DOI: 10.5061/dryad.cm50gk1
title: Data from: Why are red flowers so rare? Testing the macroevolutionary causes of tippiness.

description: Traits that have arisen multiple times yet still remain rare present a
 curious paradox. A number of these rare traits show a distinct tippy
 pattern, where they appear widely dispersed across a phylogeny, are
 associated with short branches, and differ between recently diverged
 sister species. This phylogenetic pattern has classically been attributed
 to the trait being an evolutionary dead end, where the trait arises due to
 some short‐term evolutionary advantage, but it ultimately leads species to
 extinction. While the higher extinction rate associated with a dead end
 trait could produce such a tippy pattern, a similar pattern could appear
 if lineages with the trait speciated slower than other lineages, or if the
 trait was lost more often that it was gained. In this study, we quantify
 the degree of tippiness of red flowers in the tomato family, Solanaceae,
 and investigate the macroevolutionary processes that could explain the
 sparse phylogenetic distribution of this trait. Using a suite of metrics,
 we confirm that red‐flowered lineages are significantly overdispersed
 across the tree and form smaller clades than expected under a null model.
 Next, we fit 22 alternative models using HiSSE (Hidden State Speciation
 and Extinction), which accommodates asymmetries in speciation, extinction
 and transition rates that depend on observed and unobserved (hidden)
 character states. Results of the model fitting indicated significant
 variation in diversification rates across the family, which is best
 explained by the inclusion of hidden states. Our best fitting model
 differs between the maximum clade credibility tree and when incorporating
 phylogenetic uncertainty, suggesting that the extreme tippiness and rarity
 of red Solanaceae flowers makes it difficult to distinguish among
 different underlying processes. However, both of the best models strongly
 support a bias towards the loss of red flowers. The best fitting HiSSE
 model when incorporating phylogenetic uncertainty lends some support to
 the hypothesis that lineages with red flowers exhibit reduced
 diversification rates due to elevated extinction rates. Future studies
 employing simulations or targeting population‐level processes may allow us
 to determine whether red flowers in Solanaceae or other angiosperms clades
 are rare and tippy due to a combination of processes, or asymmetrical
 transitions alone.
description: Ancestral state
 reconstruction R scriptAncestral state
 reconstruction R script used to produce Figure 1ASR_Bisse_Red.RTippyMetricCalculationsR script used to calculate tippy metricsTippyMetrics_functionsR script used to calculate tippy metricsBAMM_RedSolanaceae_controlFileInput file used for BAMM analysisBAMM_RedSolanaceae_SamplingFractionsInput file used for BAMM analysisAllGenes_wOutgroup_Mcoccinea_ndhFndhF sequence alignment fileAllGenes_wOutgroup_Mcoccinea_trnLFtrnLF sequence alignment fileAllGenes_wOutgroup_Mcoccinea_matKmatK sequence alignment fileAllGenes_wOutgroup_Mcoccinea_Waxywaxy sequence alignment fileAllGenes_wOutgroup_Mcoccinea_ITSITS sequence alignment fileBEAST_Solanaceae_BeautiPhylogenetic reconstruction BEAST file with priors following Sarkinen et al. 2013BEAST_Solanaceae_Beauti_diffPriorsPhylogenetic reconstruction BEAST file with priors following De-Silva et al. 2017BEAST_MCC_SolanaceaeTreeSolanaceae MCC phylogeny from BEAST reconstruction with priors following Sarkinen et al. 2013BEAST_MCC_SolanaceaeTree.tre_diffPriorsSolanaceae MCC phylogeny from BEAST reconstruction with priors following De-Silva et al. 2017READMEDescriptions of Dryad files