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Home , Armen Takhtajan, Red algae

BIOL 317: Identification and Classification Summer 2015 - Notes

Week 1 – Tuesday Course info

Course objectives

What is a plant? • Definition varies, but the one we will use in this defines “” as the green plants or Viridiphytes • Green plants have (organelles in which occurs), which originated as independent that were incorporated into a eukaryotic through endosymbiosis. This makes them autotrophs – they produce their own food. • Fungi and are - they must eat other organisms as food - and are very distantly related to plants. • Chloroplasts originated once in the ancestor of green plants and other photosynthetic organisms, like brown , , , and . • Green plants share a unique suite of traits. We will not focus on learning them, but they include biochemical and anatomical features like chlorophyll b, starch storage, stellate flagella base, and genomic similarities. of plants (up to seed plants) • Viridiphytes include the and land plants • Land plants or include the and vascular plants • Bryophytes, or non-vascular plants, include liverworts, , and • Living on land, versus in water, presented a new set of challenges: dessication, difficulty in exchanging nutrients between the body and the environment, less support in holding up the body • A suite of innovations evolved in the ancestor to land plants that enabled them to deal with these challenges § cuticle - waxy layer on body surface reduces water loss § sporopollenin - resistant chemical makes up wall of propagules that allow them to be dispersed through air § retained embryo - zygote formed after fertilization is retained on the mother plant, where it is protected and nurtured § stomata - occurs in some bryophytes (mosses and hornworts) and all vascular plants - holes on body surface which can be opened or closed allow for controlled gas exchange between the body interior and the environment • Vascular plants or Tracheophytes include the seedless plants and seed plants • Seedless plants include (club mosses) and monilophytes (, horsetails) • Vascular plants were able to grow larger and more complex with the evolution of: § tracheids - specialized cells for water transport, with elongate shape and thickened cell walls. They form strands in bundles or rings, called xylem tissue, which conduct water throughout the plant body and give it structural support § megaphylls - occurs in monilophytes and all seed plants – usually large, complex leaves with multiple vascular strands. Lycophytes have microphylls, leaves with a single vascular strand • Seed plants or include the and angiosperms • Gymnosperms include the , , ginkgo, and gnetophytes. • Seed plants became less dependent on water for reproduction with the evolution of: § pollen – -producing structure is encased in a protective sporopollenin wall, which allows it to be dispersed in air or by animals to the female organ of other plants § seeds - dormant embryo is encased in a protective coat and provided with food, allowing it to be dispersed

Systematics - study of biological diversity and its relationships - science of organizing biological diversity into groups (classification) and naming those groups (nomenclature) • Classification • organizes understanding of biological diversity and facilitates communication • hierarchical system - has nested ranks or levels • (most inclusive) /Division Class Family Genus Species (least inclusive) • example: in the plant evolution scheme above, the gymnosperms and angiosperms are groups nested within the group spermatophytes; the spermatophytes, lycophytes, and monilophytes are nested within the tracheophytes; the tracheophytes and bryophytes are nested within the embryophytes; the embryophytes and green algae are nested within the viridiphytes • additional ranks can be inserted between the traditional ranks or below the rank of species, eg. superorder, subfamily, subspecies. The number of ranks is potentially limitless. • in plant systematics literature, the ranks of species, genus, family, and order have traditionally been more important • - named group at any rank • eg. Solanales is a taxon at the rank of order. • Nomenclature • Common names are not an efficient or effective means of communication in science • same name applies to different things, eg. football, yam • different names apply to same thing, eg. sweet potato, yam • Scientific names should be: • systematic - each thing gets one accepted name; each name is unique • standardized - rules govern how a name is created • stable - the same name is used for the same thing over time and in different situations • Species names • binomial nomenclature - two-part name: Genus specific-epithet § eg. Ipomoea batatas (sweet potato) - Ipomoea is genus, batatas is specific epithet • genus part is capitalized; specific epithet is in lower-case • should be italicized or underlined • Genus names • Genus, eg. Ipomoea • should be capitalized, and italicized or underlined • Family names • -aceae, eg. Convolvulaceae • should be capitalized; usually has ending -aceae • Order names • -ales, eg. Solanales • should be capitalized; usually has ending -ales

Week 1 - Thursday History of plant systematics • Humans have needed to identify and categorize plants across all cultures and since even before the beginning of civilization • The modern science of plant systematics comes from a European legacy • Ancient Greek and Roman scholars were among the first to systematically study and describe plants • Theophrastus (c. 371-287 BC) - his multi-volume Historia Plantarum described many aspects of plant growth, structure, and use, and categorized plants according to their growth form • Dioscorides (c. 40-90) - his De Materia Medica described plants and their medicinal uses, and was followed for hundreds of years in European and the Middle Eastern medicine • Beginning in the 15th century, during the Age of Discovery and Exploration, the introduction of new plants into Europe spurred renewed interest in studying plant diversity • John Ray (1627-1705) - categorized plants using careful observation of many morphological traits in his Historia Plantarum • during this period, species were given long descriptive names • Carl Linnaeus (1707-1778) - "father of modern taxonomy" • popularized binomial nomenclature for species names and hierarchical classification systems • first to consistently use binomical nomenclature in his book describing all known plant species Species Plantarum (1753) • classified plants in nested ranks according to number and structure of sexual parts (classes defined by male parts, orders defined by female parts) – called the sexual system - in his book Systema Naturae (1735) • example of artificial classification system - does not reflect evolutionary relationships • Charles Darwin (1809-1882) - described and explained evolution in Origin of Species (1859) • all is related through descent with modification from common ancestors • evolutionary relationships between organisms present a natural way to classify life in a hierarchical manner • "all true classification is genealogical" • Modern classification systems • authority-based classification systems • depend on observations, experience, and intuition of expert • interpretation of how traits reflect relationships may differ • often tried to classify groups from primitive to derived • Some influential examples: § George Bentham (1800-1884) and Joseph D. Hooker (1817-1911) § Adolf Engler (1844-1930) - system still used to organize many herbaria § Charles Bessey (1845-1915) § (1910-2009) § (1919-1992) - co-author of several floras, including Flora of the Pacific Northwest, which is organized according to his system • phylogenetic classification • data and methods used are transparent and objective • hierarchical grouping of taxa according to phylogenetic relationships § eg. Angiosperm Phylogeny Group (1998, 2003, 2009)

Practice of plant systematics - i.e. phylogenetic classification • After choosing a group to study, conduct background research - what is currently known? • Flora - published treatment of all plants in a geographic area • Monograph - published treatment of all species in a taxon • Herbarium - library of preserved plant specimens, usually pressed and dried, with associated collection information • Collect data with which to compare taxa in group • some terms: • character - shared trait - eg. flower color • character state - form of trait - eg. white flower color, yellow flower color • homologous character (homology) - trait shared due to inheritance from common ancestor • analogous character (analogy/convergence/homoplasy) - trait that evolved multiple times independently • collecting data on states of homologous characters for each taxon is the goal • data used in modern studies are usually genetic sequences, but can also include morphology, anatomy, chemistry, etc. • data can be gathered from herbarium specimens or live specimens growing wild in the field or cultivated in botanical gardens • Phylogenetic inference - reconstruction of phylogenetic tree from character data • most commonly used methods compare all possible trees and choose the tree which fits the character data best according to some criteria • parsimony - simplest explanation is best - choose tree that requires fewest changes to explain character data • other methods - distance, maximum likelihood, Bayesian • the number of possible trees that can be compared becomes astronomically large with even a moderate number of taxa - most inference is done computationally • Create classifcation based on phylogenetic tree • example: Alaska yellow cedar, Chamaecyparis, and Xanthocyparis • Ultimately, a recontructed phylogenetic tree is a hypothesis of what the true evolutionary history is based on some specific set of data. New data may result in a different tree and change our understanding of relationships. What never changes is the true evolutionary history; our understanding of that history, and its reflection in our classification systems, are what can change. • Explore other questions based on understanding of relationships from phylogenetic tree • , evolution of traits, speciation, ecology... Understanding phylogenies • Parts of a tree • tips - extant taxa under study • branches - connect tips via common ancestors; show relationships • nodes - where branches meet; represent common ancestor of set of tips • root - node which connects all tips in tree; common ancestor of all tips • axis from root to tips represents time - root is in past, tips are in present • other axis from tip on one side of tree to tip on opposite side has no significance • Topology - pattern of branching • sister group - most closely related taxon to taxon of focus • shares most recent common ancestor • reciprocal relationship • tips can be rotated around nodes without changing the topology