DOI: 10.5061/dryad.8kprr4xk7
title: Pleistocene aridification underlies the evolutionary history of the Caribbean endemic, insular giant, Consolea (Opuntioideae)

description: Premise: The Caribbean islands are renowned for their small size but high
 species diversity, and cacti make up a fascinating component of seasonally
 dry tropical forest (SDTF) there. Consolea consist of
 nine species of dioecious, hummingbird pollinated trees endemic to the
 West Indies, which form a conspicuous element of the SDTF. Several species
 are threatened by anthropogenic disturbance, disease, sea-level rise and
 invasive species, and are of conservation concern. However, no
 comprehensive phylogeny yet exists for the clade.  Methods: We
 reconstructed the phylogeny of Consolea, sampling all
 species using plastome data to determine relationships, understand the
 evolution of key morphological characters and test their biogeographic
 history. We estimated divergence times to determine the role climate
 change may have played in shaping the current diversity of the
 clade.  Results: Consolea appears to have
 evolved very recently during the latter part of the Pleistocene on
 Cuba/Hispaniola likely from a South American ancestor, and from there
 moved into the Bahamas, Jamaica, Puerto Rico, Florida and the Lesser
 Antilles. The tree growth form is a synapomorphy
 of Consolea and likely aided in the establishment and
 diversification of the clade.  Conclusions: Pleistocene
 aridification associated with glaciation likely played a role in shaping
 the current diversity of Consolea, and insular gigantism may have
 been a key innovation leading to the success of these species to invade
 the often dense SDTF. This in-situ Caribbean radiation provides a window
 into the generation of species diversity and the complexity of the SDTF
 community within the Antilles.
description: We used raw reads from genome skimming derived from paired-end
 reads from the Illumina HiSeq X platform (generating 150 bp reads) for
 reference-guided plastome assembly based on the Cylindropuntia bigelovii
 plastid genome after trimming using an error probability limit of 5%.
 Majority consensus sequences were generated from our reference guided
 assemblies of raw reads and were used for building our alignment
 with MAFFT, which yielded a final alignment of 124,606 bp, which lacks one
 copy of the inverted repeat. Unalignable areas based on chloroplast
 structural complexities or pseudogenes were removed from the
 dataset. Our ETS/ITS data were acquired likewise
 through raw read guided assembly, using the above parameters. Majority
 consensus sequences were generated from reference guided assemblies of raw
 reads and were used for building our alignment with MAFFT, which yielded a
 final alignment of 6891 bp. 
description: Our plastome dataset consists of 124,606 bp generated from
 reference-guided assemblies from raw reads. We have included the most
 likely tree from our RAxML search.  Two ETS/ITS
 datasets are given, one with complete taxon sampling and another with taxa
 of <em>Consolea </em>reduced to just one accession each. Both
 msot likely RAxML trees generated from those datasets are
 given.