Nov 10; Plant Communication and Behavior

Plant communication and behavior relies on phenotypic plasticity. Plants are unable to run away, they have to live with the consequences of their behaviors.

The various cues that a plant recieves can affect a number of things including, shoot phenotype and root development. How do plants respong to shading, shade from their own leaves and shade from others?

They either confront, avoid, or tolerate. When a plant confronts a competitor the plant will have an elongation response, and increase apical dominance. When a plant avoids a competitor the plant will grow away from the competitor or have dependent germination. When a plant tolerates a competitor it will just be tolerant to the shade morphologically and physiologically.

How do plants perceive light levels and wavelengths? They possess photoreceptors, phytochromes, crytochromes, phototropins, and some unidentified UVB sensitive to particular wavelengths.

Plants can tell the difference between being in the shade of a building or a rock, versus shade of another plant. This is because of the different wavelengths of light that are absorbed by other objects. Red light is absorbed by plant canopy, far-red isn’t. That means a plant with full sun is being exposed to different ratios of red and far-red wavelengths opposed to plants which are being shaded.

Shade avoidance is a collection of responses to vegetative shading. Plants can anticipate and respond to future shade. Plants elongate less when wearing a collar that filters out far-red light reflected from adjacent leaves. Another example of this is Portulaca oleracea, or common parsalin, grows and branches in a wa that minimizs self-shading. When lower red/far-red ratios occuring in one direction the plant grows away from it.

Shade tolerant species tend to be very slow growing. The differences in allocation cause long-lived shade-tolerant plants that invest relatively more resources into defense against herbivores and pathogens.

Ligh information is more than just quantity and spectrum. It is likely that plants respond to a richer range of light cues. Vertical, mid-day shade might indivate a very tall neighbor where the plant would not want to compete to grow larger. Horizontal and late-day low r:fr cues might indivate similarly sized neighbors where the plant would compete with its neighbor.

Somatic Competition happens when plants compete with themselves. There are many redundant organs that compete with each other. In “Somatice Competition” the plant can increase performance by putting more resources into more successful organs. The growth rate can vary. Experimental evidence supports the 3 types of responses; independant, cooperative, competitive.



Nov. 8th; Plant Development and Hormones

Male Gametophytes:  Pollen

Female Gametophytes: Embryo Sac

Generative Cell will divid to become the two sperm. The tube cell makes up the pollen tube into the pistil of the plant.

One sperm fertilizes the egg, the other will fuse with the polar nucei. The fertilized egg will become the embryo. The two polar nuclei and sperm will be the endosperm that provides nutrients to the embryo. This is known as Double Fertilization.

Embryo Development

The last step of seed development is that they become desiccated, they only have 5-20% water. The seeds coat will harden.

Inside of the seed will be the seed coat, the radicle (embryonic root), Cotyledon, Epicotyl (above cotyledon), Hypocotyl (below cotyledon).

Cotyledon are seed leaves that are packed with nutrients. In monocots, the cotyledon will wrap to become the Coleoptile.

Plant Hormones

Five Main Classes of Plant Hormones

The five hormones: Auxin, Cytokinins, Gibberellins, Ethylene, Abscisic Acid

Other Plant Growth Requlators: Salicylic Acid, Jasmonic Acid, Systemin

Working with Coleoptiles Charles Darwin and son Francis studies phototrophism. They found that cutting the tip prevents it from bending. They put an opaque cap on the tip and it did not bend. If covered with a clear cap it did. If they covered the bottom with a cap it still bent. This means that there was a signal from the tip of the plant that must have been responsible for this phototrophism. Peter Boysen Jensen took it a step further and studied the chemical signal. Fritz went isolated the chemical responsible for the signal. This chemical was an AUXIN.


This is a the first plant hormone discovered. It is the Greek word for increases. Natural auxins consist of things like indole acetic acid (IAA) and relate to molecultes. They are produced in the apical meristems of shoots. They are usually transported from the top down, basipetal transport. This gradient become really important.

The process in which auxin phototrophism occurs is the ACID GROWTH HYPOTHESIS. Auxin increases proton pump activity. The cell wall becomes more acidic, and unzips the hydrogen bonds. This makes the wall soft allowing turgor pressure to push cell wall outward.

Auxin is also involved in gravitrophism. The starch-statolith hypothesis is an explaination of gravitrophism. The amyloplasts, leucoplasts that store starch, are used to figure out what is up and what is down. Whe the weight of the amyloplasts hit it triggers auxin production. Auxin is produces in the shoots.

Auxin is really important for apical dominance, tissue differentiation, lateral roots, fruit development, leaf abscission, and herbicide. In tissue differentaitaion, if you damage the vascular tissues, auxin initiates formation of vascular tissue to heal the wound. Auxin stimulates pericycl cells to divide.  The auxin enhances fruit growth, developing seeds are the source of IAA. The absicssion, or dropping of leaves and other plant parts, are a cause of a drop in auxin that drops the part. Synthestic auxins are used as weed killers.


Johannes van Overbeek discovered that coconut milk possessed factors that accelerated the growth of plant embryo and isolted tissues and cells in test tubes. 

They are found in actively dividing tissues, cytokinesis. The are shown to cause plant cells to grow in an undifferentiated mass of cells (callus). The combination of auxin from above and cytokinin from the root tell the tissue what to differentiate into. Cytokinen is produced from the roots. They can delay and reverse senescence (the process of ageing) in plants. They release buds from apical dominance.


E. Kurosawa was working on the disease of rice that produced fast growing, pale-colored and sickly plants. This was caused by a fungus isolated from the rice and later bean plants. The bean plants showed gibberellins were being released from the plant itself instead of the fungus.

Gibberellins are all about stem elongation. Dwarf plants are a varity of mutations that cause a lack of gibberellins or the inability to process gibberellins. Bolting, or the sudden verticle growth associated with flowering and death, is mediated by gibberellins. There is a spike in the gibberellins concentration. They are also really important for germination.  Gibberellins will induce genes to make enzymes that break down starch in the remaining endosperm. The biggest current use of gibberellins today is in Thompson’s seedless grapes.

Abscisic Acid

Abscisic acid causes stomatal closure, and prevents premature germination of seeds. It is very important for water regulation.


Ethylene is a gas that was discovered by accident by citrus growers. They noticed that if they kept them in a warm shed they could ripen the fruit faster. Ethylene gas hastens the ripening of fruits. It is importatn in seed germination, fruit ripening, and absission.




Oct 27; Coevolution

What is coevolution?

Coevolution involves two or more species which exert selective pressures on each other and evolve in response to each other.

The key idea is because each species involves in response to each other the selective environments is constantly changing.

When does coevolution occur?

Selective pressure will be strongest when there is a close ecological relationship. Close relative in terms as species who are specialists rather than generalists.

How do we study Coevolution?

There are different levels that we look at coevolution. The study of adaptations of the individuals, interactions between species or broad evolutionary patterns.

Does coadaptation demonstrate coevolution?

Some biologist would say that having coadaptation does not give evidence to the parallel evolution between taxa. To convincingly show coevolution you must show a parallel evoltuion between taxa.

An example of this would be the Fig Trees and Fig Wasps.

The figs have a specialist relationship with the wasps. The wasps act as pollinators for the figs. Coadaptations happen with these species. The receptive figs produce scents that are specific to a particular pollinator species. The shape of the ostiole is specifically shapped to the head of the particular wasp species. The morphology of individuals flowers specialized to a particular wasp species.
The Fig starts to develope and the ostiole opens up. The female wasp crawls in and lays here eggs in the plant with pollen from the fig she was born from. The eggs hatch and the females fly out and find another fig.


Congruent phylogenies due to cospeciation is strong evidence for coevolution.

Oct. 27, Seed Dormancy and Seed Banks

Seed dormancy means that seed is in a state of suspended growth and development. This is a reduction in the metabolic rate. This gives resistance to adverse environmental conditions.

The conditions that must be present to break dormancy differs by species. Some species germinate as soon as the environment is suitable for growth. Other species need something else such as; An intial drying period, exposure to a long period of cold, scarification of the seed coat, or intense heat.

There are possible selective advantages to these cues to break dormancy. The cue for long periods  of cold are advantagious for species because of long winters.

Different species of plants produce seeds that require different cues to grow. A seed bank is produced by the different speices’ seeds waiting for these cues. A seed bank is a collection of dormant seeds in the soil. Seed banks allow dispersal in time as well as space.

There is a broad inverse correlation between the lifespan of adult plant and longevity in the seed bank. Annual plants will tend to have seeds that last for a long time . The storage effect is a model that shows the environment varies over time, and different species respond to the environment each year. An environment good for one species may not be good for another species. As long as the species has atleast one tough life storage stage that can get you from one good year to another good year this prevents the population from crashing. Populations stores up the good years to make it through the bad ones.

Long lived seeds do not need long live matured plants, but long lived matured plants do not need long lived seeds.


Oct. 11; Sexual Reproduction

Sexual Reproduction in Plants

Alternation of Generations
Alternation of generations is when you have life history that alternates between free-living multi-cellular diploid stage (sporophyte) and the free-living multi-cellular haploid stage (gametophyte).

Image result for alternation of generations
“Diagram showing the alternation of generations between a diploid sporophyte (bottom) and a haploid gametophyte (top)” Retrieved from Wikipedia Article on Alternation of Generations

Alternation of generation can be applied to green algae. In the case of Ulva, the gametophytes and the sporophytes look exactly the same. This is call isometric alternation of generation. (Iso = same)

The general trend is to have sporophytes be the more common stage of reproduction. However, with moss this has not happened.

Alternation of generation can be applied to mosses. The sporophyte grow above the female moss.

Alternation of generation can be applied to ferns. The spores are located under the fern leaf. Each spore becomes a heart shaped gametophytes. Some ferns are hetero- or homo-sporophytes. They create male and female or just female ferns.

Alternation of generation can be applied to gymnosperms. The tree is the sporophytes. The gametophyes are located in the cones of the trees. The male cones are only on the tree for 3-4 weeks before completing the reproductive cycle. The female cones can stay on the tree for 3-4 years.

Alternation of generation can be applied to angiosperms.

Flower Review

“A diagram of the parts of flowers” Photo credit to Science & Plants for Schools retrieved from

Ovule contains the embryo sac surrounded by integuments. Three cells are located at the bottom, the center one is the egg and the two that surround it are synergids. The three cells located at the top are antipodals. Two haploid polar nuclei are located in the middle. Ovule is the female gametophyte.

Embryo Sac = Female Gametophyte
Pollen Grain = Male Gametophyte

Double Fertilization is unique to angiospersms. A double fertilization occurs when a female gametophyte (embryo sac) and two male gametophytes (sperm) encounter each other. The sperm make its way down the pollen tube . One sperm produces endosperm, and one produce embryo. The endosperm is a nutritive tissue in seeds to feed the embryo.

Plant reproduction is complex.
There are sexual and asexual reproduction, but there are also apomictic seeds, agamospermy. The agamospermy produce seeds that are clones of themselves. This occurs in dandelions.

Perfect Flowers vs. Stamenate or Pistillate Flowers

Monoecious vs. Dioecious Plants

Androdiecy vs. Gynodiecy
Some individuals produce perfect flowers and some produce only male or female flowers.

Some of these species are obligate outcrossers. These outcrosser needs pollen from another plant and cannot self pollinate
Some of these species are obligate selfers. These selfers can only self pollinate.
A lot are flexible enough for both outcrossing and selfing to happen.

How does mating system influence geographic range size for selfers vs. outcrossers?
Selfers have a bigger geographic range because they can spread even with low densities. They have reproductive assurance.


Sept. 6th; The Plant Cells and Tissue

In this lesson we learn about what makes up plant cells and tissue.

The plant cell is made up of a rigid cell walls and protoplast which contains cytoplasm, membrance bound organelles, a system of membrane, and non-membrane bound things.

The membrane bound organelles consist of things such as mitochondria and plastids. Plastids are only found in plants and algea. They are surrounded by two membranes; the internal system of membranes form flattened sacs called thylakoids, when theses are stacked up they are called grana.

The direct movement of organelles is known as Cytoplastic Streaming. It is a good idea for chloroplast to be able to move around in the cell to increase photosynthesis, when in low light, or to decrease photo damage, when in high light.

Chloroplasts are the only Plastids with Thylakoids and Grana, but there are other types of Plastids that include: Chromoplasts and Leucoplasts.

Contain no chlorophyll and retain carotenoid pigment. The chromoplasts are responsible for yellow, orange, and red colors of plants.

Are the least differentiated and contain no pigment. They synthesis/store starch, oils, or proteins.

Helpful Video on various Plastids

Plastid Conversions show that plastids can interconverse between these types of plastids. Here is where we see etioplast show up. They are chloroplasts that lack chlorophyll, so technically they are leucoplasts. Chloroplasts convert to etioplasts when under stress.


Vacuoles are membrance bound organelles that make up 90%-95% of the volume of a cell. As adolesence there are multiple vacuoles that converge into one upon the cell reaching maturity. The membrane encapsolating the vacuole is called tonoplast. The vacuole contains “cell sap” that is a solution of water, saltst, sugars, amino acids, and inorganic ions. They breakdown and recylce macromolecules that are then repurposed in the sell. Also, it is the site for water-soluble pigment deposits and can act as the site where it sequesters toxic secondary metabolites such as; tannins, nicotine, and capsasin, which are used as defense for the plant.

An example of a water soluble pigment is Anthocyanin. This flavenoid, or class of plant pigment having a structure based on flavone, changes color based on the pH and can be seen as red, purple, or blue. The color can be so vivid that it maskes the chlorophyll in leaves. This phenomenon can be see in the ornimental red maple. This can also explain why we see a change of leaf color as seasons change. The down regulation of chlorophyll with the change in temperature and moisture allows the anthocyanin pigments to be visible in leaves.

Cell Wall

The cell wall determine the shape and size of a cell and gives it rigidity. Cell walls are mainly made up of cellulose. The secondary cell wall is deposited by protoplast after the primary wall has stopped growing to size. The secondary cell wall contains lignin, a polymer for structural material, is important for structure and water movement

Three Tissue Systems in Plants

Quick Video on Tissue Systems **Start at 2:32 and stop around 6:49**

  1. Dermal
    Has two sub categories, Epidermis and Protoderm. The  epidermis is covered in cuticle and possesses gaurd cells, trichomese and other specialized cells. The gaurd cells consist of pores and stoma, and the trichomese are little hairs that main purpose is to slow down small herbivores from consuming the plant. The protoderm is meristematic tissue that gives rise to dermal tissue
  2. Ground Tissue
    Has three sub categories, Parenchyma, Collenchyma, and Sclerenchyma. Parenchyma is found in generic plant cells, leaf mesophyll, fruit flesh, and in the cortex and pith, or center, of stems and roots. They are living cells and their functions  include wound healing, advantageous growth, storage, secreation, and are involved in photosynthesis.
    Collenchyma are found in distinct strands right under the epidermis in the stems and petioles. They are living cells with uneven primary walls and their main function is for structure.
    Sclerenchyma can be found anywhere depending on the plant. They are often dead at maturity and contain thick seconday walls. Their main function is for support and structure.
  3. Vascular Tissue
    Has two sub categories which were brought up in a previous lesson; xylem and phloem.
    Xylem, “Tracheary Elements”, and elongated cells with seconday walls. Their function is to bring water, marco-, and micro-nutrients into the cell. They are dead upon maturity and have spiral thickening lignin. There are two types of Xylem; Trachieds and Vessels. Trachieds are long tappered cells with pits found within  all plants including angiospersm and Vessels are grated cells found only in angiosperms.

    Tracheid and Vessel
    “Tracheids and Vessels”

    Phloem, “Sieve Elements”, are elongated cells with primary cell walls and are living at maturity, but they do not have a nucleus. They have companion cells that bracket to the seive tube. These companion cells control the metabolic function inside.

Aug. 30th & Sept. 1st; Introduction & Plant Diversity/Evolutionary History

In this course we will cover the Basic Botany Core Concepts including; Plant Phsiology, Anatomy, Life History, and Ecology. The main goal is to tailor this course to what we want to learn and create an open source webpage that compile our research to teach others about different aspects of Botany.

KINGDOM : Plantae

What makes a plant a plant?

There are different traits that are associated with plants. These traits include:

Photosynthesis in double membrane organelles called chloroplasts, they are multicellular, and  they have cell walls made of cellulose.

We can further explore the Plantae Kingdom by looking at the Phylogeny


We can tell by fossil records that the first photosynthetic organisms were the cyanobacteria in the mid archaeon eon.
The first land plants evolved after the cambarian explosion at approximately c450 M.A.

The advantages to colonizing land:
No competition with other photsynthetic things and no predators.

The Challenges of moving to land:
Plants now needed to fight against gravity, new was of dispersal for reproduction had to be aquired, the chance of dehydrationg needed to be overcome, and a mode of transportation for water and nutrients to be moved within the system needed to be derived.

Adaptations that were made include:
1. A waxy cuticle and stomata on plants leaves and stems.
The cuticle prevents water lose, and the stomata allows CO2 to pass through for photosynthesis.

2.Gametangia are found in algae, ferns, and some other plants. They are protective chambers of sterile cells wher egametes are produced.

3.Embryos in a protective structure developed from female gametangia.

4. Vasculate Tissues were adaptive.

5. Mutualistic relationships with the fungus, mycorrhizea, was formed as the funfus pulled in more nutrients for the plant.

6.Lignin and cellulose were adaptive polymers that added rigidity to plant structure.

7. Seeds with hard coating to protect the developing embryo

8. Fruit and Flowers were a way to get animals to help with dispersal

Maulucioni, Phylogenetic plant tree, showing the major clades and traditional groups. Monophyletic groups are in black and paraphyletics in blue. 13 February 2016

Examining the phylogenetic tree the first plant group is Non-vascular plants. Node traits include Cuticle/Stoma formation and Mutualistic relationship with mycorrhizae. Given by its name Non-vascular plants have no vascular system and include Bryophytes, such as; moss, liverworts, and hornworts. They have no true roots and absorb nutrients across their whole body. The lack of lignin in the plant makes it soft and squishy as opposed to ridgid. They are good at tolerating water lose.

The next node in the tree sections off Seedless Plants. Node traits include vascular tissue and lignin. The Seedless Vascular Plants include Horsetails and Ferns. Vascular tissue can be divided into two categories, xylem and phloem. Xylem moves water and nutrients into the plant and phloem moves them out. These terms will be described more in depth in future lessons.

Gymnosperms fall under seeded plants and the node trait includes production of seeds. the gymnosperms produce “naked seeds.” These seeds are not packafed in fruit like angiosperms.

Angiosperms are also under the seeded plants and the node trait is the formation of flowers and fruits.

Plant Evolution History

Part 1

Part 2