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Plant Evolution an Introduction to the History of Life
Plant Evolution An Introduction to the History of Life KARL J. NIKLAS The University of Chicago Press Chicago and London CONTENTS Preface vii Introduction 1 1 Origins and Early Events 29 2 The Invasion of Land and Air 93 3 Population Genetics, Adaptation, and Evolution 153 4 Development and Evolution 217 5 Speciation and Microevolution 271 6 Macroevolution 325 7 The Evolution of Multicellularity 377 8 Biophysics and Evolution 431 9 Ecology and Evolution 483 Glossary 537 Index 547 v Introduction The unpredictable and the predetermined unfold together to make everything the way it is. It’s how nature creates itself, on every scale, the snowflake and the snowstorm. — TOM STOPPARD, Arcadia, Act 1, Scene 4 (1993) Much has been written about evolution from the perspective of the history and biology of animals, but significantly less has been writ- ten about the evolutionary biology of plants. Zoocentricism in the biological literature is understandable to some extent because we are after all animals and not plants and because our self- interest is not entirely egotistical, since no biologist can deny the fact that animals have played significant and important roles as the actors on the stage of evolution come and go. The nearly romantic fascination with di- nosaurs and what caused their extinction is understandable, even though we should be equally fascinated with the monarchs of the Carboniferous, the tree lycopods and calamites, and with what caused their extinction (fig. 0.1). Yet, it must be understood that plants are as fascinating as animals, and that they are just as important to the study of biology in general and to understanding evolutionary theory in particular. -
Number of Living Species in Australia and the World
Numbers of Living Species in Australia and the World 2nd edition Arthur D. Chapman Australian Biodiversity Information Services australia’s nature Toowoomba, Australia there is more still to be discovered… Report for the Australian Biological Resources Study Canberra, Australia September 2009 CONTENTS Foreword 1 Insecta (insects) 23 Plants 43 Viruses 59 Arachnida Magnoliophyta (flowering plants) 43 Protoctista (mainly Introduction 2 (spiders, scorpions, etc) 26 Gymnosperms (Coniferophyta, Protozoa—others included Executive Summary 6 Pycnogonida (sea spiders) 28 Cycadophyta, Gnetophyta under fungi, algae, Myriapoda and Ginkgophyta) 45 Chromista, etc) 60 Detailed discussion by Group 12 (millipedes, centipedes) 29 Ferns and Allies 46 Chordates 13 Acknowledgements 63 Crustacea (crabs, lobsters, etc) 31 Bryophyta Mammalia (mammals) 13 Onychophora (velvet worms) 32 (mosses, liverworts, hornworts) 47 References 66 Aves (birds) 14 Hexapoda (proturans, springtails) 33 Plant Algae (including green Reptilia (reptiles) 15 Mollusca (molluscs, shellfish) 34 algae, red algae, glaucophytes) 49 Amphibia (frogs, etc) 16 Annelida (segmented worms) 35 Fungi 51 Pisces (fishes including Nematoda Fungi (excluding taxa Chondrichthyes and (nematodes, roundworms) 36 treated under Chromista Osteichthyes) 17 and Protoctista) 51 Acanthocephala Agnatha (hagfish, (thorny-headed worms) 37 Lichen-forming fungi 53 lampreys, slime eels) 18 Platyhelminthes (flat worms) 38 Others 54 Cephalochordata (lancelets) 19 Cnidaria (jellyfish, Prokaryota (Bacteria Tunicata or Urochordata sea anenomes, corals) 39 [Monera] of previous report) 54 (sea squirts, doliolids, salps) 20 Porifera (sponges) 40 Cyanophyta (Cyanobacteria) 55 Invertebrates 21 Other Invertebrates 41 Chromista (including some Hemichordata (hemichordates) 21 species previously included Echinodermata (starfish, under either algae or fungi) 56 sea cucumbers, etc) 22 FOREWORD In Australia and around the world, biodiversity is under huge Harnessing core science and knowledge bases, like and growing pressure. -
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 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. -
Chlorophyta Is a Division of Green Algae, Informally Called
Chlorophyta is a division of green algae, informally waters of the Sargasso Sea. Many brown algae, such as called chlorophytes. The name is used in two very members of the order Fucales, commonly grow along different senses so that care is needed to determine the rocky seashores. Some members of the class are used as use by a particular author. In older classification food for humans. systems, it refers to a highly paraphyletic group of all Worldwide there are about 1500–2000 species of brown the green algae within the green plants (Viridiplantae), algae.[4] Some species are of sufficient commercial and thus includes about 7,000 species [4] [5] of mostly importance, such as Ascophyllum nodosum , that they aquatic photosynthetic eukaryotic organisms. Like the have become subjects of extensive research in their own land plants (bryophytes and tracheophytes), green algae right.[5] [4] contain chlorophylls a and b, and store food as starch Brown algae belong to a very large group, the in their plastids. Heterokontophyta, a eukaryotic group of organisms In newer classifications, it refers to one of the two distinguished most prominently by having chloroplasts clades making up the Viridiplantae, which are the surrounded by four membranes, suggesting an origin chlorophytes and the streptophytes or charophytes.[6][7] from a symbiotic relationship between a basal In this sense it includes only about 4,300 species.[3] eukaryote and another eukaryotic organism. Most brown algae contain the pigment fucoxanthin, which is responsible for the distinctive greenish-brown color that The red algae, or Rhodophyta ( / r o ʊ ˈ d ɒ f ɨ t ə / or / gives them their name. -
Aquatic and Wet Marchantiophyta, Order Metzgeriales: Aneuraceae
Glime, J. M. 2021. Aquatic and Wet Marchantiophyta, Order Metzgeriales: Aneuraceae. Chapt. 1-11. In: Glime, J. M. Bryophyte 1-11-1 Ecology. Volume 4. Habitat and Role. Ebook sponsored by Michigan Technological University and the International Association of Bryologists. Last updated 11 April 2021 and available at <http://digitalcommons.mtu.edu/bryophyte-ecology/>. CHAPTER 1-11: AQUATIC AND WET MARCHANTIOPHYTA, ORDER METZGERIALES: ANEURACEAE TABLE OF CONTENTS SUBCLASS METZGERIIDAE ........................................................................................................................................... 1-11-2 Order Metzgeriales............................................................................................................................................................... 1-11-2 Aneuraceae ................................................................................................................................................................... 1-11-2 Aneura .......................................................................................................................................................................... 1-11-2 Aneura maxima ............................................................................................................................................................ 1-11-2 Aneura mirabilis .......................................................................................................................................................... 1-11-7 Aneura pinguis .......................................................................................................................................................... -
Mitochondrial Genomes of the Early Land Plant Lineage
Dong et al. BMC Genomics (2019) 20:953 https://doi.org/10.1186/s12864-019-6365-y RESEARCH ARTICLE Open Access Mitochondrial genomes of the early land plant lineage liverworts (Marchantiophyta): conserved genome structure, and ongoing low frequency recombination Shanshan Dong1,2, Chaoxian Zhao1,3, Shouzhou Zhang1, Li Zhang1, Hong Wu2, Huan Liu4, Ruiliang Zhu3, Yu Jia5, Bernard Goffinet6 and Yang Liu1,4* Abstract Background: In contrast to the highly labile mitochondrial (mt) genomes of vascular plants, the architecture and composition of mt genomes within the main lineages of bryophytes appear stable and invariant. The available mt genomes of 18 liverwort accessions representing nine genera and five orders are syntenous except for Gymnomitrion concinnatum whose genome is characterized by two rearrangements. Here, we expanded the number of assembled liverwort mt genomes to 47, broadening the sampling to 31 genera and 10 orders spanning much of the phylogenetic breadth of liverworts to further test whether the evolution of the liverwort mitogenome is overall static. Results: Liverwort mt genomes range in size from 147 Kb in Jungermanniales (clade B) to 185 Kb in Marchantiopsida, mainly due to the size variation of intergenic spacers and number of introns. All newly assembled liverwort mt genomes hold a conserved set of genes, but vary considerably in their intron content. The loss of introns in liverwort mt genomes might be explained by localized retroprocessing events. Liverwort mt genomes are strictly syntenous in genome structure with no structural variant detected in our newly assembled mt genomes. However, by screening the paired-end reads, we do find rare cases of recombination, which means multiple concurrent genome structures may exist in the vegetative tissues of liverworts. -
Shaping the Evolutionary Tree of Green Plants: Evidence from the GST Family
www.nature.com/scientificreports OPEN Shaping the evolutionary tree of green plants: evidence from the GST family Received: 15 June 2017 Francesco Monticolo1, Chiara Colantuono1 & Maria Luisa Chiusano1,2 Accepted: 5 October 2017 Glutathione-S-transferases (GSTs) are encoded by genes belonging to a wide ubiquitous family Published: xx xx xxxx in aerobic species and catalyze the conjugation of electrophilic substrates to glutathione (GSH). GSTs are divided in diferent classes, both in plants and animals. In plants, GSTs function in several pathways, including those related to secondary metabolites biosynthesis, hormone homeostasis, defense from pathogens and allow the prevention and detoxifcation of damage from heavy metals and herbicides. 1107 GST protein sequences from 20 diferent plant species with sequenced genomes were analyzed. Our analysis assigns 666 unclassifed GSTs proteins to specifc classes, remarking the wide heterogeneity of this gene family. Moreover, we highlighted the presence of further subclasses within each class. Regarding the class GST-Tau, one possible subclass appears to be present in all the Tau members of ancestor plant species. Moreover, the results highlight the presence of members of the Tau class in Marchantiophytes and confrm previous observations on the absence of GST-Tau in Bryophytes and green algae. These results support the hypothesis regarding the paraphyletic origin of Bryophytes, but also suggest that Marchantiophytes may be on the same branch leading to superior plants, depicting an alternative model for green plants evolution. Glutathione-S-transferases (GSTs) are enzymes encoded by a ubiquitous gene family in aerobic species, able to conjugate electrophilic xenobiotics and endogenous cell components with glutathione (GSH)1. -
A Brief History of Plants by Luke Wallace
A Brief History of Plants by Luke Wallace Let us skip the first two and a half their success on land. Today, these plants new group, the seed-bearing gymnosperms, billion years of the Earth’s history from only survive in the groups known as the Club came to dominate. Placed in this group is when organic compounds in our early mosses, Whisk fern, Horsetails and, a group I Ginkophyta (Ginkgo biloba being the only Evidence shows that atmosphere made the transition to single am sure we are all familiar with, the Ferns. extant member of this group), Gnetophyta, during the Permian celled organisms via the creation of It is in a small number of Fern species that Cycads and, of course, the Conifers. For the nucleotides, RNA and DNA. For the sake of era a new group, we first see the production of separate male most part, gymnosperms did relatively well brevity, we will also have to gloss over the the seed-bearing sperm cells and female egg cells, the earliest throughout the Permian, Triassic and Jurassic adaptive radiation of early multicellular known plant lineage capable of this biological periods, exhibiting much more diversity and gymnosperms, organisms that would eventually lead phenomenon. This is thought to be crucial abundance than we see now. to the colonisation of the land 425 - 475 came to dominate. to the evolution of seed-bearing plants. million years ago. These stories could not However, during the Jurassic, another group of Placed in this group Simply put, up until this point plants produced be done justice here! plants were rapidly growing in dominance and identical sex cells and relied on water to by the Cretaceous this new plant superpower is Ginkophyta, Mosses, Liverworts and Hornworts (known bring these together. -
Plant Evolution and Diversity B. Importance of Plants C. Where Do Plants Fit, Evolutionarily? What Are the Defining Traits of Pl
Plant Evolution and Diversity Reading: Chap. 30 A. Plants: fundamentals I. What is a plant? What does it do? A. Basic structure and function B. Why are plants important? - Photosynthesize C. What are plants, evolutionarily? -CO2 uptake D. Problems of living on land -O2 release II. Overview of major plant taxa - Water loss A. Bryophytes (seedless, nonvascular) - Water and nutrient uptake B. Pterophytes (seedless, vascular) C. Gymnosperms (seeds, vascular) -Grow D. Angiosperms (seeds, vascular, and flowers+fruits) Where? Which directions? II. Major evolutionary trends - Reproduce A. Vascular tissue, leaves, & roots B. Fertilization without water: pollen C. Dispersal: from spores to bare seeds to seeds in fruits D. Life cycles Æ reduction of gametophyte, dominance of sporophyte Fig. 1.10, Raven et al. B. Importance of plants C. Where do plants fit, evolutionarily? 1. Food – agriculture, ecosystems 2. Habitat 3. Fuel and fiber 4. Medicines 5. Ecosystem services How are protists related to higher plants? Algae are eukaryotic photosynthetic organisms that are not plants. Relationship to the protists What are the defining traits of plants? - Multicellular, eukaryotic, photosynthetic autotrophs - Cell chemistry: - Chlorophyll a and b - Cell walls of cellulose (plus other polymers) - Starch as a storage polymer - Most similar to some Chlorophyta: Charophyceans Fig. 29.8 Points 1. Photosynthetic protists are spread throughout many groups. 2. Plants are most closely related to the green algae, in particular, to the Charophyceans. Coleochaete 3. -
Aquatic and Wet Marchantiophyta, Class Jungermanniopsida, Orders Porellales: Jubulineae, Part 2
Glime, J. M. 2021. Aquatic and Wet Marchantiophyta, Class Jungermanniopsida, Orders Porellales: Jubulineae, Part 2. Chapt. 1-8. In: 1-8-1 Glime, J. M. (ed.). Bryophyte Ecology. Volume 4. Habitat and Role. Ebook sponsored by Michigan Technological University and the International Association of Bryologists. Last updated 11 April 2021 and available at <http://digitalcommons.mtu.edu/bryophyte-ecology/>. CHAPTER 1-8 AQUATIC AND WET MARCHANTIOPHYTA, CLASS JUNGERMANNIOPSIDA, ORDER PORELLALES: JUBULINEAE, PART 2 TABLE OF CONTENTS Porellales – Suborder Jubulineae ........................................................................................................................................... 1-8-2 Lejeuneaceae, cont. ........................................................................................................................................................ 1-8-2 Drepanolejeunea hamatifolia ................................................................................................................................. 1-8-2 Harpalejeunea molleri ........................................................................................................................................... 1-8-7 Lejeunea ............................................................................................................................................................... 1-8-12 Lejeunea aloba .................................................................................................................................................... -
Plant Diversity Ecol 182 – 3-1-2007 Posted on Web – 2-28-07 at 5:30 Pm Summary from Last Time
Plant Diversity Ecol 182 – 3-1-2007 Posted on web – 2-28-07 at 5:30 pm Summary from last time • We talked about? The Tracheophytes •A leaf is a flattened photosynthetic structure emerging laterally from a main axis or stem and possessing true vascular tissue. • Two leaf types: microphylls and megaphylls. •The microphyll has a single vascular strand that has departed from the stem without disturbing the stem’s vascular structure. – Club mosses have microphylls. – Microphylls may have evolved from sterile sporangia. Figure 29.13a The Evolution of Leaves The Tracheophytes • The megaphyll is larger, and more complex found in ferns and seed plants. • May have arose from flattening of stems and development of overtopping (one branch differentiates from and extends beyond rest). Introducing the Tracheophytes • Plants that bear a single type of spore are said to be homosporous. – The most ancient tracheophytes were all homosporous. – Both the gametophyte and the sporophyte are independent and usually photosynthetic. – A single type of gametophyte bears both female and male reproductive organs. Introducing the Tracheophytes • Plants with two distinct types of spores evolved later, and are said to be heterosporous. – In heterosporous plants, the megaspore develops into a larger, specifically female gametophyte (megagametophyte). – The microspore develops into the smaller, male gametophyte (microgametophyte). • Heterospory evolved independently and repeatedly, suggesting that it affords selective advantages. Figure 29.14a & b Homospory and Heterospory The Surviving Nonseed Tracheophytes • The club mosses (phylum Lycophyta) have microphylls, exhibit apical growth, and have roots that branch dichotomously. • Sporangia in many Lycophyta are contained within structures called strobili (clusters of spore-bearing leaves) – There are both homosporous and heterosporous species.