Kenneth C. Oberlander

Origin and diversification of the Greater Cape flora: Ancient species repository, hot-bed of recent radiation, or both?

Like island-endemic taxa, whose origins are expected to postdate the appearance of the islands on which they occur, biome-endemic taxa should be younger than the biomes to which they are endemic. Accordingly, the ages of biome-endemic lineages may offer insights into biome history. In this study, we used the ages of multiple lineages to explore the origin and diversification of two southern African biomes whose remarkable floristic richness and endemism has identified them as global biodiversity hotspots (succulent karoo and fynbos). We used parsimony optimization to identify succulent karoo- and fynbos-endemic lineages across 17 groups of plants, for which dated phylogenies had been inferred using a relaxed Bayesian (BEAST) approach. All succulent karoo-endemic lineages were less than 17.5 My old, the majority being younger than 10 My. This is largely consistent with suggestions that this biome is the product of recent radiation, probably triggered by climatic deterioration since the late Miocene. In contrast, fynbos-endemic lineages showed a broader age distribution, with some lineages originating in the Oligocene, but most being more recent. Also, in groups having both succulent karoo- and fynbos-endemic lineages, there was a tendency for the latter to be older. These patterns reflect the greater antiquity of fynbos, but also indicate considerable recent speciation, probably through a combination of climatically-induced refugium fragmentation and adaptive radiation.

Phylogenetic marker development for target enrichment from transcriptome and genome skim data: the pipeline and its application in southern African Oxalis (Oxalidaceae).

Phylogenetics benefits from using a large number of putatively independent nuclear loci and their combination with other sources of information, such as the plastid and mitochondrial genomes. To facilitate the selection of orthologous low‐copy nuclear (LCN) loci for phylogenetics in nonmodel organisms, we created an automated and interactive script to select hundreds of LCN loci by a comparison between transcriptome and genome skim data. We used our script to obtain LCN genes for southern African Oxalis (Oxalidaceae), a speciose plant lineage in the Greater Cape Floristic Region. This resulted in 1164 LCN genes greater than 600 bp. Using target enrichment combined with genome skimming (Hyb‐Seq), we obtained on average 1141 LCN loci, nearly the whole plastid genome and the nrDNA cistron from 23 southern African Oxalis species. Despite a wide range of gene trees, the phylogeny based on the LCN genes was very robust, as retrieved through various gene and species tree reconstruction methods as well as concatenation. Cytonuclear discordance was strong. This indicates that organellar phylogenies alone are unlikely to represent the species tree and stresses the utility of Hyb‐Seq in phylogenetics.

High ploidy diversity and distinct patterns of cytotype distribution in a widespread species of Oxalis in the Greater Cape Floristic Region

BACKGROUND AND AIMS Genome duplication is widely acknowledged as a major force in the evolution of angiosperms, although the incidence of polyploidy in different floras may differ dramatically. The Greater Cape Floristic Region of southern Africa is one of the worlds biodiversity hotspots and is considered depauperate in polyploids. To test this assumption, ploidy variation was assessed in a widespread member of the largest geophytic genus in the Cape flora: Oxalis obtusa. METHODS DNA flow cytometry complemented by confirmatory chromosome counts was used to determine ploidy levels in 355 populations of O. obtusa (1014 individuals) across its entire distribution range. Ecological differentiation among cytotypes was tested by comparing sets of vegetation and climatic variables extracted for each locality. KEY RESULTS Three majority (2x, 4x, 6x) and three minority (3x, 5x, 8x) cytotypes were detected in situ, in addition to a heptaploid individual originating from a botanical garden. While single-cytotype populations predominate, 12 mixed-ploidy populations were also found. The overall pattern of ploidy level distribution is quite complex, but some ecological segregation was observed. Hexaploids are the most common cytotype and prevail in the Fynbos biome. In contrast, tetraploids dominate in the Succulent Karoo biome. Precipitation parameters were identified as the most important climatic variables associated with cytotype distribution. CONCLUSIONS Although it would be premature to make generalizations regarding the role of genome duplication in the genesis of hyperdiversity of the Cape flora, the substantial and unexpected ploidy diversity in Oxalis obtusa is unparalleled in comparison with any other cytologically known native Cape plant species. The results suggest that ploidy variation in the Greater Cape Floristic Region may be much greater than currently assumed, which, given the documented role of polyploidy in speciation, has direct implications for radiation hypotheses in this biodiversity hotspot.

A model of bulb evolution in the eudicot genus Oxalis (Oxalidaceae)

The origins and monophyly of the bulbous habit in the eudicot genus Oxalis are uncertain, but key character state transitions in the evolution of true bulbs are currently thought to be reflected in extant pseudobulbous and other geophytic taxa. We test the relationships between the two major groups of bulbous Oxalis taxa, namely the southern African lineage which is centered in the speciose Cape Floristic Region (CFR), and the New World section Ionoxalis, by including the rhizomatous geophyte Oxalis acetosella, the caudiciform stem succulent Oxalis articulata, and the rhizomiform pseudobulbous Oxalis triangularis, in combined phylogenetic analyses of nrITS and trnL-F sequence data. We optimize several key bulbous characters in ancestral state reconstructions on produced phylogenies. Results of our analyses indicate that the evolution of bulbous characters in the genus is more complex than previously thought. Although the two major bulb types are homologous, the rhizomiform pseudobulbous habit arises from within true bulbs, and in most reconstructions the caudiciform stem succulent O. articulata is inferred to have secondarily lost several distinctive bulbous characters. O. acetosella is not as closely related to the bulbous lineage as previously thought. More sampling from other key taxa are needed before the order in which key bulbous characters were acquired can be verified. We discuss these results in terms of the taxonomic and ecological implications for the CFR Oxalis taxa.

Systematic relationships in southern African Oxalis L. (Oxalidaceae): congruence between palynological and plastid trnL-F evidence

In the most recent morphology-based taxonomic classification of African Oxalis L., 206 species were recognized in nine indigenous southern African sections. A subsequent palynological review of these taxa conflicted with their taxonomic classification. In the present study, phylogenetic relationships within section Angustatae subsection Lineares are re-assessed, using plastid trnL-F non-coding DNA sequence data. The results of this study clearly indicate that, based on the DNA evidence, subsection Lineares is non-monophyletic. Previously hypothesized relationships within the subsection are also refuted. In contrast, molecular and palynological data are highly congruent, and both differ substantially from the current morphological classification for subsection Lineares.

New species of Ophiostomatales from Scolytinae and Platypodinae beetles in the Cape Floristic Region, including the discovery of the sexual state of Raffaelea

Olea capensis and Rapanea melanophloeos are important canopy trees in South African Afromontane forests. Dying or recently dead individuals of these trees are often infested by Scolytinae and Platypodinae (Curculionidae) beetles. Fungi were isolated from the surfaces of beetles emerging from wood samples and their galleries. Based on micro-morphological and phylogenetic analyses, four fungal species in the Ophiostomatales were isolated. These were Sporothrix pallida and three taxa here newly described as Sporothrix aemulophila sp. nov., Raffaeleavaginata sp. nov. and Raffaelea rapaneae sp. nov. This study represents the first collection of S. pallida, a species known from many environmental samples from across the world, from Scolytinae beetles. S. aemulophila sp. nov. is an associate of the ambrosia beetle Xyleborinus aemulus. R. rapaneae sp. nov. and R.vaginata sp. nov. were associated with a Lanurgus sp. and Platypodinae beetle, respectively, and represent the first Raffaelea spp. reported from the Cape Floristic Region. Of significance is that R.vaginata produced a sexual state analogous with those of Ophiostoma seticolle and O. deltoideosporum that also grouped in our analyses in Raffaelea s. str., to date considered an asexual genus. The morphology of the ossiform ascospores and anamorphs of the three species corresponded and the generic circumscription of Raffaelea is thus emended to accommodate sexual states. The two known species are provided with new combinations, namely Raffaelea seticollis (R.W. Davidson) Z.W. de Beer and T.A. Duong comb. nov. and Raffaelea deltoideospora (Olchow. and J. Reid) Z.W. de Beer and T.A. Duong comb. nov.

Cytogeography of Oxalis pes-caprae in its native range: where are the pentaploids?

Due to its instantaneous effects on the genetics, phenotype, physiology and/or ecology of a plant, polyploidy can play an important role in facilitating plant invasions. Understanding the determinants of invasiveness in species with multiple ploidy levels requires a detailed knowledge of ploidy composition in native versus invaded ranges. Using DNA flow cytometry, we performed representative ploidy screening (277 localities, 333 individuals) across the native range of Oxalis pes-caprae and compared the data with those from invaded ranges. Both ranges showed striking differences in ploidy composition: whereas tetra- and especially pentaploids successfully colonized secondary areas, only di-, (very rare) tri- and tetraploids (dominant) were found in the native range of this species. Disregarding the diploid var. sericea, diploids and tetraploids of the nominate variety showed largely parapatric distribution in the native range, with a zone of overlap in the Northern Cape Province. Our results challenge the conventional scenario of the introduction of pentaploid individuals from the Greater Cape Floristic Region. The origin of the pentaploid cytotype is unclear and molecular tools applied in a large scale screening are needed to understand the invasion history of the species.

Species-rich and polyploid-poor: Insights into the evolutionary role of whole-genome duplication from the Cape flora biodiversity hotspot

PREMISE OF THE STUDY Whole-genome duplication (WGD) in angiosperms has been hypothesized to be advantageous in unstable environments and/or to increase diversification rates, leading to radiations. Under the first hypothesis, floras in stable environments are predicted to have lower proportions of polyploids than highly, recently disturbed floras, whereas species-rich floras would be expected to have higher than expected proportions of polyploids under the second. The South African Cape flora is used to discriminate between these two hypotheses because it features a hyperdiverse flora predominantly generated by a limited number of radiations (Cape clades), against a backdrop of climatic and geological stability. METHODS We compiled all known chromosome counts for species in 21 clades present in the Cape (1653 species, including 24 Cape clades), inferred ploidy levels for these species by inspection or derived from the primary literature, and compared Cape to non-Cape ploidy levels in these clades (17,520 species) using G tests. KEY RESULTS The Cape flora has anomalously low proportions of polyploids compared with global levels. This pattern is consistently observed across nearly half the clades and across global latitudinal gradients, although individual lineages seem to be following different paths to low levels of WGD and to differing degrees. CONCLUSIONS This pattern shows that the diversity of the Cape flora is the outcome of primarily diploid radiations and supports the hypothesis that WGD may be rare in stable environments.

Consistent phenological shifts in the making of a biodiversity hotspot: the Cape flora

BackgroundThe best documented survival responses of organisms to past climate change on short (glacial-interglacial) timescales are distributional shifts. Despite ample evidence on such timescales for local adaptations of populations at specific sites, the long-term impacts of such changes on evolutionary significant units in response to past climatic change have been little documented. Here we use phylogenies to reconstruct changes in distribution and flowering ecology of the Cape flora - South Africas biodiversity hotspot - through a period of past (Neogene and Quaternary) changes in the seasonality of rainfall over a timescale of several million years.ResultsForty-three distributional and phenological shifts consistent with past climatic change occur across the flora, and a comparable number of clades underwent adaptive changes in their flowering phenology (9 clades; half of the clades investigated) as underwent distributional shifts (12 clades; two thirds of the clades investigated). Of extant Cape angiosperm species, 14-41% have been contributed by lineages that show distributional shifts consistent with past climate change, yet a similar proportion (14-55%) arose from lineages that shifted flowering phenology.ConclusionsAdaptive changes in ecology at the scale we uncover in the Cape and consistent with past climatic change have not been documented for other floras. Shifts in climate tolerance appear to have been more important in this flora than is currently appreciated, and lineages that underwent such shifts went on to contribute a high proportion of the floras extant species diversity. That shifts in phenology, on an evolutionary timescale and on such a scale, have not yet been detected for other floras is likely a result of the method used; shifts in flowering phenology cannot be detected in the fossil record.

Reassessment of the taxonomic status of Oxalis fabaefolia (Oxalidaceae) and the description of a unique variety of Oxalis flava from the Northern Cape Province of South Africa

Jacquin (1794) also described another seemingly related group of species, O. asinina Jacq., O. crispa Jacq., O. fabaefolia Jacq., O. lanceaefolia Jacq. and O. leporina Jacq., and distinguished between them based on corolla colour, leaf shape and stylar morph type. Salter (1944) synonymised all of the species in this group under O. fabaefolia, placing O. asinina, O. lanceaefolia and O. leporina under O. fabaefolia Form B, but maintained O. fabaefolia and O. flava as separate species based on the presence of winged petioles in the former. He did, however, concede that certain forms of O. flava are scarcely distinguish- able from O. fabaefolia Form B. Abstract Southern African Oxalis taxonomy is complicated by tremendous morphological variation. The widely distributed Oxalis flava, for example, currently contains eight morphologically distinct forms. The remaining members of sect. Crassulae display morphological characters distinctive enough to retain specific status, despite resemblance to forms of the broadly defined O. flava. Recent collection of a taxon with strong morphological affinities to species in sect. Crassulae generated much interest. In this study we assess the placement of this new taxon to members of sect. Crassulae based on analyses of DNA sequence data of the Internal Transcribed Spacer (ITS) region and morphological comparisons. Results show that most members of sect. Crassulae are distantly related to O. flava. However, our morphological and molecular data strongly suggested that the newly collected taxon represents yet another form of O. flava. In addition, these data show O. fabaefolia to be nested within O. flava, suggesting that it should be synonymised under this broadly defined species. Both the new taxon and O. fabaefolia display unique morphological characters, allowing them to be considered separate subspecific taxa of O. flava. Thus the taxa O. flava var. fabaefolia and O. flava var. unifoliolata are here proposed.