ⑦ 미나리아재비 양귀비 Ranunculales Euptelea Ceratophyllales 붕어마름 벼, 백합 ③ ④ 옥수수 MONOCOTS Acorus 창포 Chloranthales 홀아비꽃대 Basal Canellales Angiosperms Piperales 후추, 족도리풀 Magnoliales 목련, 튜립나무 magnoliids Laurales 녹나무, 아보카도 ① Austrobailales 붓순나무, 오미자 ② Nymphaeaceae 수련 Hydatellaceae Amborella EXTENT GYMNOSPERMS Amborella is a sister to all other angiosperms! Amborella trichopoda KIM, et al., (2004) Phylogeny and diversification of B-function MADS-box genes in angiosperms: evolutionary and functional implications of a 260-million-year-old duplication. American Journal of Botany 21: 2102-2118. Journal cover http://www.amborella.org/ Manatee is a sister to elephant! Whales are sister to hippos! Birds are originated from dinosaurs! 9 66 d1 Mich. cavaleriei Phylogeny of Magnoliaceae 1 8 68 d1 M. pealiana Mi 2 3 Mich. baillonii Michelia Terminal flower 72 d1 5 2 Mich. champaca Elmerrillia 11 4 3 Mich. odora sect. Maingola 2 98 d4 91 d3 Mich. figo sect. Alcimandra A 12 9 E. ovalis sect. Aromadendron 86 d4 6 3 M. cathcartii Al 64 d1 16 M. elegans Ar 5 8 M. biondii Bu 100 d8 3 M. kobus Bu 5 77 d2 M. dawsoniana Yu 3 8 14 100 d8 100 d13 3 M. campbellii Yu subgen. Yulania 2 B 11 7 M. denudata Yu Base changes 95 d5 2 100 d6 M. cylindrica Cy 29 M. acuminataTu 80 d1 5 Bootstrap /Decay value 2 M. sinica Mt sect. Manglietiastrum 20 d0 3 1 C 18 P. praecalva Pachylarnax 100 d15 1 M. nitida Gy sect. Gynopodium 3 D 28 K. duperreana 100 d26 2 K. septentrionalis Kmeria 12 1 66 d2 M. panamensis Th 2 9 20 d0 M. virginiana Ma 2 E 15 M. tamaulipana Th sect. Theorhodon s.s. 100 d14 3 sect. Magnolia 1 M. grandiflora Th 6 Axillary flower 48 d1 M.guatemalensis Th 31 d1 70 d1 5 Gw 3 2 M. coco 7 M. gigantifolia Bl sect. Gwillimia F 17 4 1 M. henryi Gw sect. Lirianthe 100 d16 6 64 d1 M. pterocarpa Li sect. Blumiana 3 6 M. liliifera Bl 7 45 d1 M. mexicana Ta G 9 4 100 d8 17 M. dodecapetala Ta sect. Talauma 82 d3 13 M. splendens Sp sect. Splendentes 33 d1 1 1 86 d2 Mang. grandis 2 H 4 Mang. aroma 17 Mang. conifera Manglietia 100 d13 6 Mang. glauca 7 4 M. officinalis Ry 9 143 I 5 98 d4 M. tripetala Ry sect. Rytidospermum s.s. 21 100 d137 92 d3 6 M. sieboldii Oy sect. Oyama 14 98 d6 M. wilsonii Oy 1 J 17 M. fraseri var. fraseri Ry 1 M. fraseri 100 d17 M. fraseri var. pyramidata Ry 5 K 19 M. macrophylla Ry M. macrophylla 4 100 d17 M. dealbata Ry M. dealbata 52 L. chinense 27 L. tulipifera Phylogeny of Magnoliaceae changes the classification of the family. • Two examples for the effect of phylogeny in the text book: 1) the phylogeny transformed to systematics (classifications) 16S rDNA phylogeny: suggested three domains in the life. 2) the phylogeny showed evolutionary information HIV gene (env) phylogeny: gave evidence of infection pathway. HIV genome stored evolutionary information recount the very recent history of its spread. ► Not only just pure application to the systematics but also the tracing evolutionary history. Phylogeny of HIV: provide an evidence of infection pathway Another example: 3) Phylogenetic tree provide molecular identification of unknown biological samples DNA barcoding: Molecular identification method of species name based on the sequences of standard gene(s). An example of my study: “DNA barcoding study of Korean Lamiaceae” based on three chloroplast DNA regions Two-dimensional barcode QR code barcode DNA-barcoding Lamiaceae (꿀풀과) Immature plants Molecular identifications of biological samples are possible EVEN in chopped or grounded samples. 황금 곽향 Scutellaria baicalensis 1 (황금) Scutellaria baicalensis 2 (황금) Scutellaria indica var. coccinea (연지골무꽃) Scutellaria indica var. tsusimensis 1 (떡잎골무꽃) Scutellaria indica var. tsusimensis 2 (떡잎골무꽃) Scutellaria insignis 1 (광릉골무꽃) Scutellaria insignis 2 (광릉골무꽃) Anayses of three Scutellaria moniliorrhiza (구슬골무꽃) Scutellaria regeliana 2 (가는골무꽃) Scutellaria strigillosa (참골무꽃) Scutellaria regeliana 1 (가는골무꽃) DNA regions in Scutellaria pekinensis var. alpina 1 (수골무꽃) Scutellaria pekinensis var. alpina 2 (수골무꽃) Scutellaria Scutellaria pekinensis var. maxima 4 (왕골무꽃) chloroplast: Scutellaria pekinensis var. ussuriensis 2 (호골무꽃) Scutellaria pekinensis var. ussuriensis 1 (호골무꽃) Scutellaria pekinensis var. maxima 1 (왕골무꽃) trnH~psbA Scutellaria pekinensis var. maxima 2 (왕골무꽃) Scutellaria pekinensis var. maxima 3 (왕골무꽃) Scutellaria pekinensis var. transitra 1 (산골무꽃) Scutellaria pekinensis var. transitra 2 (산골무꽃) atpF~atpH Scutellaria pekinensis var. transitra 3 (산골무꽃) Scutellaria pekinensis var. ussuriensis 3 (호골무꽃) Lamium album var. barbatum 1 (광대수염) psbK~psbI Lamium album var. barbatum 2 (광대수염) Lamium album var. album 1 (왜광대수염) Lamium takesimense 1 (섬광대수염) Lamium takesimense 2 (섬광대수염) Lamium Lamium album var. album 2 (왜광대수염) Stachys japonica 1 (석잠풀) Stachys japonica 3 (석잠풀) Stachys japonica 2 (석잠풀) Stachys Lamium amplexicaule 1 (광대나물) Lamium amplexicaule 2 (광대나물) Lamium amplexicaule 3 (광대나물) Leonurus japonicus 1 (익모초) Lamium Leonurus japonicus 2 (익모초) Leonurus macranthus 1 (송장풀) Leonurus macranthus 2 (송장풀) Leonurus Phlomis umbrosa (속단) Dysophylla stellata (물꼬리풀) Phlomis Neighbor joining Dysophylla yatabeana (전주물꼬리풀) Ajuga decumbens 1 (금창초) Dysophylla Ajuga decumbens 2 (금창초) Ajuga decumbens 3 (금창초) tree Ajuga spectabilis (자란초) Ajuga multiflora 1 (조개나물) Ajuga Ajuga multiflora 2 (조개나물) Teucrium japonicum (개곽향) Teucrium veronicoides 1 (곽향) Teucrium veronicoides 2 (곽향) Teucrium viscidum (덩굴곽향) Teucrium Clinopodium chinense (층층이꽃) Clinopodium micranthum (두메층층이) Clinopodium gracile (애기탑꽃) Clinopodium Agastache rugosa 1 (배초향) Agastache rugosa 2 (배초향) Dracocephalum rupestreAgastache 1 (벌깨풀) Dracocephalum rupestre 2 (벌깨풀) Meehania urticifolia 1 (벌깨덩굴) Dracocephalum Meehania urticifolia 2 (벌깨덩굴) Lycopus maackianus 1 (애기쉽싸리) Meehania Lycopus maackianus 2 (애기쉽싸리) Lycopus maackianus 3 (애기쉽싸리) Lycopus ramosissimus (개쉽싸리) Lycopus Prunella asiatica (꿀풀) Salvia chanroenica (참배암차즈기) Prunella Salvia plebeia (배암차즈기) Perilla frutescens var. frutescens 1 (들깨) Salvia Perilla frutescens var. frutescens 2 (들깨) Mosla chinensis (가는잎산들깨) Perilla Mosla dianthera (쥐깨풀) Elsholtzia minima (좀향유) Mosla Elsholtzia splendens 1 (꽃향유) Elsholtzia splendens 2 (꽃향유) Elsholtzia Isodon inflexus (산박하) Isodon japonicus (방아풀) Isodon 0.005 substitutions/site Q1 Scutellaria pekinensis var. transitra 2 (산골무꽃) Scutellaria pekinensis var. transitra 3 (산골무꽃) Scutellaria pekinensis var. ussuriensis 3 (호골무꽃) Q2 Q3 Scutellaria pekinensis var. alpina 2 (수골무꽃) Scutellaria pekinensis var. maxima 1 (왕골무꽃) Scutellaria pekinensis var. maxima 2 (왕골무꽃) Scutellaria pekinensis var. maxima 3 (왕골무꽃) Identifying unknown samples (Qs) Scutellaria pekinensis var. maxima 4 (왕골무꽃) Scutellaria pekinensis var. ussuriensis 2 (호골무꽃) Scutellaria pekinensis var. ussuriensis 1 (호골무꽃) Scutellaria pekinensis var.
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    T.C. BATMAN ÜNİVERSİTESİ FEN BİLİMLERİ ENSTİTÜSÜ ENDEMİK Ajuga vestita BOISS. BİTKİSİNİN FARKLI EKSPLANTLARINDAN İTİBAREN KALLUS OLUŞTURMA POTANSİYELİ VE OLUŞAN KALLUSUN BİYOLOJİK AKTİVİTESİNİN ARAŞTIRILMASI Şerife (AYDINARIĞ) BULUŞ YÜKSEK LİSANS TEZİ Biyoloji Anabilim Dalını Nisan-2019 BATMAN Her Hakkı Saklıdır ÖZET YÜKSEK LİSANS TEZİ ENDEMİK Ajuga vestita BOISS. BİTKİSİNİN FARKLI EKSPLANTLARINDAN İTİBAREN KALLUS OLUŞTURMA POTANSİYELİ VE OLUŞAN KALLUSUN BİYOLOJİK AKTİVİTESİNİN ARAŞTIRILMASI Şerife (AYDINARIĞ) BULUŞ Batman Üniversitesi Fen Bilimleri Enstitüsü Biyoloji Anabilim Dalı Danışman: Doç. Dr. Filiz AKBAŞ 2019, 63 Sayfa Jüri Doç. Dr. Çiğdem IŞIKALAN Doç. Dr. Filiz AKBAŞ Doç. Dr. Nesrin HAŞİMİ Ajuga vestita BOISS. bitkisi, tıbbi öneme sahip, endemik ve “EN-Tehlikede”kategorisinde olan Ajuga cinsine ait bir türdür. Bu çalışmada Ajuga vestita BOISS.’in in vitro sürgünlerinden elde edilen fidelerin farklı kısımlarından, literatür taramalarında daha önce hiç çalışılmamış olan kallus kültürlerinin başlatılması ve optimizasyonu ile kallustan sürgün elde etme potansiyelinin belirlenmesi amaçlandı. Bu amaçla öncelikle yüzey sterilizasyonu tamamlanan Ajuga vestita BOISS.’in olgun tohumları hormonsuz 1/4 MS besi ortamında çimlendirildi. Aksenik sürgün uçları, 0.125 mg/L-1 Kin içeren 1/1 MS besi yerinde çoğaltılarak kallus oluşturma çalışmalarında başlangıç materyali olarak kullanılacak in vitro sürgünler elde edildi. İn vitro ortamda yetiştirilen sürgünlerin yaprak, gövde, kök kısımları ve testası çatlatılmış olgun tohumlar, sitokinin (Kin, BAP) ve oksinin (2,4-D) farklı konsantrasyonlarının bulunduğu 1/1 MS besi ortamında ayrı ayrı kültüre alındı. Çalışma sonucunda, kültüre alınan tüm eksplant çeşitlerinde kallus oluşumu gözlendi. Ancak, tüm eksplant tiplerinde en iyi kallus oluşumunun 0.5 mg/L-1 Kin+2.0 mg/L-1 2,4-D içeren besi ortamında olduğu belirlendi.
  • Chemical and Pharmacological Research on the Plants from Genus Ajuga

    Chemical and Pharmacological Research on the Plants from Genus Ajuga

    Heterocycl. Commun. 2017; 23(4): 245–268 Review Xia Qing, Hui-Min Yan, Zhi-Yu Ni, Christopher J. Vavrickaa, Man-Li Zhang, Qing-Wen Shi*, Yu-Cheng Gu and Hiromasa Kiyota* Chemical and pharmacological research on the plants from genus Ajuga DOI 10.1515/hc-2017-0064 Received March 24, 2017; accepted June 15, 2017; previously perennial herbaceous flowering plants mainly distrib- published online July 22, 2017 uted throughout the temperate regions of Asia, Europe, Australia, North America and Africa. These species have Abstract: The genus Ajuga, a member of the Lamiaceae been used as common house plants and are called bugle family, is comprised of more than 300 species of annual or bugleweed. They are mainly characterized by the color and perennial herbaceous flowering plants mainly distrib- and shape of the flower. For example, the flower of Ajuga uted throughout the temperate regions of Asia, Europe, reptans is somewhat tall and blue, while that of Ajuga Australia, North America and Africa. These plants are used decumbens is short and purple. Many of these plants are as folk medicines effective for rheumatic fevers, dysen- of medicinal importance and are traditionally used as tery, malaria, hypertension, diabetes and gastrointestinal remedies for rheumatic fevers, dysentery, malaria, hyper- disorders, as well as anthelmintic, astringent, febrifuge tension, diabetes and gastrointestinal disorders, as well diuretic, antifungal and anti-inflammatory agents. A vari- as anthelmintic, astringent, febrifuge diuretic, antifun- ety of constituents has been isolated from these plants. gal and anti-inflammatory agents [1]. The genus Ajuga This review summarizes the phytochemical progress of the has attracted attention since the report in 1976 that Ajuga genus Ajuga and lists the compounds isolated up to 2014.
  • UC San Diego Dissertation

    UC San Diego Dissertation

    UNIVERSITY OF CALIFORNIA, SAN DIEGO Enhancing Natural Products Structural Dereplication and Elucidation with Deep Learning Based Nuclear Magnetic Resonance Techniques A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in NanoEngineering by Chen Zhang Committee in charge: William H. Gerwick, Chair Garrison W. Cottrell, Co-Chair Gaurav Arya Seth M. Cohen Chambers C. Hughes Preston B. Landon Liangfang Zhang 2017 Copyright Chen Zhang, 2017 All rights reserved The Dissertation of Chen Zhang is approved, and it is acceptable in quality and form for publication on microfilm and electronically: ____________________________________________ ____________________________________________ ____________________________________________ ____________________________________________ ____________________________________________ ____________________________________________ Co-Chair ____________________________________________ Chair University of California, San Diego 2017 iii DEDICATION I dedicate my dissertation work to my family and many friends. A special feeling of gratitude to my beloved parents, Jianping Zhao and Xiaojing Zhang whose words of encouragement and push for tenacity ring in my ears. My cousin Min Zhang has never left my side and is very special. I also dedicate this dissertation to my mentors who have shown me fascinating views of the world throughout the process, and those who have walked me through the valley of the shadow of frustration. I will always appreciate all they have done, especially Bill Gerwick, Gary Cottrell and Preston Landon for showing me the gate to new frontiers, Sylvia Evans, Pieter Dorrestein, Shu Chien, Liangfang Zhang, and Gaurav Arya for their great encouragement, and Wood Lee and Yezifeng for initially showing me the value of freedom, and continuously answering my questions regarding social sciences, humanities, literature, and arts.
  • Ethnopharmacology of the Plants of Genus Ajuga

    Ethnopharmacology of the Plants of Genus Ajuga

    ETHNOPHARMACOLOGY OF THE PLANTS OF GENUS AJUGA ZAFAR H. ISRAILI AND BADIÂA LYOUSSI* Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA *UFR Physiology – Pharmacology, Laboratory of Physiology-Pharmacology – Environmental Health, Faculty of Sciences, Dhar El Mehraz, Fez, Morocco ABSTRACT The plants of genus Ajuga are evergreen, clump-forming rhizomatous perennial or annual herbaceous flowering species, with Ajuga being one of the 266 genera of the family Lamiaceae. There are at least 301 species of the genus Ajuga with many variations. These plants, growing in Europe, Asia, Africa, Australia and North America, are used in gardens as ground cover or border for their foliage and beautiful flowers. Many of these plants have been used in traditional medicine as a remedy for fever, toothache, dysentery, malaria, high blood pressure, diabetes, gastrointestinal disorders, as anthelmintic, diuretic and antifungal, anti-inflammatory, and antimycobacterial agents. They are also used as insect growth inhibitor s. A large number of compounds have been isolated from the Ajuga plants, including phytoecdysteroids, neo-clerodane-diterpenes and diterpenoids, triterpenes, sterols, anthocyanidin-glucosides and iridoid glycosides, withanolides, flavonoids, triglycerides and essential oils. These compounds possess a broad spectrum of biological, pharmacological and medicinal properties, such as anabolic, analgesic, antibacterial, antiestrogenic, antifungal, anti-inflammatory, antihypertensive, antileukemic, antimalarial, antimycobacterial,
  • Biologically Active Compounds from Salvia Horminum L

    Biologically Active Compounds from Salvia Horminum L

    University of Bath PHD Phytochemical and biological activity studies on Salvia viridis L Rungsimakan, Supattra Award date: 2011 Awarding institution: University of Bath Link to publication Alternative formats If you require this document in an alternative format, please contact: [email protected] General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. • Users may download and print one copy of any publication from the public portal for the purpose of private study or research. • You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying the publication in the public portal ? Take down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. Download date: 09. Oct. 2021 Phytochemical and biological activity studies on Salvia viridis L. Supattra Rungsimakan A thesis submitted for the degree of Doctor of Philosophy University of Bath Department of Pharmacy and Pharmacology November 2011 Copyright Attention is drawn to the fact that copyright of this thesis rests with the author. A copy of this thesis has been supplied on condition that anyone who consults it is understood to recognise that its copyright rests with the author and that they must not copy it or use material from it except as permitted by law or with the consent of the author.
  • 6.Aptosimum Literature Chapter 2

    6.Aptosimum Literature Chapter 2

    Chapter 2 Phytochemistry of Aptosimum procumbens 2.1 Introduction Aptosimum procumbens Burch (= A. depressum) of the tribe Aptosimae belongs to the Scropulariaceae sensu stricto family of the order Lamiales.1 Scrophulariaceae is one of the largest plant families and is comprised of about 190 genera and 4000 species. Plants from this family are mostly woody herbaceous shrubs and are found predominantly in the temperate regions of the world.2 They are distinguished from related families with relative ease, but many plants are assigned to this family because they lack distinguishing characteristics that would place them in the other specific families. Therefore, Scrophs share some of the characteristics of plants of related families and this may negate the possibility that Scrophulariaceae is a distinct clade. As a result of this, there are doubts as to whether the family is monophyletic or should rather be classified as polyphyletic or paraphyletic.1 Phytochemical investigations can provide a valuable input with regards to the chemotaxanomical studies of this family. A. procumbens (Fig. 1) is mainly referred to as “carpet flower” but shares a variety of vernacular names such as “brandbossie/blare”, “Karoo violet/flower” and “kankerbos” with other related species of Aptosimum. A common name is given to a plant based on certain characteristics of the plant. A. procumbens is a prostrate mat-forming species hence the name “carpet flower”. The plant has strong woody procumbent stems with short lateral, dense leafy and floriferous branches. Another characteristic feature is the violet trumpet-like flowers that bloom in the summer or after rainfall (hence the name “Karoo violet”).