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Progress in Reconstructing the Green Plant Tree of Life with an Emphasis on Angiosperms

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Progress in reconstructing the green plant tree of life with an emphasis on angiosperms Goals •Highlight recent developments in our understanding of green plant phylogeny •Overview of our improved understanding of angiosperm phylogeny and evolution •Emphasis will be on molecular insights secondary symbiosis Keeling 2004. American Journal of Botany 91:1481-1493 Palmer et al. 2004. American Journal of Botany 91: 1437-1445 Green plant phylogeny True green algae Chlorophytes Ulva Chlamydomonas Volvox Acetabularia Streptophytes Spirogyra Chara plus land plants Green plant phylogeny: embryophytes or land plants “Bryophytes”-sister to other land plants moss liverwort hornwort MLH tracheophytes Branching order uncertain All have dominant gameto- phyte, reduced sporophyte (photosynthetic part is gametophyte) Base of embryophytes: “LMH” vs. “LHM” Liverwort phylogeny based nuclear and plastid loci J. Shaw, pers. comm. Phylogenetic status of haplolepideous moss families (J. Shaw) Para- or polyphyletic Monophyletic Bruchiaceae (Archidiaceae) Dicnemonaceae (Bryoxiphiaceae) Dicranaceae Calymperaceae 4/8 Ditrichaceae (Cinclidotaceae) Ephemeraceae (Drummondiaceae) Erpodiaceae (Eustichiaceae) Grimmiaceae (Fissidentaceae) Leucobryaceae Rhachitheciaceae 3/7 Pottiaceae (Schistostegaceae) Ptychomitriaceae (Serpotortellaceae) Rhabdoweisiaceae (Wardiaceae) Seligeriaceae How “distinct” are genera of mosses, on average? Phylogeny of tracheophytes (vascular plants) Phylogeny of tracheophytes: Lycophytes Lycophyte Diversity Selaginella Lycopodium • Lycopodiaceae – Lycopodium – Huperzia • Selaginellaceae Iso. Sel. Lyco. – Selaginella • Isoetaceae – Isoetes Lepidodendron Phylogeny of tracheophytes: Euphyllophytes Diagram of the chloroplast genome of grape (Vitis vinifera) Phylogeny of tracheophytes (vascular plants) Monilophytes--Characteristic stem anatomy Clade is well-supported by DNA data From Kenrick and Crane 1997 Phylogeny of tracheophytes: Monilophytes Unexpected sister-group Psilotales Ophioglossales Equisetophytes Fossils from the Devonian strobilus leaves Leptosporangiate ferns In the shadow of angiosperms And old lineage (Devonian)... But ferns diversi`fied In the “shadow of the Angiosperms” Schneider et al. (2004). Nature 428: 553 Cretaceous Phylogeny of tracheophytes: seed plants Seed plant phylogeny Cycads, Ginkgo, Conifers megastrobilus Cycas revoluta Ginkgo biloba Pinus aristata Gnetales Gnetum Ephedra Welwitschia Relationships among extant seed plants morphology molecules “Gnepine” hypotheses Gnetales placed within conifers gymnosperms Gordon Burleigh and Sarah Mathews 2004 Am. J. Botany 2004 91: 1599-1613 Gnetales and conifers share morphological similarities • linear leaves • wood anatomy (circular bordered pits with tori in the protoxylem, interspersed with annular thickenings) Angiosperms: one of the greatest terrestrial radiations • Ecologically Dominant – Approximately 300,000 species QuickTime?and a TIFF (Uncompressed) decompressor are needed to see this picture. QuickTime?and a QuickTime?and a TIFF (Uncompressed) decompressor TIFF (Uncompressed) decompressor are needed to see this picture. are needed to see this picture. QuickTime?and a TIFF (Uncompressed) decompressor are needed to see this picture. QuickTime?and a TIFF (Uncompressed) decompressor are needed to see this picture. QuickTime?and a QuickTime?and a TIFF (Uncompressed) decompressor TIFF (Uncompressed) decompressor are needed to see this picture. are needed to see this picture. QuickTime?and a QuickTime?and a QuickTime?and a TIFF (Uncompressed) decompressor TIFF (Uncompressed) decompressor are needed to see this picture. QuickTime?and a TIFF (Uncompressed) decompressor TIFF (Uncompressed) decompressor are needed to see this picture. are needed to see this picture. are needed to see this picture. …the rapid rise and early diversification of angiosperms is “an abominable mystery” --Charles Darwin letter to J. D. Hooker 22 July 1879 Early Cretaceous Angiosperms: Archaefructus • ~127 mya • China • Spiral/whorled carpels • Paired stamens • Aquatic First Flower? Sun et al. (2002) Molecular estimates for age of the angiosperms are converging 158-179 mya Wikström et al. (2001) 140-190 mya Sanderson & Doyle (2001) 127-132 mya Soltis et al. (2002) 140-180 mya Bell et al. (2005) 155-198 mya Bell et al. (2005) First angiosperm ? Overview of Angiosperm Phylogeny • Molecular data from chloroplast, mitochondrial and nuclear genomes are congruent • Repeated patterns of resolution and polytomies: repeated radiations • Focus on basal lineages Angiosperm phylogeny--3 gene 100 Fagales Fig. 2.3 60 100 Cucurbitales fabids I eurosid 68 100 Rosales 98 Fabales 77 Zygophyllales 100 Celastrales 62 rosids Oxalidales 51 100 Malpighiales 99 malvids II eurosid Sapindales 100 99 51 Malvales 95 100 Brassicales CORE EUDICOTS NO 100 Crossosomatales Model organism 100 Myrtales 100 Geraniales EUDICOTS 80 Arabidopsis Saxifragales “DICOTS”! 98 lamiids I euasterid Lamiales 100 Solanales 84 99 96 Gentianales 56 100 Garryales 55 campanulids II euasterid asterids Asterales 89 94 Dipsacales 97 86 Apiales 100 88 Aquifoliales 96 Ericales 100 99 98 Cornales 98 Caryophyllales 87 100 Berberidopsidales 100 Santalales 100 Gunnerales EUDICOTS DIVERGING EARLY- 75 59 Buxaceae Antirrhinum 100 Trochodendraceae 100 Proteales 84 100 Sabiaceae 100 Ranunculales magnoliids 98 56 Canellales “Survivors” 100 ANGIOSPERMS BASAL 75 Piperales 100 52 78 Magnoliales 100 98 Laurales 100 98 Chloranthaceae 100 98 Ceratophyllaceae 57 monocots 100 Trimeniaceae 91 100 Schisandraceae 100 Austrobaileyaceae 100 100 Nymphaeaceae Amborellaceae extant gymnosperms 100 Amborella Cabomba Amborella trichopoda Poster Child for the angiosperms • Shrub, cloud forests of New Caledonia • Small flower • Spiral arrangement of parts • Moderate number of parts • Undifferentiated perianth (“tepals”) Sandy Floyd Early-branching Angiosperms closed carpels Rest of angiosperms vessels Austrobaileyales Illicium Water Lilies Cabomba Amborella Summary of Angiosperm Phylogeny Eudicots (75%) Monocots (22%) Easy to Magnoliids resolve Ceratophyllaceae Mesangiosperms Chloranthaceae Austrobaileyales Water lilies Amborella Using complete chloroplast genome sequences to resolve recalcitrant nodes in deep-level angiosperm phylogenetics Michael J. Moore1*, Charles D. Bell2, Pamela S. Soltis3, & Douglas E. Soltis1 1Dept. of Botany, University of Florida 2Dept. of Ecology & Evolutionary Biology, Tulane University 3Florida Museum of Natural History *[email protected] 454 Sequencing Lots of short reads Very high coverage 20 mil+ bases in 4 hrs From Margulies et al., 2005 AToL: 30 Plastid Genomes Sequenced Ceratophyllum Ceratophyllaceae Liquidambar Altingiaceae Tradescantia Commelinaceae Heuchera Saxifragaceae Vallisneria Hydrocharitaceae StaphyleaStaphyleaceae Lilium Liliaceae Bulnesia Zygophyllaceae Spathiphyllum Araceae Euonymus Celastraceae Nandina Berberidaceae Oxalis Oxalidaceae Meliosma Meliosmaceae Ficus Moraceae Nelumbo Nelumonaceae Quercus Fagaceae Platanus Platanaceae Cornus Cornaceae Trochodendron Trochodendraceae Rhododendron Ericaceae Gunnera Gunneraceae Ehretia Boraginaceae Berberidopsis Berberidopsidaceae Aucuba Aucubaceae Dillenia Dilleniaceae Nerium Apocynaceae PlumbagoPlumbaginaceae Antirrhinum Plantaginaceae Phoradendron Viscaceae Ilex Aquifoliaceae Ximenia Olacaceae Lonicera Caprifoliaceae Moore et al. Angiosperms: the “Big Bang” eudicot Monocots plus Eudicots + Ceratophyllum Ceratophyllum Diversified in monocot <5 million years Chloranthaceae magnoliid 61 genes Eudicots • 75% of all angiosperm species • Triaperturate pollen • Origin of clade 125 mya • Relationships among major clades unclear Flowering plants:the“Dirty Dozen” FIG. 1B Amborellaceae FIG. 1A Nymphaeaceae Austrobaileyales monocots Ceratophyllaceae Chloranthaceae magnoliids Ranunculales Trochodendraceae Buxaceae .l. 1. BASALANGIOSPERMS Proteales 4. SAXIFRAGALES Sabiaceae Gunnerales Saxifragaceae alliance 2. BASALEUDICOTS Crassulaceae alliance Altingiaceae Cercidiphyllaceae Peridiscaceae Hamamelidaceae Daphniphyllaceae Paeoniaceae Gisekiaceae Nyctaginaceae 5. CARYOPHYLLIDS Phytolaccaceae Sarcobataceae Aizoaceae Molluginaceae Basellaceae Didiereaceae Halophytaceae Cactaceae Portulacaceae Stegnospermnataceae Achatocarpaceae Assembling the Tree of Life of Tree Assembling the Amaranthaceae Caryophyllaceae Asteropeiaceae Physenaceae Simmondsiaceae Polygonales Rhabdodendraceae Dilleniaceae asterids e Myrtales Vitaceae Crossosomatales s. l. Geraniales eurosid II (malvids) Oxalidales 3. COREEUDICOTS Huaceae Goupiaceae Euphorbiaceae Putranjivaceae Caryocaraceae Linaceae Malpighiaceae Elatinaceae Clusiaceae Podostemaceae Bonnetiaceae Hypericaceae Ochnaceae s.l. Violaceae Passifloraceae s.l. Chrysobalanaceae s.l. Balanopaceae Achariaceae Salicaceae 6. BASALROSIDS Humiriaceae Irvingiaceae s Lacistemataceae ae Ctenolophonaceae Pandaceae Phyllanthaceae 7. BASALFABIDS Picrodendraceae Lophopyxidaceae Ixonanthaceae Erythroxylaceae 8. MALPIGHIALES Rhizophoraceae Zygophyllaceae Krameraceae Celastrales Rosales Fabales Fagales e Cucurbitales Santalales Berberidopsidales rosids Resolving the saxifragales eudicots: asterids a “sneak peak” caryophyllids eudicots santalales pp BS Resolving the Rosids: 12 genes Rosid II 100% Bootstrap (malvid) Rosid I (fabid) 100% Bootstrap GARLI Rapid rise of the rosids: diversification rate shifts Bursts in diversification correspond to rapid rise of angiosperm dominated forests 83 - 112 mya Angiosperm summary •With enough data (plastid genome) deep level problems can be solved •Initial
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  • 584 *Monocots, Basal Angiosperms, Chloranthales, Magnoliids

    584 *Monocots, Basal Angiosperms, Chloranthales, Magnoliids

    584 584 584 *Monocots, basal angiosperms, Chloranthales, magnoliids Subdivisions are added for monocots, basal angiosperms, Chloranthales, magnoliids together; for monocots alone See Manual at 583–585 vs. 600; also at 583–584 .2 *Basal angiosperms, Chloranthales, magnoliids Standard subdivisions are added for basal angiosperms, Chloranthales, magnoliids together; for basal angiosperms alone .22 *Amborellales Class here Amborellaceae .23 *Nymphaeales Including Cabombaceae, Hydatellaceae, Nymphaeaceae Including water lilies .24 *Austrobaileyales Including Austrobaileyaceae, Schisandraceae, Trimeniaceae Including magnolia vine, star anise .26 *Chloranthales Class here Chloranthaceae .28 *Magnoliids .282 *Canellales Including Canellaceae, Winteraceae Including wild cinnamon, winter’s barks .284 *Piperales Including Aristolochiaceae, Hydnoraceae, Saururaceae Including birthwort, black pepper, lizard’s-tails, peperomias Class here Piperaceae Class here peppers Class comprehensive works on peppers in 583.9593 .286 *Magnoliales Including Annonaceae, Magnoliaceae, Myristicaceae Including cherimoya, cucumber tree, custard apples, lancewoods, mace, magnolias, michelias, nutmegs, papaws, tulip tree, yellow poplar See also 583.78 for papaws of family Caricaceae * *Add as instructed under 583–588 1 584 Dewey Decimal Classification 584 .288 *Laurales Including Atherospermataceae, Calycanthaceae, Hernandiaceae, Monimiaceae, Siparunaceae Including avocados, bay laurel, California laurel, cinnamon, Oregon myrtle, sassafras, sweet bay; comprehensive works

  • Angiosperm Phylogeny Inferred from Sequences of Four Mitochondrial Genes 1Yin-Long QIU∗ 1Libo LI 1Bin WANG 1,2Jia-Yu XUE 1Tory A

    Journal of Systematics and Evolution 48 (6): 391–425 (2010) doi: 10.1111/j.1759-6831.2010.00097.x Angiosperm phylogeny inferred from sequences of four mitochondrial genes 1Yin-Long QIU∗ 1Libo LI 1Bin WANG 1,2Jia-Yu XUE 1Tory A. HENDRY 1Rui-Qi LI 1Joseph W. BROWN 1Ya n g L I U 1Geordan T. HUDSON 3Zhi-Duan CHEN 1(Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA) 2(School of Life Sciences, Nanjing University, Nanjing 210093, China) 3(Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China) Abstract An angiosperm phylogeny was reconstructed in a maximum likelihood analysis of sequences of four mitochondrial genes, atp1, matR, nad5, and rps3, from 380 species that represent 376 genera and 296 families of seed plants. It is largely congruent with the phylogeny of angiosperms reconstructed from chloroplast genes atpB, matK, and rbcL, and nuclear 18S rDNA. The basalmost lineage consists of Amborella and Nymphaeales (including Hydatellaceae). Austrobaileyales follow this clade and are sister to the mesangiosperms, which include Chloranthaceae, Ceratophyllum, magnoliids, monocots, and eudicots. With the exception of Chloranthaceae being sister to Ceratophyllum, relationships among these five lineages are not well supported. In eudicots, Ranunculales, Sabiales, Proteales, Trochodendrales, Buxales, Gunnerales, Saxifragales, Vitales, Berberidopsidales, and Dilleniales form a basal grade of lines that diverged before the diversification of rosids and asterids. Within rosids, the COM (Celastrales–Oxalidales–Malpighiales) clade is sister to malvids (or rosid II), instead of to the nitrogen-fixing clade as found in all previous large-scale molecular analyses of angiosperms. Santalales and Caryophyllales are members of an expanded asterid clade.