Taxonomic uncertainty and decision making for biosecurity: spatial models

for myrtle/guava rust: Online Supplementary material

J. Elith, J. Simpson, M. Hirsch and M. A. Burgman

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Online Appendix 1: Species locations

sp nativeuredo27 x y country location source1

puccinia 1 0 -65.50000 -27.00000 Argentina Tucuman Simpson unpubl. – USDA (2009)puccinia 1 0 -58.98333 -27.45000 Argentina Resistencia Simpson unpubl. – Di Fonzo (1946)puccinia 1 0 -56.10000 -27.40000 Argentina Encarnacion Simpson unpubl. – Acuna & Garran (2004)puccinia 1 0 -59.53333 13.16667 Barbados Bridgetown Simpson unpubl. – Baker & Dale (1948)puccinia 1 0 -43.31667 -15.80000 Brazil Janauba Simpson unpubl. – USDA (2009)puccinia 1 0 -44.66667 -14.18333 Brazil Itaguai Simpson unpubl. – USDA (2009)puccinia 1 0 -41.10000 -18.10000 Brazil Espirito Santo Simpson unpubl. – Hennen et al. (2005)puccinia 1 0 -40.10000 -18.10000 Brazil Teixeira de Freitas Simpson unpubl. – USDA (2009)puccinia 1 0 -42.81667 -5.08333 Brazil Teresina Simpson unpubl. – USDA (2009)puccinia 1 0 -42.90000 -20.40000 Brazil Pomte Nova Simpson unpubl. – USDA (2009)puccinia 1 0 -40.26667 -19.81667 Brazil Aracruz Simpson unpubl. – USDA (2009)puccinia 1 0 -43.33333 -22.95000 Brazil Sao Francisco Simpson unpubl. – USDA (2009)puccinia 1 0 -43.23333 -22.90000 Brazil Rio de Janeiro Simpson unpubl. – Hennen et al. (2005)puccinia 1 0 -49.05000 -26.93333 Brazil Blumenau Simpson unpubl. – USDA (2009)puccinia 1 0 -35.71667 -9.66667 Brazil Maceio Simpson unpubl. – USDA (2009)puccinia 1 0 -48.93333 -27.10000 Brazil Brusque Simpson unpubl. – USDA (2009)puccinia 1 0 -34.90000 -8.05000 Brazil Recife Simpson unpubl. – USDA (2009)puccinia 1 0 -51.38333 0.71667 Brazil Porto Grande Simpson unpubl. – USDA (2009)puccinia 1 0 -51.28333 -0.11667 Brazil Mazagao Novo Simpson unpubl. – USDA (2009)puccinia 1 0 -51.05000 0.03333 Brazil Macapa Simpson unpubl. – USDA (2009)puccinia 1 0 -75.58333 6.25000 Colombia Medellin Simpson unpubl. – Hennen et al. (2005)puccinia 1 0 -75.59203 6.24115 Colombia Medellin USDA (2010)puccinia 1 0 -84.10000 9.93333 Costa Rica Ciudad Colon Simpson unpubl. – USDA (2009)puccinia 1 0 -79.98333 21.80000 Cuba Trinidad Simpson unpubl. – Arnold (1986)puccinia 1 0 -82.76667 22.81667 Cuba Artemisa Simpson unpubl. – Arnold (1986)puccinia 1 0 -74.50000 20.35000 Cuba Baracoa Simpson unpubl. – Arnold (1986)puccinia 1 0 -70.51667 19.21667 Dominican Republic La Vega USDA (2010)puccinia 1 0 -70.51667 19.38333 Dominican Republic Moca USDA (2010)

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puccinia 1 0 -69.90000 18.46667 Dominican Republic Santo Domingo Simpson unpubl. – Kern et al. (1933)puccinia 1 0 -70.71700 19.73300 Dominican Republic Puerto Plata Cupey USDA (2010)puccinia 1 0 -78.98330 -2.28330 Ecuador Huigra USDA (2010)puccinia 1 0 -78.41667 -1.40000 Ecuador Banos Simpson unpubl. – Stevenson (1926)puccinia 1 0 -72.33333 18.53333 Haiti Port-au-Prince Simpson unpubl.puccinia 1 0 -76.80000 18.00000 Jamaica Kingston Simpson unpubl. – USDA (2009)puccinia 1 0 -77.45000 18.38300 Jamaica Stewart Town USDA (2010)puccinia 1 0 -77.36667 18.03333 Jamaica Mandeville Simpson unpubl. – USDA (2009)puccinia 1 0 -77.11670 18.26670 Jamaica Moneague USDA (2010)puccinia 1 0 -76.71670 18.03330 Jamaica Gordon Town USDA (2010)puccinia 1 0 -77.48333 18.16666 Jamaica Christiana USDA (2010)

puccinia 1 0 -77.71670 18.25000 JamaicaQuickStep, St Elizabeth USDA (2010)

puccinia 1 0 -76.71670 18.06670 Jamaica Newcastle USDA (2010)puccinia 1 0 -57.00000 -24.50000 Paraguay Rosario Simpson unpubl. – Hennen et al. (2005)puccinia 1 0 -66.16667 18.11667 Puerto Rico Cayey Simpson unpubl. – Arthur (1915)puccinia 1 0 -66.00000 18.40000 Puerto Rico Bayamon Simpson unpubl. – Arthur (1915)puccinia 1 0 -66.08425 18.05150 Puerto Rico Guayama USDA (2010)puccinia 1 0 -66.39139 18.22888 Puerto Rico Orocovis USDA (2010)puccinia 1 0 -67.07563 18.17455 Puerto Rico Mayaguez USDA (2010)puccinia 1 0 -66.98028 18.18278 Puerto Rico Maricao USDA (2010)puccinia 1 0 -66.70000 18.16667 Puerto Rico Adjuntas Simpson unpubl. – USDA (2009)puccinia 1 0 -61.51667 10.65000 Trinidad Lady Chancellor Hill Simpson unpubl. – USDA (2009)puccinia 1 0 -60.80000 11.20000 Trinidad Plymouth Simpson unpubl. – Baker & Dale (1951)puccinia 1 0 -66.89828 10.49605 Venezuela Caracas USDA (2010)puccinia 0 0 -96.13333 19.16000 Mexico Veracruz USDA (2010)puccinia 0 0 121.60000 23.98333 Taiwan Hualien Simpson unpubl. – Wang (1992)puccinia 0 0 -117.01746 33.23657 USA San Diego USDA (2010)puccinia 0 0 -156.56667 20.56667 USA Makiki Simpson unpub - Hawaiipuccinia 0 0 -157.85000 21.30000 USA Manoa Simpson unpub - Hawaiipuccinia 0 0 -82.45000 27.93333 USA Tampa Simpson unpub - Floridapuccinia 0 0 -81.86667 26.63333 USA Fort Myers Simpson unpub - Floridapuccinia 0 0 -157.71667 21.35000 USA Waimanalo Simpson unpub - Hawaii

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puccinia 0 0 -82.66667 27.76667 USA St Petersburg Simpson unpub - Floridapuccinia 0 0 -80.31667 27.43333 USA Fort Pierce Simpson unpub - Floridapuccinia 0 0 -156.50000 20.88333 USA Wailuku Simpson unpub - Hawaiipuccinia 0 0 -159.36667 21.96667 USA Lihue Simpson unpub - Hawaiipuccinia 0 0 -80.18333 25.76667 USA Miami Simpson unpub - Floridapuccinia 0 0 -80.05000 26.70000 USA West Palm Beach Simpson unpub - Floridapuccinia 0 0 -80.13333 26.11667 USA Fort Lauderdale Simpson unpub - Floridapuccinia 1 1 -58.45000 -34.60000 Argentina BuenosAires Simpson unpubl. – Spegazzini (1898)puccinia 1 1 -54.63333 -26.40000 Argentina Eldorado Simpson unpubl. – Spegazzini (1898)puccinia 1 1 -47.63333 -22.71667 Brazil Piracicaba Simpson unpubl. – USDA (2009)puccinia 1 1 -48.31667 -21.26667 Brazil Jaboticabal Simpson unpubl. – USDA (2009)puccinia 1 1 -42.88333 -20.75000 Brazil Viçosa Simpson unpubl. – USDA (2009)puccinia 1 1 -51.91667 -23.41667 Brazil Maringa Simpson unpubl. – USDA (2009)puccinia 1 1 -47.08333 -22.90000 Brazil Campinas Simpson unpubl. – USDA (2009)puccinia 1 1 -48.43333 -22.86667 Brazil Botucatu Simpson unpubl. – USDA (2009)puccinia 1 1 -43.93333 -19.91667 Brazil Belo Horizonte Simpson unpubl. – USDA (2009)puccinia 1 1 -45.00000 -21.23333 Brazil Lavras Simpson unpubl. – USDA (2009)puccinia 1 1 -46.61667 -23.53333 Brazil Sao Paulo Simpson unpubl. – Hennen et al. (2005)puccinia 1 1 -47.93333 -15.78333 Brazil Brasilia Simpson unpubl. – USDA (2009)puccinia 1 1 -43.76667 -21.23333 Brazil Barbaccena Simpson unpubl. – Hennen et al. (2005)puccinia 1 1 -51.31667 -30.10000 Brazil Guaiba Simpson unpubl. – USDA (2009)puccinia 1 1 -49.23333 -25.28333 Brazil Colombo Simpson unpubl. – USDA (2009)puccinia 1 1 -51.16667 -29.83333 Brazil Sao Leopoldo USDA (2010)puccinia 1 1 -58.00000 -31.40000 Uruguay Concordia Simpson unpubl. – Perez et al. (2010)uredo 1 1 -58.51667 -34.46667 Argentina Acussuso Simpson et al. (2006)uredo 1 1 -58.08333 -33.25000 Uruguay Paysandu Perez et al. (2010)uredo 1 1 -56.33330 -34.66670 Uruguay Canelones Perez et al. (2010)uredo 1 1 -57.36667 -32.41667 Uruguay Rio Negro Perez et al. (2010)uredo 1 1 -55.95000 -31.68333 Uruguay Tacuarembo1 Perez et al. (2010)uredo 1 1 -55.95000 -31.58333 Uruguay Tacuarembo2 Perez et al. (2010)uredo 1 1 -55.95000 -31.55000 Uruguay Tacuarembo3 Perez et al. (2010)uredo 1 1 -54.73333 -34.31667 Uruguay Maldonado Perez et al. (2010)uredo 1 1 -55.15000 -34.55000 Uruguay Lavalleja Perez et al. (2010)

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uredo 0 1 -76.71700 18.08300 Jamaica Hardwar Gap Simpson et al. (2006)1Footnote regarding sources: Simpson unpubl. is a draft Pest Risk Analysis report for Guava Rust – this included distribution records collated before 2009 from diverse sources, all of which were supported by voucher herbarium specimens. We have attributed all records to their original sources, where known, as detailed in the following list:

- Floridao Alfieri Jr., S.A., Langdon, K.R., Wehlburg, C., Kimbrough, J.W. (1984). Index of Plant Diseases in Florida (Revised). Florida Dept. Agric. and Consumer Serv., Div. Plant Ind.

Bull. 11: 1-389.o Leahy, R. (2004) Recent history of Puccinia psidii on Myrtaceae in Florida. FDACS-DPI. http://pestalert.ifas.uft.edu/tmm-0209.htm (accessed 18 January 2006) o Marlatt, R.B., Kimbrough, J.W. (1979). Puccinia psidii on Pimenta dioica in south Florida. Pl. Dis. Reporter 63: 510-512.o Rayamajhi, M., Van, T. (2005). Impact of Puccinia psidii on the performance of invasive tree, Melaleuca quinquenervia in Florida. Phytopathology 95: s87. o Rayachhetry, M.B., Elliott, M.L., Van, T.K. (1997). Natural epiphytotic of the rust Puccinia psidii on Melaleuca quinquenervia in Florida. Pl. Dis. 81: 831. o Rayamajhi, M.B., Pratt, P.D., Center, T.D., Wheeler, G.S. (2010). Differential response by Melaleuca quinquenervia trees to attack by the rust fungus Puccinia psidii in

Florida. Pl. Dis. 94: 1165.o Rayachhetry, M.B., Van, T.K., Center, T.D., Elliott, M.L. (2001). Host range of Puccinia psidii, a potential biological control agent of Melaleuca quinquenervia in Florida. Biol.

Control 22: 38-45.- Hawaii

o Killgore, E.M., Heu, R.A. (2005) A rust disease of O'hia. State of Hawaii, Dept. Agric., New Pest Advisory 05-04: 1-2.o Loope, L. (2010) A summary of information on the rust Puccinia psidii Winter (guava rust) with emphasis on means to prevent introduction of additional strains to Hawaii:

U.S. Geological Survey Open-File Report 2010-1082: 1- 31. - Acuña, M., Garran, S.M. (2004) Detección de Kirramyces epicoccoides, Puccinia psidii y Coniothyrium zuluense agents causales de enfermedades en Eucalyptus spp. En la zona de

Concordia, entre rios, Argentina. Ria 33: 135-148.- Arnold, G.R.W. (1986). Lista de Hongos Fitopatogenos de Cuba. Ministerio de Cultura Editorial Cientifico-Tecnica, 207 pages.- Arthur, J.C. (1915) Uredinales of Poerto Rico based on collections by F. L. Stevens. Mycologia 7: 227-255.- Di Fonza, M.A. (1946) Las Uredinas del Chaco. Publicaçăo Misceláneo Ministério Agricultura Buenos Aires Series A, ii, 12: 1-12.- Baker, R.E.D., Dale, W.T. (1948) Fungi of Barbados and the Windward Islands. Mycological Papers 25: 1-26.- Baker, R.E.D., Dale, W.T. (1951) Fungi of Trinidad and Tobago. Mycological Papers 33: 1-123.- Hennen, J.F., Figueiredo, M.B., Carvelho, A.A. de.Jr., Hennen, P.G. (2005) Catalogue of the species of plant rust fungi (Uredinales) of Brazil. Instituto de Pesquisas, Jardim Botănico do

Rio de Jane, Rio de Janeiro.- Kern, F.D., Ciferri, R., Thurston, H.W.Jr. (1933) The rust-flora of the Dominican Republic. Annales Mycologici 31: 1-40.- Nolan, Zambino: Nolan P., Zambino P (2010) Eucalyptus/Guava/Myrtle rust. In 2010 Forest Pest Conditions California, p.46. California Forest Pest Council.

http://www.fs.usda.gov/Internet/FSE_DOCUMENTS/stelprdb5346910.pdf.; Zambino, P.J., Nolan, P.A. (2011). First report of rust caused by Puccinia psidii on paperbark, Melaleuca quinquenervia, in California. Pl. Dis. 95: 1314.

- Spegazzini, C. (1898) Fungi Argentini novi vel critici. Anals del Museo Nacional de Historia Natural de Buenos Aires 6: 81-288.- Stevenson, J.A. (1926) Foreign Plant Diseases. USDA Fed. Hortic. Board Bureau, Plant Ind., Government Printing Office, Washington D.C.- USDA (2009): from Farr, D.F., Rossman, A.Y., Palm, M.E. and Mccray, E.B. 2006. Fungal Databases, Systematic Botany and Mycology Laboratory, ARS, USDA.

(http://nt.arsgrin.gov/fungaldatabases/). Accessed November 2009- Wang, W. (1992) Survey of Eucalyptus diseases in Taiwan. Bulletin Taiwan Forest Research Institute, New Series 7: 179-194.

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The USDA (2010) records were sourced from records from the United States Dept of Agriculture (USDA 2010) agricultural research service, and specifically their documentation of Specimens in the U.S. National Fungus Collections (BPI). These record 177 specimens; for this project all records were checked against the set of 66 locations already available. Records where locations were too vague were excluded. Records already represented in the set 66 were excluded. The remaining locations were investigated and city name used to assign coordinates for each record. In some cases there were multiple records within close proximity, sampling similar environments. From these, one representative was used rather than multiple, to avoid introducing uneven survey effort across the native range. Farr, D.F., & Rossman, A.Y. Fungal Databases, Systematic Mycology and Microbiology Laboratory, ARS, USDA. Accessed May, 2010, from http://nt.ars-grin.gov/fungaldatabases/

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Online Appendix 2Pairwise correlations between the initial candidate sets, in the regions used for background in the Puccinia models (see main paper, Figure 1). The variable names are on the diagonals, with absolute Pearson correlation coefficients in the upper right (font sized proportional to strength of correlation), and plots of the variables and a smoothed (red) line of best fit in the lower half.

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Online Appendix 3 – global predictionsLegend as for Figure 2, main paper. Note that any predictions in regions with novel climates (see Appendix 4) should be treated with great caution, and interpreted in light of the fitted functions for the model.

Uredo_10

Uredo_27

Puccinia_94

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Puccinia_84

Puccinia_67

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Online Appendix 4: Novel environmentsOrange indicates environments outside the range of the training data for at least one predictor. In orange areas one should be cautious about what predictions mean, because the model is extrapolating outside of the data on which the model was fitted. However, nearly all of the predictions of suitable environments (Appendix 3) are within the blue areas, and therefore within the range of the training data. These were estimated using the background data for the models, since the background data are the major contribution to the environmental coverage of the model.

1. Uredo background:

2. Puccinia background:

1.

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Online Appendix 5

Modelled responses (red lines) for all variables. The y axes show variation in the logistic prediction over the range of the given environmental variable (x axes). For each plot, all other variables are held at their mean value.

Below the blue areas are from cross-validated models, indicating the main trends plus uncertainty. Cross-validation was not attempted for the smallest dataset, because there were too few records for a reliable error estimate.

Variable Uredo_10 Uredo_27 Puccinia_94 Puccinia_84 Puccinia_67prec_min

prec_max

tmin_min

tmax_max

tmean_wetq

aridity

humidity

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Online Appendix 6Exploring other uncertainties: Using Uredo_27 and Puccinia_94 (which accord with a generous interpretation of Uredo and P.psidii sensu lato) and changing:

(a) Predictors a. Drop tmean_wetq, which is correlated ~ 0.80 with the min and max temperaturesb. Include a larger suite of candidate variables: add these bioclim variables which could be considered

also possible predictors (though bio18 and bio19 have the problem of mixing rainfall and temperature, which can cause problem patterns in projections) Bio2: Mean Diurnal Range ("annual temperature range") Bio15: Precipitation Seasonality(Coefficient of Variation) Bio18: Precipitation of Warmest Quarter Bio19: Precipitation of Coldest Quarter

(b) Feature classes allowed in Maxent:a. Include product features (this allows simple interactions)b. Instead use hinge features (in contrast to the initial choice of linear and quadratic, this will produce more

skewed and less smooth functions); use regularization of 1.25 so they are not too complex.

Summary: northern Australia starts to get higher predictions if include extra variables predictions in New Zealand are sensitive to the settings for some model

Uredo_27 : Minus tmean_wetq Uredo_27 : Minus tmean_wetq but Include extra variables

Uredo_27 : linear, quadratic and product features Uredo_27 : hinge features

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Puccinia_94 : Minus tmean_wetq Puccinia_94 : Minus tmean_wetq but include extra variables

Puccinia_94 : linear, quadratic and product features Puccinia_94 : hinge features

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