Botany III�Plant Diversity

Diversity of plants, algae,

fungi, & prokaryotes

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Course #: BOT 317

Instructor: Jamie Boyer, Ph.D.

Dates: Mon., Apr 8 – Jun 3

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Final: June 10

Topics

Session 1: Evolution & Bacteria / Archaea

Session 2: Non-vascular plants

Session 3: Spore-bearing, Vascular plants

Session 4: Cone-bearing plants with Seeds

Session 5: Flowering plants

Session 6: Algae and Protists

Session 7: Fungi and Slime Molds

Session 8: Ecology

Grading

• Attendance 5%
• Quizzes (7) 30%
• Each week we will have an quiz that covers

the previous session’s content

• Final Exam 30%
• Lab Notebook 25%
• Procedures and labeled diagrams

for all viewed material

• Journal Article Assignment 10%
• See additional sheet in email

Topics for Tonight

• Evolutionary Theory
• Binomial Nomenclature
• Taxonomy
• Cladistics Methodolgy
• Prokaryotic organisms
• Bacteria
• Archaea (or Archaebacteria)

Evolutionary Theory

• What is Evolution?
• Descent with modification
• Not just change over time
• Changes in properties of populations, which transcend the lifetime of single individual.
• Individuals do not evolve.
• Evolutionary changes are inheritable from one generation to the next.

(Young) Charles Darwin

Modern Evolutionary Synthesis

• Population Genetics merged Darwinian evolution and Mendelian principles
• Evolution needed an explanation for inheritance of information
• Population: localized group of individuals belonging to the same species
• Species: a group of populations, which could interbreed
• Phenotype: the physical appearance of an organism
• Genotype: all genes in an organism
• Allele: one form of a gene (e.g. “A” and “a”)
• Gene pool: sum total of all alleles, of all the genes, of all individuals, in a population.

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For example, if the proportion of allele A in the population

changed from 90% to 50% over time

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Evolution is …

…the change in the frequency of alleles,

within a gene pool,

from generation to generation

(Old) Charles Darwin

Gregor Mendel

1

2

1

2

Cell with chromosomes

Trillium grandiflorum

Trillium grandiflorum 

forma roseum

Individual #1

Individual #2

Individual #3

How do alleles change?�Agents of Evolution

1. Mutations: changes in genotype of an individual
• Most are detrimental; raw material for evolution; add new alleles
2. Migration: movement of alleles into/out of population
• New alleles will change proportions or frequencies in population
3. Genetic Drift: changes due to pure chance or luck
• Laws of probability will greatly affect small populations
• Founder effect & bottleneck effect
4. Selective mating: non-random mating
• Inbreeding: mating of closely-related individuals
5. Natural selection…

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The Process of Evolution

• Natural selection: the process by which favorable traits that are heritable become more common in successive generations of a population of reproducing organisms
• Acts on the physical traits (phenotype) of an organism
• More fit traits allow the organism to survive and reproduce
• Less fit traits that are heritable become less common.
• Over time this creates adaptations that specialize organisms to a particular ecological niche and new species

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• Artificial selection: similar process controlled by humans to breed favorable features in organisms.

Brassica oleracea

Speciation

• Speciation: the origin of new species
• Allopatric speciation: geographic barrier separates populations, which evolve “away” from each other.
• e.g. Islands, Mountains, Waterfalls
• may lead to adaptive radiation of species (e.g. Galapagos Islands)
• Sympatric speciation: genetic changes create a reproductive barrier which allow new species to arise even though within breeding distance
• e.g. Reproductive or Phenotypic barriers
• Polyploidy: having more than two sets of chromosomes

Evolution & Geologic time

• What is microevolution?
• Evolution on a small scale (species level)
• Within a single population of a species
• Takes place over thousands and millions of years.
• What is macroevolution?
• Evolution above the species level, assessing the diversity of an entire clade and its position on the tree
• Takes place over tens and hundreds of millions of years
• Are they separate processes?
• No… microevolution leads to macroevolution, over time.

Convergent Evolution

• Unrelated species evolve a similar form or function, due to environment forces
• e.g. Adaptations to arid environments

Euphorbiaceae - spurges

Apocynaceae - milkweeds

Cactaceae - cactuses

Pine (Pinus)

Cycad (Cycas)

Date palm (Phoenix)

Whistling pine (Casuarina)

Sarracenia

Cephalotus

Nepenthes

Various pitcher plants

That’s the process…

…but how do we represent

evolutionary change

or species differences?

Binomial System of Nomenclature

• Carl Linnaeus: (1707-1778)
• Species Plantarum: 1753
• 1^st official reference of scientific names
• Each name has 2 parts: binomial system
• Generic epithet
• Specific epithet
• Binomial System of Nomenclature
• All organisms are named with this system
• Organisms are also placed in a taxonomic classification

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e.g. Homo sapiens;

Trillium grandiflorum

Taxonomy

A classification system used to sort organisms based upon similarities

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Classic Hierarchy:

Kingdom

Phylum

Class

Order

Family

Genus

Species

e.g. Plantae: photosynthetic organisms with embryos

e.g. Anthophyta: flowering plants

e.g. Magnoliopsida: dicotyledons

e.g. Rosales: specific order of dicots

e.g. Rosaceae: rose family

e.g. Rosa; always capitalized; always underlined or italicized

e.g. Rosa multiflora Thunb.; always underlined or italicized

Cladistics

Methodology used to determine the evolutionary relationships of taxa using their “features”, and generate a visual representation of their evolutionary history.

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Characters are “coded” for each taxon in the study…

• Feature is present: “+”
• Feature is absent: “-”
• Feature is unknown: “?”

A computer program sorts and organizes the taxa based on similarities and differences

Cladistics

This method assumes that taxa with more characters in common are more likely to be closely related

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• Results are visually represented as a phylogenetic tree or cladogram

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• Groups, taxa, or features appearing a long time ago are called ancestral
• Notice we don’t use the term “primitive”
• Groups, taxa, or features appearing more recently in history are derived
• Notice we don’t use the term “advanced”

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Cladistics (cont.)

Now we can add these features to the tree to show that they define each clade

P

F

O

M

…F-P-O clade =

…P-O clade =

…O clade =

M = moss

F = fern

P = pine

O = oak

vascular tissue

seeds and wood

flowers

Vascular

tissue

Seeds

& Wood

Flowers

(M)

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(F)

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(P)

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(O)

Feature for…

Let’s assume…

• the presence of features is derived
• the absence of features is ancestral
• More absent traits = more ancestral on tree
• More present traits = more derived on tree

Mono-, Para- and Polyphyletic�Groups

F

E

G

A

B

C

D

Monophyletic: a group with one common ancestor, and all descendants

Paraphyletic: group with an ancestor, that doesn’t include one branch of descendants

Polyphyletic: group with an ancestor, that doesn’t include many descendant branches

Examples

• Land plants
• Angiosperms

Examples

• Gymnosperms
• Reptiles

Examples

• Algae
• Protists

Diversity of Life

2 Kingdoms

1750s

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Plants

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Animals

3 Kingdoms

1860s

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Protists

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Plants

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Animals

4 Kingdoms

1930s

Monerans

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Protists

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Plants

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Animals

5 Kingdoms

1960s

Monerans

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Protists

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Fungi

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Plants

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Animals

3 Domains

1990s

Bacteria

Archaea

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Eukarya

• Chromoalveolata
• Excavates
• Unikonts
• Archeaplastida

Why has the science changed over time?

What technologies have aided the change in thinking?

Diversity of Life:�“Prokaryotes”

1. Domain* Bacteria�2. Domain* Archaea

*“Domain” is considered above the Kingdom level

“Prokaryotes”�Organisms without organelles

• Oldest organisms on Earth (at least 3.5 billion years old)
• Ancestral, but not primitive
• Each prokaryotic group has feature(s) that defines it
• Dominant form of life on earth
• Found everywhere (even in & on other organisms)
• Photosynthetic, chemosynthetic, and heterotrophic forms
• Aerobic and anaerobic forms
• Prokaryote domains
1. Bacteria
2. Archaea

Bacteria

Archaea

Domains

Last Universal Common Ancestor

(LUCA)

Slime molds

Green algae

Red algae

Other algae

Archaea

Domains

Last Universal Common Ancestor

(LUCA)

Bacteria

In a later event, the mitochondria and chloroplasts are the evolutionary results of ingestion of different bacteria by the eukaryotic host over time

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Mitochondria

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Endosymbiont theory predicts that a eukaryote is the evolutionary result of bacteria host ingesting an archaean

Last Eukaryotic Common Ancestor

(LECA)

Domain: Bacteria

• Features
• Cell wall & Nucleoid (area with cicular DNA)
• Flagella, in some
• Pilus (hair-like structure for attaching and sharing genes)
• Forms
• Coccus (ball-shaped)
• Bacillus (rod-shaped)
• Spirillus (spiral-shaped)
• Ecological Importance
• Global carbon balance
• “Fix” free nitrogen (into nitrate)
• Decompose toxic substances
• Negative interactions
• Plants: most blights, soft rots, and wilts are bacterial

Bacteria�“Nitrogen-fixers”

Cyanobacteria

• Photosynthetic
• Heterocyst: fix nitrogen; turn gaseous N2 into solid nitrate or nitrite
• e.g. symbiosis with cycads, Azolla, bryophytes, green algae, etc.
• Stromatolites

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Rhizobia

• Nitrogen-fixing bacteria associated

with legumes

• Form nodules on roots
• Distantly related to cyanobacteria

Sharks Bay, Australia

coralloid roots of cycads

x2,000

Stromatolite fossils from 2 billion years ago

Bacteria�Prochlorophytes

• Photosynthetic and very small, between 0.2 and 2.0 µm (width of a human hair is ~100 µm)
• Important (pico-)plankton in ocean
• Live in nutrient-poor water
• Similar in appearance to cyanobacteria

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Prochlorothrix

Prochloron

Bacteria�Purple / Green Sulfur

• Cyanobacteria & plants use chlorophyll to split water in photosynthesis
• H2O + CO2 🡪 CH2O + O2
• These bacteria use split hydrogen sulfide in photosynthesis
• H2S + CO2 🡪 CH2O + S2
• Some live in bright, oxygen-less (anaerobic) environments; others in dark, aerobic env’ts
• They reduce harmful organic compounds (e.g. methane, hydrogen sulfide) and odors in manure wastewater ponds
• Thought to be the origin of the mitochondria

Bacteria�Mollicutes

• Lack cell walls
• Very small (~0.2μm)
• Parasites on plants and animals
• Infect the phloem cells (sieve elements)
• Can cause phyllody in plants
• Mycoplasma causes “walking pneumonia” in humans
• e.g. Citrus stubborn disease,
• Peach X-disease,
• Pear decline,
• Aster-yellows (carrots),
• Lethal yellowing of coconuts

Domain: Archaea

• Originally called Archaebacteria
• Genome more closely related to eukaryotes, than Bacteria
• Use more energy sources than eukaryotes
• Metal ions, ammonia, hydrogen gas
• Do not use sun to “fix” carbon
• Major part of ocean plankton (<2 μm)
• Soil dwelling, frequently in extreme environments

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Archaea�Halophiles

• Thrive on high salt concentrations
• Live in salt concentrations 5x ocean water
• Heterotrophic and aerobic
• Evaporation ponds, Great Salt Lake, Dead Sea

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Archaea�Methanogens

• Organisms that produce methane (CH₄)
• CO₂ + 4 H₂ → CH₄ + 2H₂O
• Live in anaerobic (oxygen-less) environments
• Common in sewage-treatment, bogs, ocean depths

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Archaea�Thermophiles

• Lives in relatively high temperatures (106-221°F)
• Found in hot springs, geysers, deep-sea vents
• There are also thermophile bacteria in these springs
• Enzymes from thermophiles used in Polymerase Chain Reaction (making many copies of DNA)

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Next week: Domain Eukaryotes

Lab Pratice: Cyanobacteria�Nostoc or Anabaena

• Heterocyst: fix nitrogen (e.g. symbiosis w/ legumes)

Modes of Macroevolution

• Phyletic Gradualism: evolution occurs at a slow but constant rate
• Species continue to adapt
• Gradually become new species.
• No clear demarcation between old and new species

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• Punctuated Equilibrium
• Most species show little change for most of geological history
• Phenotypic evolution it is localized in rare events
• Branching speciation occurs relatively quickly