DOCSLIB.ORG

Euap1 FUL FUL-Like Euap3

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Euap1 FUL FUL-Like Euap3 Nymphaelaes A Magnolids Monocots Ranunculales Proteales Trochodendrales Buxales Gunnerales Saxifragales Vitales Rosids Caryophyllales Cornales FUL-Like Ericales Asterids Gunnerales Saxifragales Vitales Rosids FUL Caryophyllales Cornales Ericales Asterids Gunnerales Saxifragales Vitales Rosids euAP1 Caryophyllales Cornales Ericales Asterids Amborellales Nymphaelaes B Austrobaileyales Magnolids Chloranthales Monocots Ranunculales Proteales Trochodendrales Buxales Gunnerales Saxifragales Vitales Rosids Dilleniales Santanales TM6 Caryophyllales Cornales Ericales Asterids Saxifragales Vitales Rosids Dilleniales Caryophyllales Cornales euAP3 Ericales Asterids Amborellales Nymphaelaes C Austrobaileyales Magnolids Chloranthales Monocots Ranunculales Proteales Trochodendrales Buxales Gunnerales Saxifragales Vitales Rosids Dilleniales Caryophyllales Cornales PI Ericales Asterids Amborellales D Nymphaelaes Magnolids Monocots Ranunculales Proteales Trochodendrales Buxales Gunnerales Saxifragales Vitales Rosids euAG Caryophyllales Cornales Ericales Asterids Gunnerales Saxifragales Vitales Rosids SHP Dilleniales Asterids Amborellales E Chloranthales Magnolids Monocots Ranunculales Proteales Buxales Gunnerales Saxifragales Vitales Rosids STK Caryophyllales Ericales Asterids Amborellales Nymphaelaes F Magnolids Monocots Ranunculales Proteales Trochodendrales Buxales Gunnerales Saxifragales Vitales Rosids Caryophyllales Cornales FBP9 Ericales Asterids Vitales Rosids Caryophyllales SEP4 Cornales Asterids Gunnerales Saxifragales Vitales Rosids SEP1/2 Caryophyllales Cornales Ericales Asterids Amborellales Chloranthales G Magnolids Monocots Ranunculales Proteales Trochodendrales Buxales Gunnerales Vitales Rosids Asterids SEP3 Caryophyllales Cornales Ericales Asterids Amborellales H Nymphaelaes Magnolids Monocots Ranunculales Proteales Buxales Saxifragales Vitales Rosids SVP Caryophyllales Cornales Ericales Asterids Saxifragales Vitales Rosids Dilleniales Caryophyllales StMADS11 Ericales Asterids Gunnerales Vitales Rosids AGL24 Dilleniales Caryophyllales Cornales Ericales Asterids Amborellales Nymphaelaes I Magnolids Monocots Ranunculales Proteales Trochodendrales Buxales Saxifragales Vitales Rosids Santanales Caryophyllales Cornales FBP22 Asterids Gunnerales Vitales Rosids Berberidopsidales AGL14 Cornales Ericales Asterids Saxifragales Vitales Rosids TM3 Dilleniales Berberidopsidales Cornales Asterids Supplemental Figure 1: Simplified phylogenetic trees of the MADS-box gene subfamilies used for ASR and selective pressure estima- tion. AP1- (A), AP3- (B), PI- (C), AG- (D), STK- (E), SEP1/2/4 (F), SEP3 (G), SVP/AGL24 (H), SOC1- (I) gene lineages. Arrows denote the nodes used for ASR before the γ triplication (blue) and at the Rosid/Asterid split (green). Red arrows denote the nodes for which no reliable ancestral genes could be reconstructed. ancAP1 pre-γ ancPI post-γ ancPI 1 1 1 0.8 0.8 0.8 0.6 0.6 0.6 0.4 0.4 0.4 0.2 0.2 0.2 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 21 31 41 51 61 71 81 91 1 21 31 41 51 61 71 81 91 21 31 41 51 61 71 81 91 11 11 11 2 2 101 121 131 141 151 161 171 181 191 201 101 121 131 141 151 161 171 181 191 201 221 231 241 251 101 121 131 141 151 161 171 181 191 201 MADS I K C MADS I K C MADS I K C anceuAP1 ancFUL-LIKE ancFUL 1 1 1 0.8 0.8 0.8 0.6 0.6 0.6 0.4 0.4 0.4 0.2 0.2 0.2 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 21 31 41 51 61 71 81 91 21 31 41 51 61 71 81 91 21 31 41 51 61 71 81 91 11 11 11 2 2 2 101 121 131 141 151 161 171 181 191 201 221 231 241 101 121 131 141 151 161 171 181 191 201 221 231 241 251 101 121 131 141 151 161 171 181 191 201 221 231 241 MADS I K C MADS I K C MADS I K C ancAP3 anceuAP3 ancTM6 1 1 1 0.8 0.8 0.8 0.6 0.6 0.6 0.4 0.4 0.4 0.2 0.2 0.2 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 21 31 41 51 61 71 81 91 21 31 41 51 61 71 81 91 21 31 41 51 61 71 81 91 11 11 11 2 2 2 101 121 131 141 151 161 171 181 191 201 221 231 101 121 131 141 151 161 171 181 191 201 221 101 121 131 141 151 161 171 181 191 201 221 MADS I K C MADS I K C MADS I K C ancAG anceuAG ancSHP 1 1 1 0.8 0.8 0.8 0.6 0.6 0.6 0.4 0.4 C 0.4 0.2 0.2 0.2 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 21 31 41 51 61 71 81 91 21 31 41 51 61 71 81 91 21 31 41 51 61 71 81 91 11 11 11 2 2 101 121 131 141 151 161 171 181 191 201 101 121 131 141 151 161 171 181 191 201 101 121 131 141 151 161 171 181 191 201 MADS I K C MADS I K C MADS I K C pre-γ ancSTK post-γ ancSTK 1 1 0.8 0.8 0.6 0.6 0.4 0.4 0.2 0.2 0 0 1 1 1 1 1 1 1 1 1 1 1 1 21 31 41 51 61 71 81 91 21 31 41 51 61 71 81 91 11 11 2 2 101 121 131 141 151 161 171 181 191 201 221 101 121 131 141 151 161 171 181 191 201 221 MADS I K C MADS I K C ancSEP1/2/4 pre-γ ancSEP3 post-γ ancSEP3 1 1 1 0.8 0.8 0.8 0.6 0.6 0.6 0.4 0.4 0.4 0.2 0.2 0.2 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 21 31 41 51 61 71 81 91 21 31 41 51 61 71 81 91 1 1 21 31 41 51 61 71 81 91 11 11 2 2 11 101 121 131 141 151 161 171 181 191 201 221 231 241 101 121 131 141 151 161 171 181 191 201 221 231 241 2 101 121 131 141 151 161 171 181 191 201 221 231 241 MADS I K C MADS I K C MADS I K C ancSEP1/2 ancSEP4 ancFBP9 1 1 1 0.8 0.8 0.8 0.6 0.6 0.6 0.4 0.4 0.4 0.2 0.2 0.2 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 21 31 41 51 61 71 81 91 1 1 1 1 21 31 41 51 61 71 81 91 21 31 41 51 61 71 81 91 11 2 11 101 121 131 141 151 161 171 181 191 201 221 231 241 251 11 2 2 101 121 131 141 151 161 171 181 191 201 221 231 241 251 101 121 131 141 151 161 171 181 191 201 221 231 241 251 MADS I K C MADS I K C MADS I K C ancSVP/AGL24 ancSVP ancAGL24 1 1 1 0.8 0.8 0.8 0.6 0.6 0.6 0.4 0.4 0.4 0.2 0.2 0.2 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 21 31 41 51 61 71 81 91 1 1 1 1 21 31 41 51 61 71 81 91 21 31 41 51 61 71 81 91 11 2 11 11 101 121 131 141 151 161 171 181 191 201 221 231 2 2 101 121 131 141 151 161 171 181 191 201 221 231 101 121 131 141 151 161 171 181 191 201 221 231 MADS I K C MADS I K C MADS I K C ancSOC1 ancFBP22 ancTM3 1 1 1 0.8 0.8 0.8 0.6 0.6 0.6 0.4 0.4 0.4 0.2 0.2 0.2 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 21 31 41 51 61 71 81 91 1 1 1 1 21 31 41 51 61 71 81 91 21 31 41 51 61 71 81 91 11 2 11 11 101 121 131 141 151 161 171 181 191 201 2 2 101 121 131 141 151 161 171 181 191 201 221 101 121 131 141 151 161 171 181 191 201 221 MADS I K C MADS I K C MADS I K C Supplemental Figure 2: Ancestral sequences and their accuracy. Dots represent the posterior probabilities (y-axis) for each amino acid site (x-axis) for all reconstructed genes. Arrows denote ambiguous sites defined as sites for which the most likely amino acid has a posterior probability lower than 0.80 and that have an alternative amino acid state with a posterior probability higher than 0.2. Green arrows represent ambiguous sites of which the most likely amino acids are biochemically similar (S and T; V, L and I; D and E; N and Q; K and R were considered similar). A Gene subfamilies AP1 SQUA/AP1/FUL CAL Overlapping FUL PPIs only in de Folter et al (2005) DEF/AP3 AP3 PPIs only in this study GLO/PI PI No interactions detected AG AG SHP1 SHP2 STK STK SEP1 SEP1/2/4 SEP2 SEP4 SEP3 SEP3 SVP SVP/ StMADS11 AGL24 AGL42 SOC1/TM3 SOC1 AP1 CAL FUL AP3 PI AG SHP1 SHP2 STK SEP1 SEP2 SEP4 SEP3 SVP AGL24 AGL42 SOC1 Gene s ubfamilies B MC TM4 Overlapping SQUA/AP1/FU L SLMBP 7 PPIs only in Leseberg et al (2008) PPIs only in this study SLMBP2 0 No interactions detected TAP3 DEF/AP 3 TM6 LeP I GLO/P I TP I TAG1 AG TAGL1 SLMBP 3 STK TAGL1 1 TM29 RIN SEP1/2 /4 LeMADS1 SLMBP21 SEP3 TM5 JOINTLESS SVP/S tMADS11 SLMBP2 4 SLMBP1 8 SOC1/TM 3 TM3 MC TM4 SLMBP7 SLMBP20 TAP3 TM6 LeP I TP I TAG1 TAGL1 SLMBP3 TAGL11 TM29 RIN LeMADS1 SLMBP21 TM5 JOINTLESS SLMBP24 SLMBP18 TM3 C Arabidopsis Interaction No interaction Total Sensitivity 0,6052632 This study Interaction 23 16 39 Accuracy 0,7973856 No interaction 15 99 114 Precision 0,5897436 Total 38 115 153 Specificity 0,8608696 Solanum Interaction No interaction Total Sensitivity 0,4125 This study Interaction 33 12 45 Accuracy 0,7445887 No interaction 47 139 186 Precision 0,7333333 Total 80 151 231 Specificity 0,9205298 Arabidopsis/Solanum Interaction No interaction Total Sensitivity 0,4745763 This study Interaction 56 28 84 Accuracy 0,765625 No interaction 62 238 300 Precision 0,6666667 Total 118 266 384 Specificity 0,8947368 Supplemental Figure 3: Comparison of the PPIs obtained in this study with the determined PPIs from previous published literature.
Load more

Recommended publications
  • Well-Known Plants in Each Angiosperm Order
    Well-known plants in each angiosperm order This list is generally from least evolved (most ancient) to most evolved (most modern). (I’m not sure if this applies for Eudicots; I’m listing them in the same order as APG II.) The first few plants are mostly primitive pond and aquarium plants. Next is Illicium (anise tree) from Austrobaileyales, then the magnoliids (Canellales thru Piperales), then monocots (Acorales through Zingiberales), and finally eudicots (Buxales through Dipsacales). The plants before the eudicots in this list are considered basal angiosperms. This list focuses only on angiosperms and does not look at earlier plants such as mosses, ferns, and conifers. Basal angiosperms – mostly aquatic plants Unplaced in order, placed in Amborellaceae family • Amborella trichopoda – one of the most ancient flowering plants Unplaced in order, placed in Nymphaeaceae family • Water lily • Cabomba (fanwort) • Brasenia (watershield) Ceratophyllales • Hornwort Austrobaileyales • Illicium (anise tree, star anise) Basal angiosperms - magnoliids Canellales • Drimys (winter's bark) • Tasmanian pepper Laurales • Bay laurel • Cinnamon • Avocado • Sassafras • Camphor tree • Calycanthus (sweetshrub, spicebush) • Lindera (spicebush, Benjamin bush) Magnoliales • Custard-apple • Pawpaw • guanábana (soursop) • Sugar-apple or sweetsop • Cherimoya • Magnolia • Tuliptree • Michelia • Nutmeg • Clove Piperales • Black pepper • Kava • Lizard’s tail • Aristolochia (birthwort, pipevine, Dutchman's pipe) • Asarum (wild ginger) Basal angiosperms - monocots Acorales
    [Show full text]
  • Supplemental Information.Pdf
    SUPPORTING INFORMATION Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous-Paleogene boundary Kevin Vanneste1,2, Guy Baele3, Steven Maere1,2,*, and Yves Van de Peer1,2,4,* 1 Department of Plant Systems Biology, VIB, Ghent, Belgium 2 Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium 3 Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium 4 Department of Genetics, Genomics Research Institute, University of Pretoria, Pretoria, South Africa *Corresponding authors Yves Van de Peer Steven Maere VIB / Ghent University VIB / Ghent University Technologiepark 927 Technologiepark 927 Gent (9052), Belgium Gent (9052), Belgium Tel: +32 (0)9 331 3807 Tel: +32 (0)9 331 3805 Fax: +32 (0)9 331 3809 Fax: +32 (0)9 331 3809 E-mail: [email protected] E-mail: [email protected] Overview Species grouping topology ................................................ 3 Calibrations and constraints .............................................. 5 Alternative calibrations and constraints ............................ 13 Relative rate tests ............................................................. 27 Re-dating the Pyrus bretschneideri WGD ......................... 30 WGD age estimates from literature ................................... 33 Eschscholzia californica and Acorus americanus ............. 34 2 Species grouping topology In order to date the node joining the homeologous pair, orthogroups were constructed consisting of both homeologs and orthologs from other plant species for which full genome sequence information was available. Different plant species were grouped into ‘species groups’ for which one ortholog was selected and added to the orthogroup, in order to keep the orthogroup topology fixed and to facilitate automation on the one hand, but also to allow enough orthogroups to be constructed on the other hand (see Material and methods).
    [Show full text]
  • 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
    [Show full text]
  • Systematic Botany. Lecture 38
    BIOL 448.38 Systematic Botany. Lecture 38 Alexey Shipunov Minot State University December 5, 2011 BIOL 448.38 Outline Questions and answers Angiosperms Rosidae, part 2 BIOL 448.38 Outline Questions and answers Angiosperms Rosidae, part 2 I The goal was to remember the key characters, plus (possibly) some representatives BIOL 448.38 Questions and answers Previous final question: the answer Give the short characteristic of any of 7 orders studied. BIOL 448.38 Questions and answers Previous final question: the answer Give the short characteristic of any of 7 orders studied. I The goal was to remember the key characters, plus (possibly) some representatives BIOL 448.38 Questions and answers General phylogeny of angiosperms groups studied so far other rosids Myrtales Geraniales Vitales Saxifragales Asteridae Dilleniales Platanales Ranunculales Liliidae Piperales Laurales Magnoliales Chloranthales ANTITA BIOL 448.38 Angiosperms Rosidae, part 2 Angiosperms Rosidae, part 2 BIOL 448.38 Angiosperms Rosidae, part 2 BIOL 448.38 Angiosperms Rosidae, part 2 BIOL 448.38 Angiosperms Rosidae, part 2 BIOL 448.38 Angiosperms Rosidae, part 2 BIOL 448.38 Angiosperms Rosidae, part 2 BIOL 448.38 Angiosperms Rosidae, part 2 BIOL 448.38 Angiosperms Rosidae, part 2 BIOL 448.38 Angiosperms Rosidae, part 2 BIOL 448.38 Angiosperms Rosidae, part 2 General phylogeny + all rosids Malpighiales Oxalidales Celastrales Cucurbitales Fagales Rosales Fabales Malvales Brassicales Sapindales Myrtales Geraniales Vitales Saxifragales Asteridae Dilleniales Platanales Ranunculales Liliidae Piperales Laurales Magnoliales Chloranthales ANTITA Give the short characteristic of any of orders studied. BIOL 448.38 Angiosperms Rosidae, part 2 Final question (3 points) BIOL 448.38 Angiosperms Rosidae, part 2 Final question (3 points) Give the short characteristic of any of orders studied.
    [Show full text]
  • 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.
    [Show full text]
  • 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.
    [Show full text]
  • 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
    [Show full text]
  • Full of Beans: a Study on the Alignment of Two Flowering Plants Classification Systems
    Full of beans: a study on the alignment of two flowering plants classification systems Yi-Yun Cheng and Bertram Ludäscher School of Information Sciences, University of Illinois at Urbana-Champaign, USA {yiyunyc2,ludaesch}@illinois.edu Abstract. Advancements in technologies such as DNA analysis have given rise to new ways in organizing organisms in biodiversity classification systems. In this paper, we examine the feasibility of aligning two classification systems for flowering plants using a logic-based, Region Connection Calculus (RCC-5) ap- proach. The older “Cronquist system” (1981) classifies plants using their mor- phological features, while the more recent Angiosperm Phylogeny Group IV (APG IV) (2016) system classifies based on many new methods including ge- nome-level analysis. In our approach, we align pairwise concepts X and Y from two taxonomies using five basic set relations: congruence (X=Y), inclusion (X>Y), inverse inclusion (X<Y), overlap (X><Y), and disjointness (X!Y). With some of the RCC-5 relationships among the Fabaceae family (beans family) and the Sapindaceae family (maple family) uncertain, we anticipate that the merging of the two classification systems will lead to numerous merged solutions, so- called possible worlds. Our research demonstrates how logic-based alignment with ambiguities can lead to multiple merged solutions, which would not have been feasible when aligning taxonomies, classifications, or other knowledge or- ganization systems (KOS) manually. We believe that this work can introduce a novel approach for aligning KOS, where merged possible worlds can serve as a minimum viable product for engaging domain experts in the loop. Keywords: taxonomy alignment, KOS alignment, interoperability 1 Introduction With the advent of large-scale technologies and datasets, it has become increasingly difficult to organize information using a stable unitary classification scheme over time.
    [Show full text]
  • Phylogeny of the SE Australian Clade of Hibbertia Subg. Hemistemma (Dilleniaceae)
    Phylogeny of the SE Australian clade of Hibbertia subg. Hemistemma (Dilleniaceae) Ihsan Abdl Azez Abdul Raheem School of Earth and Environmental Sciences The University of Adelaide A thesis submitted for the degree of Doctor of Philosophy of the University of Adelaide June 2012 The University of Adelaide, SA, Australia Declaration I, Ihsan Abdl Azez Abdul Raheem certify that this work contains no materials which has been accepted for the award of any other degree or diploma in any universities or other tertiary institution and, to the best of my knowledge and belief, contains no materials previously published or written by another person, except where due reference has been made in the text. I give consent to this copy of my thesis, when deposited in the University Library, being made available for photocopying, subject to the provisions of the Copyright Act 1968. I also give permission for the digital version of my thesis to be made available on the web, via the University digital research repository, the Library catalogue, the Australian Digital Thesis Program (ADTP) and also through web search engine, unless permission has been granted by the University to restrict access for a period of time. ii This thesis is dedicated to my loving family and parents iii Acknowledgments The teacher who is indeed wise does not bid you to enter the house of his wisdom but rather leads you to the threshold of your mind--Khalil Gibran First and foremost, I wish to thank my supervisors Dr John G. Conran, Dr Terry Macfarlane and Dr Kevin Thiele for their support, encouragement, valuable feedback and assistance over the past three years (data analyses and writing) guiding me through my PhD candidature.
    [Show full text]
  • Reconstructing the Basal Angiosperm Phylogeny: Evaluating Information Content of Mitochondrial Genes
    55 (4) • November 2006: 837–856 Qiu & al. • Basal angiosperm phylogeny Reconstructing the basal angiosperm phylogeny: evaluating information content of mitochondrial genes Yin-Long Qiu1, Libo Li, Tory A. Hendry, Ruiqi Li, David W. Taylor, Michael J. Issa, Alexander J. Ronen, Mona L. Vekaria & Adam M. White 1Department of Ecology & Evolutionary Biology, The University Herbarium, University of Michigan, Ann Arbor, Michigan 48109-1048, U.S.A. [email protected] (author for correspondence). Three mitochondrial (atp1, matR, nad5), four chloroplast (atpB, matK, rbcL, rpoC2), and one nuclear (18S) genes from 162 seed plants, representing all major lineages of gymnosperms and angiosperms, were analyzed together in a supermatrix or in various partitions using likelihood and parsimony methods. The results show that Amborella + Nymphaeales together constitute the first diverging lineage of angiosperms, and that the topology of Amborella alone being sister to all other angiosperms likely represents a local long branch attrac- tion artifact. The monophyly of magnoliids, as well as sister relationships between Magnoliales and Laurales, and between Canellales and Piperales, are all strongly supported. The sister relationship to eudicots of Ceratophyllum is not strongly supported by this study; instead a placement of the genus with Chloranthaceae receives moderate support in the mitochondrial gene analyses. Relationships among magnoliids, monocots, and eudicots remain unresolved. Direct comparisons of analytic results from several data partitions with or without RNA editing sites show that in multigene analyses, RNA editing has no effect on well supported rela- tionships, but minor effect on weakly supported ones. Finally, comparisons of results from separate analyses of mitochondrial and chloroplast genes demonstrate that mitochondrial genes, with overall slower rates of sub- stitution than chloroplast genes, are informative phylogenetic markers, and are particularly suitable for resolv- ing deep relationships.
    [Show full text]
  • 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.
    [Show full text]
  • Bilirubin: an Animal Pigment in the Zingiberales and Diverse Angiosperm Orders Cary L
    Florida International University FIU Digital Commons FIU Electronic Theses and Dissertations University Graduate School 11-5-2010 Bilirubin: an Animal Pigment in the Zingiberales and Diverse Angiosperm Orders Cary L. Pirone Florida International University, [email protected] DOI: 10.25148/etd.FI10122201 Follow this and additional works at: https://digitalcommons.fiu.edu/etd Part of the Biochemistry Commons, and the Botany Commons Recommended Citation Pirone, Cary L., "Bilirubin: an Animal Pigment in the Zingiberales and Diverse Angiosperm Orders" (2010). FIU Electronic Theses and Dissertations. 336. https://digitalcommons.fiu.edu/etd/336 This work is brought to you for free and open access by the University Graduate School at FIU Digital Commons. It has been accepted for inclusion in FIU Electronic Theses and Dissertations by an authorized administrator of FIU Digital Commons. For more information, please contact [email protected]. FLORIDA INTERNATIONAL UNIVERSITY Miami, Florida BILIRUBIN: AN ANIMAL PIGMENT IN THE ZINGIBERALES AND DIVERSE ANGIOSPERM ORDERS A dissertation submitted in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY in BIOLOGY by Cary Lunsford Pirone 2010 To: Dean Kenneth G. Furton College of Arts and Sciences This dissertation, written by Cary Lunsford Pirone, and entitled Bilirubin: An Animal Pigment in the Zingiberales and Diverse Angiosperm Orders, having been approved in respect to style and intellectual content, is referred to you for judgment. We have read this dissertation and recommend that it be approved. ______________________________________ Bradley C. Bennett ______________________________________ Timothy M. Collins ______________________________________ Maureen A. Donnelly ______________________________________ John. T. Landrum ______________________________________ J. Martin Quirke ______________________________________ David W. Lee, Major Professor Date of Defense: November 5, 2010 The dissertation of Cary Lunsford Pirone is approved.
    [Show full text]