ELEMENTAL ECOLOGY FALL 2023

Instructors

Seth Newsome (SDN)

[email protected]

Emma Elliott Smith (EES)

[email protected]

Teaching Assistant

Joshua Cortez (JC)

[email protected]

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 19th: Introductions, Expectations, and Isotopic Definitions

Lab (8/20): Group Project Discussion and Form Groups

August 21st Definitions and Fractionation* (EES)

Reading: *Ben-David and Flaherty 2012.pdf; Newsome et al. 2007.pdf

Week 2

August 26th: Isotopes in Water (SDN)

Lab (8/27): Research Questions and Experimental Design

August 28th: Isotopes in Plant Water* (SDN)

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

Assignment Due (9/1): Ideas for Group Projects (10 Points)

Week 3

September 2nd: Primary Producer Carbon I (EES)

Lab (9/3): Introduction to Gear I: CSI Tour (EA/TCEA/GB–IRMS)

September 4th: Primary Producer Carbon II* (EES)

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

Week 4

September 9th: Consumer Carbon (EES)

Lab (9/10): Sample Preparation I: Decalcification, Lipid-Extraction, Microbalance; Sample Preparation Protocols

September 11th: Primary Producer Nitrogen* (SDN)

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

Assignment Due (9/15): Project Description and References Guidelines (40 points)

Week 5

September 16th: Primary Producer Nitrogen (SDN)

Lab (9/17): Sample Preparation II: Sample Homogenization, Cryodistillation

September 18th: EXAM #1 (High School IsoCamp)

Reading: Kelly 2000.pdf

Week 6

September 23rd: Consumer Carbon* (EES)

Lab (9/24): Introduction to Gear II: CSI Tour (GCC–IRMS and Picarro)

September 25th: Consumer Nitrogen (SDN)

Reading: *Kurle et al. 2014.pdf; Vanderklift and Ponsard 2003.pdf

Week 7

September 30th: Consumer Nitrogen* (SDN)

Lab (10/1): Mixing Models (SDN); Linear Mixing Model Exercise; Phillips and Koch 2002.pdf

October 2nd: Isotopic Incorporation (SDN)

Reading: *Croll et al. 2005.pdf, Moore et al. 2016.pdf

Week 8

October 7th: Consumer Hydrogen* (SDN)

Lab (10/8): FALL BREAK (NO CLASS)

October 9th: FALL BREAK (NO CLASS)

Reading: *Estep and Dabrowski 1980.pdf; Hobson et al. 1999.pdf

Assignment Due (10/11): Experimental Design and Methods Guidelines (50 Points); Example: SEV Smammals

Week 9

October 14th: Consumer Sulfur (SDN)

Lab (10/15): Data Reduction: IsoCamp 2022 Plants RAW; CSI Working Standard Values

October 16th: Consumer Oxygen (EES)

Assignment Due (10/20): Linear Mixing Models

Week 10

October 21st: Amino Acid Carbon (EES)

Lab (10/22): Bayesian Mixing Models (SIMMR); R Installation Instructions; SIMMR Assignment; SIMMR Assignment Data

October 23rd: Amino Acid Carbon* (EES)

Reading: *Elliott Smith et al. 2021.pdf; Larsen et al. 2009.pdf; O'Brien et al. 2002.pdf; Phillips et al. 2014.pdf

CLASS SIMMR DEMO: SIMMR Code; geese; sources; corrections; SIMMR GitHub

Week 11

October 28th: Producer Amino Acid Nitrogen (SDN)

Lab (10/29): Group Work Time

October 30th: Consumer Amino Acid Nitrogen* (SDN)

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

Assignment Due: Bayesian Mixing Model Exercise (November 3rd)

Week 12

November 4th: GUEST LECTURE (Mertz)

Lab (11/5): Spatial Metrics (SIBER); SIBER Assignment; SIBER Assignment Data

November 6th: GUEST LECTURE (Murrell)

Reading: Newsome et al. 2020.pdf (11/7); Busquets-Vass et al. In Review.pdf (11/9)

CLASS SIBER DEMO: SIBER Code; Demo Sea Otter Data

Week 13

November 11th: Amino Acid Hydrogen* (SDN)

Lab (11/12): Group Work Time: Draft Figures

November 13th: Fatty Acid Carbon and Hydrogen (SDN)

Reading: *Fogel et al. 2016.pdf; Wang et al. 2015.pdf; Ruess and Chamberlain 2010.pdf

Assignment Due: SIBER Exercise (November 17th)

Week 14

November 18th: Data Statistical Session: Essential AA LDA Demo; LDA Assignment; Producer_Library

Lab (11/19): NO LAB (THANKSGIVING)

November 20th: GUEST LECTURE (NEFF)

Project Pre-Proposal Guidelines; Oral Presentation Evaluation

Week 15

November 25th: Data Statistical Session: Essential AA LDA Demo; LDA Assignment; Producer_Library

Lab (11/26): NO LAB (THANKSGIVING)

November 27th: NO CLASS (THANKSGIVING)

Assignment Due: Submit Project Pre-Proposal for Peer Evaluation (Wednesday November 26th); Peer Review Guidelines

Week 16

December 2nd: Group Project Presentations

Lab (12/3): Group Project Presentations

December 4th: Group Project Presentations

Assignment Due (12/4): Project Pre-Proposal Peer Evaluations

Final Pre-Proposal Due: Monday December 11th

Supplemental Readings