library(ecoevoapps)
sim_df_pos <- run_exponential_model(time = 50)
plot_continuous_population_growth(sim_df_pos)
What is ecology, and how is it done?
Principles of Ecology Week 1
Course introduction
Questions about the bats
What are some questions an ecologist might want to ask about these bats?
Two minutes to generate as many questions as you can
Take a few minutes to share your favorite questions with your neighbors
Classroom challenge: can we break 50 questions?
About me
How did I get to be here?
Back to the bats.
How many bats live under the bridge?
How many bats live under the bridge?
A simple question that is not so simple to answer.
General theme in ecology: How many are there, and how are their numbers changing?
Relevant in a wide range of settings:
tracking populations of invasive species,
managing populations in fisheries,
controlling spread of infectious disease,
estimating flux of atmospheric CO2, …This includes human health, e.g. Why do cancers spread faster in some contexts than others?
How many bats live under the bridge?
Mark-Recapture as a method to generate estimates of population size:
Capture and mark (tag) some number of individuals
Release tagged individuals and allow the population to re-equilibrate
Once population is settled (e.g. in the case of bats - on a different night), capture some number of individuals
The proportion of individuals that are marked in your second sample can give you a good estimate of the total population size
How many bats live under the bridge?
\(N_{Marked}\): number of individuals marked in first sample
\(N_{Captured}\): number of individuals captured in second sample
\(N_{Captured,\ Marked}\): number of individuals in the second sample that are marked
\(N_{Total,\ Estimated}\): estimate of total population size
\[N_{Total,\ Estimated} = \frac{N_{Marked}*N_{Captured}}{N_{Captured,\ Marked}}\]
Worked example:
On day 1, you catch and mark 200 bats
On day 8 (in the following week) you catch 1000 bats, of which 175 are marked
\[N_{Total,\ Estimated} = \frac{N_{Marked}*N_{Captured}}{N_{Captured,\ Marked}}\]
\[N_{Total,\ Estimated} = \frac{200*1000}{175} = 1143 \mathrm{\ bats}\]
Semester overview
Our goal over the next semester will be to develop skills to:
- Describe how the field of ecology tackles the complexity of nature
- Explain how mathematical thinking helps generate ecological insights
- Interpret figures and results from published ecological literature
- Discuss the role of ecology in addressing major societal challenges.
Next class
- Overview of course structure
- Introduction to population ecology
Principles of Ecology
Day 2
Course Structure - Logistics
Course overview
Ecology - a field motivated by human efforts to describe, understand, predict, and modify nature
In the Western tradition of ecology, a classical focus on what determines where organisms live, and how their numbers change over time?
As the field evolves, a new emphasis to describe, understand, predict, and modify life under global change
Course overview
This course aims to develop your skills in four areas:
- Describe how the field of ecology tackles the complexity of nature
- Explain how mathematical thinking helps generate ecological insights
- Interpret figures and results from published ecological literature
- Discuss the role of ecology in addressing major societal challenges.
Course structure and evaluation
Your grade will reflect your performance in three areas:
- Weekly self-reflections
- Weekly activities
(mostly completed outside of class; some in-class) - Semester project
(more on this next week)
Weekly self-reflections
- The goal is to help you take a step back and reflect more generally on your growth as a scientist over the semester
- I encourage you to think about how the material we are learning in-class relates (or doesn’t relate) to your life more generally
- I will include a list of potential reflection topics, but I encourage you to think broadly about what matters to you.
- First weekly reflection due this Sunday night.
Weekly self-reflections
Why are we doing this??
- Metacognition – thinking about your own thinking – a key ingredient in academic and career success
Weekly self-reflections
Why are we doing this??
- Make space for deliberately thinking about how lessons from basic ecology apply to our increasingly complex and “weird” environment
Weekly self-reflections
- Due on Sunday night every week
24-hour grace period - You are in charge of grading your own weekly reflections
- Each week starting in Week 2, you will be asked to reread and grade your previous week’s submission
- Assign yourself a grade out of 5 (whole numbers only, please).
- I will read self-reflections to get a sense of how things are progressing, and to identify areas of potential improvement/adjustment
Weekly self-reflections
Potential ideas for this week’s reflection:
- What are some things you are excited about for this semester? What are some things you are nervous about?
- What does the word “ecology” mean to you? How do you think it is relevant to your life?
- What is your relationship with “nature”? In your mind, how can humans have a healthy relationship with nature?
- Is there a particular place that comes to your mind when you think of “being out in nature”? What kinds of characteristics define that space for you?
Weekly activities
- Each week starting in Week 2, you will be asked to complete an activity related to course content
- Format will vary by week
e.g. reading primary ecological literature; quantitative worksheet, etc. - Typically due on Thursday nights
- These activities will form the focus of in-class activities on Fridays
Weekly activities
- The goal of these activities is to encourage your deep engagement with course material
- As with self-reflections, you are in charge of evaluating your submissions (whole numbers only, please)
- To help with grading, I will share an ‘exemplar’
Weekly activities
No ‘weekly activity’ this week; please complete the “Who’s in class” survey on Moodle.
Co-working sessions
Starting in Week 2, I will be available for two co-working sessions per week:
- Wednesday afternoon from 3.30-4 over Zoom (link in Moodle)
- Friday morning at 10.30-11.30, in the Student Union (exact location announced next week)
- Contact me if you cannot attend either.
Course Stucture - Content
Levels of ecological organization
- Population
- How do individuals of a given species interact with the abiotic environment, and with each other?
- How do these interactions affect population dynamics?
- Community
- How do individuals of different species interact with each other?
- How are diverse ecological communities organized and structured?
Levels of ecological organization
- Landscape
- What drives the turnover (change) in community types across space?
- How can habitat structure across large distances affect population dynamics?
- Ecosystem
- How do energy and nutrients flow across entire ecosystems?
- What are the consequences of disruptions to ecosystems cycles?
Approaches to ecology
- Observational studies
- The bedrock of ecology: capturing what is happening, with all the ‘messiness’ of nature
- Essential at all levels of organization; especially so at the ecosystem level
- Strengths and limitations
- While these can provide compelling - even incontrovertible evidence - it is almost impossible to assign causality
Approaches to ecology
- Experimental studies
- Control specific factors of interest
- Critical for assigning causality
- Ethical and practical considerations
- Strengths and limitations
Approaches to ecology
- Mathematical modeling
- Essential for integrating complexity (e.g. projecting over long time frames)
- Generate predictions from simple principles + data
- Helps us look in the right places
- Strengths and limitations
Approaches to ecology
- Integration of observation, experiment, and modeling
Where does ecology happen?
Where does ecology happen?
Where does ecology happen?
Principles of Ecology
Day 3
Reminders
- Weekly reflection due on Sunday night
- Potential questions listed on Moodle
- Length guidelines
Reminders
- First Weekly Activity due next Thursday night
- Expect this to take ~3-4 hours to read the paper and fill out a worksheet
Paper for next week
Paper for next week
https://unidecology.org/
How ecologists deal with uncertainty
When I saw the forecast yesterday morning, the prediction was for a hot and sunny day.
But around 3pm, there was a massive (and very local) rainstorm that dumped a lot of water over my neighborhood
Was the forecast wrong?
Why are our best estimates/predictions sometimes off?
Mark-recapture method
- What is it??
Today’s Activity
Mark-recapture in real life
(Kind of.)
Today’s Activity
- Groups of 3 (4 of needed)
- Upto ten groups total
- In each group, at least one person should have a computer with internet access
Today’s Activity
Details available at https://ecology.gklab.org/ –> Weekly Activities –> Week 1 –> Click on “Mark-Recapture Activity” button
Stuff we didn’t get to this week
Population ecology
What defines a population?
Individuals of the same species living together
Individuals interact with one-another
e.g. mating, facilitating, competing
How does a population grow or shrink?
How does a population grow or shrink?
Consider a ‘closed’ population
no movement in or out of a populationChange in population size (\(N\)) only driven by births and deaths
There is some per-capita birth rate (\(b\)), and some per-capita death rate (\(d\))
Total number of births = \(b*N\)
Total number of deaths = \(d*N\)
How does a population grow or shrink?
- Change in population size over time is determined by total births (\(bN\)) minus total deaths (\(dN\))
\[\frac{dN}{dt} = bN - dN\]
\[\frac{dN}{dt} = (b - d) N\]
How does a population grow or shrink?
\[\frac{dN}{dt} = (b - d) N\]
- Define \(b-d\) into one integrative term \(r\)
\[\frac{dN}{dt} = r N\]
Populations growt when there are more births than deaths (\((b-d) > 0\); aka \(r > 0\))
Populations shrink when there are more deaths than births (\((b-d) > 0\); aka \(r < 0\))
How can such a simple population model help?
Next class
- Hands-on activity for estimating population sizes
- If time, build on population growth model
- Continuous vs. Discrete time
- Adding biological constraints