DOI: 10.5061/dryad.31zcrjdhw
title: Polyploids increase overall diversity despite higher turnover than diploids in the Brassicaceae

description: Although polyploidy is widespread across the plant Tree of Life, its
 long-term evolutionary significance is still poorly understood. Here we
 examine the effects of polyploidy in explaining the large-scale
 evolutionary patterns within angiosperms by focusing on a single family
 exhibiting extensive inter-specific variation in chromosome numbers. We
 inferred ploidy from haploid chromosome numbers for 80% of species in the
 most comprehensive species-level chronogram for the Brassicaceae. After
 evaluating a total of 94 phylogenetic models of diversification, we found
 that ploidy influences diversification rates across the Brassicaceae. We
 also found that despite diversifying at a similar rate to diploids,
 polyploids have played a significant role in driving present-day
 differences in species richness among clades. Overall, in addition to
 highlighting the complexity in the evolutionary consequences of
 polyploidy, our results suggest that rare successful polyploids persist
 while significantly contributing to the long-term evolution of clades. Our
 findings further indicate that polyploidy has played a major role in
 driving the long-term evolution of the Brassicaceae and highlight the
 potential of polyploidy in shaping present-day diversity patterns across
 the plant Tree of Life.
description: All references in accordance to the Main Text
 Data S1. The Brassicaceae phylogeny was extracted using the
 extract.clade function in the ape R package version 5.2 [31] from Smith
 and Brown [22]. <br> <br> Data S2–S3: We used ChromEvol to
 infer ploidy for the maximum number of species included in our tree (1,667
 species). First, we estimated the median chromosome number across all the
 available counts for each species (see also [34]). Second, we extracted
 all possible subtrees from the Brassicaceae phylogeny using the subtrees
 function implemented in the ape R package. We then selected subtrees with
 (i) sizes between 25 and 550 species, and (ii) a maximum of 70% of missing
 data (i.e., species in tree lacking chromosome counts). This produced 342
 subtrees that we used to run the Ploidy Inference Pipeline (PIP) and infer
 ploidy. The newly developed R function used to partition the Brassicaceae
 phylogeny into optimal subtrees for ChromEvol analyses is provided in Data
 S3. <br> <br> Data S4: Brassicaceae phylogeny used to analyzed
 the phylogenetic signal of ploidal level variation across the Brassicaceae
 phylogeny using Pagel’s Lambda [38] and the D-statistics [39]. The same
 tree was used to fit Binary State Speciation and Extinction models (BiSSE
 [28,29]) and Hidden State Speciation and Extinction models (HiSSE [27])
 using the diversitree R package version 0.9-10 [42] and hisse R package
 version 1.8.9 [27,43]. <br> <br> Data S5: We analyzed the role
 of polyploid species in influencing species richness among Brassicaceae
 genera using phylogenetic regressions [41] and phylogenetic path analyses
 [30,46]. We first constructed a generic-level phylogeny for the family by
 pruning from each genus in tree, all species except for one. The resulting
 generic-level tree (one species per genus) is provided in Data
 S5.
description: We recommed using R (https://www.r-project.org) and figtree
 (http://tree.bio.ed.ac.uk/software/figtree/) for accessing these files.