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FOR 332 - Forest Ecology


Ruth Yanai, Associate Professor, tel: 470-6955, e-mail:

Kimberly Bohn, Visiting Instructor, tel: 470-4877, e-mail:

Materials Provided by Instructors

  • Syllabus (updated 9/05)
  • Guidelines for Grading Assignments (updated 9/05)
  • Writing a Lab Report
  • Lab Observation Sheet
  • Critique of a Journal Article 
  • Klenner and Sullivan article
  • An Exemplary Critique
  • Tips on reading scientific literature

Class Notes

Quiz Question:  What is ecology?

Ecology:  How living things are interrelated to each other and the environment.  Distribution and abundance of organisms.  From Greek: oikos (household) and logos (science): the study of the household of nature.

Includes ecotypes such as forests, streams, lakes, oceans.  In this course, we will focus on forest ecology, where trees dominate the processes.

Ecosystem Ecology focuses on the relationship of the biotic system to the abiotic (atmosphere, soil) at scale larger than..

Instructors: Ruth Yanai, does research more than teaching, has taught Forest Ecology three times.

Kimberly Bohn has been a TA in this course twice and is now a Visiting Instructor.  It is her last semester as a PhD student.

Steve is a junior in FRM, this course is required for his major.

Kent is a senior taking Forest Ecology as an elective, he’s from near Keuka Lake, and lives on Westcott Street.

Chad is a sophomore in FRM.

John is also in FRM.  They’ve taken a lot of classes together.

Tom is a Dual major (EFB and FRM), he’s 19 and live in Lawrinson, he’s a sophomore.

Jose is a sophore in Environmental Studies.  He wants to learn more about forests.  He’s from Columbia and he was in the learning community last year.

Nathan is a first-year graduate student, with an undergraduate degree in English from Binghamton.  He’s in Forestry, Ecosystem Science and Applications.

James is from Long Island, he’s in his third year in FRM, he did the SPFF this summer

Eric is a senior in FRM, he’s from Ohio.

Pam is from Rochester, she’s a part-time student with a background in electrical engineering.

What helps you get something out of assigned reading?

Discuss with other people, in class or outside of class.

Questions can guide your thinking about the reading.

Open ended questions that test your understanding.

Taking notes in the reading helps you remember it if you look at it again.

Highlighting important things helps identify what to go back and read again.

Knowing your own learning style will help you optimize your use of these tools.

Our reading guides help you know what’s important to get out of the reading.  Your quiz questions will be based on the reading guide.

Quiz:  Describe the difference in wood structure between diffuse porous and ring porous trees.

Meristem- key to tree growth, Undifferentiated  cells, located on surface area of tree, apical and lateral

Growth of individual tree parts

  1. Branches (akaShoots) and Leaves:

Growth: primordia located in buds, leaves grow out first and then shoot elongation. Elongation stimulated by auxins.

Indeterminate vs. determinate (free vs. fixed)

IND- can grow throughout growing season, multiple flushes; maples, birches, cherries

Determinate- only one set of leaves and shoots per season- oaks and pines

Early Leaves vs. Late leaves

  1. Roots:

Growth similar to shoot growth (cells)- at apical meristem.

Correlation of elongation to root diameter. Elong. Also affected by temperature, excess water (because of oxygen losses), compaction

  1. Bole

Growth: Meristem divides into fusiform cells and ray cells ( both are in xylem),

Ring width and area: Wood is produced along perimeter,

From base of crown downwards

Types of Wood: Coniferous wood- tracheids, no differentiation in function (support or transport) of tracheids.

Diffuse porous- small vessels spread throughout wood used for water transport

Ring porous- large vessels in early wood and smaller vessels in late wood

Diffuse vs. Ring Porous wood

Early vs. late wood

Reaction Wood

Compression – conifers, forms on underside

Tension- hardwoods, forms on the upperside

Which paragraph starts with a topic sentence?  Can you add one?

Many variables affect intensity of light on forests’ floors.  Plots with high crown density and basal area, for example, might be more shaded than

The characteristics of the trees, specifically height, crown ratio, size, and density, could be related to the pattern of red pine mortality and to the light environment. 

One evaluation of the stand characteristics was done by Team Gray Van in the measuring live-crown ratio and tree height.  The results show…  However, The Other Guys found that…  Team Xtreme shows how…  (can you also make these verb tenses consistent?)

There were four groups in this lab.  Each group tested a different variable…

What’s necessary in your Methods section?  Just enough so that someone else could replicate your experiment.

The diameter and species of all trees > 2” dbh were determined on two 50’ by 50’ plots in each stand. 

When should you be more specific?  Which examples are too specific?

The light environment was related to the stem density.

The failed pine plantation had more intense sunlight on the forest floor than did the more intact pine plantation.

Can you improve these sentences?

Comparison of Red Pine Live Crown Ratios between a Failed and an Intact Red Pine Plantation

The study areas in this experiment were two 50x50’ plots in each of two even-aged stands of red pine (Pinus resinosa), established on land previously used for agriculture.

Given the relatively small change in elevation, ...

Beech has become less commercially valuable since the spread of beech bark disease throughout the Northeast.

In contrast, in site two, there was greater plant diversity and a greater amount of sunlight.

When is it important to double-space your assignments?

Make-up exercise for the last Individual Report

The central concept for the red pine lab was “demography”; we also studied regeneration and life history strategies.  So you should be able to tell us why we had more regeneration in one site than another, and what life history strategies made some species successful in regenerating (why is the understory a different species than the overstory in these stands?)

3 pts:  Thorough definition of the concept, using examples from the text or from class to demonstrate understanding.

Part c.  An example of the same concept applied to another context.

Next lab the central concept is Population Dynamics

Study Guide:Barnes; CH 19

Concept: Nutrient Cycling

6 macronutrients: N, Ca, P, K, Mg, S

micronutrients: Fe, Zn, Bo, Mn, Cu, Ni essential for plant growth

What nutrients are most commonly limiting in what kinds of ecosystems?

N is most commonly limiting in boreal, temperate and some tropical forests: only certain organisms can fix N.  The atmosphere is mostly N; why is N ever limiting?  N2 gas is not available to plants. 

P is most commonly limiting in wet tropical forests.  High rainfall, high temperature, and old soils mean that most of the available nutrients have already been weathered.  Ultisols, Oxisols

Describe three sources of nutrients to forest ecosystems.  Which nutrients are supplied by each source?

  1. Atmospheric deposition (wet and dry):  S: pollution from burning of fossil fuels containing S (SO4). N in NOx: automobile emissions.
  2. N fixation
  3. Mineral weathering:  all the ones in rocks: Ca, Mg, K, (major in rocks) S, P (small amounts)

Compare wet and dry deposition (differences in particle size, distance that particles are transported, etc.)

Larger particles come down in wet deposition; only small particles are transported a long way in the air. 

How do legumes add N to soil?

Only bacteria can do it.  Plants form associations with these bacteria (rhizobium for legumes, Frankia for alder, myrica); the bacteria fix N, the plant supplies the bacterium with energy in the form of carbohydrate.

Describe the 2 mechanisms by which nutrients move towards root surfaces.

Diffusion: ions move from high to low concentration by random movement.

Mass flow:  water moves towards the root driven by transpiration

Explain the relationship between mycorrhizae and plants.

Symbiosis between a fungus and a plant.  It can’t fix N.  The fungus can explore the soil and take up nutrients.  The plant provides C to the fungus.

What is nutrient-use-efficiency?  How does it vary with climate?

Most common definition: Crop yield/fertilizer applied. 

In your textbook: Leaf production/leaf nutrient content.

The graphs illustrate N limitation, except in tropical forests, where P seems to control litter production.

Study Guide:Barnes; CH 19, part 2

Concept: Nutrient Cycling 2

1.  How does the accumulation of organic matter in the forest floor vary by climate and species composition? Why?

Forest floor (organic horizon >40% OM or 20% organic C) retains nutrients, water; improves infiltration and reduces erosion.

In very cold climates, decomposition is slow, and SOM accumulates.  Arctic and boreal forests can have thick organic layers.  In hot and humid climates, decomposition is rapid, and forest floors are less massive.

Deciduous leaves decompose more readily than conifer needles.

2.  What chemical compounds found in plant litter are broken down during microbial decomposition, and which break down faster than others?

Proteins are rapidly broken down; there’s a big demand by decomposers.

Carbohydrate: glucose is most available, more complex sugars, cellulose and hemicellulose go more slowly.

Lignin goes the slowest.

3.   What other factors besides the chemical constituents of plant litter affect the rate of decomposition?

Temperature and soil water potential (availability of water)

The common earthworm is a European exotic, which speeds up decomposition and incorporates OM into the mineral soil.  Microarthropods are important to breaking down material into smaller pieces.  Bacteria and fungi do most of the work.

Chemical symbols you should know:

NO3 nitrate (most oxidized)

NH4 ammonium

SO4 sulfate




PO4 phosphate

  1. What are the processes for  N immobilization, N mineralization, nitrification and denitrification . (Also, try drawing the N cycle within an ecosystem)
  1. N immobilization
  2. mineralization
  3. Nitrification
  4. Denitrification
  5. N fixation

5.  Which elements are more likely to be leached from an ecosystem? Why?

 Nitrate is more readily leached than ammonium (which is held by cation exchange).

Ca, K elements that are weathered in large amounts will be important in streamwater.

6.  When is nutrient leaching greatest in temperate deciduous forests? 

Early spring:  trees are not taking up much water yet, so there is more to lose; snowmelt has high nitrate.

Article: Canham et al. Windthrow

When you read a journal article (or write a lab report), you should be able to find the following information.

  1. What was the problem the authors addressed?

Relationship of storm severity and differential response of tree species had not been previously quantified.

Why is it important?

Knowing which trees withstand windthrow can help predict future forest development after storms, frequency and severity of storms could be changing with climate change.

  1. What are the objectives or hypotheses?

Develop a NEW IMPROVED method for distinguishing the effects of storm severity and species susceptibility, depending on the size of a tree.

Shade tolerant species should invest more in wood strength.

  1. What did the authors do, and where (methods)?

They measured windthrow in 43 plots in the Adirondacks, second growth and old growth.  They had a variety of degrees of disturbance.

  1. What did the authors find out (results)?

Intermediate sized trees: black cherry and red spruce showed highest rates of windthrow; yellow birch and sugar maple were low

Small trees: beech hemlock and sugar maple (shade tolerant trees) were less susceptible.  CONSISTENT WITH HYPOTHESIS

Big trees: Beech (very shade tolerant) was likely to break, maybe due to beech bark disease.  NOT CONSISTENT WITH HYPOTHESIS

Species composition affects amount of windthrow for same storm severity

  1. What are the conclusions?  Do they answer the original question?


When you critique a journal article (which you will do later this semester), you will also address questions such as the following.

  1. What background information or ecological understanding is needed
    to understand the research?

Need to explain the equations that they use.

Disturbance, classification of wind disturbances, severity.

Shade tolerance, life history characteristics.

Previous methods, previous research results (suggesting relationship of shade tolerance to disturbance)

  1. What are the strengths of the study?  Do you have suggestions for

The problem is important, and the study design is broad (old-growth and secondary forest)  They provide a new method.  Conifers weren’t important in this study system.

The time at which measurements were taken could affect the results.

  1. Are the conclusions supported by the results?

Yes, there was a relationship between tree species and susceptibility.  They were able to address storm severity.

How far could the conclusions be extrapolated?

They only learned about the species that they studied.  Making a generalization about shade tolerance class means that hypotheses could be posed in other systems.

  1. What new research could be stimulated by the results of this study?

Apply this approach in other systems.

The difference between large and small stems could be further explored.  For example, is the difference due to dimensions or also to the material properties of the wood.

The time of year at which the storm occurred: compare lots of sites with storms at different times.

How long does it take for a forest to become wind-firm?  Simulation modeling might be one way to address this.

Critique of a journal article


  1. Include background material beyond that in Intro of paper (full credit for papers not cited in your paper). 
  2. To describe this paper include info on: wind disturbance regimes in NE (known rates of severe or intermediate storms); other known work on windthrow in this region, or species composition in areas disturbed by wind, or other work done on the same research site.
  3. For those studying animals, tell us about the animal (habitat, etc).  Describe the ecosystem it is found in. Pictures help.
  4. End with why research is important (usually stated in their Intro):  understanding freq and susc of species to windthrow under differing severities could be important for modelling the change in forest composition under future climate conditions.

Strengths of presentation

  1. Intro- placed their problem in context of current knowledge ; makes it easier to understand why their study is important
  2. Methods- for those interested in statistics, they provide a thorough description of what they did to calculate MLE; this makes their methods repeatable
  3. Results- despite the difficult math, they describe the results clearly, relating it to species characteristics; this makes paper accessible to non-stats people

Suggestions for improved presentation

  1. Figure 3: hard to tell species apart by symbols; use more contrasting symbols
  2. Results: 2nd paragraph of Old vs young was confusing and seemed contradictory. They explained why windthrow RATE was higher in old stands, but they should also explain why SUSCEPTIBILITY was lower

Strengths of experimental design (why did authors choose this design?)

  1. Took a transect perpendicular to wind path; this is important because wind (and thus windthrow) probably decreases somewhat as it moves through the forest (parallel)
  2. They included a wide range of topographies (most likely to account for any variation associated with this feature)
  3. 20 plots in both old and young stands seems like an ample sampling scheme

Suggestions for improved experimental design (or describe an alternate design?)

  1. Statistics- they say their predicted values shows an “excellent” fit to observed data, but they should use a goodness of fit test (chi-sq) to actually prove that their model  is accurate.
  2. Improvements to design (from conclusions after the study)- a) since species affects their storm severity index, they really need to find plots with similar species compositions (or put various compositions into different categories and evaluate separately), b) they conclude that height/diameter ratios are probably more important to susceptibility than diameter alone, so height info would have been useful

Are the conclusions supported by the results? Why or Why not?

  1. “Life history characteristics suggest that late successional species invest more in resistance to windthrow”:  their results only found a relationship between susceptibility and late successional (or shade-tolerant) species for smaller trees. It was somewhat true for intermediate sized trees (though I think that was more a function of height). Results for old trees were confounded by beech (BBD)
  2. “Height/diameter ratio explains differences in susceptibility in old vs. young stands… because trees in old growth have likely been suppressed and have denser wood”: it’s true that the older stands had smaller trees (they show a signif. diff. in dbh), but there is no data regarding suppression or wood density (I do think this is a valid SUGGESTION as a possible explanation though)
  3. “Our results suggest that distinctive abundance of yellow birch in old-growth… is due to its ability to survive the intermediate-scale disturbance events”: I thought this was kind of a stretch. What about the fact that the regeneration niche for YB is often on downed logs?


  1. windthrow susc. Of a conifer forest type
  2.  Application/ incorporation of results into a model evaluating forest dynamics under climate change

Materials Provided by Instructors

Observing the Forested Landscape





Boundaries and size:





Bedrock geology:

Surficial geology:

Today’s conditions:

Sketch map


Layer Height and Continuity Dominant Species (% cover or basal area)

Articles and Questions

When you read a journal article (or write a lab report), you should be able to find the following information.

  1. What was the problem the authors addressed? Why is it important?
  2. What are the objectives or hypotheses?
  3. What did the authors do, and where (methods)?
  4. What did the authors find out (results)?
  5. What are the conclusions?  Do they answer the original question?

When you critique a journal article (which you will do later this semester), you will also address questions such as the following.

  1. What background information or ecological understanding is needed
    to understand the research?
  2. What are the strengths of the study?  Do you have suggestions for
  3. Are the conclusions supported by the results? How far could the conclusions be extrapolated?
  4. What new research could be stimulated by the results of this study?