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Hunting the treasure of Cape Oxalis diversity

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Poster presented at Botany 2018 conference of the Botanical Society of America titled Hunting the treasure of Cape Oxalis diversity (Zeisek, Oberlander, Dreyer, Schmickl, Schneeweiss):
Evolution of phenotypic and cytogenetic traits goes hand-in-hand with biodiversity and speciation, as new species occupy new ecological niches and undergo reproductive isolation. These processes must be seen in a historical, phylogenetic context of evolutionary relationships among species. Phylogeny explains a significant portion of species' traits in radiating organismal groups. One of the best geographic regions where we can study these processes is the Cape in southernmost Africa, long known for its enormous plant diversity and richness. One prominent if understudied Cape clade is Oxalis (Oxalidaceae). The monophyletic southern African Oxalis lineage accounts for nearly half the species diversity of the genus (ca. 230 spp.). Species are universally tunicate bulbous geophytes but exhibit substantial diversity in leaf, stem and bulb morphology. In addition, they show substantial karyological complexity. We reconstructed the phylogeny of the vast majority of southern African Oxalis (over 500 accessions) by developing a novel bioinformatics pipeline for the design of low-copy nuclear probes for target enrichment, which we used in the Hyb-Seq approach. We obtain a robust, well-resolved tree, and based on this novel phylogenetic backbone, we study phenotypic trait evolution in this genus at an unprecedented resolution and certainty.
On the same conference, Roswitha Schmickl had talk on the same topic titled Massive polyploidization but no obvious role for polyploids in the radiation of southern African Oxalis L.: insights from phylogenomics and cytogenetics (Schmickl, Oberlander, Zeisek, Liston, Schneeweiss, Záveská, Emshwiller, Dreyer, Suda):
Every extant angiosperm species has undergone multiple rounds of whole genome duplication (WGD), which implies a major role for polyploidy in the evolutionary history of the clade. Paradoxically, recently originated polyploids seem to have lower diversification rates compared to their diploid congeners. The flora of the extremely diverse Greater Cape Floristic Region (Cape) in southern Africa is particularly polyploid-poor compared to non-Cape floras. An exception is the species-rich eudicot genus Oxalis, a lineage of extraordinary vegetative diversity and karyological complexity. The southern African (SoA) Oxalis lineage accounts for nearly half the species diversity (230 spp.) of the genus and is thus a prime candidate to address the following questions: What is the frequency of WGDs in SoA Oxalis? Are the polyploids of relatively recent origin? How have WGDs influenced the radiation of SoA Oxalis? We answered these questions based on a phylogenomic hypothesis using a targeted sequence capture approach involving over 1100 genes and flow cytometric data for over 2200 accessions of 122 SoA Oxalis species. We first tested if phylogenetic relationships were indeed tree-like rather than reticulate and then modeled chromosome number evolution and addressed ploidy-associated diversification rate shifts on reconstructed phylogenetic trees. WGD in SoA Oxalis is rife, with ca. 53% of sampled species containing polyploids. Despite this, we find very little evidence for allopolyploidy, almost all sampled species contain diploids, reconstructed WGD events occur almost entirely along the tips of the tree, and polyploids are almost always inferred to have lower diversification rates than diploids. Consequently, despite being present in over half of present-day species, polyploids have played a remarkably small role in the evolution of SoA Oxalis. More generally, SoA Oxalis fits in well in a polyploid-poor Cape flora and our findings agree with hypotheses considering WGD to be mostly an evolutionary dead end.
On similar topic, we presented poster about our prepared Genome size database of the Greater Cape flora titled The role of genome duplication and variation in nuclear genome size in the evolution of the Cape flora (Chumová, Zeisek, Trávníček, Suda):
Genomes represent a distinct and legitimate level of biological organization within cells, having their own unique evolutionary histories and with genome size (GS) as one of their inherent properties. One feature that has long puzzled researchers measuring nuclear GS is the tremendous variation encountered in many different groups of organisms.This project aims to fill the knowledge gap regarding the GS and ploidy diversity across one of the most species- and endemic-rich floras of the world --- Cape Floristic Region (CFR; it has nearly 9400 species of which approximately 68 % are endemic). It is relatively well-explored in comparison with other world hotspots, with available data on species distribution, phylogeny, ecological preferences, functional traits and/or biotic interactions.Currently, representative GS data are available only for a few Cape genera (e.g. Agapanthus, Eucomis, Gasteria, Nerine, Oxalis), while the great majority of Cape groups remain unexplored. Therefore, we want to unravel the extent of ploidy and genome size variation across the Cape flora and assess the evolutionary role of genome-wide processes (genome duplication, genome down-/up-sizing) in the genesis of the Cape hyperdiversity. In particular, we are determining holoploid genome sizes and AT/GC contents in a representative set of Cape plants using DNA flow cytometry. We are developing a public online database, which will store all available GS data of Cape plants and will serve as a primary source of GS values for this biodiversity hotspot. Around 1000 species have already been subjected to flow cytometric analyses by our team using both intercalating (to estimate GS in absolute units) and AT-selective (to determine the proportion of AT/GC bases) fluorochromes. Our goal is to fill the database not only by GS data, but also by chromosome counts and exact information of investigated individuals, including georeferenced locality, high-resolution scan of preserved herbarium vouchers, etc. The database should provides fundamental source of unequivocal and easily checked data on incidence, frequency and distribution of taxa with ploidy heterogeneity and genome size variation. Meta-analyses of such data will shed new light into extent of polyploid speciation in CFR. (poster)

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