Floral biology and taxonomic complexity in the genus Alpinia Roxb. (Zingiberaceae)

The tropics harbour the highest number of species in the world. Uncovering why and how these regions are so species-rich has been a central theme in evolutionary biology. When it comes to plants, about two-thirds of the plant species are present in the tropics. Research on tropical plants is impeded by an array of taxonomic challenges. To understand these challenges in more detail, I have focused on the genus Alpinia Roxb. from the Zingiberaceae. It is the largest genus in the ginger family (c.250 species) and one of the most taxonomically complex. Molecular phylogenetic studies have revealed that this genus is polyphyletic. Moreover, nomenclatural confusion is an issue in Alpinia as many species with validly published names were described before the development of the type concept which has led to taxonomic confusion regarding species identities. Several Alpinia species also possess intermediate morphological characters that cause difficulty in delimiting species. Understanding the extent of reproductive isolation and hybridisation is crucial in this case. These species also possess a unique stylar dimorphism termed flexistyly, a strategy used to promote outcrossing. Many studies have investigated the reproductive biology of flexistylous species in Alpinia, but not much is known about the genetic basis of this trait. Accordingly, the aims of my thesis are: • To understand the taxonomic challenges present in the tropics. • To resolve taxonomic uncertainty in a group of Indian Alpinia species. • To investigate the crossing barriers and the potential for hybridisation in the genus Alpinia. • To elucidate the genetic basis of flexistyly. I conducted a survey of plant biologists to investigate the taxonomic problems faced when working on tropical taxa, and reviewed the literature to find case studies where taxonomic issues impede research. I found that taxonomic challenges in the tropics are caused by practical issues associated with fieldwork and herbarium collections and biological factors such as rapid radiations, hybridisation, and phenotypic plasticity. To resolve the nomenclatural confusion in a group of Indian Alpinia species, I examined a range of original material and have resolved the confusion associated with the name A. bracteata used by Roscoe and Roxburgh. I have also assigned a lectotype for the name A. calcarata (Haw.) Roscoe. To investigate crossing barriers, I performed artificial hybridisation between and within clades of Alpinia s.l. I found that Alpinia species show widespread interspecific cross compatibility, especially within clades, and in a few instances, between divergent clades as well as genera. I also found a negative correlation between the genetic distance and the seed set, but this correlation was not significant. To investigate the genetic basis of flexistyly, I assembled a draft genome of Alpinia nigra that served as a reference for downstream analysis. I used a Pool-Seq approach to investigate the allele frequency differences between bulks of the anaflexistylous and cataflexistylous morphs. Most of the genome showed low differentiation (average genome-wide FST=0.04), with no clear outlier regions. This is consistent with the lack of evidence for a large inversion. This might be due to the complex nature of the genomic region(s) that govern this trait or it could be a single gene that might be difficult to detect. The potential for hybridisation and the lack of reproductive isolation might be common in gingers, and overlooked in many tropical taxa. It may be a critical factor that caused taxonomic complexity within this tropical genus