Seth Newsome (SDN)

[email protected]

Alexi Besser (ACB)

[email protected]

BIOL 409/509

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 24th: Introductions, Expectations, and Ecological Origins

August 26th: Definitions and Fractionation (ACB)

Reading: *Ben-David and Flaherty 2012.pdf

Lab (8/25): Group Project Discussion and Form Groups

Week 2

August 31st: Isotopes in Water (SDN)

September 2nd: Isotopes in Plant Water* (SDN)

Reading: *Dawson 1998; Bowen et al. 2005.pdf

Lab (9/1): Experimental Design and Field Methods

Assignment Due (9/3): Ideas for Group Projects

Week 3

September 7th: Primary Producer Carbon (ACB)

September 9th: Primary Producer Carbon* (ACB)

Reading: *Driscoll et al. 2020.pdf; Cerling et al. 1997.pdf

Lab (9/8): Introduction to Gear I: CSI Tour (EA/TCEA/GB–IRMS)

Week 4

September 14th: Primary Producer Nitrogen I (SDN)

September 16th: Primary Producer Nitrogen II* (SDN)

Reading: *Austin and Vitousek 1998.pdf; Amundson et al. 2003.pdf

Lab (9/15): Sample Preparation I: Decalcification, Lipid-Extraction, Microbalance; Sample Preparation Protocols

Assignment Due: Project Description and References Guidelines (50 points)

Week 5

September 21st: Consumer Carbon I (ACB)

September 23rd: Consumer Carbon II* (ACB)

Reading: *Kurle et al. 2014.pdf; Kelly 2000.pdf

Lab (9/22): Introduction to Gear II: CSI Tour (GCC–IRMS and Picarro)

Week 6

September 28th: Consumer Nitrogen (SDN)

September 30th: Consumer Nitrogen* (SDN)

Reading: *Croll et al. 2005.pdf; Vanderklift and Ponsard 2003.pdf

Lab (9/29): Sample Preparation II: Sample Homogenization, Cryodistillation

Assignment Due: Experimental Design and Methods Guidelines (50 Points); Example: SEV Smammals

Week 7

October 5th: Consumer Hydrogen (SDN)

October 7th: Isotopic Niches* (Dr. Philip Manlick)

Reading: *Newsome et al. 2007.pdf; Clegg et al. 2003.pdf

Lab (10/6): Group Work Time

Week 8

October 12th: Consumer Oxygen* (ACB)

October 14th: FALL BREAK (NO CLASS)

Reading: *Wang et al. 2009.pdf


Assignment Due: Final Sample Submission Deadline (CSI)

Week 9

October 19th: Isotopic Incorporation (SDN)

October 21st: IsoClocks* (Dr. Oliver Shipley)

Reading: *Moore et al. 2016.pdf; Martinez del Rio and Carleton 2012.pdf

Lab (10/20): Mixing Models (SDN); Linear Mixing Model Exercise (Group Work Time)

Week 10

October 26th: Amino Acid Carbon (ACB)

October 28th: Amino Acid Carbon Fingerprints (Dr. Philip Manlick)

Reading: *Elliott Smith et al. 2021.pdf; Larsen et al. 2009.pdf

Lab (10/27): 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 11

November 2nd: Producer Amino Acid Nitrogen (ACB)

November 4th: Consumer Amino Acid Nitrogen* (SDN)

Reading: *McMahon and McCarthy 2016.pdf; Ramirez et al. 2021.pdf

Lab (11/3): Visualizing Data and Data Reduction; CN Data Corrections

Assignment Due: Bayesian Mixing Model Exercise (Thursday November 4th)

Week 12

November 9th: Consumer Amino Acid Hydrogen (SDN)

November 11th: Forensic Applications* (Dr. Christy Mancuso)

Reading: *West et al. 2009.pdf; Fogel et al. 2016.pdf

Lab (11/10): Spatial Metrics (SIBER); SIBER Assignment

CLASS SIBER DEMO: SIBER Code; Demo Sea Otter Data


Week 13

November 16th: Fatty Acid Carbon and Hydrogen (ACB)

November 18th: Fatty Acid Carbon and Hydrogen* (ACB)

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 23rd: Triple Oxygen Isotopes* (Dr. Nico Lubcker)


Reading: *Whiteman et al. 2019.pdf


Assignment Due: LDA Exercise (Tuesday November 30th)

Project Pre-Proposal Guidelines; Oral Presentation Evaluation

Week 15

November 30th: Marine Mammal Applications (Drs. Geraldine Busquets Vass and Nico Lubcker)

December 2nd: Marine Mammal Applications (Drs. Geraldine Busquets Vass and Nico Lubcker)

Lab (12/1): Group Work Time

Assignment Due: Submit Project Pre-Proposal for Peer Evaluation (Wednesday December 1st); Peer Review Guidelines

Week 16

December 7th: Group Project Presentations

December 9th: Group Project Presentations

Lab (12/8): Group Project Presentations

Assignment Due: Submit Project Pre-Proposal Peer Evaluations (Wednesday December 8th)

Final Pre-Proposal Due: Monday December 13th

Supplemental Readings