**7. Future perspectives and conclusions**

*Begonia* is a remarkable genus both for its size and diversity. As a pantropical genus, it provides the opportunity to compare biogeographic patterns in different regions using like to like. It also offers the chance to examine the reasons behind the high levels of tropical diversity through comparisons with speciation patterns in correspondingly widespread temperate genera.

Major progress has been made clarifying the evolutionary relationships in the genus *Begonia* at the sectional level. Further work is required at the species level, to assess lower level relationships, and reveal biogeographic patterns. The lack of a fossil record for the genus has been a stumbling block to the generation of detailed evolutionary scenarios (Goodall-Copestake et al., 2009). Moreover, more informative genetic markers are needed to obtain well-resolved phylogenies of the recent rapid radiations that have occurred in different regions.. However, the development of barcoded next generation sequencing techniques holds out the promise that phylogenies of many hundreds of accessions could be produced en-mass, transforming our ability to detect speciation patterns. The decreasing cost of sequencing means that transcriptomes, whole plastid genomes and even draft nuclear genomes can be produced for reasonable amounts of money (Ng & Kirkness, 2010).

The prevalence of geographic isolation between *Begonia* species may be one of the factors explaining the limited postzygotic reproductive isolating barriers between species. The lack of interspecific crossing barriers has contributed to its success as a horticultural subject, and provides us with the opportunity to use classical and quantitative genetic techniques to study the genes that vary between species.

On one level such analysis can be done by transcriptome or genome comparisons and the screening for genes that show the signature of diversifying or purifying selection (Biswas & Akey, 2006). However, these techniques can provide only statistical support for the importance of any one locus, and are not informative about which traits are affected. In a non-model group the link between locus and function can only be based on comparisons with model species which may be misleading.

A second approach works in the other direction, from the trait down to the locus. Once a genetic map has been constructed, quantitative trait locus (QTL) analysis can reveal the genetic architecture of species level differences: the number of loci that affect a trait, along with their sizes and interactions (Zeng, 2005). The traits most divergent between species may be related to the selective forces that drove speciation and can be linked to plant fitness as measured by seed production or to relative growth rate (Taylor et al., 2009). An ideal experiment would combine both approaches, mapping highly divergent genes relative to QTLs.

One of the great advantages of *Begonia* for this work is the parallel evolution that is common in the genus on many levels. Given sufficient genetic resources, comparisons can be made between the genetic architecture of traits independently evolved within and between sections and continents. This allows hypothesises about trait evolution to be tested using multiple replicates, providing greater robustness than is usually possible for evolutionary studies.

One topic that has yet to be studied in depth and deserves further attention is natural hybridisation and hybrid speciation. Hybrid speciation seems very likely within the genus, and interspecific processes may be the cause of the hard incongruence of phylogenetic trees derived from plastid and nuclear ribosomal data within some species-rich sections (*Platycentrum*, *Petermannia*) (Goodall-Copestake (2010), Thomas (2010). However, homoploid hybrids are hard to detect; and only a handful of species in evolutionary model systems have proven to be hybrids without a change in ploidy level (e.g. *Helianthus, Argyranthemum, Ceanotus, Pinus* (listed in Gross & Rieseberg, 2005). Investigation of the frequency of natural hybridisation, together with studies of genome stabilisation after polyploidisation and more karyomorphological data may be useful to understand chromosome evolution within the genus. The use of molecular techniques, such as comparative transcriptional profiling or targeted genome resequencing of species and their hybrids (see Twyford & Ennos, 2011), or cytological techniques such as GISH, may shed light on the role of natural hybridisation.

The genus *Begonia* has been studied for many reasons, including: horticulture, taxonomy, as an indicator for biogeographic variation, to understand the development of their distinctive leaf forms and their aberrations, population genetics of endemic species, hybridisation and genome dynamics. As the distinction between model plants with extensive genetic resources, and non-models without these resources becomes less well defined, we expect that *Begonia* will continue to provide insights into the nature and origin of tropical plant diversity.
