Seth Newsome (SDN)
Emma Elliott Smith (EES)
BIOL 419/519
PAIS 2120
Lecture: Tuesday & Thursday 9:30–10:45AM
Lab: Wednesday 2:00–4:00PM
Course Syllabus
Reading Report Form
CSI Sample Submission Form
Course Schedule
Week 1
August 22nd: Introductions, Expectations, and Ecological Origins
August 24th: Definitions and Fractionation (SDN)
Reading: *Ben-David and Flaherty 2012.pdf
Lab (8/23): Group Project Discussion and Form Groups
Week 2
August 29th: Isotopes in Water (SDN)
August 31st: Isotopes in Plant Water* (SDN)
Reading: *Dawson 1998; Bowen et al. 2005.pdf
Lab (8/30): Experimental Design and Field Methods
Assignment Due (9/1): Ideas for Group Projects
Week 3
September 5th: Primary Producer Carbon (EES)
September 7th: Primary Producer Carbon* (EES)
Reading: *Driscoll et al. 2020.pdf; Cerling et al. 1997.pdf
Lab (9/6): Introduction to Gear I: CSI Tour (EA/TCEA/GB–IRMS)
Week 4
September 12th: Primary Producer Nitrogen I (SDN)
September 14th: Primary Producer Nitrogen II* (SDN)
Reading: *Austin and Vitousek 1998.pdf; Amundson et al. 2003.pdf
Lab (9/13): Sample Preparation I: Decalcification, Lipid-Extraction, Microbalance; Sample Preparation Protocols
Assignment Due (9/15): Project Description and References Guidelines (50 points)
Week 5
September 19th: Isotopic Incorporation (EES/SDN)
September 21st: Isotopic Incorporation (EES/SDN)
Reading: *Moore et al. 2016.pdf; Martinez del Rio and Carleton 2012.pdf
Lab (9/20): Mixing Models (SDN); Linear Mixing Model Exercise (Group Work Time)
Week 6
September 26th: Consumer Carbon I (EES)
September 28th: Consumer Carbon II* (EES)
Reading: *Kurle et al. 2014.pdf; Kelly 2000.pdf
Lab (9/27): Introduction to Gear II: CSI Tour (GCC–IRMS and Picarro)
Week 7
October 3rd: Consumer Nitrogen (SDN)
October 5th: Consumer Nitrogen* (SDN)
Reading: *Croll et al. 2005.pdf; Vanderklift and Ponsard 2003.pdf
Lab (10/4): Sample Preparation II: Sample Homogenization, Cryodistillation
Assignment Due: Experimental Design and Methods Guidelines (50 Points); Example: SEV Smammals
Week 8
October 10th: Consumer Hydrogen (SDN)
October 12th: FALL BREAK (NO CLASS)
Reading: *Newsome et al. 2007.pdf; Clegg et al. 2003.pdf
Lab (10/11): Group Work Time
Week 9
October 17th: Consumer Sulfur (SDN)
October 19th: Consumer Oxygen (SDN)
Reading: *Moore et al. 2016.pdf; Martinez del Rio and Carleton 2012.pdf
Lab (10/18): Mixing Models (SDN); Linear Mixing Model Exercise (Group Work Time)
Week 10
October 24th: Producer Amino Acid Nitrogen (SDN)
October 26th: Consumer Amino Acid Nitrogen* (SDN)
Reading: *McMahon and McCarthy 2016.pdf; Ramirez et al. 2021.pdf
Lab (10/25): Visualizing Data and Data Reduction; CN Data Corrections
Assignment Due: Bayesian Mixing Model Exercise (Thursday November 4th)
Week 11
October 31st: Producer Amino Acid Carbon (EES)
November 2nd: Consumer Amino Acid Carbon (EES)
Reading: *Elliott Smith et al. 2021.pdf; Larsen et al. 2009.pdf
Lab (11/1): Bayesian Mixing Models (SIMMR); R Installation Instructions; SIMMR Assignment; SIMMR Assignment Data
CLASS SIMMR DEMO: SIMMR Code; geese; sources; corrections
Assignment Due: Linear Mixing Model Exercise
Week 12
November 7th: Consumer Amino Acid Carbon (EES)
November 9th: Consumer Amino Acid Hydrogen (EES)
Reading: *West et al. 2009.pdf; Fogel et al. 2016.pdf
Lab (11/8): Spatial Metrics (SIBER); SIBER Assignment
CLASS SIBER DEMO: SIBER Code; Demo Sea Otter Data
Week 13
November 16th: Spillover/Choose Your Own Adventure
November 18th: Spillover/Choose Your Own Adventure
Reading: *Wang et al. 2015.pdf; Ruess and Chamberlain 2010.pdf
Lab (11/17): Linear Discriminant Analysis (Group Work Time); LDA Assignment; Producer_Library
CLASS LDA DEMO: Essential AA LDA Demo; Consumers; Producers
Assignment Due: SIBER Exercise (Tuesday November 23rd)
Week 14
November 21st: OPEN LECTURE
November 23rd: THANKSGIVING (NO CLASS)
Lab (11/22): NO LAB
Assignment Due: LDA Exercise (Tuesday November 30th)
Project Pre-Proposal Guidelines; Oral Presentation Evaluation
Week 15
November 28th: Jon Dombrosky (Historical Ecology)
December 30th: Nadia Neff (Human Nutrition)
Lab (11/29): Group Work Time
Assignment Due: Submit Project Pre-Proposal for Peer Evaluation (Wednesday December 1st); Peer Review Guidelines
Week 16
December 5th: Group Project Presentations
December 7th: Group Project Presentations
Lab (12/6): Group Project Presentations
Assignment Due: Submit Project Pre-Proposal Peer Evaluations (Wednesday December 8th)
Final Pre-Proposal Due: Monday December 13th