No description available.

No description available.

The plastid genomes of land plants are generally highly conserved in gene content and order, genome organization, and rates of sequence evolution; however, a few groups have experienced genomic change. The previously published sequence of Pelargonium X hortorum (Geraniaceae) reveals the largest, most rearranged plastid genome among land plants, and rate heterogeneity and genomic change have been documented in the monocot family Poaceae. Three initiatives were taken to characterize plastid genome evolution better in these groups. First, I estimate and compare genome-wide rates of sequence evolution in Geraniaceae genes relative to other angiosperms. An analysis of nucleotide substitutions for 72 plastid genes from 47 angiosperms, including nine Geraniaceae, shows that values of dN are accelerated in ribosomal protein and RNA polymerase genes. dN/dS, an indicator of selection, is significantly elevated in the same two classes of genes and ATPase genes. Second, I sequenced three additional Geraniaceae plastid genomes (Erodium texanum, Geranium palmatum, and Monsonia speciosa) and compare these sequences to each other, P. X hortorum, and other rosids. Geraniaceae plastid genomes are highly variable in size, gene content and order, and base composition. The genome of M. speciosa is among the smallest land plant plastid genomes, and one copy of the IR region in E. texanum has been lost. Gene/intron loss and gene duplication are rampant in Geraniaceae plastid genomes, and a number of losses are phylogenetically inconsistent. To explain the unusual rates and patterns of genome evolution in Geraniaceae, I propose a model of aberrant DNA repair coupled with altered gene expression. Lastly, I characterize genome evolution in the family Poaceae and order Poales. There has been a recent surge in the availability of Poaceae sequences, but a comprehensive analysis of genome evolution had not been performed that included any non-grass Poales taxa. I present the sequence of Typha latifolia (Typhaceae), the first non-grass Poales sequenced to date, and I show that Poaceae plastid genomes exhibit increased genomic rearrangements and nucleotide substitutions. These analyses show the extent of lineage-specific rate acceleration on the branch leading to Poaceae and deceleration during the diversification of the family. / text

Thesis (MSc)--Stellenbosch University, 2011. / ENGLISH ABSTRACT: Species’ seasonal behaviour is of paramount importance in understanding community functioning and dynamics. Recently, plant phenology has further gained significance as a reliable indicator of climate change impacts. Despite the importance of understanding plant dynamics, there are relatively few plant phenological records for the sub-Antarctic region, and where records exist they are often not extensive. Sub-Antarctic Marion Island, typical of Southern Ocean Islands, offers a useful setting for addressing these knowledge gaps. This study documented the vegetative and reproductive phenologies (or aggregate phenological patterns) of twelve indigenous and three alien vascular plant species on the island. The phenological differences among the species and distinct seasonal groupings (e.g. early, intermediate and late species) were examined. I also investigated the phenological differences among the indigenous and alien plant species. Furthermore, the onset of selected reproductive phenophases from the current records was compared with historical records for determining the extent of climate change-related alterations in phenology. Phenological data were collected fortnightly on five, 5 m x 5 m permanent plots per species (except for a few species) for a full growing season. Thus the sample size is n = 5 for all plant species except for Crassula moschata (n = 4), Juncus effusus (n=4) and Rumex acetosella (n=1). Sites of the same species were separated by at least 500 m except for the alien plant, Juncus effusus, where all four known populations were selected despite two of these populations being < 500 m apart. This study indicated that Marion Island plants grow throughout the year with no major peaks except in Azorella selago and Acaena magellanica which showed winter dormancy. However, reproduction in most plant species predominately occurred in spring and summer months. Pringlea antiscorbutica and Poa cookii were the first two species to set flower buds in September while most species dispersed their seeds in summer except for Agrostis magellanica and Crassula moschata which dispersed in early autumn. Distinct from most temperate systems, the reproductive seasonality displayed by Marion Island plant species is explained more by daylength than by temperature, perhaps due to the region’s typical thermal aseasonality. Interestingly, many cooccurring species and/or clades across the Falkland, Kerguelen, Macquarie and South Georgia Islands also showed similar flowering onset date to the Marion Island plants, further confirming their daylength sensitivity. However, other external factors seem to come into play at later events of reproduction. Consequently, fruit maturation time of similar species across the sub-Antarctic islands varied substantially despite the plants having flowered in the same month. Although plant species showed similar reproductive seasonality, there were significant differences among species phenologies i.e. phenophase timing, duration and peak occurrence dates. However, using 95% confidence intervals of Generalized Linear Models weighted means, and/or one-way ANOVA (Tukey post hoc test), three homogenous sets of species (early, late, or intermediate onsets) were identified based on flower bud, flowering and seed dispersal phenophase onset dates. The homogenous species groupings observed for flower buds also remained unchanged during flowering onset except for Cotula plumosa and Callitriche antarctica which switched groups. As for the seed dispersal timing, the pattern was not consistent with that of the flower bud and flowering onset homogenous groupings, except for Acaena magellanica and Agrostis magellanica which remained in the early and late groups, respectively. Conversely, in the case of the timing of other phenophases (pollen release, fruit set and fruit ripening), entire phenophase durations, and peak occurrence dates, species overlapped greatly, resulting in an unbroken progression or continuum of phenology among species. Similarly, the three alien plant species investigated here (Cerastium fontanum, Juncus effusus and Rumex acetosella) showed no consistent phenological differences from the rest of the species. However, a widespread alien plant species on Marion Island, C. fontanum, reproduced for most of the year, although its reproduction peak was in summer months as was the case for the rest of the species. This study also indicated that indigenous plant species have altered their reproductive phenologies since 1965. Although the response was species-specific, the majority of plant species significantly delayed the onset of reproductive activities in 2007 by comparison with 1965. However, it is not clear if the observed species response was caused by the now drier and warmer Marion Island climate or by discrepancies in reporting in the earlier studies and/or sampling differences between the recent and historical records. Therefore, these results should be taken with caution. In conclusion, this research provided a detailed phenological dynamics record for vascular plant species on the island. Over time these records may be used as a basis for monitoring and modelling the impact of climate on plant phenology on the island. / AFRIKAANSE OPSOMMING: Spesies se seisoenale gedrag is van die allergrootste belang in die begrip van gemeenskapsfunksionering en dinamika. Meer onlangs het plant fenologie verdere betekenis verwerf as ‘n betroubare indikator vir die impakte van klimaatsverandering. Ondanks die belangrikheid om plant dinamika te verstaan, is daar relatief min plant fenologiese rekords vir die sub-Antarktiese streek en waar rekords wel bestaan is dit dikwels nie omvangryk nie. Sub- Antarktiese Marion Eiland, tipies van Suidelike Oseaan Eilande, bied ‘n nuttige ligging om hierdie kennis gapings aan te spreek. Hierdie studie het die vegetatiewe en voorplantingsfenologieë (of gesamentlike fenologiese patrone) van elf inheemse en drie uitheemse vaatplantspesies op die eiland gedokumenteer. Die fenologiese verskille tussen die spesies en duidelike seisoenale groeperings (bv. vroeë, intermediêre en laat spesies) is ondersoek. Ek het ook die betekenisvolle fenologiese verskille tussen die inheemse en uitheemse plantspesies ondersoek. Voorts, die aanvang van gekose voortplanting feno-fases van huidige rekords is vergelyk met historiese rekords om die mate van klimaatsverandering verbandhoudende veranderings in die fenologie te bepaal. Fenologiese data is twee weekliks ingesamel op vyf, 5 m x 5 m permanente plotte per spesie (behalwe vir ‘n paar spesies) vir ‘n volle groei seisoen. Dus, die insamelings grootte is n = 5 vir al die plantspesies behalwe vir C. moschata (n = 4), Juncus effusus (n=4) en Rumex acetosella (n=1). Persele vir dieselfde spesies is geskei deur ten minste 500 m, behalwe vir die uitheemse plant, Juncus effusus, waar al vier populasies wat bekend is gekies is, ten spyte daarvan dat twee van hierdie populasies < 500 m uitmekaar is. Hierdie studie het aangedui dat Marion Eiland plante regdeur die jaar groei, met geen belangrike spitstye nie, behalwe in Azorella selago en Acaena magellanica wat ‘n winter rusperiode wys. Hoe ookal, voortplanting in meeste van die plantspesies het hoofsaaklik voorgekom tussen die lente en somermaande. Pringlea antiscorbutica en Poa cookii was die eerste twee spesies om blomknoppe uit te stoot in September, terwyl die meeste spesies hulle sade versprei het gedurende die somer, behalwe vir Agrostis magellanica en Crassula moschata wat versprei het in vroeg herfs. Duidelik van meeste gematigde sisteme, word die voortplanting seisoenaliteit, getoon deur die Marion Eiland plantspesies, verduidelik meer deur daglengte as deur temperatuur, moontlik weens die streek se tipiese termiese a-seisoenaliteit. Interessant, baie spesies en/of afstameling-groeperings wat saam aangtref word dwarsoor die Falkland, Kerguelen, Macquarie en Suid Georgia Eilande wys ook soortgelyke bloei aanvangsdatums as die Marion Eiland plante, nog meer bevestigend van hulle dag-lengte sensitieweteit. Hoe ookal, ander eksterne faktore blyk betrokke te raak by latere gebeure van voortplanting. Gevolglik het vrug rypwordingstyd van dieselfde spesies oor die sub-Antarktiek noemenswaardig verskil, ten spyte daarvan dat die plante in dieselfde maand geblom het. Alhoewel plantspesies dieselfde voortplanting seisoenaliteit gewys het, was daar ‘n noemenswaardige veskil tussen spesie fenologieë, m. a. w. feno-fase tydsberekenning, tydsduur en spits voorkomsdatums. Hoe ookal, deur gebruik te maak van 95% betroubaarheid intervalle van Algemene Lineêre Modelle gewigte gemiddelde en/of een rigting ANOVA (Turkey post hoc toets), is drie homogene stelle van spesies (vroeë, laat en intermediêre aanvang) geïdentifiseer gebasseer op blomknop, bloei en saad verspreiding feno-fase aanvangsdatums. Die homogene spesie groeperings waargeneem op blomknoppe het ook onveranderd gebly gedurende bloei aanvang behalwe vir Cotula plumosa en Crassula antarctica wat groepe geruil het. Vir die saadverspreiding tydsberekenning was die patroon nie konstant met die van die blomknop en bloei aanvang homogene groepe nie, behalwe vir Acaena magellanica en Agrostis magellanica wat in die vroeë en laat groepe respektiewelik gebly het. Omgekeerd, in die geval van tydsberekenning van ander feno-fases (stuifmeel vrysetelling, vrugwerp, vrugrypwording), volledige feno-fase tydsduur en spits voorkomsdatums het spesies grootliks oorvleuel, wat ‘n ongebroke vordering of deurlopendheid van fenologie tussen die spesies tot gevolg het. Ooreenkomstig het die drie uitheemse spesies wat hier ondersoek is (Cerastium fontanum, Juncus effusus en Rumex acetosella) geen bestendige fenologiese verskille van die res van die spesies gewys nie. Hoe ookal, ‘n wydverspreide uitheemse spesie op Marion Eiland, Cerastium fontanum, het deur die meeste van die jaar voortgeplant, hoewel met ‘n voorplanting spits in die somer maande soos die res van die spesies. Hierdie studie dui ook aan dat inheemse plantspesies hulle voortplanting fenologieë verander het sedert 1965. Alhoewel die reaksie spesiespesifiek was, het die meerderheid van die plantspesies hulle voortplanting aanvang aansienlik vertraag gedurende 2007 in vergelyking met 1965. Hoe ookal, dis nie duidelik of die waargeneemde spesie reaksie was as gevolg van die nou droër en warmer Marion Eiland klimaat of deur teenstrydighede in verslagewing gedurende die vroëre studies en/of insameling verskille tussen die onlangse en historiese rekords. Daarom moet hierdie resultate met versigtigheid hanteer word. In samevatting, hierdie navorsing voorsien ‘n gedetaileerde fenologiese dinamieka rekord vir vaatplantspesies op die eiland. Oor tyd kan hierdie rekords gebruik word as basis vir monitering en modellering van die impak van klimaat.

The aim of this dissertation is to study the systematics and evolution of Euphorbiaceae vines (tribe Plukenetieae), a diverse pantropical lineage (~365 species and 18 genera) composed of three morphologically distinct subtribes, Dalechampiinae, Plukenetiinae, and Tragiinae. Through the course of my research I largely resolved the evolutionary history of Plukenetieae and made broader contributions to the study of pollen and seed evolution, pantropical biogeography, and plant diversification. In chapter two I developed the first well-sampled molecular phylogeny for Plukenetieae (154 terminals, ~93 species, 2,207 character dataset composed of ITS and psbA-trnH with indel gap-scored data), and determined baseline species group relationships of the tribe. Molecular phylogeny largely agreed with pollen morphology hypotheses and confirmed that the large genus Tragia was para- and/or polyphyletic and should be split into smaller genera. Analysis of pollen morphology revealed a trend towards aperture reduction and loss in Tragiinae, with four origins of weakly defined apertures and up to three origins of inaperturate pollen. In chapter three, I studied the seed size evolution of Plukenetia, a pantropical genus with large edible oil-rich seeds, by developing a near-exhaustive phylogeny (83 terminals, 20 of ~24 species, 5,069 bp dataset of ETS, ITS, KEA1 introns 11 and 17, TEB exon 17, matK, ndhF) and conducting ancestral state estimation and phylogenetic regression. Seed size evolution in Plukenetia was dynamic and associated with competing selective pressures of plant size, fruit type (and inferred dispersal syndrome), and seedling ecology. In chapter four I presented a revised sectional classification of Plukenetia based on phylogeny and morphological evidence, including three new taxa from South America. Chapters three and five included biogeographical investigations on Plukenetia and Plukenetieae. Analyses revealed that pantropical disjunct distributions arose one to three times in each subtribe via periodic long-distance dispersals from the Oligocene to the Pliocene, most often from South America to Africa and then Southeast Asia. Lastly, in chapter five, I developed an improved phylogeny for Plukenetieae (289 terminals, ~109 species, 5,160 bp dataset of ETS, ITS, KEA1 intron 11, TEB exon 17, matK, ndhF) to study the influence of innovative traits (twining growth form, stinging hair defences, and pseudanthial inflorescences) on diversification in the tribe. However, increased diversification was not associated with innovative traits. Instead, diversification was associated with clades that shifted into drier open habitats, aided by habitat expansion following the Late Miocene cooling period.

The interaction between pollinators and flowers affects the fitness of both pollinators and flowering plants, which can result in the co-evolution of pollinator and floral traits. Some pollination systems contain flower-dwelling ambush predators that attack visiting pollinators. This interaction could result in co-evolution of predator and pollinator traits as is typical in predator-prey systems. The presence of these predators could also have indirect negative fitness effects on flowering plants by killing or deterring pollinators. This raises the possibility that predator and floral traits also co-evolve. Furthermore, it is possible that this system is best described as a three-species game where predator, pollinator, and floral traits all co-evolve. The ultimate goal of my thesis is to explore this possibility. This is achieved in Chapter 5, which consists of a game theory model of the co-evolution of floral colour with predator and pollinator behavioural strategies. This model is novel, both within the pollination context described here and within a wider context. Furthermore this model is the first to propose that the evolution of floral colour might be affected by the presence of flower-dwelling ambush predators. This is particularly significant given that there has been little discussion about what floral traits might be adaptations to the presence of these predators. A secondary goal of this thesis is to explore how pollinators detect and respond to the presence of flower-dwelling ambush predators as an important subcomponent of predator-pollinator-flower co-evolutionary dynamic. Chapter 2 demonstrates that bumblebees avoid evidence of past predation events, and Chapter 3 demonstrates that the honeybee recruitment dance is affected by exposure to cues of predation risk in a way that should reduce the colony's exposure to predators. Chapter 4 is a model that suggests novel factors that might affect how a population of pollinators distributes itself between predator-free and predator-containing flowers. / Thesis / Doctor of Philosophy (PhD)

Future global change scenarios predict a dramatic loss of biodiversity for many regions in the world, potentially reducing the resistance and resilience of ecosystem functions. Once before, during Plio-Pleistocene glaciations, harsher climatic conditions in Europe as compared to North America led to a more depauperate tree flora. Here we hypothesize that this climate driven species loss has also reduced functional diversity in Europe as compared to North America. We used variation in 26 traits for 154 North American and 66 European tree species and grid-based co-occurrences derived from distribution maps to compare functional diversity patterns of the two continents. First, we identified similar regions with respect to contemporary climate in the temperate zone of North America and Europe. Second, we compared the functional diversity of both continents and for the climatically similar subregions using the functional dispersion-index (FDis) and the functional richness index (FRic). Third, we accounted in these comparisons for grid-scale differences in species richness, and, fourth, investigated the associated trait spaces using dimensionality reduction. For gymnosperms we find similar functional diversity on both continents, whereas for angiosperms functional diversity is significantly greater in Europe than in North America. These results are consistent across different scales, for climatically similar regions and considering species richness patterns. We decomposed these differences in trait space occupation into differences in functional diversity vs. differences in functional identity. We show that climate-driven species loss on a continental scale might be decoupled from or at least not linearly related to changes in functional diversity. This might be important when analyzing the effects of climate-driven biodiversity change on ecosystem functioning.

Extreme haustorial parasites have long captured the interest of naturalists and scientists with their greatly reduced and highly specialized morphology. Along with the reduction or loss of photosynthesis, the plastid genome often decays as photosynthetic genes are released from selective constraint. This makes it challenging to use traditional plastid genes for parasitic plant phylogenetics, and has driven the search for alternative phylogenetic and molecular evolutionary markers. Thus, evolutionary studies, such as molecular clock-based age estimates, are not yet available for all parasitic lineages. In the present study, we extracted 14 nuclear single copy genes (nSCG) from Illumina transcriptome data from one of the “strangest plants in the world”, Hydnora visseri (Hydnoraceae). A ~15,000 character molecular dataset, based on all three genomic compartments, shows the utility of nSCG for reconstructing phylogenetic relationships in parasitic lineages. A relaxed molecular clock approach with the same multi-locus dataset, revealed an ancient age of ~91 MYA for Hydnoraceae. We then estimated the stem ages of all independently originated parasitic angiosperm lineages using a published dataset, which also revealed a Cretaceous origin for Balanophoraceae, Cynomoriaceae and Apodanthaceae. With the exception of Santalales, older parasite lineages tend to be more specialized with respect to trophic level and have lower species diversity. We thus propose the “temporal specialization hypothesis” (TSH) implementing multiple independent specialization processes over time during parasitic angiosperm evolution.

No description available.

Future global change scenarios predict a dramatic loss of biodiversity for many regions in the world, potentially reducing the resistance and resilience of ecosystem functions. Once before, during Plio-Pleistocene glaciations, harsher climatic conditions in Europe as compared to North America led to a more depauperate tree flora. Here we hypothesize that this climate driven species loss has also reduced functional diversity in Europe as compared to North America. We used variation in 26 traits for 154 North American and 66 European tree species and grid-based co-occurrences derived from distribution maps to compare functional diversity patterns of the two continents. First, we identified similar regions with respect to contemporary climate in the temperate zone of North America and Europe. Second, we compared the functional diversity of both continents and for the climatically similar subregions using the functional dispersion-index (FDis) and the functional richness index (FRic). Third, we accounted in these comparisons for grid-scale differences in species richness, and, fourth, investigated the associated trait spaces using dimensionality reduction. For gymnosperms we find similar functional diversity on both continents, whereas for angiosperms functional diversity is significantly greater in Europe than in North America. These results are consistent across different scales, for climatically similar regions and considering species richness patterns. We decomposed these differences in trait space occupation into differences in functional diversity vs. differences in functional identity. We show that climate-driven species loss on a continental scale might be decoupled from or at least not linearly related to changes in functional diversity. This might be important when analyzing the effects of climate-driven biodiversity change on ecosystem functioning.