Whole genome sequencing is helping generate robust phylogenetic hypotheses for a range of taxonomic groups that were previously recalcitrant to classical molecular phylogenetic approaches. As a case study, we performed a shallow shotgun sequencing of eight species in the tropical tree family Chrysobalanaceae to retrieve large fragments of high-copy number DNA regions and test the potential of these regions for phylogeny reconstruction. We were able to assemble the nuclear ribosomal cluster (nrDNA), the complete plastid genome (ptDNA) and a large fraction of the mitochondrial genome (mtDNA) with approximately 1000×, 450× and 120× sequencing depth respectively. The phylogenetic tree obtained with ptDNA resolved five of the seven internal nodes. In contrast, the tree obtained with mtDNA and nrDNA data were largely unresolved. This study demonstrates that genome skimming is a cost-effective approach and shows potential in plant molecular systematics within Chrysobalanaceae and other under-studied groups.

Some plant families show a striking imbalance in species diversity between the Neotropics and the Palaeotropics. The woody plant family Chrysobalanaceae is a typical example of this pattern, with 80% of the 531 species in the Neotropics. In order to test alternative interpretations for this pattern, we generated a dated phylogenetic hypothesis for Chrysobalanaceae, using DNA sequence data from one nuclear and six plastid markers. Using a maximum likelihood approach, we jointly inferred ancestral areas and diversification rates in the Neotropics and Palaeotropics. We found that Chrysobalanaceae most probably originated in the Palaeotropics about 80 Mya. The family dispersed into the Neotropics at least four times beginning 40–60 Mya, with at least one back‐dispersal to the Palaeotropics. Members of Chrysobalanaceae have experienced higher extinction, speciation and net diversification rates in the Neotropics. Hence, the high species diversity of Chrysobalanaceae in the Neotropics appears to be primarily caused by a higher speciation rate in this region. Several recent studies have shown high diversification rates in Neotropical plant families, but have focused on Andean‐centred taxa. Ours is the first study to find a similar pattern in a family for which the centre of diversity is in eastern and central Amazonia. © 2012 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, ••, ••–••.