a b s t r a c tThe economically important soapberry family (Sapindaceae) comprises about 1900 species mainly found in the tropical regions of the world, with only a few genera being restricted to temperate areas. The infrafamilial classification of the Sapindaceae and its relationships to the closely related Aceraceae and Hippocastanaceae -which have now been included in an expanded definition of Sapindaceae (i.e., subfamily Hippocastanoideae) -have been debated for decades. Here we present a phylogenetic analysis of Sapindaceae based on eight DNA sequence regions from the plastid and nuclear genomes and including 85 of the 141 genera defined within the family. Our study comprises 997 new sequences of Sapindaceae from 152 specimens. Despite presenting 18.6% of missing data our complete data set produced a topology fully congruent with the one obtained from a subset without missing data, but including fewer markers. The use of additional information therefore led to a consistent result in the relative position of clades and allowed the definition of a new phylogenetic hypothesis. Our results confirm a high level of paraphyly and polyphyly at the subfamilial and tribal levels and even contest the monophyletic status of several genera. Our study confirms that the Chinese monotypic genus Xanthoceras is sister to the rest of the family, in which subfamily Hippocastanoideae is sister to a clade comprising subfamilies Dodonaeoideae and Sapindoideae. On the basis of the strong support demonstrated in Sapindoideae, Dodonaeoideae and Hippocastanoideae as well as in 14 subclades, we propose and discuss informal groupings as basis for a new classification of Sapindaceae.

AimThe aim was to characterize the temporal dynamics of the Sahul-Sunda floristic exchange using published dated molecular phylogenies.Location The Sahul and Sunda shelves in Australasia and Southeast Asia.Methods Dated molecular phylogenies were compiled from the literature for plant clades that contained at least one node representing a biogeographical disjunction between the Sahul and Sunda shelves. For these nodes the age, ancestral geographical area and propagule type were determined.Results We analysed 49 clades from 21 published phylogenies representing a diverse set of angiosperm lineages. The inferred age of the disjunctions ranged from c. 33 Ma to c. 1 Ma; the earliest age marked the onset of the SahulSunda floristic exchange. Disjunctions (resulting from dispersal/migration events) occurred at the rate of 0.41 per 2 Myr between 34 and 12 Ma. Thereafter the rate sharply increased, coincident with the shelves effectively merging. For nearly two-thirds (63%) of the nodes Sunda was the ancestral area, and for 90% the ancestral species possessed zoochorous propagules.Main conclusions There is strong support for a dynamic model of floristic exchange between Sahul and Sunda. Fewer (18%) disjunctions occurred prior to Sahul and Sunda merging around 12 Ma, which we attribute to a combination of the effect of overwater dispersal barriers and relatively stable, saturated species assemblages resistant to the establishment of newly arrived lineages. The exchange, once underway, was strongly asymmetrical; eastwards migration into Sahul predominated over the reverse by a factor of c. 2.4. As zoochorous lineages were overrepresented among the successful dispersers, we infer a strong role for localized animal dispersal across narrow water barriers.

Fleshy fruits have evolved independently in Syzygieae and Myrteae, and this is accompanied by exceptional diversification rate shifts in both instances, suggesting that the evolution of fleshy fruits is a key innovation for rainforest Myrtaceae. Noting the scale dependency of this hypothesis, more complex explanations may be required to explain diversification rate shifts occurring within the fleshy-fruited tribes, and the suggested phylogenetic hypothesis provides an appropriate framework for this undertaking.

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BackgroundWidespread uptake of DNA barcoding technology for vascular plants has been slow due to the relatively poor resolution of species discrimination (∼70%) and low sequencing and amplification success of one of the two official barcoding loci, matK. Studies to date have mostly focused on finding a solution to these intrinsic limitations of the markers, rather than posing questions that can maximize the utility of DNA barcodes for plants with the current technology.Methodology/Principal FindingsHere we test the ability of plant DNA barcodes using the two official barcoding loci, rbcLa and matK, plus an alternative barcoding locus, trnH-psbA, to estimate the species diversity of trees in a tropical rainforest plot. Species discrimination accuracy was similar to findings from previous studies but species richness estimation accuracy proved higher, up to 89%. All combinations which included the trnH-psbA locus performed better at both species discrimination and richness estimation than matK, which showed little enhanced species discriminatory power when concatenated with rbcLa. The utility of the trnH-psbA locus is limited however, by the occurrence of intraspecific variation observed in some angiosperm families to occur as an inversion that obscures the monophyly of species.Conclusions/SignificanceWe demonstrate for the first time, using a case study, the potential of plant DNA barcodes for the rapid estimation of species richness in taxonomically poorly known areas or cryptic populations revealing a powerful new tool for rapid biodiversity assessment. The combination of the rbcLa and trnH-psbA loci performed better for this purpose than any two-locus combination that included matK. We show that although DNA barcodes fail to discriminate all species of plants, new perspectives and methods on biodiversity value and quantification may overshadow some of these shortcomings by applying barcode data in new ways.