Elemental Ecology (CRN 30535/53802)

University of New Mexico, Fall 2015

Tuesday & Thursday 11:00AM–12:15PM (Castetter Hall 107)

Office Hours: Wednesday 2:00–3:00PM (Castetter Hall 190)

Primary Instructor

Dr. Seth Newsome (Animal Ecology)

Guest Instructors

Dr. Dave Hanson (Plant Eco-Physiology)

Dr. Sherry Nelson (Evolutionary Anthropology)

Dr. Blair Wolf (Animal Eco-Physiology)


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


            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


            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 (August 8 & 20)

      8/18: Introductions, Expectations, Ecological Origins

        8/20: Definitions & Fractionation

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

Week 2 (August 25 & 27)

        8/25: Center for Stable Isotopes Tour & Gear

        8/27: Water Isotopes

        Required Reading: Brooks et al. 2010, Jasechko et al. 2013

Week 3 (September 1 & 3)

        9/1: Plant Water Isotopes

        9/3: Paper Discussion (Dawson 1998) & Sample Preparation

        Required Reading: Dawson 1998

Week 4 (September 8 & 10)

        9/8: Primary Producer Carbon

        9/10: Paper Discussion (Ehleringer et al. 1997, Cerling et al. 2009)

        Required Reading: O'Leary 1988, Pataki et al. 2003, Raven et al. 2002

Week 5 (September 15 & 17)

        9/15: Guest Instructor Dr. Dave Hanson & Paper Discussion (Bloemen et al. 2013)

        9/17: Primary Producer Nitrogen

        Required Reading: Handley and Raven 1992, Austin and Vitousek 1998, Evans 2001

Week 6 (September 22 & 24)

        9/22: Animal Carbon

        9/24: Guest Instructor Dr. Sherry Nelson & Paper Discussion (Nelson 2013)

        Required Reading: Fry et al. 1978, Cerling et al. 1998, Nelson 2013,

        Sterner & Elser Chapter 4

Week 7 (September 29 & October 1)

        9/29: Animal Carbon

        10/1: Animal Carbon

        Required Reading: Polischuk et al. 2001, Vanderklift and Ponsard 2003

Week 8 (October 6 & 8)

        10/6: Guest Instructor Dr. Blair Wolf & Paper Discussion (Wolf et al. 2002)

        10/8: Fall Break

        Required Reading: Wolf et al. 2002

Week 9 (October 13 & 15)

        10/13: Animal Carbon

        10/15: Animal Carbon & Animal Nitrogen

        Required Reading: Clegg et al. 2003, Rubenstein and Hobson 2004

Week 10 (October 20 & 22)

        10/20: Animal Hydrogen

        10/22: Animal Hydrogen & Paper Discussion (Wunder et al. 2012)

        Required Reading: Carleton et al. 2004, Martinez del Rio et al. 2009

Week 11 (October 27 & 29)

        10/27: Isotopic Incorporation

        10/29: Mixing Models

        Required Reading: Phillips and Koch 2002, Parnell et al. 2010, Phillips 2012

Week 12 (November 3 & 5)

        11/3: Interpretive Tools: SIAR & Classroom Exercise (Parnell et al. 2010)

        11/5: Interpretive Tools: Trophic Level & Spatial Metrics (Jackson et al. 2011)

        Required Reading: Post 2002, Layman et al. 2007

Week 13 (November 10 & 12)

        11/10: Amino Acid Carbon

        11/12: Amino Acid Carbon & Paper Discussion (O'Brien et al. 2002)

        Required Reading: Hare et al. 1991, O'Brien et al. 2002, Newsome et al. 2011

Week 14 (November 17 & 19)

        11/17: Amino Acid Nitrogen

        11/19: Amino Acid Nitrogen & Paper Discussion (Bradley et al. 2015)

        Required Reading: McClelland and Montoya 2002, Popp et al. 2007

Week 15 (November 24 & 26)

        11/24: Amino Acid Hydrogen & Paper Discussion (Fogel et al. 2016)

        11/26: Thanksgiving

Week 16 (December 1 & 3)

        12/1 & 12/3: Student Presentations

Elemental Ecology Syllabus

Reading Report Form

Pre-Proposals due September 1st (Guidelines)

CSI Sample Submission Form.xlsx

Project Paper Guidelines

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 Files:

Exercise #2

        Excel File (Exercise #2.xlsx)