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Pleistocene aridification underlies the evolutionary history of the Caribbean endemic, insular giant, Consolea (Opuntioideae)

Citation

Majure, Lucas et al. (2021), Pleistocene aridification underlies the evolutionary history of the Caribbean endemic, insular giant, Consolea (Opuntioideae) , Dryad, Dataset, https://doi.org/10.5061/dryad.8kprr4xk7

Abstract

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.

Methods

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. 

Usage Notes

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 Consolea reduced to just one accession each. Both msot likely RAxML trees generated from those datasets are given. 

Funding

National Science Foundation, Award: DEB-1735604

National Geographic Society, Award: 9939–16

National Science Foundation, Award: DEB-0818399

National Science Foundation, Award: GSS-1461496