High species richness and endemism in tropical mountains are recognized as major contributors to the latitudinal diversity gradient. The processes underlying mountain speciation, however, are largely untested. The prevalence of steep ecogeographic gradients and the geographic isolation of populations by topographic features are predicted to promote speciation in mountains. We evaluate these processes in a species-rich Neotropical genus of understory herbs that range from the lowlands to montane forests and have higher species richness in topographically complex regions. We ask whether climatic niche divergence, geographic isolation, and pollination shifts differ between mountain-influenced and lowland Amazonian sister pairs inferred from a 756-gene phylogeny. Neotropical Costus ancestors diverged in Central America during a period of mountain formation in the last 3 My with later colonization of Amazonia. Although climatic divergence, geographic isolation, and pollination shifts are prevalent in general, these factors don’t differ between mountain-influenced and Amazonian sister pairs. Despite higher climatic niche and species diversity in the mountains, speciation modes in Costus appear similar across regions. Thus, greater species richness in tropical mountains may reflect differences in colonization history, diversification rates, or the prevalence of rapidly evolving plant life forms, rather than differences in speciation mode.

The repository is organized in three main folders comprising the three main set of analyses presented in the paper.

Folders are organized sequentially according to the order they appear in the manuscript, with titles indicating the specific analysis associated with the file contents.

Inside each one of the folders you will find the code used for every component of the pipeline and the main inputs and outputs.

Code in the repository have the following suffixes:

.sh	= to be executed in bash
.r .R	= to be executed in R
.py	= to be executed in python 2

Fasta and tree files have additive inserts in the name to indicate their processing:

.mafft	= aligned with MAFFT
.norr	= outgroups removed and tree is rooted in ingroup
.oc	= columns with less than 95% occupancy were removed from the alignment
.pr	= tree pruned to match climatic data occupancy
.rd	= alignment/tree reduced to monophyletic taxa
.rr	= tree was re-rooted
.spur	= outliers individual sequences were removed with TrimAl
.trim	= sections for the alignment were trimmed with TrimAl
s.ts	= extreme long branches and/or taxa with long branches flagged by TreeShrink exclude