DOI: 10.5061/dryad.ghx3ffbkp
title: Data from: Rapid diversification rates in Amazonian Chrysobalanaceae inferred from plastid genome phylogenetics

description: We studied the evolutionary history of Chrysobalanaceae with phylogenetic
 analyses of complete plastid genomes from 156 species to assess the tempo
 of diversification in the Neotropics and help to unravel the causes of
 Amazonian plant diversification. These plastid genomes had a mean length
 of 162,204 base pairs, and the nearly complete DNA sequence matrix, with
 reliable fossils, was used to estimate a phylogenetic tree.
 Chrysobalanaceae diversified from 38.9 Mya (95% highest posterior density,
 95%HPD: 34.2-43.9 Mya). A single clade containing almost all Neotropical
 species arose after a single dispersal event from the Palaeotropics into
 the Amazonian biome c. 29.1 Mya (95%HPD: 25.5-32.6 Mya), with subsequent
 dispersals into other Neotropical biomes. All Neotropical genera
 diversified from 10 to 14 Mya, lending clear support to the role of Andean
 orogeny as a major cause of diversification in Chrysobalanaceae. In
 particular, the understory genus Hirtella diversified extremely rapidly,
 producing &gt; 100 species in the last 6 My (95% HPD: 4.9-7.4 My). Our
 study suggests that a large fraction of the Amazonian tree flora has been
 assembled in situ within the last 15 My.  
description: This dataset contains aligned DNA sequences of the plastid genome
 for species in Chrysobalanaceae and outgroups in Malpighiales. Usage notes
 describe the four files included as part of this package.
 Tissue was taken from herbarium collections or leaf samples dried
 in silica. Total DNA was extracted using standard methods. A separate
 Illumina library was prepared for each sample, and the libraries were then
 multiplexed in groups of 24 or 48. The pools were sequenced on HiSeq
 2000-2500 high-throughput sequencers, yielding 101-nucleotide pair-ended
 DNA reads, or the more recent HiSeq 3000 sequencer, yielding 150
 pair-ended reads. Plastome assembly was performed on a local cluster
 running Linux CentOS version 6.7. We used the NOVOplasty organelle genome
 assembler version 2.7.2. We obtained unique circularized plastid genomes
 for 54 specimens. For another 58 specimens, we set a reference sequence to
 guide the assembly (using <i>Li</i>c<i>ania
 canescens</i> Benoist available in NCBI NC300566). In some cases,
 NOVOplasty returns two or more optional genomes, corresponding to large
 inversions, and we manually selected the option matching gene order.
 Points of reference of the circularized plastid genomes were aligned using
 the CSA software. For the remaining 51 specimens (30% of our final
 dataset), we mapped the reads directly against a reference plastid genome
 using the ‘map to reference’ option in Geneious version 9.0.5.
description: Four files are included in this package: 
 Chryso8_final_annotated-2.geneious is a geneious native file
 26.64 MB in size and it was generated with Geneious 9.0.5. It contains all
 Chrysoabalanaceae plastome data with annotations.
 Chryso8_final_annotated.nex is a Nexus file 31.79 MB in size
 generated with Geneious 9.0.5. It contains all plastome data without
 annotations. Chryso_dated3 is a Nexus tree file 213
 KB generated from BEAST 2.5.1 and associated post-processing routines. It
 is in Nexus format and opens with FigTree v.1.4.4.
 Malpighiales_master15b.geneious is a geneious native file 235 kB
 in size and it was generated with Geneious 9.0.5. It contains CDS of
 plastomes for 20 species in Malpighiales used to date the crown age of
 Chrysobalanaceae.