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. Gómez

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. β1.0 = trait relationship with average growth or survival, β2.0 = 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. σgrowth = standard deviation of error in stem growth, σindividual = standard deviation of individual random effects for seedling survival models (where many individuals surveyed repeatedly, σcensus = standard deviation of random effects for seedling census intervals, and σplot = standard deviation of random effects for seedling plots.

TableA3

 

FigA1

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.


 

FigA2

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.


 

FigA3

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


 

FigA4

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.


 

FigA5

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.


 

FigA6

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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