Rapid diversification rates in Amazonian Chrysobalanaceae inferred from plastid genome phylogenetics

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 > 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.  

Methods
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 Licania canescens 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.