DOI: 10.5061/dryad.0rxwdbs22
title: Acaulescence promotes speciation and shapes the distribution patterns of palms in Neotropical seasonally dry habitats

description: Rainforests have been a source of lineages to open and seasonally dry
 habitats throughout Angiosperm evolution, especially in the Neotropics.
 However, the underlying mechanisms that allow such shifts remain poorly
 understood at large spatial scales. Here, we test whether acaulescence (an
 underground stem or a very short stem concealed in the ground) has
 affected the colonization and speciation in Neotropical seasonally dry
 habitats by cocosoid palms (Cocoseae). Acaulescent species maintain their
 growth underground, which increases their chances of survival from
 prolonged seasonal dry season and frequent fires. We use an integrative
 approach based on trait‐dependent diversification models, phylogenetic
 comparative methods, and ecological niche models. We found that shifts
 towards acaulescent growth form were accompanied by evolutionary
 transitions to seasonally dry habitats. Acaulescent lineages had higher
 speciation rates than non-acaulescent ones. However, the interaction
 between acaulescence and seasonally dry habitats had no significant effect
 on Cocoseae speciation rates. Acaulescent palms are primarily distributed
 in Neotropical seasonally dry habitats and non-acaulescent palms are
 concentrated in Amazonian rainforests. Our results suggest that an
 underground stem, with high carbohydrate and water storage capacity, is a
 preadaptation by which rainforest lineages were able to colonize and
 diversify in new fire-prone, increasingly seasonal and drier adaptive
 zones. The projected global expansion of dry seasonal habitats requires an
 understanding of how drought-avoidance functional traits evolve and how
 they are linked to seasonally dry habitats. Our results are, thus, a step
 forward in determining plant response mechanisms to drier and seasonal
 conditions.
description: <b>Cocoseae_Data.xlsx</b> contains metadata for each
 of the following datasheets: <b>Table_S1</b>: Data on the
 growth form and habitat type for all Cocoseae species (i.e. n= 334)
 obtained from Kissling et al. 2019 and Cassia-Silva et al. 2019 datasets,
 respectively. <b>Table_S2</b>: Key identification of
 occurrences records downloaded from the Global Biodiversity Information
 Facility – GBIF (https://www.gbif.org).
 <b>Table_S3: </b>Species’ occurrence records individually
 checked. Table S3 contains the number of records of each species (Records)
 and metrics widely used to assess model accuracy in the Ecological niche
 modeling procedure: <b>deviance, COR</b>, and true skill
 statistic (<b>TSS</b>). The area under the receiver operating
 characteristic curve (<b>AUC)</b> and initial distribution
 size (<b>iniDist</b>).
 <b>Cocoseae_tree_MCC.txt</b> contains the maximum
 credibility clade (MCC) tree of the Cocoseae palm tribe.
 <b>Cocoseae_tree_100.txt</b> contains 50 phylogenetic
 trees randomly sampled from the posterior distribution of an all-evidence
 species-level supertree of palms (Faurby et al. 2016/https://doi.org/10.1016/j.ympev.2016.03.002). <b>sdm_DRYAD.r</b> contains the script used to run the ecological niche models. <b>HiSSE.r </b>contains the script used to run all 24 models to the Cocoseae phylogeny<br> that differed on how their parameters were constrained. Two models were BiSSE-like models (i.e. without hidden states), where turnover (τ = l + m) parameters were free to 100 vary, and extinction fraction (ε) or transitions rates (q) were constrained between growth forms states, depending on the model. Four models corresponded to different CID models, which assumed that rate differences are associated with two (CID-2) or four (CID-4) hidden states and extinctions or 105 transitions were constrained between states. The remaining HiSSE models were trait-dependent diversification models with hidden states, different combinations of parameter constraints, and two different types of transition matrices,one restricted (default) and the other allowing all transitions between character states (Beaulieu and O’Meara 2016). <b>MuHiSSE.r</b> contains the script used to run all nine MuHiSSE (Multistate Speciation and Extinction with hidden traits) models. One of these was a ‘null model’ where no diversification rate variation is caused by character states. One model was a character-dependent diversification without (i.e. MuSSE-like model) a hidden state and the last seven models included two to eight hidden states (MuHiSSE 2-8 models). <b>Mapas_global_extent.rar</b> contains all maps generated for the Ecological niche modeling procedure.