Physiological models of climate change impacts on reptiles and amphibians

CANBERRA, Australia Feb 3-7 2014, immediately after ASH, 2014

(delivered in Sao Paulo, Brazil, Dec. 2012 and Puerto Madryn, Sept 2013) Sinervo, Miles – co-instructors (though R. B. Huey and J. Rohr have contributed pptx’s).

Files labeled TBMA=“To Be Made Available” the week of the workshop

Reading to kick off the course: Behavioral Drive vs. Behavioral Inertia (Huey_et_al_AmNat_2003.pdf).

Day 1 – Feb 3

Readings:

HijmansIJC2005.pdf for an introduction to worldclim.org (I have surfaces in [R] workspaces).

SinervoSci2010.pdf  SinervoSciSOM2010.pdf is key (and ClusellaTrullasSci2011.pdf, SinervoSci2011.pdf).

Useful Historical papers on a variety of taxa:

Amphibians and Disease: PoundsNature_2006.pdf

Species Range Model: ThomasNature2004.pdfThomasNatureSI2004.doc

Coral: Jokiel_et_al_08_coral_mesocosm_oa.pdf

Riebesell_etal_2007_Nature.pdf

Trophic Mismatch:EdwardsRichardsonNature2004_trophic_mismatch.pdf

Southern Oceans: AtkinsonNature2004_salps_seaice.pdf

TreeFLIR_8_hours.mov

BlowOutHoles_8_hours.mov

Mini-Workshop [R] climate surfaces ą xls sheets

BNLL_hr_to_Extinct.pptx

GopherusTb.csv

outputGopherusTb_h_r_Extinct.xls

myExtinctionFunction.docx

PlotExtinction.docx

Te example: Zimmerman_ThermalEcology_Gopherus_1994.pdf

 

 

 

Times

Professor

Schedule

08h30

Sinervo

Introduction to the Course

08h45 - 10h15

1. Introduction to EcoPhysiology

10h15 - 10h30

Questions

10h30 - 11h30

11h20 - 12h00

Miles

Sinervo

2. Operative Env. Temp.

3. Climate Big Facts

4. Climate Models

12h00 - 14h00

lunch

14h00 - 15h15

 

15h30 - 17h00

Sinervo

1. Practical: R climate surfaces mapped onto xls sheets (worldclim.org)

Miles

2. Operative Env. Temp. Models: Frogs and Tortoises

 

Day 2 – Feb 4

 


Topics: How you measure performance and thermal sensitivity. Correlative climate envelop methods (example with Blunt-nosed leopard lizards) vs. Causal Mechanistic Models (Energy-mass balance Eqns., Operative Environmental models).Coding
[R] for global climate Download: HeliothermicSim.rThermoconformerSim.r

Write and modify code for MyExtinctionFn.r.txt, PlotExtinction.r.txt, and simulate climate envelops.

Readings:

HueyPRSB2012.pdf a paper describing ectotherm and endotherm general methods

DzialowskiJThermBiol2005.pdf review of operative environmental temperature methods, How many Te models do you need?

MitchellPRSB2008.pdf a paper on Tuatara and distributional limits set by incubation

PorterTracyLizardEcology.pdf a classic chapter on Energy-Mass Balance methods (TBMA)

BarrowsJAridEnv_Chucks_Torts_2011.pdf a nice Habitat Niche Modeling Approach

Barrows_etal_Uma_climate_change.pdf a nice case study we can analyze for climate extinction

Angilletta2006ThermPerfCurvJThermBiol.pdf How to estimate TPCs

Huey_etalProcRSocB2009.pdf Tb of Thermoconformers

Izam_Kingsolver2005AmNat.pdf Another paper on TPC estimation (Function Value Traits)

Zajitschek_etal2012_BiolJournal.pdf Generalized Additive Mixed Models (GAMMs)

 

08h30

08h45 - 10h15

Miles

1. Metabolism & Peformance and Tb, Tpref

10h15 - 10h30

Questions

10h30 - 12h00

Sinervo

2. Climate Envelopes vs Ecopysiological Envelopes: Why a physiological filter is necessary to estimate extinction risk. a. Hours of Restriction: Integrating Te, Ta, and Behavior, b. Ecophysiological filter models (Lizards – Tb & Te, Frogs – Temp/Hydric Operative Env., Plants – PLCs, Polar Bears – TNZ)

12h00 - 14h00

lunch

14h00 - 17h00

1. Practical – R workspaces for ecophysiology – BNLL and Gopherus data sets

2. Readout Operative Env. Temp. dataloggers

3. performance demo, Tpref demo

4. We will also cover MAXENT modeling in R, in addition to our focus on ecophysiological climate methods

 

Day 3 – Feb 5

 

Topical papers for lizards and other reptiles:

AdolphPorterAmNat.pdf 

DoakEcolApp.pdf

SinervoGopherus_ms.pdf (TBMA)

 

Topics: Species Interactions and climate forcing:

Parasites (Bd) and frogs
Readings:

– de-trending climate data to search for associations

Rohr_and_Raffel_PNAS_2010.pdf (Rohr_and_Raffel_PNAS_2010Supp_Mat.pdf)

Rohr_et_ al_PNAS_2008.pdf 

(Rohr_et_al_PNAS_2008_Supporting_Material.pdf)

Ecophysiological models for host-parasite

Raffel_et_al_NCC_2012.pdf (Raffel_et_al_NCC_2012_Supplement.pdf)

Meylan_etal_2012.pdf 

Paranjpe_etal_EcoEvo_2013.pdf – A case of Behavioral Inertia

 

EXERCISE 1 – [R] code (recreate the Chelo maps)

[R]_console_from_the_CheloBarry_example

CheloBarry.csv

myExtinctionFunctionSouth.doc

 

EXERCISE 2 – [R]: Using this example from Liolaemus, compute extinction risk for each species. For those species without Tb, assume their Tb is the average of the known species. What is the probability of extinction of each species in the year 2080 assuming that the months of reproduction are simply Nov-Jan (three months). You must derive the h_r_critical for each species and compute extinction risk for each separately.  Use the h_r equation from Sinervo et al. 2010 for Liolaemus.

Species_ExamplesSort.xls

 

TECHNIQUE File: For a data file with many replicated sites, this is an xls macro that computes the nearest neighbor distances.

Species.ExamplesPRE-Sort.xls, with the following STEPS:

1)    Sort by species, Lat, Lon

2)    Copy the first >1km column that is updated dynamically and paste it into the second column >1km, USE Paste Special VALUES

3)    Now sort on the second column, delete all the values with 1 and leave the values with 0

4)    You now have a file with duplicate values in a “1km” distance summarized by a single value

 

EXERCISE 3 – Compute h_restriction and h_activity using xls equations =IF(Te model >29.1,1,0) to compute h_restriction and

=IF(Te model > 20, 1, 0) to compute h_activity

Tortuga_Te_PuertoMadrynBigCh1SmallCh2.csv

 

EXERCISE 4 – Temperature Sensitivity of Performance

Compute the instantaneous performance of Anolis in each environment over the course of the 24-h day at PtaSalinas using the non-linear equation in CurveFitting, below.

ThermalSens.csv

Curve_Fitting.xlsx  -- setting up performance calcs for xls

PtaSalinasFebTe.csv – data on Te of Anolis in the Shade and Open

code_for_digitalTime_and_Rplots_of_AnolisTe.doc

 

 

 

08h30

Notes and revisions

08h45 - 10h15

Sinervo

1. a) Climate Variability-Bd-Frog Extinctions b) Hydric restriction, Te and Frogs

10h15 - 10h30

Questions

10h30 - 11h30

Sinervo

1. Why are tropical lizards more vulnerable to extinction

11h30 - 12h00

Miles

2. Plasticity and Maternal Effects

12h00 - 14h00

lunch

14h00 - 17h00

1. Practical

xls interpolation of thermal performance curves and Te

2. Thermal preference demo

 

Day 4 – Feb 6

 

 

08h30

Notes and Revisions

Topics: An introduction to population dynamic methods for developing causal mechanistic models, the Leslie matrix, Population Viability Analyses Cellular Automata approaches in [R],paleoclimate, Adaptation to Climate Change
Readings: [R code for a cellular automata TBMA]

Nogues-Bravo_GlobalEcolBiogeogr_2009.pdf

Bartlein1998_21K_paleoclimate.pdf

Hoffmann_Sgro_nature_2011_adaptation.pdf

 

08h45 - 10h15

Miles

1. Population Ecology and Demography; Leslie Matrix and Population Projection

10h15 - 10h30

Preguntas

10h30 - 11h15

Sinervo

2. a) Population Dynamics and Mechanistic Models; Paleoclimates, pptx TBMA

11h15 - 12h00

Sinervo

b) Cellular Automata Approaches; Evolutionary Response to Climate Warming, pptx TBMA

c) Building in the impacts of other Anthropogenic forcers: impacts of forest fragmentation and solar farms, pptx TBMA

12h00 - 14h00

14h00 - 17h00

Sinervo Miles

1. Practical R code for Population ecology as a function of climate

 

Day 5 – Feb 7

Readings on phylogeny:

Freckleton_2009.pdf

Revell_2009.pdf

OMeara2012EvolutionaryInterencesPhylogeniesAREES.pdf

Pagel_1999_Inferring_Rate_of_Evolution.pdf

Schluter_et_al_1997_evolution_likelihood_of_ancestor_states.pdf

08h30

Notes and Revisions

08h45 - 10h15

Miles

1. Mesquite and Comparative Phylogenetic Methods. 1. Introduction to Mesquite and R. Ancestor Character Estimation, Phylogenetic Signal

10h15 - 10h30

Questions

10h30 - 12h00

2. Statistical methods incoporating phylogenetic information.

12h00 - 14h00

Lunch

14h00 - 17h00

1. Practical – [R] and Mesquite phylogenetic methods