Elemental Ecology (CRN 59996/60066)

University of New Mexico, Fall 2017

Lecture: Tuesday & Thursday 9:30AM–10:45PM (Castetter Hall 107)

Lab: Wednesday 2:00–4:00PM (Location Varies)

Office Hours:

    Newsome: Tuesday 11:00–12:00 (Castetter Hall 190)

    Pages Barcelo: Thursday 11:00–12:00 (Marron Hall 216)

Primary Instructor

Dr. Seth Newsome (Animal Ecology and Eco-Physiology)


Teaching Assistant

Laura Pages Barcelo (Animal Ecology)


Guest Instructors

Dr. John Whiteman (Animal Eco-Physiology)

Laura Pages Barcelo (Animal Ecology)

Emma Elliott Smith (Animal Ecology)

 

Isotopic Ecology Overview

            Newsome et al. 2007c.pdf; Wolf et al. 2008.pdf


Carbon Isotopes in Primary Producers, Soils, and Sediments

            Farquhar et al. 1982.pdf; Fogel and CIfuentes 1991.pdf; Ehleringer et al. 2000.pdf;

            Dawson et al. 2002.pdf; Raven et al. 2002.pdf


Carbon Isotopes in Animals

            Kelly 2000.pdf; Howland et al. 2003.pdf; Sponheimer et al. 2003.pdf; Passey et al. 2005.pdf


Notation and Gear

            Fry et al. 1992.pdf; Hayes 2001.pdf; Groning et al. 2009.pdf


C3/C4 Applications

            Koch et al. 1995.pdf; O'Brien et al. 2002.pdf; McCullagh et al. 2005.pdf


Australia (OZ)

            Johnson et al. 1998.pdf; Johnson et al. 1999.pdf; Johnson et al. 2005.PDF; Miller et al. 2005.pdf


Nitrogen Isotopes in Primary Producers, Soils, and Sediments

            Peterson and Fry 1987.pdf; Fogel and Cifuentes 1991.pdf; Evans 2001.pdf;

            Dawson et al. 2002.pdf


Nitrogen Isotopes in Animals

            Minagawa and Wada 1984.pdf; Kelly 2000.pdf; Pearson et al. 2003.pdf;

            Sponheimer et al. 2003.pdf; Murphy and Bowman 2006.pdf


Trophic Discrimination Factors

            Sick et al. 1997.pdf; Schoeller 1999.pdf; Post 2002.pdf; Pearson et al. 2003.pdf;

            Vanderklift and Ponsard 2003.pdf; Trueman et al. 2005.pdf; Tibbets et al. 2008.pdf


Mangroves

            Cifuentes et al. 1996.pdf; McKee et al. 2002.pdf; Bouillon et al. 2008.pdf; Fogel et al. 2008.pdf


Hydrogen Biochemistry

            Estep and Hoering 1980.pdf; Sessions et al. 1999.pdf; Whiticar 1999.pdf; Hayes 2001.pdf


Hydrogen in Primary Producers

            Estep 1981.pdf; Estep and Hoering 1981.pdf; Wassenaar and Hobson 1998.PDF;

            Terwilliger et al. 2002.pdf


Hydrogen in Animals Avian Ecology

            Hobson et al. 1999.pdf; Kelly et al. 2002.pdf; Hobson et al. 2004.pdf; Bowen et al. 2005.pdf;

            Bearhop et al. 2005.pdf; Wunder et al. 2005.pdf; Wunder and Norris 2008.pdf;

            Farmer et al. 2008.pdf


Laboratory Protocols

            Koch et al. 1997.pdf; Teece and Fogel 2004.pdf; Sessions 2006.pdf


Animal Movement and Migration

            Hobson et al. 1999.pdf; Rubenstein and Hobson 2004.pdf


Tracing Foodwebs with Oxygen Isotopes

            Sternberg et al. 1984.pdf; Guy et al. 1993.pdf; Gat 1996.pdf; Kohn et al. 1996.pdf;

            Colman et al. 2005.pdf; Kreuzer-Martin et al. 2005.pdf; O'Brien and Wooller 2007.pdf


Isotope Fractionation by Microorganisms

            Macko and Estep 1984.pdf; Coffin et al. 1990.pdf; Habicht and Canfield 1997.pdf;

            Fogel and Tuross 1999.pdf; Hobbie et al. 2005.pdf; Ziegler et al. 2005.pdf;

            Glaser et al. 2006.pdf


Isotopic Incorporation

            McKechnie et al. 2004.pdf; Martinez del Rio and Wolf 2005.pdf;

            Carleton and Martinez del Rio 2005.pdf; Carleton et al. 2006.pdf; Cerling et al. 2007.pdf;    

            Carleton et al. 2008.pdf; Martinez del Rio et al. 2009.pdf


Astrobiology

            Farquhar et al. 2000.pdf; House et al. 2000.pdf; Orphan et al. 2001.pdf;

            Eigenbrode et al. 2006.pdf; Grady and Wright 2006.pdf; Schweizer et al. 2007.pdf


Compound Specific Isotope Analysis

            Macko et al. 1987.pdf; Freeman et al. 1990.pdf; Hare et al. 1991.pdf; Stott et al. 1997.pdf;

            Fogel and Tuross 2002.pdf; Scott et al. 2006.pdf; Sessions 2006.pdf


Isotopic Routing and Mixing Models

           Ambrose and Norr 1993.pdf; Phillips and Koch 2002.pdf; Phillips and Gregg 2003.pdf;

            Moore and Semmens 2008.pdf; Martinez del Rio et al. 2009.pdf; Kelly and Martinez del Rio 2009;


Pregnancy, Nutritional Stress, and Nursing

            Fogel et al. 1989.pdf; Hobson et al. 1993.pdf; Polischuk et al. 2001.pdf;

            Oelbermann and Scheu 2002.pdf; Fuller et al. 2004.pdf; Fuller et al. 2005.pdf

Other Topics and Related Publications

Week 1

      8/22: Introductions, Expectations, Ecological Origins

        8/23: Project Discussion (Ben-David and Flaherty 2012)

        8/24: Definitions & Fractionation

        More Reading: Sharp Chapter 2, Sterner & Elser Chapter 2


Week 2

        8/29: Water Isotopes

        8/30: Introduction to Gear I: Conflo and IRMS.pptx (Castetter 41)

        8/31: Water Isotopes (Bowen et al. 2005)

        More Reading: Jasechko et al. 2013


Week 3

        9/5: Plant Water Isotopes (Dawson 1998)

        9/6: Experimental Design and Campus Fieldwork (Castetter 41)

        9/7: Primary Producer Carbon

        More Reading: O'Leary 1988

        Assignment Due (9/7): Project Description and Reference List


Week 4

        9/12: Primary Producer Carbon (Ehleringer et al. 1997)

        9/13: Introduction to Gear II: EA and TCEA (Castetter 41)

        9/14: Primary Producer Carbon

        More Reading: Raven et al. 2002, Pataki et al. 2003


Week 5

        9/19: Primary Producer Nitrogen

        9/20: Introduction to Gear III: Gas-Bench, PICARRO, and GC-C (Castetter 41)

        9/21: Primary Producer Nitrogen (Austin and Vitousek 1998)

        More Reading: Handley and Raven 1992, Evans 2001

        Assignment Due (9/21): Project Experimental Plan and Methods


Week 6

        9/26: Animal Carbon

        9/27: Sample Preparation I (Castetter 237)

        9/28: Animal Carbon (Cerling et al. 1998)

        More Reading: Fry et al. 1978, Sterner & Elser Chapter 4


Week 7

        10/3: Animal Carbon

        10/4: Sample Preparation II (Castetter 237)

        10/5: Animal Nitrogen (Carleton et al. 2006)

        More Reading: Vanderklift and Ponsard 2003


Week 8

        10/10: Animal Nitrogen

        10/11: FALL BREAK

        10/12: FALL BREAK

        More Reading: Post 2002


Week 9

        10/17: Animal Nitrogen

        10/18: Raw Data Corrections & Graphing Data

        10/19: Isotopic Incorporation (Tieszen et al. 1983)

        More Reading: Martinez del Rio et al. 2009


Week 10

        10/24: Animal Hydrogen

        10/25: Mixing Models I

        10/26: Animal Hydrogen (Clegg et al. 2003)

        More Reading: Rubenstein and Hobson 2004, Wunder et al. 2012


Week 11

        10/31: Mixing Models

        11/1: Mixing Models II

        11/2: Amino Acid Carbon (Phillips 2012)

        More Reading: Phillips and Koch 2002, Parnell et al. 2010


Week 12

        11/7: Amino Acid Carbon (O'Brien et al. 2002)

        11/8: Spatial Metrics

        11/9: Amino Acid Carbon – Emma Elliott Smith

        More Reading: Hare et al. 1991, Newsome et al. 2011


Week 13

        11/14: Amino Acid Nitrogen (McMahon et al. 2016)

        11/15: Spatial Metrics (Jackson et al. 2011)

        11/16: Amino Acid Nitrogen (McClelland and Montoya 2002)

        More Reading: Layman et al. 2007, Popp et al. 2007,


Week 14

        11/21: Amino Acid Hydrogen (Fogel et al. 2016)

        11/22: THANKSGIVING

        11/23: THANKSGIVING

        More Reading:


Week 15

        11/28: Alkanes

        11/29:

        11/30: Fatty Acid Carbon and 17O – Dr. John Whiteman

        More Reading:


Week 16

        12/5–12/7: Student Presentations

        Assignment Due (9/7): Pre-Proposal

Exercise #1

        Excel File (Exercise #1.xls)

        Clark and Fritz 1997 Inside Cover

In Class Exercise #2

    SIAR (Stable Isotope Analysis in R)

            SIAR for Ecologists

            SIAR Commands   

            UHURU Rodents

                Rodents (TAHA.txt, SAME.txt, GERO.txt, ELRU.txt)

                Food (UHURU_Sources.txt)

                Trophic Discrimination Factors (UHURU_TDF.txt)

            Alaskan Wolves

                Wolves (NAPCA.txt, NAPCB.txt, NAPCC.txt)

                Prey (NAPC_Sources.txt)

                Trophic Discrimination Factors (NAPC_TDF.txt)

In Class Exercise #2   

    SIBER (Stable Isotope Bayesian Ellipses in R)

            SIBER_Code.R

            SIBER Files:

Exercise #2

        Excel File (Exercise #2.xlsx)