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Overview

This is a 2-week INTENSIVE field course. Intensive means your typical schedule will look like this:

Time Activity
07:30 Breakfast
08:30 Morning Tutorials
10:30 Field Activities (Pack Lunch)
17:30 Dinner
18:30 Evening Tutorials
21:30 Finish

Schedule & Grades

Deadlines

Check back regularly; these will be updated as the schedule gets set:

Date Assignment
May 16 (8:30) Submit paper choices
May 17 (8:30) Bring samples for DNA extraction
May 18 (evening) 1. Finish collections
2. Combine & visualize GM dataset
3. Present assigned readings

DRAFT Schedule

This schedule is tentative:

DRAFT schedule

DRAFT schedule

Grading Scheme

Note: This grading scheme has changed from the OUPFB Syllabus.

The main reason is to shorten the final project and replace it with two smaller projects that can be completed during the field course. This also reduces the amount of work to be completed after the field course has finished.

Group Projects (50%)

  • Herbarium Collections (10) – Due May 20
  • Insect Collections (10) – Due May 20
  • Final Project (30)
    • Project Proposal (5) – Due May 26
    • Code and Data Quality (10) – Due June 10
    • Final write-up (15) – Due June 10

Peer Evaluation & Participation (20%)

Individual Marks (30%)

  • Field & Lab notes (10)
  • Paper Presentation 1 – May 20
  • Paper Presentation 2 – May 22

Grading Rubrics

Natural History Collections

Each group member should produce at least 5 specimens. Submit 5 from each group member and note ‘best’ 5 (must include at least 1 from each group member). Grading will be based on:

  1. Variety (10 marks) – specimens differ from other students, represent a broad range of taxonomic groups, geographical locations, and habitat types.
  2. Data & Metadata (20 marks) – labels with correct scientific name, GPS location and datum type; clear & detailed meta-data demonstrating careful attention to detail.
  3. Preservation (10 marks) – specimen dried sufficiently, mounted properly, all structures visible (e.g. beetle wings extended; both sides of leaves visible), tidy and aesthetic presentation, secure mounting.

Paper presentations

15 minute presentations + 5 minutes for questions & discussion. Grade (10%) based on

  1. Content (20 marks) – Presentation is an accurate representation of the paper. No important points are left out.
  2. Clarity (10 marks) – Paper is explained well; complex or detailed material is summarized clearly; questions are answered well
  3. Presentation (10 marks) – clean, clear slides; good eye contact; speaking at a good pace with good projection.

Tutorials & Activities

Tutorials

Resources:

Datasets:

Tutorials:

  1. Data Carpentry: Data Organizing with Spreadsheets
    • Example of Messy Data Data
  2. Data Carpentry: Working with data using OpenRefine
  3. R FUNdamentals
    • Fallopia community ecology experiment Data
  4. Visualizations with qplot()
  5. Some analysis of the Lythrum dataset
  6. The magic of regular expressions (regex)
  7. Combining datasets: Lythrum 2017 data and metadata. If you get stuck, take a look at the LythrumDataMerge.R code with PL_complete.csv and Lythrum2017FieldData.csv, or skip to the merged dataset
  8. DNA barcode analysis
  9. Differential expression analysis. You will need access to a unix server running SLURM scheduler, and you will need to upload the tutorial.tar.gz file.

Assignments

Journal Discussion:

  1. Read the intro an eDNA paper.
  2. Choose a paper from the list below that interests you*.
  3. Coordinate so that everyone presents a different paper.
  4. Submit list of papers and presenters Wednesday Morning (May 16)
  5. Prepare to teach the paper to the class (15 min + discussion). You will be the only one to read the paper.
  6. While you prepare, discuss confusing terms and concepts to improve your understanding.
  7. Pesent Friday evening (May 18)

*You can propose another eco/env genomics paper that is not on the list, but also choose one from the list as a backup in case the one you choose doesn’t fit with the theme.

Natural History Collections

  1. Collect & Preserve the Specimen (and meta-data)
  2. Identify the Species
    • Reference manuals in the lab
    • Go Botany Website
  3. Mount and Submit the Specimen
  4. Organize and upload meta-data

You will have all day Wednesday and Thursday morning to make collections. You should have at least 15 specimens ready for preservation before lunch on Thursday, May 17. There may not be much time to make more collections after this, and you will still have to mount and label the specimens.

Select two plants for DNA extraction and bring them to the Brown Lab after lunch on Wednesday (May 16).

Day 1 (May 14)

Intro to QUBS

QUBS Website and Key Links

Safety Information

Exercise 1:

Working in your groups, identify potential risks and a plant to mitigate risk the hazards assigned to your group (from handout).

Example:

Hazard: Thin ice in winter

Risk: Hypothermia and/or drowning

Plan: Make sure that ice thickness is adequate for your planned activities. Carry ‘polar picks’.

  • Never go on ice alone. It is best to wear a floater suit and carry a rope.

  • Be sure to bring a complete change of clothes in a dry bag.

  • If you do go through the ice:
    1. Call for help
    2. Do not try to climb out in the same direction where you went through the ice
    3. Use the air trapped in your clothing to get into a floating position on your stomach.
    4. Reach onto the broken ice without pushing down, and then kick your legs to push your torso on the ice.
    5. Once on the ice, crawl on your stomach or roll away from the open area with your arms and legs spread out as far as possible to evenly distribute your body weight. Do not stand until well away from the open water and thin ice.

Exercise 2:

Fill out OCASP Forms (check for email invite):

Compare your groups answers to the risks and plans on the OCASP form.

  • What was obvious
  • What was surprising or something you didn’t think of?

Safety Information

Course goals

3 Pillars:

  1. Learn by doing
    • Field Activities
    • Hands-on tutorials
  2. Emphasis on transferrable skills
    • Coding
    • Experimental Design
    • Data Science! (collect manage  visualize  analyze  report)
    • Communication
    • Teamwork
  3. Cumulative learning – each day builds on previous activities/tutorials

Code of Conduct

In this course we follow a code of conduct based on The Carpentries.

They can be summarized by two Main rules:

  1. Be professional
  2. Be inclusive

Zero-tolerance policy: Harassment is any form of behaviour intended to exclude, intimidate, or cause discomfort. Because we are a diverse community, we may have different ways of communicating and of understanding the intent behind actions. Therefore we have chosen to prohibit certain forms of behaviour in our community, regardless of intent. Prohibited harassing behaviour includes but is not limited to:

  • written or verbal comments which have the effect of excluding people on the basis of membership of a specific group (ethnicity, religious belief, gender, sexual orientation, etc.)
  • causing someone to fear for their safety, such as through stalking, following, or intimidation
  • the display of sexual or violent images
  • unwelcome sexual attention
  • nonconsensual or unwelcome physical contact
  • sustained disruption of talks, events or communications
  • incitement to violence, suicide, or self-harm
  • continuing to initiate interaction (including photography or recording) with someone after being asked to stop
  • publication of private communication without consent

The list above should not be taken as exhaustive but rather as a guide to make it easier to enrich all of us and the communities in which we participate.

Tutorials

Setup:

Software to install:

Datasets:

  • Spreadsheet Tutorial Data
  • OpenRefine Tutorial Data

Data Carpentry:

  1. Data Organizing with Spreadsheets
    • Spreadsheet Tutorial Data
  2. Working with data using OpenRefine
    • OpenRefine Tutorial Data

Day 2 (May 15)

CDE

Read through the website for the Global Garlic Mustard Field Survey (GGMFS) project: garlicmustard.org

As you read through the pages, keep in mind the questions below. Be prepared to discuss your findings with the class:

  1. What is a Coordinated Distributed Experiment?
  2. What are the major aims or goals of the project?
  3. Create a flow chart or concept map describing the data collection protocol (see protocol pdf)
  4. What biological questions can be addressed with the data?
  5. What are some potential problems or difficulties with the protocol?

Journal Article Assignment

  1. Read the intro an eDNA paper.
  2. Choose a paper from the list below that interests you*.
  3. Coordinate so that everyone presents a different paper.
  4. Submit list of papers and presenters Wednesday Morning (May 16)
  5. Prepare to teach the paper to the class (15 min + discussion). You will be the only one to read the paper.
  6. While you prepare, discuss confusing terms and concepts to improve your understanding.
  7. Pesent Friday evening (May 18)

*You can propose another eco/env genomics paper that is not on the list, but also choose one from the list as a backup in case the one you choose doesn’t fit with the theme.

Natural History Collections

  1. Collect & Preserve the Specimen (and meta-data)
  2. Identify the Species
    • Reference manuals in the lab
    • Go Botany Website
  3. Mount and Submit the Specimen
  4. Organize and upload meta-data

You will have all day Wednesday and Thursday morning to make collections. You should have at least 15 specimens ready for preservation before lunch on Thursday, May 17. There may not be much time to make more collections after this, and you will still have to mount and label the specimens.

Select two plant specimens per person for DNA sequencing (e.g. difficult to ID).

Day 3 (May 16)

1. Collections

  • Meet at 8:30 in front of the Lodge. A packed lunch will be provided.
  • Have everything packed ahead of time:
    • Field clothes, sunhat, sunscreen bug spray, etc.
    • Maps
    • Plant pressing equipment
    • Killing jars and falcon tubes with slightly moist paper towels
    • To kill insect humanely: place in freezer in Brown Lab when you return
  • Spend full day hiking QUBS trails collecting plants and insects.
  • Claire will continue collecting garlic mustard data (give her data sheets)
  • Aim to have enough specimens to mount and submit for final project

2. Prep paper presentation

3. Data entry

Enter garlic mustard data as a .csv file

Day 4 (May 17)

DNA Barcodes

  1. Read instructions on the PCR protocol handout
  2. Draw a flowchart or diagram to summarize the protocol
  3. What are some potential errors or difficult steps?

Day 5 (May 18)

Deadlines

  1. Finish collecting data from Garlic Mustard Arrays and Common Garden Plots 1, 2 & 4
  2. Enter and save data as .csv files in the shared dropbox folder
  3. Finish Assigned Reading Presentations

13:00 Metabarcoding & metagenomics (Kat)

18:30 Paper presentations

Day 6 (May 19)

Rainy Day #1

08:30 Collections

Plant Mounting Demonstration (Kat)

Inspect & Mount Specimens

  • See if plants are dry or need more time in oven
  • Be VERY CAREFUL, they are very fragile when dry
  • Remove insects from freezer and mount on boards
  • Look for specimens that did not preserve well and might need to be collected again

12:00 Lunch & Reflections:

  • Private self-reflection (not shared)
    • Consider everything in the last 5 days (activities listed on website)
    • What were some personal highlights, challenges
    • What was unexpected, what was as expected
  • Annonymous course feedback
    • Green Sticky: 1 or more positive things
    • Red Sticky: 1 or more suggestions for improvement
    • For each sticky:
      1. Content
      2. Delivery

13:00 Lythrum Paper Discussion

  1. Read a paper testing rapid evolution of local adaptation in invading populations of Lythrum salicaria
  2. Private reflection
    • What is this paper testing?
    • How do they test it? What are the main analytical methods?
    • HINT: You might want to look at the supplementary methods
    • Are the data publicly available? If so, where?
    • What are some potential limitations of this research?
    • What are some potential areas for future research?
  3. Discuss with partner
  4. Discuss with class

18:30

Lythrum 2013 Data

  1. Locate the data in the online repository
  2. Inspect the comon garden data from the paper
  3. Make sense of the column names
    • Note: What is missing that could help us interpret these?
  4. Introduction to lm(), glm() and lmer()
  5. Attempt to reconstruct (or jury-rig):
    1. Test for local adaptation
    2. Test for natural selection

GM Data

Working with your partner:

  1. Finish entering GM data (on .csv file for each block or array)
  2. Use OpenRefine to create two data sheets:
    1. Import & combine GM data from all three GM common garden plots into a single data sheet.
    2. Import & combine GM data from all three GM arrays into a single data sheet.
  3. Clean your data:
    1. Check for mis-spelling
    2. Look for possible measurement errors
    3. Ensure zeros and missing data are coded properly
    4. Find columns containing >1 piece of information and separate into new column(s)
  4. Save the data sheets (as .csv) and the JSON script recording of your edits in the R Project file you made during the R tutorial.

Working individually:

  1. Visualize your data in R and inspect your graphs carefully
    1. Import one of your ‘cleaned’ and combined .csv files (arrays OR common garden)
    2. Use qplot() to visualize your data
    3. Create an .Rmd notebook file to generate a report
    • Describe in normal language the steps you made to clean the data
    • Include a hyperlink to the JSON text file
    • Include your figures and your interpretation of what they mean
      • e.g. Is there a postive/negative correlation? What might have caused this?
    1. ‘Preview’ your .Rmd file and save it as an .html file in you working directory

Day 7 (May 20)

7:30 Breakfast (cereal and toast available)

8:30 Lythrum Field Experiment (Eugene)

18:30 Lythrum project (Eugene)

Lythrum data

  1. Enter your groups data into a spread sheet and save to the dropbox.
  2. Import, combine & clean data from all pairs into a single data sheet using OpenRefine.
  3. Save the data sheet (as .csv) and the JSON script recording of your edits in the R Project file you made during the R tutorial.

Day 8 (May 21)

8:30 Tick sampling

12:00 Lunch

13:30 Data & Collections work

18:30 Tutorial

  • Lythrum 2013 Data parse & local adaptation test
  • Lythrum Test for genetic variation (lmer)
  • Git with R Studio

Day 9 (May 22)

8:30 Gene flow experiment set-up

Outreach Day (Emily)

Outreach Assignments

  1. Tweet your paper : Start with something that will grab attention, then sumarize the highlights of the paper in 280 characters.
  2. 8.5 x 11 poster or pamphlet communicating your paper to a 1st year biology undergraduate.

18:30 Unix/Bash

Day 10 (May 23)

8:30 Aquatic Sampling Day (Aaron)

19:00 QUBS Seminar: Dr. Rute Clemente-Carvalho

“The striking biodiversity of the Brazilian Atlantic Forest. New species discoveries and the extraordinary miniaturised toads in the genus Brachycephalus.”

20:00 Reflections and Discussion

21:00 Inspect gene flow experiment

Day 11 (May 24)

8:30 Plant surveys & soil sampling (Kat)

12:00 Packed Lunch

18:30 Microbial Metagenomics Tutorial (Kat)

Day 12 (May 25)

8:30 Final Project Day #1

13:00 Hiking @ Rock Dunder

18:30 DNA Barcoding Analysis

Day 13 (May 26)

8:30 Final Project Day #2

13:00 Lock Hike

18:30 Wrap-up Tutorial

Day 14 (May 27)

8:30 Depart QUBS

Other Notes:

Data Management Mini-Workshop

Project Start: Create a Data Management Plan (DMP)

  • DMP Assistant is an online portal to help you create a data management plan
  • portagenetwork.ca –> DMP Assistant –> Sign Up for a new account (or Sign in if you already have one)

Project Finish: Publish your data