### Class Meeting: Friday, 31 August 2012

Announcements:
• HW3: Practicing decifering experimental designs with cane toad paper. Pushed back to Wednesday 9/5/12 before class. We will practice this in class today.
• A great place for more information on the process of science!
http://undsci.berkeley.edu/article/intro_01
• HW4: due next Wednesday. We will talk about that later today.
• HW5: Group contract. Will have assignment and sample contract up this afternoon. Due next Friday (9/7/12)
• My office is changing. I am now in Biology 1112B (1st floor office suite)

### Objectives:

1. Distinguish questions that can be answered scientifically from those that cannot. Given a question or results from a "study" explain whether the results or question can or cannot be answered scientifically. chapter 1
2. Identify the pattern of scientific reasoning and investigation. Given a question/statement, create a testable hypothesis including...
• Null and alternative hypotheses
• Independent and dependent variables
Given an experimental design identify those same elements. Cane toad paper Chapter 1
3. Distinguish the difference among Observations, hypotheses, and theories. Given a statement identify whether it is an observation, hypothesis or theory. Be prepared to explain your rational Chapter 1
4. Determine whether a hypothesis has been supported through statistics using a p-value. Given a hypothesis with a p-value, state whether the hypothesis has been supported.
5. Identify the relationship between births and deaths that result in population change. given the birth rate and death rate determine whether a population is increasing or decreasing in size. determine the number of eggs surviving to reproductive age to maintain a population. chapter 36
6. Reproduce/identify exponential and logistic growth curves and all important features relative to both (including growth phases and carrying capacity). Given a population, show an expected growth curve and identify the important points in the curve. given a scenario determine whether the population is under exponential or logistic growth Chapter 36
7. Identify the intrinsic characteristics of growth (includes r vs k strategies). Given an organisms life history is it likely an r or K strategist. Given environmental conditions predict whether r or k strategists are more likely to succeed. for a given r is the population increasing, decreasing, or stable? Chapter 36
8. Distinguish between density dependent and density independent limiting factors. Given a population list a density dependent and density independent limiting factor. State whether the factor is biotic or abiotic. Explain your answer. chapter 36

### Evaluating Data

Objective(s): 1, 2
Scientific tests must have clearly defined variables and a null hypothesis

Types of variables
• Dependent - What investigator thinks is affected (plotted on y-axis)(effect)
• Independent - Often what the investigator varies/manipulates, usually cause (plotted on x-axis)(cause)
• Controlled - Variables held constant (control for other alternative hypotheses)
the independent variable causes the dependent response

#### What is a null hypothesis?

• H0 (Null hypothesis) = no difference, independent does not effect dependent
• HA (alternate hypothesis) = a difference exists, a relationship exists, independent causes change in dependent
Sample experiment: 12 plants: 6 with nutrients added, 6 with no nutrients added, measure growth (grams biomass) after 6 weeks. Water same amount, keep at same temperature, give same amount of light
1. List the alternative hypothesis: plants that receive nutrients will have higher biomass than plants that do not receive nutrients(note that plants that receive nutrients will have lower biomass is another alternative hypothesis)
2. List the null hypothesis: plants that receive nutrients will have the same biomass as plants that receive no nutrients (only one null hypothesis)
3. List the dependent, independent and any control variables
• Dependent variable: Plant biomass at 6 weeks (in grams)
• Control variables: water, temperature, light

### P-value

Objective(s): 4

Scientists use p-values to provide information on the probability that a relationship occurred by chance. The higher the p-value, the less likely that the independent variable caused the change in the dependent variable (ie the relationship is not significant).

If the p-value <0.05, then there is less than a 5% chance that the difference seen or relationship observed was caused by chance alone.

so...

p-value >=0.05 then not significant

p-value < 0.05 then significant

Note: Error bars (vertical lines in the graphs below) show how much variability is in the values used to calculate a mean.  If the error bars overlap, the differences probably are not significant.

 small error bars that do not overlap p<0.05 maybe p=0.005 error bars overlap and extend beyond average represented by bar p>0.05, maybe p=0.08

### Clicker questions

Objective(s): 2, 3, 4

Passages from Cane Toad Paper (Brown et al 2007)

para 1 pg 17698, fig 2a. size
The arthritic condition is absent in smaller toads (logistic regression with toad body size vs. arthritis occurrence: X2 = 13.94; df = 1; P < 0.0002; see Fig. 2A).
 1. Independent Variable 2. Dependent Variable 3. Control Variable a. whether the toads have arthritis b. there are none evident from the statement c. small toads d. large toads e. toad size f. none of the toads had arthritis g. both toad types had the same amount of arthritis h. toads with arthritis i. toads without arthritis

para 1 pg 17698, fig 2a. size
The arthritic condition is absent in smaller toads (logistic regression with toad body size vs. arthritis occurrence: X2 = 13.94; df = 1; P < 0.0002; see Fig. 2A).
 4. Null Hypothesis 5. Alternative Hypothesis 6. Was the alternative hypothesis supported (significant or not significant) a. there are none evident from the statement b. large toads have more arthritis than small toads c. none of the toads had arthritis d. both toad types had arthritis e. both toad types had the same amount of arthritis

Radio-tracking of free-ranging toads shows that the arthritic animals continue to move at least as far and fast under field conditions as do nonaffected conspecifics (mean distances 157 vs. 144 m per day respectively, based on 11 pairs of size-matched animals monitored over the same time periods: F1,20=0.06; P=0.81).
 1. Independent Variable 2. Dependent Variable 3. Control Variable whether the toads have arthritis none of the toads traveled time period sampled, toad size distance traveled toads with and without arthritis travel the same distance arthritic toads nonarthritic toadslong distance traveled there are none evident from this statement

Radio-tracking of free-ranging toads shows that the arthritic animals continue to move at least as far and fast under field conditions as do nonaffected conspecifics (mean distances 157 vs. 144 m per day respectively, based on 11 pairs of size-matched animals monitored over the same time periods: F1,20=0.06; P=0.81).
 4. Null Hypothesis 5. Alternative Hypothesis 6. Was the alternative hypothesis supported (significant or not significant) whether the toads have arthritis none of the toads traveledtoads with and without arthritis travel the same distance toads without arthritis travel a longer distance than toads with arthritis arthritic and non-arthritic toads both travel long distances

### Q1 - What do you need to know to predict population change?

objective: 4, 7

As a group, on paper, answer the following questions regarding the deer population scenario.

You are responsible for maintaining the deer herd of Kentucky. Answer the following questions to predict next years population size.
1. What limits deer population size?
2. What increases deer population size?
1. What counts from this year do you need to know?
2. What rates do you need to know?
3. Is there anything else you need to know?

### What factors determine population growth rate?

objective: 4, 6

Population growth rate depends on

1. the current size of the population
2. the contribution of each individual to the population growth rate
3. survival/death rate

Intrinsic growth rate of a population depends on the species

Intrinsic growth = how fast a population can grow.

Pianka ER. 1988. Evolutionary Ecology. New York: Harper Collins Publishers Inc. p. 140

Pianka ER. 1988. Evolutionary Ecology. New York: Harper Collins Publishers Inc. p. 162

### When does a population size change?

objective: 4, 5

births = deaths, the population size stays the same [zero population growth]

births>deaths, the population size increases

births<deaths, the population size decreases

"r" = per capita rate of increase

Within populations, r varies through time and can be positive (increase), negative (decrease) or zero (no change).

Exponential growth

If all individuals are reproducing at their maximum potential, the population size increases exponentially.

Figure 52.5 Freeman 2005

### Population growth model

objective: 4, 6, 7

Population - a group of organisms of the same species within a defined area. Often the population is determined by the question being asked. (ie the kentucky deer population, population of bacteria in a test tube, population in a river or bay)

Variables
• rd = death rate (deaths per unit time ie year)
• rb = birth rate (births per unit time ie year)
• n1 = population size at time 1 (number of individuals in population now)
• n2 = population size at time 2 (number of individuals in population 1 year from now)
Survival and reproductive success depends upon
• biotic factors - living things such, competition, predation, and food production
• abiotic factors - non-living things such as weather, water availability, and nutrient availability
with this information you can calculate the number of individuals at the end of one unit of time.

 number of births - number of deaths + population at start = population in one year rb*n1 - rd*n1 + n1 = n2
note: the book uses r. r = intrinsic growth rate = rb - rd
therefore we can rewrite our equation as:
• r*N1 + N1 = N2

### What is in these carboys?

objective: 4, 5, 7

1. If left in a wort (sugar solution used to grow yeast), predict the change in population size in the carboy over time (draw figure)
2. Will the population increase indefinitely? Why or why not?
3. Identify the different phases of growth in your diagram and identify any biotic or abiotic factors that may be affecting growth

Do most natural populations exhibit exponential growth? Why?

objective: 5, 7

### Logistic growth

objective: 5

Figure 52.5 Freeman 2005

### What limits growth rates and population size?

objective: 7

Density-independent factors

• change birth rates and death rates regardless of the number of individuals in the population.
• usually triggered by changes in abiotic environment (environmental resistance)
• Weather including hurricanes
• volcanoes
• forest fire
• pollution

Density-dependent factors

...usually biotic and change in intensity as a function of population size.

e.g., increase in intensity as population size approaches carrying capacity.
Carrying capacity depends upon the quality of the habitat.

e.g., predation

e.g., trees: if crowded have less sunlight, nutrients, water - therefore produce fewer seeds.

(competition for resources)

How does carrying capacity fit into our prior growth model?
New variables
• K = carrying capacity = maximum sustainable population size
• G = population growth = growth including other factors (ie K )
 Exponential growth model G=rN Logistic growth model G=rN[(K-N)/K]

### r & k strategies

objective: 4, 5, 6, 7

1. Imagine a site where every day there is abundant food, but organisms are likely to be killed getting the food. Which organism would you expect have more offspring?
• hundreds of offspring, little parental care
• only a few offspring, lots of parental care/teaching
2. Assuming that reproductive aged adults are likely to survive and reproduce, would it make more sense for an organism to have lots of offspring if a site is stable or if a site is unpredictable?

### r & k strategies

objective: 4, 5, 6, 7

• r strategist
• r because (intrinsic growth rate) maximized
• little parental care
• high mortality rate
• short lived
• k strategist
• k because tends to live near carrying capacity
• large bodies
• long life
• few, well cared for offspring
Name three examples of r-strategists and three examples of k-strategists in your groups

### r & k strategies

objective: 4, 5, 6, 7

• Examples
• r = cockroach, rat, dandelion
• k = elephant, human, coconut
• r and k strategies are extremes and most organisms fall somewhere in the middle
• r strategists tend to favor areas with high disturbance, k strategists often have difficulty surviving in areas with frequent disturbance
• Humans tend to cause frequent disturbance, hence we tend to encourage r-strategist organisms (see list above)

### Modeling deer population growth

objective: 4, 5, 6, 7

birth rate = 1.5 faun per female
percent of births male = 50%
rdn = natural death rate = 10% of total deer population
rdh = harvest rate = 15% of total deer population (can be divided among males and females differently)
n1 = deer population size at year 1 = 10,000 (6,000 female, 4,000 male) Here is a relatively simple example using a spreadsheet

Population counter

Analyzing the change in the growth rate of human populations:

From Freeman 2005, Figure 52.13

Scenario depends on female fertility rate - now 2.7 worldwide.

Replacement rate: if at zero for one generation, r=0, ZPG (Zero Population Growth).

### Homework 4: design an experiment: step 1

to be complete next week, so think about ideas over the weekend. The hypothesis does not have to be biologically related and must be completed within 1 week.

As a group, submit online in Blackboard
1. Observation:
1. What observation/s did you make that lead to your question?(ie Why are you interested in this problem?)
2. Question:
1. What is your research question?
3. Hypothesis: how will you test your question?
1. Write out the hypothesis
2. List your dependent variable - response - needs to be quantifiable (counts, measurement, time, etc)
3. List your Independent variable - the cause - can be manipulated or observed
4. List any controls - accounts for any competing hypotheses
5. Describe your proposed Method -
• How will you carry out the experiment
• There should be replication

Note 1: Do not conduct the experiment yet You will conduct the experiment in Part 2.
Note 2: Do not use Human Subjects in your experiment unless you are only observing. Do not use vertebrates, including fish in your study unless you are only observing. Therefore, no surveys and no asking other students to be in your study and no using pets (unless you have a pet snail, cricket or amoeba).

Rubric for homework

• 1 pt - Assignment completed on blackboard on-time
• 1 pt - Observations lead to testable hypothesis
• 1 pt - Identifies dependent and independent variables
• 1 pt - Description of experiment would allow another student to repeat the experiment
• 1 pt - Experiment includes replication - more than one sample per treatment