Progress in reconstructing the green 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 Green plant phylogeny: 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 is well-supported by DNA data

From Kenrick and Crane 1997 Phylogeny of tracheophytes: Monilophytes Unexpected sister-group

Psilotales Ophioglossales Equisetophytes Fossils from the

strobilus 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 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

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--Charles Darwin letter to J. D. Hooker 22 July 1879 Angiosperms: Archaefructus

• ~127 mya • China • Spiral/whorled carpels • Paired • Aquatic

First ?

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 lineages Angiosperm phylogeny--3 gene

100 Fig. 2.3 60 100 fabids eurosid I 68 100 98 77 100 62 51 100 99 malvids eurosid II 100 99 51 95 100 CORE NO 100 Model organism 100 100

Geraniales EUDICOTS 80 Arabidopsis “DICOTS”! 98 lamiids euasterid I 100 84 99 96 56 100

55 campanulids euasterid II 89 94 97 86 100 88 96 100 99 98 98 87 100 100 100

Gunnerales EUDICOTS DIVERGING EARLY- 75 59 Buxaceae Antirrhinum 100 100 84 100 Sabiaceae 100

Ranunculales 98 56 “Survivors” 100 ANGIOSPERMS BASAL 75 100 52 78 100 98 100 98 100 98 57 monocots 100 Trimeniaceae 91 100 Schisandraceae 100 Austrobaileyaceae 100 100 Nymphaeaceae Amborellaceae extant gymnosperms 100 Cabomba Amborella trichopoda Poster Child for the angiosperms

• , 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 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

Diversified in monocot <5 million years

Chloranthaceae magnoliid 61 genes Eudicots

• 75% of all angiosperm species • Triaperturate • Origin of clade 125 mya • Relationships among major unclear Flowering plants:the“Dirty Dozen” FIG. 1B

Amborellaceae FIG. 1A Nymphaeaceae Austrobaileyales monocots Ceratophyllaceae Chloranthaceae magnoliids Trochodendraceae Buxaceae .l. 1. BASALANGIOSPERMS Proteales 4. SAXIFRAGALES Sabiaceae 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 Amaranthaceae Caryophyllaceae Asteropeiaceae Physenaceae Simmondsiaceae Polygonales Rhabdodendraceae Dilleniaceae asterids e Myrtales Crossosomatales s. l. 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 rise of angiosperms was not rapid; the initial rapid radiation came later

•Angiosperms characterized by a series of rapid radiations Reclassifying the angiosperms

Angiosperm Phylogeny Group (APG) APG classification QuickTime?and a QuickTime?and a TIFF (Uncompressed) decompressor TIFF (Uncompressed) decompressor are needed to see this picture. are needed to see this picture.

Recent advances--the flower

Angiosperm phylogeny + Floral developmental genetics

“Evo-Devo”

Evo-devo = permits rapid advances in understanding floral evolution Molecular Genetics of Flower Development

Arabidopsis Antirrhinum

mutant

identify gene

ab Elliot Meyerowitz and Enrico Coen Mutant phenotype of B-function genes (b) Compared to wild type (a) Origin and Diversification of The Flower

100 Fagales Fig. 2.3 60 100 Cucurbitales fabids eurosid I 68 100 Rosales 98 Fabales 77 Zygophyllales 100 Celastrales 62 rosids Oxalidales 51 100 Malpighiales 99 malvids eurosid II Sapindales 100 99 51 Malvales 95 100 Brassicales EUDICOTS CORE 100 Crossosomatales Model organism 100 Myrtales 100

Geraniales EUDICOTS 80 Arabidopsis Saxifragales 98 Lamiales lamiids euasterid I 100 Solanales 84 99 96 Gentianales 56 100 Garryales

55 campanulids euasterid II 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

g P P P StSt P C St St St StSt Eudicots PP P Core- Fagales Walnuts, chestnut Se Se Cucurbitales Squash eudicots Rosales Apples, strawberries Fabales Legumes G f Se Zygophyllales Creosote plant P Celastrales PP P Oxalidales Star fruit C Malpighiales Passion fruit Se Sapindales Citrus, cashews P Malvales Cotton, cocoa Classic Brassicales Arabidopsis, mustard B Crossosomatales e ABC model Myrtales Pomegranate T Gernaliales AC StSt T T Saxifragales Gooseberry St St Lamiales Antirrhinum, olive C is derived! St St Solanales Tomato, green pepper T T T Gentianales Coffee St T Garryales Asterales Sunflower Dipsacales Elderberry d T T Apiales Dill, fennel T Aquifoliales T Cornales T T Ericales Blueberry, cranberry Berberidopsidales Santalales Caryophyllales Buckwheat, quinoa Gunnerales c T Trochodendrales B T T T Proteales Macadamia nut T Sabiaceae AC T Ranunculales Poppy T Chloranthales Magnoliales Nutmeg, cherimoya Laurales Avocado b T Piperales Black pepper T Winterales St C T Monocots Grains (Oryza), palms, tulip T Ceratophyllales Illiciaceae Star anise T Schisandraceae Kim et al. Austrobaileyaceae B Nymphaeaceae a Amborellaceae AC CC T Gymnosperms C C T Sm

T General take home message

The “Abominable mystery” is far from solved, but progress is being made!

Charles Darwin British Naturalist

1809 -1882 General take home message “Nothing in Biology Makes Sense Except in the Light of Evolution”

Things make a lot more sense in light of a phylogeny

Theodosius Dobzhansky (1900-1975) Invest time and $ to study the hang-gliders of evolution Thank you

• NSF Plant Genome Program

• NSF AToL program

Amborella trichopoda Baill. female flower Photo by Sangtae Kim QuickTime?and a QuickTime?and a TIFF (Uncompressed) decompressor TIFF (Uncompressed) decompressor are needed to see this picture. are needed to see this picture.

Acknowledgements

postdocs - Andre Chanderbali, Sangtae Kim, Matyas Buzgo students - Sam Brockington, Mi-Jeong Yoo, Jin Koh ABC model (Coen and Meyeorowitz, 1991): Genetic Control of Floral Organ Identity in Model Plants

B A C

A A+B B+C C Carpel

Carpel Petal Stamen

Sepal MADS-box Gene Phylogeny * New basal sequences * *Homologs of A,B,C genes *

*

* * Amborella: B-function genes

CLASSIC ABC MODEL STAMINODE Whorl 1 2 3 4 B A C

Organ type sepal petal stamen carpel 1.2 STAMEN 1. 2 1

1 0.8

0.8 0.6

0.6 0.4 TEPAL 0.4

0.2 0.2

0 TE ST SD CA 18S 0 TE ST SD CA LEAF Internal control 12345 12 345

Expected band AP3 PI CARPEL

B-class genes expressed throughout all floral organs in Amborella Kim et al. (2005) The Perianth of Amborella

Gradual transition from bracts to perianth to stamens Amborella: developmental morphology

• Gradual transition from bracts to tepals

• Gradual transition from tepals to stamens

• Developmental similarities between stamens and carpels

Gradual transition from outer to inner organs Floral Genome Project: Questions 1. Are homologs of ABC genes found in ? YES 2. If expression implies function, does the ABC model hold for basal angiosperms? Floral Genome Project: Questions 1. Are homologs of ABC genes found in basal angiosperms? 2. If expression implies function, does the ABC model hold for basal angiosperms?

no; expression is consistent with ABC model but broader (B class); an alternative model is needed Implications for Floral Genetics & Evolution: Fading Borders Model

ABC model B

A C

Sliding boundaries (Kramer et al.) B

A C

Fading borders B

A C

"reproductive bract-like, petaloid staminode stamen carpel placenta, shoot" sepaloid integument Euphyllophytes: synapomorphies •Multiflagellate sperm

•leaves = megaphyll (“true leaves”)

•Overtopping (main stem and side branches)

•Chloroplast DNA inversion