Ecological Archives E096-190-A1

Ecological Archives E096-190-A1

Jesse R. Lasky, Bénédicte Bachelot, Robert Muscarella, Naomi Schwartz, Jimena Forero-Montaña, Christopher J. Nytch, Nathan G. Swenson, Jill Thompson, Jess K. Zimmerman, and María Uriarte. 2015. Ontogenetic shifts in trait-mediated mechanisms of plant community assembly. Ecology 96:2157–2169. http://dx.doi.org/10.1890/14-1809.1

Appendix A. Supplemental methods for Markov Chain Monte Carlo and additional results for ontogenetic changes in growth and survival.

For Gibbs sampling using JAGS, we sampled 35k steps of burn-in and 25k steps with thinning to every 100th step to obtain posterior distributions. For Hamiltonian Monte Carlo sampling using Stan, we sampled 25k steps of burn-in and 50k steps to obtain posterior distributions.

Table A1. Species list, indicating whether species were found in seedling plots or in trees at least 1 cm DBH.

Family	Species	Seedling	Tree at least 1 cm DBH
Euphorbiaceae	Alchorneopsis floribunda (Benth.) Müll. Arg.	TRUE	TRUE
Euphorbiaceae	Alchornea latifolia Sw.	TRUE	TRUE
Fabaceae-Faboideae	Andira inermis (W. Wright) Kunth ex DC.	TRUE	TRUE
Rubiaceae	Stenostomum obtusifolium (Urb.) Britton & P. Wilson	FALSE	TRUE
Primulaceae	Ardisia glauciflora Urb.	FALSE	TRUE
Moraceae	Artocarpus altilis (Parkinson) Fosberg	FALSE	TRUE
Combretaceae	Buchenavia tetraphylla (Aubl.) R. A. Howard	TRUE	TRUE
Malpighiaceae	Byrsonima spicata (Cav.) DC.	TRUE	TRUE
Malpighiaceae	Byrsonima wadsworthii Little	TRUE	TRUE
Calophyllaceae	Calophyllum brasiliense	TRUE	TRUE
Melastomataceae	Henriettea squamulosa (Cogn.) Judd	FALSE	TRUE
Salicaceae (Flacourtiaceae)	Casearia arborea (Rich.) Urb.	TRUE	TRUE
Salicaceae (Flacourtiaceae)	Casearia decandra Jacq.	TRUE	FALSE
Salicaceae (Flacourtiaceae)	Casearia sylvestris Sw.	TRUE	TRUE
Urticaceae (Cecropiaceae)	Cecropia shreberiana Miq. subsp. shreberiana	TRUE	TRUE
Solanaceae	Cestrum macrophyllum Vent.	FALSE	TRUE
Oleaceae	Chionanthus domingensis Lam.	TRUE	TRUE
Rubiaceae	Chione venosa (Sw.) Urb. var. venosa	FALSE	TRUE
Sapotaceae	Chrysophyllum argenteum Jacq.	FALSE	TRUE
Lauraceae	Cinnamomum elongatum (Nees) Kosterm.	TRUE	TRUE
Lauraceae	Cinnamomum montanum (Sw.) Bercht. & J. Presl	FALSE	TRUE
Verbenaceae	Citharexylum caudatum L.	FALSE	TRUE
Clusiaceae	Clusia rosea Jacq.	FALSE	TRUE
Polygonaceae	Coccoloba diversifolia	FALSE	TRUE
Polygonaceae	Coccoloba pyrifolia Desf.	FALSE	TRUE
Rubiaceae	Coffea arabica L.	FALSE	TRUE
Anacardiaceae	Comocladia glabra Spreng.	TRUE	TRUE
Boraginaceae	Cordia borinquensis Urb.	TRUE	TRUE
Boraginaceae	Cordia sulcata DC.	FALSE	TRUE
Euphorbiaceae	Croton poecilanthus Urb.	TRUE	TRUE
Rhizophoraceae	Cassipourea guianensis Aubl.	TRUE	TRUE
Cyatheaceae	Cyathea arborea (L.) Sm.	FALSE	TRUE
Cyatheaceae	Cyathea borinquena (Maxon) Domin	TRUE	FALSE
Cyrillaceae	Cyrilla racemiflora L.	FALSE	TRUE
Burseraceae	Dacryodes excelsa Vahl	TRUE	TRUE
Araliaceae	Dendropanax arboreus (L.) Decne. & Planch.	TRUE	TRUE
Euphorbiaceae	Drypetes alba Poit.	FALSE	TRUE
Putranjivaceae (Euphorbiaceae)	Drypetes glauca Vahl	TRUE	TRUE
Myrtaceae	Eugenia domingensis O. Berg	TRUE	TRUE
Myrtaceae	Eugenia stahlii (Kiaersk.) Krug & Urb.	TRUE	TRUE
Rubiaceae	Faramea occidentalis (L.) A. Rich.	TRUE	TRUE
Moraceae	Ficus citrifolia Mill.	FALSE	TRUE
Rubiaceae	Genipa americana L.	FALSE	TRUE
Rubiaceae	Gonzalagunia spicata (Lam.) M. GÃ³mez	TRUE	TRUE
Meliaceae	Guarea glabra Vahl	TRUE	TRUE
Meliaceae	Guarea guidonia (L.) Sleumer	TRUE	TRUE
Rubiaceae	Guettarda valenzuelana A. Rich.	TRUE	TRUE
Annonaceae	Guatteria caribaea Urb.	TRUE	TRUE
Melastomataceae	Henriettella fascicularis (Sw.) C. Wright	FALSE	TRUE
Chrysobalanaceae	Hirtella rugosa Pers.	TRUE	TRUE
Salicaceae (Flacourtiaceae)	Homalium racemosum Jacq.	TRUE	TRUE
Fabaceae-Mimosoideae	Inga laurina (Sw.) Willd.	TRUE	TRUE
Fabaceae-Mimosoideae	Inga vera Willd.	TRUE	TRUE
Rubiaceae	Ixora ferrea (J. F. Gmel.) Benth.	TRUE	TRUE
Salicaceae (Flacourtiaceae)	Laetia procera (Poepp.) Eichler	FALSE	TRUE
Fabaceae-Faboideae	Lonchocarpus heptaphyllus (Poir.) Kunth ex DC.	TRUE	FALSE
Malpighiaceae	Malpighia fucata Ker Gawl.	TRUE	TRUE
	Manilkara bidentata (A. DC.) A. Chev.	TRUE	TRUE
Anacardiaceae	Mangifera indica L.	FALSE	TRUE
Phyllanthaceae (Euphorbiaceae)	Margaritaria nobilis L. f.	TRUE	TRUE
Sapindaceae	Matayba domingensis (DC.) Radlk.	TRUE	TRUE
Celastraceae	Maytenus elongata (Urb.) Britton	FALSE	TRUE
Sabiaceae	Meliosma herbertii Rolfe	FALSE	TRUE
Melastomataceae	Miconia impetiolaris (Sw.) D. Don ex DC.	TRUE	TRUE
Melastomataceae	Miconia laevigata (L.) D. Don	FALSE	TRUE
Melastomataceae	Miconia mirabilis (Aubl.) L. O. Williams	FALSE	TRUE
Melastomataceae	Miconia prasina (Sw.) DC.	TRUE	TRUE
Melastomataceae	Miconia racemosa (Aubl.) DC.	TRUE	TRUE
Melastomataceae	Miconia tetrandra (Sw.) D. Don	TRUE	TRUE
Sapotaceae	Micropholis guyanensis (A. DC.) Pierre	FALSE	TRUE
Sapotaceae	Micropholis garciniifolia Pierre	FALSE	TRUE
Myrtaceae	Myrcia deflexa (Poir.) DC.	TRUE	TRUE
Myrtaceae	Myrcia fallax (Rich.) DC.	FALSE	TRUE
Myrtaceae	Myrcia leptoclada DC. (syn. Myrcia amazonica)	TRUE	TRUE
Myrtaceae	Myrcia splendens (Sw.) DC.	TRUE	TRUE
Lauraceae	Ocotea floribunda (Sw.) Mez	TRUE	TRUE
Lauraceae	Ocotea leucoxylon (Sw.) Laness.	TRUE	TRUE
Lauraceae	Ocotea moschata (Meisn.) Mez	FALSE	TRUE
Lauraceae	Nectandra turbacensis (Kunth) Nees	TRUE	TRUE
Fabaceae-Faboideae	Ormosia krugii Urb.	TRUE	TRUE
Annonaceae	Oxandra laurifolia (Sw.) A. Rich.	FALSE	TRUE
Rubiaceae	Palicourea croceoides Ham.	TRUE	TRUE
Piperaceae	Piper blattarum Spreng.	TRUE	TRUE
Piperaceae	Piper glabrescens (Miq.) C. DC.	TRUE	TRUE
Piperaceae	Piper hispidum Sw.	TRUE	FALSE
Arecaceae	Prestoea acuminata (Willd.) H. E. Moore var. montana (Graham) A. J. Hend. & Galeano	TRUE	TRUE
Moraceae	Pseudolmedia spuria (Sw.) Griseb.	TRUE	TRUE
Rubiaceae	Psychotria berteroana DC.	TRUE	TRUE
Rubiaceae	Psychotria brachiata Sw.	TRUE	TRUE
Rubiaceae	Psychotria deflexa DC.	TRUE	TRUE
Rubiaceae	Psychotria grandis Sw.	FALSE	TRUE
Clusiaceae	Garcinia portoricensis (Urb.) Alain	TRUE	TRUE
Arecaceae	Roystonea borinquena O. F. Cook	TRUE	TRUE
Salicaceae (Flacourtiaceae)	Samyda spinulosa Vent.	TRUE	TRUE
Euphorbiaceae	Sapium laurocerasus Desf.	TRUE	TRUE
Araliaceae	Schefflera morototoni (Aubl.) Maguire	TRUE	TRUE
Elaeocarpaceae	Sloanea berteroana Choisy ex DC.	TRUE	TRUE
Bignoniaceae	Spathodea campanulata P. Beauv.	FALSE	TRUE
Meliaceae	Swietenia macrophylla King	FALSE	TRUE
Symplocaceae	Symplocos martinicensis Jacq.	TRUE	TRUE
Myrtaceae	Syzygium jambos (L.) Alston	TRUE	TRUE
Bignoniaceae	Tabebuia heterophylla (DC.) Britton	TRUE	TRUE
Burseraceae	Tetragastris balsamifera (Sw.) Oken	TRUE	TRUE
Meliaceae	Trichilia pallida Sw.	TRUE	TRUE
Staphylaceae	Turpinia occidentalis (Sw.) G. Don	FALSE	TRUE
Urticaceae	Urera baccifera (L.) Gaudich. ex Wedd.	TRUE	TRUE
Rutaceae	Zanthoxylum martinicense (Lam.) DC.	TRUE	TRUE

Table A2. Spearman’s rank correlation coefficients among studied traits.

	Wood density	SLA	Max. height	Seed mass

Leaf N	-0.38	0.48	-0.29	-0.23
Wood density		-0.32	0.01	0.10
SLA			-0.16	-0.30
Max. height				0.30

Table A3. Potential scale reduction factor convergence diagnostics (Gelman and Rubin 1992) for main model parameters of interest. β_1.0 = trait relationship with average growth or survival, β_2.0 = trait relationship with response to NCI, β₁ = mean of species specific intercepts for growth or survival, β₁ = mean of species specific responses to NCI, β₃ = mean of species specific responses to NCIS, β₄ = mean of species specific responses to DBH, β₅ = mean of species specific responses to DBH*NCI interaction. σ with numbered subscripts are standard deviations of hyper-distributions of species parameters, for which means are given by similarly numbered β. σ_growth = standard deviation of error in stem growth, σ_individual = standard deviation of individual random effects for seedling survival models (where many individuals surveyed repeatedly, σ_census= standard deviation of random effects for seedling census intervals, and σ_plot = standard deviation of random effects for seedling plots.

TableA3

Fig. A1. The distribution of size class DBH thresholds among species for growth models. Individuals of each species were evenly divided into two bins at the median.

Fig. A2. The distribution of size class DBH thresholds among species for survival models. Individuals of each species were evenly divided into two bins at the median.

Fig. A3. Additional parameters estimated in DBH size class and trait-specific models of growth. Closed circles represent parameters significantly different from zero.

Fig. A4. Additional parameters estimated in DBH size class and trait-specific models of survival. Note that seedling survival is measured at 1- to 3-year intervals, while stems in size classes 1–3 are measured across 5-year intervals. Also note that crowding * DBH interactions were not modeled for seedlings. Closed circles represent parameters significantly different from zero.

Fig. A5. Estimated species average growth rates in the smallest DBH size class vs. growth in the largest size class. Three different traits are indicated as circle color, while circle size is proportional to the square root of mean species relative abundance among trees with at least 1 cm DBH. Gray lines represent 95% CIs.

Fig. A6. Estimated growth and survival parameters for models where size class thresholds are equal for all species. Compare to Fig. 1 of the main text, which is based on results where species are divided into species-specific size classes.

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