The recognition of ecological speciation and hybridisation as key components of speciation has led to a major shift in evolutionary biology over the last decade. The mimetic Heliconius butterflies of the Neotropics have served as a prominent example of both, although the vast majority of studies have focused exclusively on very recent divergences and on colour pattern adaptation, neglecting deeper timescales and patterns across the rich diversity of the adaptive radiation. The relative importance across adaptive radiations of allopatry, changing ecological pressures, adaptive morphology and introgression promoted by natural and sexual selection remains unknown. I combine phylogenetics, genomics and comparative approaches to elucidate the patterns and identify the key drivers of diversification in the continental-scale radiation of Heliconius and nine related genera. I present the first comprehensive, multilocus and time-calibrated phylogeny of the group and find that shifts in diversification rate cannot be unequivocally attributed to a single environmental factor. The potential role of coevolution with the obligatory host plants Passiflora is examined with the aid of a new phylogeny of the passion vines. Evidence is found for diffuse coevolution, as the diet of most Heliconiini is not predicted by their phylogeny and varies at short timescales. Although passion vine butterflies are the leading example of speciation by hybridisation, this process has been described in only one subgenus. I utilise whole exome data to examine the morphologically suggestive case of a putative hybrid from another clade and find no evidence of introgression. The data is further used to answer long-standing questions about the origins of the most phenotypically diverse species. In the final chapter whole genome data are applied to characterise the patterns of divergence and gene flow across the entire genera Heliconius and Eueides, characterising the patterns of conflicting signal and comparing the performance of philosophically distinct approaches to reflect the heterogeneity across the genome. I find that the phylogeny is unstable due to a combination if incomplete lineage sorting and introgression and may never be fully resolved, perhaps necessitating a network representation. Genomic admixture is a unique property of just one clade comprising a quarter of all species, and involves primarily the adaptive wing pattern loci. Surprisingly, the sex-linked Z chromosome shows a different order of speciation events. Altogether my results show unexpectedly limited role of allopatry, geoclimatic variables and host plant adaptation in the diversification of a major insect radiation, thus confirming the importance of ecological speciation driven by selection on wing patterns. However, I also demonstrate that introgression may be less important in this group than previously thought.

Seminal fluid proteins (SFPs) have been shown to affect the physiology,behaviour and immune responses of mated females in some species. Thisopen window for manipulation of female’s fitness allows the possibility forcomplex evolutionary dynamics between the SFPs and proteins of femalesthat would counter the effects of the former, the female reproductive proteins (FRPs). Also, the bean beetles of the Bruchinae subfamily are pests to pre-ferred species of plant hosts. The hosts have a great variety of secondary defensive metabolites between them and to detoxify those compounds, each beetle species is expected to have a well adapted arsenal of digestive proteinsfor a specific host. I carried out a comparative study with four species of bean beetles with the aim to identify patterns of selection in the proteins mentioned. Expression data for one of those species, Callosobruchus maculatus, has allowed to identify its SFPs, FRPs and digestive proteins and with orthology inference I identified their orthologues in the other three species. Then I estimated theratio of non-synonymous to synonymous substitution rates (ω) for each protein by using codeML of the PAML package and used them as a proxy for estimating selection. FRPs had about the same ω values as conserved genes found across the Arthropod phylum, while the SFPs and digestive proteins hadhigher ω values, indicating more relaxed purifying selection. I also performed tests of positive selection and have identified 92 digestive proteins, 9 FRPs and 26 SFPs as potential targets for future functional work. Finally, I examined the scenario of co-evolution between SFPs and FRPs because of direct interaction. By correlating branch-specific ω values for each possible pairs of proteins I found that SFPs are associated on average more with FRPs than with digestive or conserved genes, as expected. The same was true for the FRPs. Also I examined the possibility of factors contributing to the association such as expression levels, sex-biased expression and protein function. Using linear regression models I found that expression levels and proteinfunction do predict in some degree the ω estimates and could thus also affectthe correlations examined. High gene expression levels reduce the overall ωvalues of genes, also known as E-R anticorrelation. Sex-biased expression does not affect the overall ω values, but does affect the intensity of the E-R anticorrelation, with it being less prominent in male-biased genes and more prominent towards female-biased genes.

No description available.

Many plant species recognize kin and respond with changes in functional traits. Researchers hypothesize that siblings compete less than strangers. However, no study has directly tested whether siblings are less competitive. Measuring natural selection on kin recognition responses in root allocation and other destructively measured traits is challenging, since trait and fitness cannot be measured on the same individual. Here, a methodology using family-level selection is developed, measuring the trait on one individual and measuring its fitness value using another related individual. Three greenhouse pot experiments were conducted using six Brassica oleracea cultivars at two nutrient levels. We investigated whether root allocation and morphological traits were under natural selection. We tested whether or not there was cultivar recognition or resource partitioning in B. oleracea. We found that putative competitive traits (size, height, emergence and root allocation) had expected patterns of individual selection for an increase in each trait and group selection for a reduction of each trait. There was no indication that resource partitioning was occurring or that B. oleracea could recognize cultivars. However, plants were experiencing competitive interactions within pots. In conclusion, we demonstrate that using family-level selection estimates the fitness consequences of root allocation and morphological traits. / Thesis / Master of Science (MSc)

No description available.

No description available.

Plants produce a vast number of low-molecular-weight chemicals (so called secondary or specialized metabolites) that confer a selective advantage to the plant, such as defense against herbivory or protection from changing environmental conditions. Many of these specialized metabolites are used for their medicinal properties, as lead compounds in drug discovery, or to impart our food with different tastes and scents. These chemicals are produced by various pathways of enzyme-mediated reactions in plant cells. It is suspected that enzymes in plant specialized metabolism evolved from those in primary metabolism. Understanding how plants evolved to produce these diverse metabolites is of primary interest, as it can lead to the engineering of plants to be more resistant to both biotic and abiotic stress, or to produce more complex small molecule compounds that are difficult to derive. To that end, the first objective was to develop a schema for rational protein engineering using meta-analyses of a well-characterized sesquiterpene synthase family encoding two closely-related but different types of enzymes, using quantitative measures of natural selection on amino-acid positions previously demonstrated as important for neofunctionalization between two terpene synthase gene families. The change in the nonsynonymous to synonymous mutation rate ratio (dN/dS) between these two gene families was large at the sites known to be responsible for interconversion. This led to a metric (delta dN/dS) that might have some predictive power. This natural selection-oriented approach was tested on two related enzyme families involved in either nicotine/tropane alkaloid biosynthesis (putrescine N-methyltransferase) or primary metabolism (spermidine synthase) by attempting to interconvert a spermidine synthase to encode putrescine N-methyltransferase activity based upon past patterns of natural selection. In contrast to the HPS/TEAS system, using delta dN/dS metrics between SPDS and PMT and site directed mutagenesis of SPDS did not result in the desired neofunctionalization to PMT activity. Phylogenetic analyses were performed to investigate the molecular evolution of plant N-methyltransferases involved in three alkaloid biosynthetic pathways. The results from these studies indicated that unlike O-MTs that show monophyletic origins, plant N-MTs showed patterns indicating polyphyletic origins. To provide the foundation for future molecular-oriented studies of urushiol production in poison ivy, the complete poison ivy root and leaf transcriptomes were sequenced, assembled, and analyzed. / Ph. D.

Thesis (PhD)--Stellenbosch University, 2012. / ENGLISH ABSTRACT: Computational molecular evolution is a field that attempts to characterize how genetic sequences evolve over phylogenetic trees – the branching processes that describe the patterns of genetic inheritance in living organisms. It has a long history of developing progressively more sophisticated stochastic models of evolution. Through a probabilist’s lens, this can be seen as a search for more appropriate ways to parameterize discrete state continuous time Markov chains to better encode biological reality, matching the historical processes that created empirical data sets, and creating useful tools that allow biologists to test specific hypotheses about the evolution of the organisms or the genes that interest them. This dissertation is an attempt to fill some of the gaps that persist in the literature, solving what we see as existing open problems. The overarching theme of this work is how to better model variation in the action of natural selection at multiple levels: across genes, between sites, and over time. Through four published journal articles and a fifth in preparation, we present amino acid and codon models that improve upon existing approaches, providing better descriptions of the process of natural selection and better tools to detect adaptive evolution. / AFRIKAANSE OPSOMMING: Komputasionele molekulêre evolusie is ’n navorsingsarea wat poog om die evolusie van genetiese sekwensies oor filogenetiese bome – die vertakkende prosesse wat die patrone van genetiese oorerwing in lewende organismes beskryf – te karakteriseer. Dit het ’n lang geskiedenis waartydens al hoe meer gesofistikeerde waarskynlikheidsmodelle van evolusie ontwikkel is. Deur die lens van waarskynlikheidsleer kan hierdie proses gesien word as ’n soektog na meer gepasde metodes om diskrete-toestand kontinuë-tyd Markov kettings te parametriseer ten einde biologiese realiteit beter te enkodeer – op so ’n manier dat die historiese prosesse wat tot die vorming van biologiese sekwensies gelei het nageboots word, en dat nuttige metodes geskep word wat bioloë toelaat om spesifieke hipotesisse met betrekking tot die evolusie van belanghebbende organismes of gene te toets. Hierdie proefskrif is ’n poging om sommige van die gapings wat in die literatuur bestaan in te vul en bestaande oop probleme op te los. Die oorkoepelende tema is verbeterde modellering van variasie in die werking van natuurlike seleksie op verskeie vlakke: variasie van geen tot geen, variasie tussen posisies in gene en variasie oor tyd. Deur middel van vier gepubliseerde joernaalartikels en ’n vyfde artikel in voorbereiding, bied ons aminosuur- en kodon-modelle aan wat verbeter op bestaande benaderings – hierdie modelle verskaf beter beskrywings van die proses van natuurlike seleksie sowel as beter metodes om gevalle van aanpassing in evolusie te vind.

Rhodopsin, a visual pigment protein found in retinal photoreceptors, mediates vision at low-light levels. Recent studies focusing primarily in human and mouse have challenged the assumption of neutral evolution of synonymous substitutions in mammals. Using recently developed likelihood-based codon models accounting for mutational bias and selection, we find significant evidence for selective constraint on synonymous substitutions in mammalian rhodopsins, and a preference for cytosine at 3rd codon positions. A second project investigated adaptive evolution in rhodopsin, in view of theories of nocturnality in early mammals. We detected a significant acceleration of non-synonymous substitution rates at the origins of therian mammals, and a tendency of synonymous substitutions towards C-ending codons prior to that. These findings suggest an evolutionary scenario in which synonymous substitutions that increase mRNA stability and/or translation efficiency may have preceded adaptive non-synonymous evolution in early mammalian rhodopsins. These findings have important implications for theories of early mammalian nocturnality.

The study of sex allocation is one of the most successful areas in evolutionary biology: its theoretical predictions have been supported by experimental, observational and comparative approaches. Here, I develop sex allocation theory as follows: (1) I use fertility insurance theory to predict the sex ratio strategy of the malaria parasite, in response to human medical interventions that increase mortality and decrease fertility of the parasite’s various sexual stages; (2) Haplodiploidy has been suggested as a driver of the evolution of eusociality, as under this genetic system a female may be more related to her sister than to her own offspring. I examine a model considering queen versus worker control over the sex ratio of the colony and show that haplodiploidy alone does not explain the evolution of helping; (3) I follow up this study of the haplodiploidy hypothesis by examining the idea that split-sex ratios may favour the evolution of eusociality in haplodiploid species. I study the two mechanisms of split sex ratios, that are found in natural populations and may have been important in the transition to eusociality: queen virginity and queen replacement. I focus on the impact of worker reproduction by considering the effect of woker producing a fraction of the colony offspring and by considering variation in the workers’ offspring sex ratio. My analysis shows that worker reproduction does not promote the evolution of helping in haplodiploid species; (4) I examine the evolution and function of a sterile soldier caste in parasitoid wasps from the genus Encyrtidae. Two main functions have been hypothesized for the emergence of soldiers: spiteful mediation of a sex ratio conflict in mixed-sex broods, and altruistic protection and 7 facilitation of the development of relatives. I develop a model considering variation in the oviposition behaviour of females, that may produce single-sex or mixed-sex broods. I show that, in accordance with previous theory, females are expected to produce more soldiers than males, under the sex ratio conflict hypothesis. I also show that one of the consequences of this costly conflict is that females are favoured to produce single-sex broods over mixed-sex broods.