Dissertations / Theses on the topic 'Colour evolution'

Kyoto University (京都大学)
0048
新制・課程博士
博士(人間・環境学)
甲第10943号
人博第230号
15||185(吉田南総合図書館)
新制||人||58(附属図書館)
UT51-2004-G790
京都大学大学院人間・環境学研究科環境相関研究専攻
(主査)教授 加藤 真, 教授 松井 正文, 助教授 宮下 英明
学位規則第4条第1項該当

The evolution and development of eyespot and non-eyespot colour pattern elements was studied in Vanessa butterflies using a phylogenetic approach. A Bayesian phylogeny of the genus Vanessa was reconstructed from 7750 DNA base pairs from 10 genes. Twenty-four non-eyespot and forty-four eyespot color pattern elements from the Nymphalid ground plan were defined and studied and their evolutionary history was traced on the Vanessa phylogeny. Ancestral character states were predicted and the direction of evolutionary changes was inferred for all characters. Five serially arranged eyespots were predicted for the ancestral Vanessa on all wing surfaces. Homologous eyespot and non-eyespot characters on the surfaces of the forewing were more similar than those on the surfaces of the hindwing. Homologous eyespot characters on the dorsal surfaces of fore and hindwings show more similarities than the ventral surfaces, in contrast to what was found for non-eyespot characters. Independent Contrast analysis was also used to study correlations between eyespot characters. Independent Contrast analysis revealed significant correlations between eyespots 2 and 5 and eyespots 3 and 4 on all wing surfaces. This consistency among highly variable eyespot characters suggested a structural hypothesis: the existence of a Far-Posterior (F-P) compartment boundary and organizer could be responsible for the observed correlations. This hypothesis was tested in several ways. First, examination of wing patterns across species from all families of butterflies revealed correspondence between wing cells 1 and 4 and between cells 2 and 3. Second, evaluation of spontaneous mitotic clones in butterflies and moths reveals a peak abundance of clonal boundaries along the vein dividing wing cells 2 and 3. Finally, experimentally generated FLP/FRT mitotic wing clones produced in Drosophila, reveal a clonal boundary posterior to the L5 wing vein, which is homologous to the vein dividing wing cells 3 and 4 in butterflies. Collectively, this suggests the existence of an additional compartment boundary associated with an organizer in wing cell 3 responsible for patterning the posterior portion of insect wings. A model is proposed that predicts that the wing developmental compartment boundaries produce unique combinations of gene expression for each wing sector, permitting eyespot individuation.
February 2016

We investigate the effects of colour evolution in QCD scattering processes and how these can be implemented in both analytical and numerical approaches. We split this in to four parts where each part is given in one chapter. In the first chapter we give a brief summary of the important aspects of QCD which are needed as a basis for the rest of the investigation. In addition to this, we describe different sets of formalisms for handling colour within interactions. We then give a brief review of the components of a Monte-Carlo event generator. In the second chapter we review previous work by the author on jet vetoes and their implementation in the Monte-Carlo event generator Herwig++. We describe the analytical method for studying jet vetoes and then discuss the differences between this method and that which is used in the original parton shower of Herwig++. Once this is done we make changes to both the analytical approach and Herwig++ in order to investigate these differences. We then show the results for an improved parton shower as a result of this investigation. In the third chapter we consider the effects of tuning the parameters within Herwig++. We investigate what parameters are likely to have the most changes to observables given the modifications made in the previous chapter. We then produce seven tunes to different sets of observables and discuss said tunes. In the fourth and final chapter we discuss the effects of sub-leading colour within the analytical approach and in a potential numerical setup. We discuss a set of potential algorithms for implementing sub-leading colour within a standalone parton shower.

This thesis investigates language acquisition and evolution, using the methodologies of Bayesian inference and expression-induction modelling, making specific reference to colour term typology, and syntactic acquisition. In order to test Berlin and Kay�s (1969) hypothesis that the typological patterns observed in basic colour term systems are produced by a process of cultural evolution under the influence of universal aspects of human neurophysiology, an expression-induction model was created. Ten artificial people were simulated, each of which was a computational agent. These people could learn colour term denotations by generalizing from examples using Bayesian inference, and the resulting denotations had the prototype properties characteristic of basic colour terms. Conversations between these people, in which they learned from one-another, were simulated over several generations, and the languages emerging at the end of each simulation were investigated. The proportion of colour terms of each type correlated closely with the equivalent frequencies found in the World Colour Survey, and most of the emergent languages could be placed on one of the evolutionary trajectories proposed by Kay and Maffi (1999). The simulation therefore demonstrates how typological patterns can emerge as a result of learning biases acting over a period of time. Further work applied the minimum description length form of Bayesian inference to modelling syntactic acquisition. The particular problem investigated was the acquisition of the dative alternation in English. This alternation presents a learnability paradox, because only some verbs alternate, but children typically do not receive reliable evidence indicating which verbs do not participate in the alternation (Pinker, 1989). The model presented in this thesis took note of the frequency with which each verb occurred in each subcategorization, and so was able to infer which subcategorizations were conspicuously absent, and so presumably ungrammatical. Crucially, it also incorporated a measure of grammar complexity, and a preference for simpler grammars, so that more general grammars would be learned unless there was sufficient evidence to support the incorporation of some restriction. The model was able to learn the correct subcategorizations for both alternating and non-alternating verbs, and could generalise to allow novel verbs to appear in both constructions. When less data was observed, it also overgeneralized the alternation, which is a behaviour characteristic of children when they are learning verb subcategorizations. These results demonstrate that the dative alternation is learnable, and therefore that universal grammar may not be necessary to account for syntactic acquisition. Overall, these results suggest that the forms of languages may be determined to a much greater extent by learning, and by cumulative historical changes, than would be expected if the universal grammar hypothesis were correct.

It is well known that the colour preferences of ganglion and LGN cells do not match the four perceptually simple colours red, green blue and yellow. It is also known that although colour perception is distorted in the peripheral visual field, there are four hues that appear stable with eccentricity. These are defined as peripherally invariant hues. Both of these observations must in some way reflect the physiological substrate of neurons at different stages of the primary visual pathway. The experiments described here are aimed at understanding the link between the physiology and the perception of colour by studying the characteristics of peripheral colour visionThe following questions have been addressed; i) to what extent does colour matching rely on the retinal physiological substrate? ii) what is the reason for the discrepancy between invariant and unique green and how is cone contrast linked to this paradox? iii) how are the `special' hues (invariant and unique) related to human evolution? iv) how does peripheral colour vision vary between males and females?An asymmetric colour matching paradigm and a colour naming task have been employed. In the colour matching task, 24 chromatic axes of variable purity are used. Observers match the chromaticity of a 3 degree peripheral spot with that of a 1 degree parafoveal spot. The results are expressed in terms of hue rotation, saturation match and cone contrast. In the colour naming experiment the observers name 40 chromatic axes as either red, blue, green or yellow and colour naming functions are derived. The central maxima of these functions are defined as the unique hues. The results suggest that colour matching and cone opponency reflect the characteristics of the retinal neural network as they exhibit nasal-temporal asymmetries, similar to known physiological asymmetries. Although three of the peripherally invariant hues match the unique counterparts, invariant and unique green are markedly different for all observers. In an important control experiment unique hues are shown to be stable with eccentricity and purity. This confirms that these attributes are not confounding factors for the observed discrepancy between invariant and unique green. Unlike for the other 'special' hues the RMS cone contrast of invariant green differs markedly between parafoveal and peripheral targets. It is likely that the cone contrast remains unchanged only if the stimuli excite the same number of cones. Two invariant and two unique hues (blue and yellow) fall on the daylight locus suggesting that discrimination in these regions of the colour space is strongly influenced by terrestrial illumination. Moreover, the inter-individual variability is found to be minimised around the daylight locus showing that the blue-yellow system is more stable across colour normal populations than the red-green system. A statistically significant difference is demonstrated between the peripheral colour vision of males and females. This may be attributed to the M-cone polymorphism which in addition to X-chromosome inactivation, results in more than three cone types in the female retina.

The diverse visual specialisations of stomatopods are an important consideration in studies of their radiation and evolution. Most stomatopods in the Superfamilies Gonodactyloidea and Lysiosquilloidea have regionally specialised eyes. A central band composed of six rows of ommatidia contains an array of photoreceptive pigments and filters that allow for finely tuned colour and polarisation vision. In other stomatopods the mid-band is reduced and unspecialised, or is absent. Previously, this has been considered to be the plesiomorphic condition. Phylogenetic analyses of the Stomatopoda show that the extant stomatopod lineages evolved from a gonodactyloid-type ancestor. Characters for phylogenetic analyses have been derived from external morphology, details of eye daslqn and mitochondrial DNA sequences. Although not wholly congruent, the results from these separate analyses indicate that species with a simpler eye design are not more primitive but have lost parts of the mid-band arrangement. This regressive evolutionary event has occurred independently on a number of occasions. Observations on the neuroanatomy of the eyes in the stomatopod Neogonodactylus oerstedii have revealed the existence of an accessory lobe located distally on the medulla externa and connecting with the six mid-band rows. The lobe is involved in processing colour and polarisation information. The discovery of the lobe in species that lack the retinal specialisations for colour vision provides further evidence that they are descended from a more advanced ancestor. Similarities in the arrangement of eye muscles between species with a two or six row mid-band also give support for this conjecture. The ancestors of the modern stomatopods are likely to have evolved in shallow water and coral reef habitats. The development of colour vision was advantageous for prey location and in interspecific encounters. Stomatopods subsequently radiated into a diverse range of habitats. For those in more spectrally limited surroundings the colour vision system has largely been lost but vestiges are still present today in the form of a reduced mid-band and medulla lobe.

This thesis addresses questions concerning the evolution of body colour in threespine sticklebacks (Gasterosteus aculeatus). Chapter 2 examines natural selection of colour in sticklebacks by investigating the possible divergence of cryptic colouration between a species pair. I determined that the upper body colour of benthics matched the littoral background (benthics’ habitat) colour more closely than did the upper body colour of limnetics, suggesting that in their own habitat benthics are more cryptically coloured than the limnetic species. Furthermore, I found that benthics exhibited a greater degree of colour plasticity and consistency in this plasticity than limnetics, which is likely an adaptive response to the greater spectral heterogeneity of the littoral zone. Chapter 3 examines sexual selection of colour in sticklebacks by investigating whether UV is a secondary sexual character on the abdomen of four stickleback populations. Using colour measurements taken from reproductive males and females during the breeding season and individuals from the non-breeding season, I found that UV did not exhibit striking patterns of sexually dimorphism or seasonality on the abdomen, suggesting that UV is not a secondary sexual character on this part of the body in these populations. The Priest benthic population, however, exhibited significant sexual dimorphism and borderline significant seasonality, leaving open the possibility that UV may be a secondary sexual character in this population.

Heliconius butterflies are found across the neo-tropics, with bright aposematic colour patterns. These Müllerian mimics show striking colour pattern convergence across species, while paradoxically showing striking diversity within species. Thus Heliconius wing patterns have become an excellent system for understanding the repeatability of evolution. This work has identified a number of genes that appear to be involved in colour pattern control across species, such as optix and cortex, which respectively control red and yellow pattern elements. However, this work has only looked at the genetic basis of colour pattern in a small number of species, and primarily focusses on just two; H. melpomene and H. erato. I first use a population genomics approach to try to identify whether optix controls the hindwing rays phenotype in two poorly studied species; H. demeter and H. aoede. I identify both divergence associated with colour pattern at this optix, as well as another putative colour pattern control locus in H. aoede, the ommochrome pathway gene cardinal. Further, I use Quantitative trait loci analysis to explore the genetics of colour pattern in H. melpomene, confirming WntA as the gene controlling the ‘broken band’ phenotype and I identify a locus associated with red-orange pigmentation, while also exploring the role of minor effect loci in quantitative colour pattern variation. Finally, I use the natural diversity at two hybrid zones, in conjunction with phylogenetic discordance at mimicry loci, to identify putative regulatory enhancers associated with colour pattern shifts, investigate introgression across species at this fine genetic scale, and the possible role of colour pattern introgression in Heliconius speciation. This work reveals both interesting cases of convergent genetic evolution, independent genetic evolution and introgression, showing that a variety of evolutionary processes have shaped Heliconius mimicry across species.

In aposematism a prey species use bright colours, often combined with a black contrasting pattern, to signal unprofitability as prey to potential predators. Although there are several different hypotheses about the presence of these internally contrasting patterns, there is little experimental evidence of any beneficial effects. In this thesis I have used bird predators and artificial prey signals to investigate if the contrasting internal patterns in warning displays may have evolved to increase signal efficacy, especially regarding the speed of avoidance learning. In paper I the relative importance of colour and pattern in avoidance learning was studied. The conclusion was that birds primarily attend to colour, not pattern, when learning the discrimination, which was further supported by the results in paper II-IV, all suggesting a secondary role of patterns. In paper II I show that predators may to some degree use patterns for discrimination, if they convey important information about prey quality. The predators showed a hierarchical way of learning warning colour components, where colour is learned to a higher degree than pattern. In paper III I investigate if internal contrasting patterns promote avoidance learning by increasing conspicuousness as prey-to-background contrast does. The study did not support this idea, as the presence of internal black patterns did not improve avoidance learning on a colour matching background. In paper IV, however, I show that the presence of many internal colour boundaries resulted in faster avoidance learning on a multi-coloured background, and predator generalization favoured more internal boundaries, while there was no effect of pattern regularity. From these studies I conclude that internal pattern contrasts may function to increase the efficacy of the warning colour, its salience, and as a means for aposematic prey to be discriminated from harmful mimics. However, the major finding is the importance of colour over pattern.
At  the time of the doctoral defence the following papers were unpublished and had a status as follows: Paper 2: Manuscript; Paper 4: Manuscript

In this thesis, I used Lathyrus to study floral colour evolution. My work builds on that of pioneer geneticists who used the sweet pea (Lathyrus odoratus) for research in early 20th century England. They used the rich horticultural resource of inbred cultivars for genetic study. More recently, studies on flavonoid biochemistry and the phylogenetics of Lathyrus lend tools to place the colour shifts in an evolutionary and molecular context. In chapter 2, I show that the A1 locus is a missense mutation (332 G/A) in the substrate recognition site (SRS1) of flavonoid 3’,5’-hydroxylase (F3’5’H) and is associated with the pink mutant cultivar ‘Painted Lady’ (‘PL’). This single base pair substitution in the mutant F3’5’H is speculated to toggle the enzyme from primary F3’5’H activity to a relatively efficient F3’H, as shown in a heterologous transformation in Arabidopsis PAP1D (a mutant line that produces anthocyanin constitutively). In chapter 3, I constructed a multi-species coalescent tree using Bayesian inference and reconstructed the ancestral states for floral colour, life history trait (perennial or annual) and floral pattern. The ancestral states for Lathyrus are anthocyanin rich (AR), annual and concolourous. However, no correlation was found between the life history trait (which is linked to breeding systems) and the loss of anthocyanin colour in the petal, when corrected for phylogenetic independence. This suggests that in Lathyrus, autogamous species are as colourful as allogamous ones even though the latter are expected to need greater floral display. In chapter 4, I found that the lack of expression in dihydroflavonol reductase (DFR) was associated with a white mutant cultivar ‘Mrs Collier’ (‘MC’) of L. odoratus via a trans-regulatory machinery. Two transcription factors, the sweet pea orthologues of AN2 (MYB) and AN1 (bHLH) were also not expressed although neither was associated with the white phenotype in an F2-cosegregation analysis. This DFR silencing was also observed in another white mutant of the domesticated grass pea (L. sativus). In contrast, when unpigmented wild species originate under natural selection, DFR expression, if at all affected, is lowered rather than fully silenced, likely due to pleiotropic effects.
Science, Faculty of
Botany, Department of
Graduate

The detrimental effects of inbreeding are well known, and they have been shown to be associated with lower levels of reproductive success, higher levels of parasitism and differences in disease susceptibility. To better understand large fitness differences between morphs in the colour polymorphic common buzzard, Buteo buteo, we investigated differences in the levels of internal relatedness between morphs. As the common buzzard mating system is non-random and the light and dark morph individuals are less abundant than the intermediates, it could be the case the extreme colour morph individuals are more inbred. However, no differences were found in levels of inbreeding. In birds, the physiological and behavioural consequences of colour polymorphisms are not widely known. Here we used an experiment to investigate the effect of this melanin-based polymorphism on nest defence behaviour in the common buzzard. Among males, light morphs were found to be significantly more aggressive to a perceived threat of nest predation than either intermediate or darkly coloured birds, while there was a non-significant tendency for the reverse among females. The level of aggression observed for each member of a pair was independent of the level of aggression shown by the other member. These results illustrate that polymorphisms can be associated with alternative reproductive tactics in birds, and suggest a possible link between the biochemistry of melanin production and individual behaviour. For most species living in seasonal environments, timing is an important determinant of the success of a breeding attempt. Individuals also face a trade off between current and future reproduction. Here we investigated whether colour morphs differed in their timing of breeding. Light-light and dark-dark pairs were found to breed earlier than the population mean, with light-dark pairs fledging chicks slightly later. Differences in reproductive strategies between morphs may account for the observed differences.

Timescales for stellar evolution and star and planet formation are critical to provide constraints on theories. The accuracy of these timescales, and therefore our ability to confidently reject a given model, rely on the accuracy of the derived ages for star-forming-regions (SFRs). In this study I have developed the new techniques and adopted or updated the existing techniques necessary to derive precise age orders for a range of SFRs. Deriving precise ages for SFRs requires precise distances and extinctions. I have applied a new technique, 2 fitting (Naylor &Je ries, 2006), to derive a set of self-consistent and statistically robust distances (and mean extinctions), with associated uncertainties for 12 SFRs. I have also revised and formalised a widely used method of deriving individual extinctions, the Q-method (Johnson &Morgan, 1953). These new data show that the largest remaining uncertainty in deriving distances to SFRs is composition. Deriving ages or age orders for pre-main-sequence (pre-MS) populations using pre-MS theoretical isochrones has been shown to be unreliable at present (Naylor et al., 2002; Bonatto et al., 2004; Pinsonneault et al., 2004), largely due to model dependencies and spreads within a colour-magnitude diagram (CMD). Therefore, I have developed a technique to model the pre-MS, generating empirical isochrones, which e ectively removes spreads in pre-MS populations in a CMD. The derived distances and extinctions have been applied to the empirical isochrones, enabling the creation of an age ordered ladder in intrinsic colour and absolute magnitude. This has been calibrated using ages for fiducial sequences and nominal ages assigned to the separable groups, which are as follows: 1 Myr, NGC2244 and IC5146. 2 Myrs, NGC6530 and the ONC. 3 Myrs, Ori, Cep OB3b, NGC2264 and Ori. 4 5 Myrs, NGC2362 and IC348. 10 Myrs, NGC7160. 13 Myrs, h and Per. 20 Myrs, NGC1960. 40 Myrs, NGC2547. 2 Once assigned the nominal ages and age orders were combined with ancillary data to investigate rotation rate and disc evolution. The general trends of rotation rate distribution evolution and disc fraction changes with age confirmed existing estimates for the disc survival, and therefore star-disc interaction through disc-locking, with a timescale of 5 Myrs. However, this study also revealed some of the first evidence of local environment e ects. IC348 appears ‘out of sequence’ in both the rotation rate distribution and disc fraction. Specifically, IC348 has a larger disc fraction than expected at its nominal age and exhibits a rotation rate distribution expected from a much younger SFR (i.e. the ONC). This could be a consequence of the lower number density of O stars (none exist in IC348) and therefore a lower density of UV flux, which acts to hasten disc dissipation. Finally, a potentially important feature of stellar populations in a CMD, the R-C gap was identified. This separation in a CMD of the fully convective pre-MS and main-sequence (MS) stars with radiative cores was found to vary as a function of age. As the R-C gap is also measurable in colour it provides a distance independent age indicator. I have explained the underlying physics of the R-C gap and discussed possible applications of this phase change of the stellar interior. In addition, an overlap between the pre-MS and MS sections of the R-C gap was apparent in all SFRs where the R-C gap could be unambiguously identified. This R-C gap overlap shows that the studied SFRs must contain a spread in isochronal ages. However, the interpretation of this spread is dependent on the underlying assumptions. If one assumes stars form by a robust slowstar- formation (SSF) mechanism and isochronal ages represent the true age of a star, then these spreads can be construed as true age spreads. Alternatively, if one adopts a rapid-star-formation model (RSF), this spread can be explained as a variation in accretion histories of the constituent stars. As found by Siess et al. (1999) and Tout et al. (1999) accretion can act to accelerate pre-MS star evolution, meaning the isochronal age does not represent the true age of the star. This increases the advantages of empirical isochrones and age ordering over the derivation of individual ages for SFRs. Indeed, this R-C gap overlap could be used to ‘normalise out’ any spread in age or accretion history and therefore increase the power of derived age orders.

Understanding how selection interacts with genetic variation to produce biodiversity is a central theme in evolutionary biology. Many studies have taken advantage of the rich diversity of colouration in animals to tackle this, as colour is both ecologically relevant and a clearly visible phenotype. This has carried over into the 'omics' era, with plenty of studies addressing evolutionary questions by examining the genomics of colouration in natural populations. These studies tend to focus on discrete colour variation and pigmentation. However, most phenotypic variation is continuous, and little is known about the genetics of structural colour. Heliconius butterflies display warning colouration that boasts both striking diversity, alongside near-perfect convergence between mimetic species. Repeated evolution of pigment colour patterns is driven by the repeated use of a small set of genes. On the western slopes of the Andes, convergent iridescence has also evolved between the co-mimics Heliconius erato and Heliconius melpomene, which appears to vary continuously. In this thesis I (1) describe clinal variation in iridescence across hybrid zones between iridescent and non-iridescent subspecies of H. erato and H. melpomene and highlight a common selective agent (mimetic warning colouration), yet different migration-selection balance between the species. 2) I demonstrate a striking difference in levels of population structure between the co-mimics across their hybrid zones. However, in both species variation in iridescence is independent of population structure and is maintained by selection despite gene flow. (3) I describe the genetic architecture of iridescence in Heliconius, for the first time, using association mapping. Lack of power to estimate genetic architecture for H. melpomene prevented a thorough between-species comparison. However, I find potential evidence of overlapping genomic regions responsible for variation in iridescence. This thesis lays the groundwork for future research narrowing down the genetic underpinnings of iridescence in this system.

Explaining the wide range of animal colouration in the natural world is a key issue in evolutionary biology. Bumble bees are often brightly coloured and show a range of colours and colour patterns in different species as well as considerable variation within species. The large garden bumble bee, Bombus ruderatus, is highly variable in its degree of black (melanic) colouration, with morphs ranging from the familiar yellow and black bands (banded) through intermediate forms to morphs that are totally melanic. The aim of this research was to determine what might be maintaining the colour polymorphism in populations of B. ruderatus in the South Island, New Zealand. Colouration of worker bees was measured using a digital photography method and found to be significantly different across sample sites. To look at potential adaptive functions of body colour in B. ruderatus, three hypotheses of thermoregulation, desiccation tolerance and Müllerian mimicry were tested by comparing patterns of variation in melanism to patterns of variation in climatic variables (temperature, rainfall, humidity) and abundance of conspecifics. In order to address the possibility that selectively neutral processes were more important than selection, the genetic structure of B. ruderatus populations was characterised and compared to the pattern of variation in melanism. The colouration of individuals from the same population collected at different times in the season was compared to evaluate whether body colour was plastic and any support for the genetic basis of melanism in B. ruderatus was also assessed by determining any relationship between relatedness and degree of melanism. The results suggest that differences in the degree of melanism between populations are greater than the differences expected through selectively neutral forces alone and, therefore, that the pattern of variation in melanism is likely a result of selection and/or phenotypic plasticity in addition to gene flow and genetic drift. Although a global model consisting of four climatic variables and the abundance of conspecifics explained a small proportion of the variation in melanism, no support was found for any specific hypothesis relating to the adaptive function for body colour. Instead the results suggest that some combination of factors, most likely including factors not measured in this study, is influencing the frequency of melanic morphs. In addition, there was evidence that body colour was influenced by phenotypic plasticity and that melanism has a low heritability in B. ruderatus. Taken together, these results imply that patterns of melanism across B. ruderatus populations are complex and it is likely that multiple factors are influencing melanism in concert.

This thesis is concerned with the colour change and microstructural evolution of wet paint when subject of shear. When different processing shear histories are applied to certain paints, the resulting colour of the paint can vary. Paint consists of pigment particles suspended in a mixture of resin and solvent, and this multi-phase structure results in a complex microstructure. For this reason there can be many possible causes of this colour change, one of which was thought to relate to the organisation of the pigment dispersion. Rheological measurements of paint were carried out to investigate whether there was a link between rheology and colour change. The measurements were performed using a Rheometrics Dynamic Spectrometer (RDS II) at low shear rates and a Multi-Pass Rheometer (MPR) at high shear rates. Although the shear ranges of the RDS II and MPR did not overlap, extrapolation of data obtained at low shear rates matched those from the MPR at high shear rates. The rheological response of the material was described using a viscoelastic K-BKZ integral constitutive equation in combination with a Wagner damping factor. Systematic tests under controlled conditions were successfully performed, and the results of three paint samples were compared. The experimental findings indicated that the observed colour change behaviour of paint was related to the modification of size and size distribution of pigment agglomerates, both during and after shear. In order to correlate pigment size with the resulting paint colour, an attempt was made to model these experimental findings. A mathematical model was developed on the basis of the Mie scattering theory. This model was verified by a case study, and its prediction gave semi-quantitative agreement with the experimental findings.

Flowers’ colours are an essential element of their ability to attract visits from pollinators. However, the colours as they appear to human observers can differ substantially from their appearance to insect pollinators, and so it is essential to consider pollinator vision in any study of the ecology of flower colour. In this thesis I describe how I have overseen the development of an online database to provide accurate information on floral spectral reflectance measured without human observational bias. This resource allows a more accurate consideration of flower colours in future studies, and permits investigations of flower colours within and across habitats. Using the records in this database, I analysed flowers from two European habitats for spatial or temporal changes, modelling the colours according to insect visual perception. I discovered that the insect-colour composition of the plant communities does not change either along an altitudinal gradient or throughout the year. These novel and ecologically-relevant analyses contradict previous observational studies, but support the theory of a pollination “market” in which flowers compete for pollinator visitation. I then describe my experimental investigations into the visual capabilities of two pollinators and how this may relate to what colours of flowers they visit. Firstly I study the foraging behaviour of bees under spatially inconsistent illumination and how this impacts on their choice behaviour. I revealed patchy light can have measurable effects on bee foraging behaviour: they intentionally choose familiar over unfamiliar illumination, which may impact on the flowers they visit in complex natural environments. Secondly, I detail the new evidence for a red-sensitive photoreceptor in South African monkey beetles, a major pollinator in a habitat containing many longwavelength- reflecting flowers, which are not classically “attractive” to bees. Throughout this thesis, I explore how pollinator vision has shaped the evolution of flower colours in different contexts.

Thesis (MScAgric) -- Stellenbosch University, 2005.
ENGLISH ABSTRACT: Winemakers or producers are under constant pressure to reduce the operational costs for the production of wine. The reason for this being threefold: Firstly, the number of cellars and estates locally, and internationally, has grown immensely. Thus, the competition on both the national and international front has put producers under pressure to reduce their production cost in order to survive the explosion of brand possibilities on the consumer's horizons. Secondly, the exchange rate has been one of the most unpredictable variables which highlight the importance of scenario planning and sufficient financial planning in order to overcome significant exchange rate fluctuations which may cause financial strain for the business. Thirdly, the benefits of using expensive oak barrels for the maturation of premium quality wines are undisputable. These benefits include the clarification and decarbonation of wines, decrease in the astringency of tannins ("softening of tannins"), the evolution of colour, providing complementary oak aromas which increase the complexity and finesse of these wines and stabilising the colloid structure of the maturing wine. The greatest disadvantages remain nevertheless that it is a costly and labour intensive operation. Oak is an essential part of the flavour profile of many premium quality wines, and there is still a growing market demand for these wines. The use of oak barrels for the maturation of premium red wines, incorporates a specific flavour dimension to the wine (and adding value), has been the traditional way of storing wines. Well known cellars and Estates all over the world have build remarkable profiles and identities for their brands. To alter any principles regarding the use of oak will alter the style of the wines and will beyond any doubt influence their brand image negatively. Chapter 1 gives an introduction and the main aims of the study. The phenolic composition of grapes and oak are a complex mixture of different molecules which are discussed in Chapter 2. These include those responsible for the colour (anthocyanins), taste (mainly the tannins) and aroma of the wine. The composition of the oak barrel can be influenced by its origin, seasoning of the oak, toasting of the staves, age of the barrel etc. These factors all affect the chemical composition of the oak (lactones, volatile phenols, carbohydrate volatiles, hydrolysable tannins etc.) and ultimately, the wine. The chemical reactions taking place in wine during ageing are also complex, which makes maturation and research of wine in oak a complex business. The challenge, thus, developed to sustain the flavour profiles (oak attributes) and to reduce the operational costs, without influencing the identity or profile of the brand negatively. The use of oak derived products like chips, dust, blocks, staves, balls and even extracts was proposed, although it is considered by-products of the cooperage profession. Some of the major disadvantages of the use of oak derived products still remain the limited control over the production process. This may lead to inconsistency in the quality of these products. Nevertheless, the use of oak derived products and the availability of these products have grown significantly and with it a need for research on this field. Chapter 3 address the results obtained from the maturation of Pinotage, which is uniquely South African, and Shiraz wines, in different oak type barrels (French vs. American vs. Russian), as well as treatments with various oak derived products, and the influence of these oak products on the evolution of colour, phenolic development and quality of the wines during ageing. The results obtained in this project correlated with findings in the literature. The colour density, percentage of red pigment colour and S02 resistant pigments increased, especially in the first three to six months during ageing in barrels as a result of ellagic tannin extraction from the barrels and polymerisation reactions, but decreased later as maturation progresses as a result of precipitation. In some cases the use of oak increased the colour density significantly with almost 40%. The colour density, total red pigment colour and total phenolic composition decreased during bottle maturation as a result of polymerisation. No significant colour differences between the barrel types could, however, be detected. The use of oak derived products showed the same tendencies for all colour dimensions, although no significant differences could be detected between the treatments. The most significant difference was that new oak barrels contributed more to the development of colour compared to the oak treatments. The Gelatine index gives an indication of the degree of polymerisation of tannins; higher values will indicate tannins which are highly reactive and will cause an astringent mouth feel. The values should decrease as maturation progresses and tannins polymerise. Little differences between barrel types (French vs. American vs. Russian) were found in the one Shiraz, but in the two Pintage wines the index was the lowest in the wines matured in French oak after 36 months bottle ageing. Sensorial tests indicated little quality differences after 36 months between the different oak types The American oak barrels had, in general, a more "oaky bouquet", even after 36 months in the bottle. Pinotage matured with different alternative oak products showed that chips added to barrels tended to give a higher oak aroma, with a lower fruit compared to the other treatments. The same wine matured in new barrels, as expected, also had a very high oak aroma compared to the same wine matured in older barrels. This led to a higher fruit perception in the latter wines. Lees contact is a practice more commonly used in the production of white wines, but may be a dangerous practice in the production of red wines. Chapter 4 reports on the effect of lees contact during ageing of red wine on the micro flora and colour after 12 month maturation. No significant differences in microbial analysis were detected during of barrel maturation between the wines matured in the lees and the filtered wines for acetic acid, yeast and lactic acid bacteria. The initial pH differences during cold maceration and fermentation, however, did influence these numbers, with higher numbers being observed at higher pH values. However, colour differences could be detected. The concentration of yellow brown pigments (measured at 420 nm) was lower in the lees matured wines than in the filtered· wines which underwent malolactic fermentation in the barrel. Other colour differences that could be detected were higher colour density and total red pigment colour in wines as a result of longer skin contact (due to slower alcoholic fermentation rate). Thus, manipulation of the skins during alcoholic fermentation, the use of barrels and/or oak derived products in various stages of vinification and maturation of wines and additional practices as maturation on lees may be thus be used to set a certain style of wine which meet a specific market demand, trend or style. Chapter 5 summarises the results obtained and future research to be done on wood and wine. This study, however, clearly showed that the origin and oak type does not influence the colour as much as the aroma and taste of red wine under South African conditions.
AFRIKAANSE OPSOMMING; Wynmakers of produsente word onder gedurige druk geplaas om die produksiekoste van wyn te verlaag. Die redes hiervoor is drieledig: Eerstens het die getal kelders en landgoedere op nasionale en internasionale vlak geweldig toegeneem. Dus, die kompetisie op beide nasionale en internasionale gebied plaas produsente onder druk om die produksie koste van die wyn te verminder om sodoende finansieel die ontploffing van nuwe moontlike wyne op die horison van die verbruiker te oorleef. Tweedens, die wisselkoers was altyd een van die meer onvoorspelbare veranderlikes wat die belangrikheid van scenario-beplanning en weldeurdagte finansiele beplanning beklemtoon om sodoende groat veranderinge in die wisselkoers, wat moontlike finansiele druk in die besigheid mag veroorsaak, te oorkom. Derdens, een van die grootste uitgawes in die produksie proses van is die verouderingskomponent van kwaliteitswyn. Die voordele van die gebruik van eikehout vate in die verouderingsproses van rooiwyne is welbekend. Hierdie voordele sluit in die suiwering van die wyn in terme van soliede partikels , dekarbonisering (C02-ontgasting}, afname in die vrank smaak ("sagtheid van die tanniene), die ontwikkeling van die kleur van die wyn, toevoeging van komplementere hout boeketstowwe wat bydrae tot die kompleksiteit van die wyn, asook die stabilisering van die kollo"idale struktuur van die wyn. Die grootste nadeel bly, nieteenstaande, die geweldige koste verbonde aan vate, asook die hantering en onderhoud daarvan. Eike hout verwante boeketstowwe is 'n onmisbare komponent van die aroma profiel van baie kwaliteitswyne. Daar is 'n groeiende mark vir hierdie tipe wyne. Die gebruik van eikehout vate vir die veroudering van kwaliteitswyne, behalwe die bydrae van belangrike geurstowwe (een waarde), was nog altyd 'n tradisionele stap in die proses. Beroemde kelders reg oor die wereld het uitmuntende mark identiteite vir hulle self geskep, asook 'n "spesifieke identiteit" vir hulle wyn. Om enige beginsels aangaande die gebruik van eikehout te verander, sal sander twyfel die wynstyl verander en moontlik 'n negatiewe effek op die kelder se identiteit he. Hoofstuk 1 gee 'n inleiding en die hoof doelstellings van die studie. Die fenoliese samestelling van druiwe en eikehout bestaan uit 'n komplekse mengsel van verskillende molekules wat in Hoofstuk 2 beskryf word. Hierdie sluit in daardie verantwoordelik vir die kleur (antosianiene), die smaak (hoofsaaklik tanniene) en die aroma van die wyn. Die samestelling van die eikevat kan beinvloed deur die oorsprong, veroudering van die hout, roostering, ouderdom van die vat ens. Hierdie faktore beinvloed almal die samestelling van die houtvat (laktone, vlugtige fenole, hidroliseerbare tanniene ens.) en uiteindelik, die wyn. Die chemiese reaksies wat plaasvind tydens die veroudering van wyn is ook kompleks, wat die veroudering en navorsing van wyn in vate 'n komplekse proses kan maak. Die uitdaging, dus, het ontstaan om die organoleptiese profiel van die wyn (eikehout boeketstowwe) te behou en terselftertyd die produksiekoste van die wyn te verlaag. Die gebruik van eikehout verwante produkte soos skaafsels, blokkies, stawe en balke en selfs eikehout ekstrakte is aanbeveel, alhoewel dit gesien word as afvalprodukte van die kuiperye Een van die grootste nadele van eikehout alternatiewe produkte is egter die beperkte kwaliteitskontrole oor die produksieproses. Dit mag lei tot wisselvalligheid in die kwaliteit van hierdie produkte. Nieteenstaande het die gebruik van eike houtverwante produkte en die beskikbaarheid van hierdie produkte geweldig toegeneem en tesame daarmee die behoefte aan navorsing hieroor. Hoofstuk 3 bespreek resultate van die gebruik van verskillende eikehout tipe vate (Frans vs Russies vs Amerikaans), asook die gebruik van eikehout verwante produkte, op die kleur ontwikkeling, fenoliese samestelling en kwaliteit van Pinotage (eie aan Suid-Afrika) en Shiraz wyne gedurende vat en bottel veroudering. Die ontwikkeling van kleur het verskeie unieke dimensies en resultate wat verkry is in hierdie projek stem ooreen met literatuur. Die kleurdigtheid, persentasie rooi pigment en 802 weerstandbiedende pigmente het toegeneem met veroudering in houtvate (veral in die eerste drie tot ses maande) as gevolg van ellagitanniene wat geekstraeer word en gepolimerisasie, maar het later gedurende veroudering afgeneem as gevolg van presipitasie reaksies. In sekere gevalle het die kontak met hout die kleurdigtheid met tot 40% vermeerder. Die kleurdighteid, totale rooi pigmente en totale fenole het tydens bottelverouding afgeneem a.g.v. polimerisasie. Geen merkwaardige verskille kon egter tussen die verskillende vattipes gevind word nie. Verskille tussen die houtverwante produkte was ook klein en het diesefde tendense getoon as die vate. Nuwe vate se impak op die kleurprofiel en ontwikkeling van verouderde rooiwyne was egter meer beduidenswaardig as die gebruik van gebruikte vate en behandelings met eikehout verwante produkte. Die gelatien indeks verwys na die toestand van polimerisasie van tanniene. Hoer waardes kan verwag word in jong wyne en dui op hoogs reaktiewe tanniene. Die waarde sal afneem soos tanniene polimere vorm met veroudering en sal dus 'n veel minder vrank mondgevoel tot gevolg he. Klein verskille tussen die vat tipes (Frans vs Amerikaans vs Russies) is opgemerk in die een Shiraz, maar in die twee Pinotage wyne was die indeks die laagste in die wyne verouder in Franse eikehout na 36 maande se bottelveroudering. Sensoriese toetse het aangedui dat daar klein verskille gevind is tussen die verskillende eiketipes. Die wyn verouder in Amerikaanse eik het, in die algemeen, 'n sterker eikehoutkarakter gehad na 36 maande bottelveroudering. Wyn verouder met verskillende alternatiewe houtprodukte het aangetoon dat eikehouskaafels in vate 'n sterker eikehoutkarakter aan die wyn gegee het met 'n laer vrugtige aroma in vergelyking met die ander behandelings. Dieselfde wyn verouder in nuwe vate het oak, soos verwag, 'n sterk hout boeket gehad in vergelyking met die verouder in ouer vate. Dit het dan oak gelei dat laasgenoemde wyne 'n sterker vrug aroma gehad het. Veroudering van wit wyne op moer is 'n algemene praktyk, alhoewel dit minder toegepas word op rooiwyne as gevolg van verwante gevare. Hoofstuk 4 bespreek die effek van moerkontak op die mikrobiese en kleursamestelling van rooiwyn tydens 12 maande se houtveroudering. Geen noemenswaardige verskille is egter verkry tussen die wyne verouder op die moer en die filtreerde wyne vir asynsuur-, melksuurbateriee en gisgetalle nie. Aanvanklike pH verskille tydens koue masserasie en alkoholiese fermentasie het egter hierdie getalle beinvloed, met hoer ·getalle verkry in die hoer pH wyn. Die wyne wat appelmelksuurgisting in die vate ondergaan het en verouder is op die moer het egter 'n laer konsentrasie geelbruin pigmente (gemeet by 420 nm) as die gefiltreerde wyne. Ander kleurverskille sluit in hoer kleurdigtheid en totale rooi pigmente as gevolg van langer dopkontak (stadiger alkoholiese fermentasie). Manipulering van die doppe voor en tydens alkoholiese gisting, die gebruik van eikehoutvate of eikehoutverwante produkte, of kombinasies daarvan tydens verskillende produksie fases en ander praktyke soos moer kontak, kan dus gebruik word am 'n sekere styl wyn op markversoek daar te stel. Hoofstuk 5 som die resultate op, asook toekomstige navorsingsmoontlikhede wat op die gebied van hout en wyn gedoen kan word. Hierdie studie het egter duidelik aangedui dat die eikehout oorsprong en tipe die kleur nie so baie beinvloed soos die aroma en smaak van die wyn onder Suid-Afrikaanse kondisies nie.

Research into speciation and t~e processes governing divergence within species has received considerable attel1tion from ecologists and evolutionary biologists in recent years. However, few empirical studies have focused on marine systems, despite the potential evolutionary consequences of the unique conditions in this environment. The coral reef fish genus Hypoplectrus represents an excellent system with which to study marine divergence and comprises 10-14 distinct colour morphotypes. This thesis focuses on the Hypolectrus colour polymorphism and considers how these morphotypes differ genetically, morphometrically and ecologically. Furthermore, the distribution of morphotypes is resolved and the potential implications of these geographical patterns considered. All of these studies include data on multiple colour morphotypes from widely dispersed geographical locations. AFLP molecular marker analysis shows morphotypes to have consistent low level genetic isolation among each other. Some of the markers tested showed significantly higher levels of isolation than expected, suggesting they may be linked to genes under selection. Stable isotope analysis shows little evidence to suggest ecological divergence between morphotypes and they do not appear to possess distinct feeding niches. Morphotypes show quite variable dietary patterns across their range, suggesting against ecological adaptation involving diet. Geometric morphometric results show small but significant differences between morphotypes, which may be due to genetic isolation rather than physical adaptation. The diversity of morphotypes across the Hypoplectrus distribution shows interesting patterns, which suggest morphotypes do not co-occur randomly and that the number of morphotypes present on a reef is positively correlated with general reef fish species richness. Following these results, we now have an improved understanding of the Hypoplectrus colour polymorphism and there are clear directions for future research into the origin of this phenotypic radiation.

The colour of guppies (Poecilia reticulata) evolves as a compromise between sexual selection (favouring conspicuousness) and natural selection (favouring crypsis). However, guppies live in a variety of habitats and with a variety of predators and consequently in a variety of selective environments. I investigated how habitat and predator's visual systems affect the evolution of colour. I used regressions to assess the importance of habitat features on the evolution of colour for 29 guppy populations. I then quantified the colour of guppies living in the presence and absence of two predators. The prawn predator is insensitive to orange light while the fish predator is insensitive to ultraviolet light. Habitat explained some variation in colour, but not in a consistent manner. Guppies living with the prawn were more orange and guppies living with the fish had more ultraviolet reflectance, providing evidence for the use of these aspects of colour as private signals.

In this thesis a critical assessment of the ages derived using theoretical pre-main-sequence (pre-MS) stellar evolutionary models is presented by comparing the predictions to the low-mass pre-MS population of 14 young star-forming regions (SFRs) in colour-magnitude diagrams (CMDs). Deriving pre-MS ages requires precise distances and estimates of the reddening. Therefore, the main-sequence (MS) members of the SFRs have been used to derive a self-consistent set of statistically robust ages, distances and reddenings with associated uncertainties using a maximum-likelihood fitting statistic and MS evolutionary models. A photometric method (known as the Q-method) for de-reddening individual stars in regions where the extinction is spatially variable has been updated and is presented. The effects of both the model dependency and the SFR composition on these derived parameters are also discussed. The problem of calibrating photometric observations of red pre-MS stars is examined and it is shown that using observations of MS stars to transform the data into a standard photometric system can introduce significant errors in the position of the pre-MS locus in CMD space. Hence, it is crucial that precise photometric studies (especially of pre- MS objects) be carried out in the natural photometric system of the observations. This therefore requires a robust model of the system responses for the instrument used, and thus the calculated responses for the Wide-Field Camera on the Isaac Newton Telescope are presented. These system responses have been tested using standard star observations and have been shown to be a good representation of the photometric system. A benchmark test for the pre-MS evolutionary models is performed by comparing them to a set of well-calibrated CMDs of the Pleiades in the wavelength regime 0.4−2.5 μm. The masses predicted by these models are also tested against dynamical masses using a sample of MS binaries by calculating the system magnitude in a given photometric band- pass. This analysis shows that for Teff ≤ 4000 K the models systematically overestimate the flux by a factor of 2 at 0.5 μm, though this decreases with wavelength, becoming negligible at 2.2 μm. Thus before the pre-MS models are used to derive ages, a recalibration of the models is performed by incorporating an empirical colour-Teff relation and bolometric corrections based on the Ks-band luminosity of Pleiades members, with theoretical corrections for the dependence on the surface gravity (log g). The recalibrated pre-MS model isochrones are used to derive ages from the pre-MS populations of the SFRs. These ages are then compared with the MS derivations, thus providing a powerful diagnostic tool with which to discriminate between the different pre- MS age scales that arise from a much stronger model dependency in the pre-MS regime. The revised ages assigned to each of the 14 SFRs are up to a factor two older than previous derivations, a result with wide-ranging implications, including that circumstellar discs survive longer and that the average Class II lifetime is greater than currently believed.

The sap beetle genus Carpophilus Stephens (Coleoptera: Nitidulidae) is a large genus consisting of over 200 species and are found worldwide. Several species are important pests of crops and stored products, and are frequently intercepted as part of biosecurity operations. The genus is poorly known taxonomically, and there are several species groups that are challenging to identify by morphological methods. In particular, two species found across the Pacific, C. maculatus Murray and C. oculatus Murray are frequently confused with each other. These two species are similar in size and colour, but differ primarily by the shape of the colour pattern on their elytra. However, this colour pattern is highly variable within both species, leading to ambiguity in the indentification of these species. Within C. oculatus, three subspecies have been described based on differences in the male genitalia and pronotal punctation: C. o. oculatus and C. o. gilloglyi Dobson are distributed widely across the Pacific, while C. o. cheesmani Dobson is known only from Vanuatu. A search of literature records and specimen collections revealed 32 species of Carpophilus recorded from the Pacific region. In addition there remain several unidentified specimens representing at least four species, two of which will be described subsequent to this research. A number of species recorded in the literature may have been misidentified, and these require further field collections and inspection of museum specimens to confirm their presence in the Pacific. To test the validity of the subspecies of C. oculatus, and its distinctiveness from C. maculatus, a phylogeny of available specimens of Carpophilus was inferred from one mitochondrial gene (cytochrome c oxidase subunit I (COI)), and two nuclear genes (28S ribsomal RNA (28S) and the internal transcribed spacer 2 (ITS2)). These data show large genetic distances between the three subspecies of C. oculatus of 7-12%. Given these distances are similar to those between other species in the genus, this indicates these subspecies may be elevated to full species. The data also consistently support a monophyletic relationship between C. o. oculatus and C. o. gilloglyi. Nuclear genes also support C. o. cheesmani as part of a clade with the other subspecies, but these relationships are unresolved in COI. Carpophilus maculatus was not supported as being the sister taxon of the C. o. oculatus and C. o. gilloglyi clade. Other relationships within Carpophilus were unresolved, possibly due to a combination of incomplete taxon sampling, and saturation of substitutions within the COI gene. Phylogeographic analysis of specimens collected from several localities within the range of C. oculatus showed that, with only one exception, there were no shared haplotypes between archipelagoes. This result suggests it may be possible to determine the provenence of intercepted specimens, providing further information regarding potential invasion pathways. A degree of geographic structuring was also present within C. o. gilloglyi, being separated into a western clade found in Fiji and Rotuma and an eastern clade distributed from the Kermadec Islands and Tonga to French Polynesia. This separation was most profound in COI data, with a mean pairwise distance between the clades of 7%. ITS2 data also demonstrates a degree of differentiation between the two clades, based on differences in the insertions and deletions between the clades. The variability in the shape and colour of the elytral pattern of C. oculatus was also investigated. Colour was quantified using a method based on Red-Green-Blue (RGB) colour values derived from digital photographs, while an outline analysis of the elytral pattern was conducted using elliptic Fourier analysis (EFA). Principal Components Analysis of the RGB values and EFA coefficients showed no clear separation between subspecies, nor were any trends correlated with host fruit or collection localities. Variation at all levels and all measures studied in this thesis show that this geographic region and this genus of beetles offer intruiging insights into speciation, biogeography and biological invasions. There is much scope for further research on the causes and consequences of this variation and the lives of these interesting insects.

Evolutionary transitions between the two major predator avoidance strategies aposematism and crypsis are expected to be associated with changes in many important traits of animals. However, empirical studies on populations experiencing ongoing or recent transitions between these strategies are rare. This thesis investigates the co-evolution of traits among populations of the Strawberry poison frog D.pumilio in Bocas del Toro, Panama. I found that all investigated populations were genetically distinct but that colour and pattern did not correlate with genetic or geographic distance, which suggests that selection needs to be invoked to explain the observed variation. Based on the chromatic contrast between frog dorsal colour and the natural habitat substrates used by the frogs, the populations were defined as bright or dull coloured. I found that frogs from bright coloured populations were larger. This is expected if aposematism is enhanced by large signals while crypsis is enhanced by small size. Further, individuals from bright coloured populations had a coarser black dorsal pattern, which is expected if crypsis is impaired by a bold pattern. The importance of pattern coarseness was confirmed by an avian detection experiment showing that coarse patterned dark green prey were more easily detected than dark green prey without pattern or with fine pattern. I put forward the hypothesis that enhanced protection, gained by aposematism, may affect behaviours that influence dispersal and pairing patterns. Indeed, males from bright coloured populations displayed at more exposed sites and showed a tendency to be more explorative and aggressive. In summary, my results show that the bright and dull coloured populations most likely represent an aposematic and a cryptic strategy, respectively. Furthermore, I show that evolutionary changes between aposematism and crypsis can be associated with coevolution of both morphology and behaviour. I argue that this coevolution may increase the likelihood of both pre- and post-zygotic reproductive isolation. This is because greater phenotypic differences between populations increase the likelihood of selection against badly adapted migrants and hybrids with intermediate traits.

Globular clusters are tracers of the formation and evolution of their host galaxies. Kinematics, chemical abundances, age and position of the clusters allows tracing interactions between Milky Way and surrounding galaxies and outlines their chemical enrichment history. In this thesis we analyse mid-resolution spectra of about 800 red giant stars in 51 Galactic globular clusters. It is the first time that [Fe/H] and [Mg/Fe] derived in a consistent way are published for such a huge sample of globular clusters, almost 1/3 of the total number of catalogued clusters. Our metallicities are showed to be more precise than previous works based on mid-resolution spectroscopy. A turnover at [Fe/H] ~ -1.0 is found in the plot [Fe/H] vs. [Mg/Fe] for bulge and halo, although bulge seems to have a more metal-rich turnover, i.e, bulge has more efficient formation than the halo. Comparing the abundances with age the timescale for SNIa to start to become important is 1Gyr. [Fe/H] vs. age corroborates the different star formation efficiency of bulge and halo while [Mg/Fe] does not follow that. Halo was formed in mini halos or dwarf galaxies, and two multiple population clusters had their origin analysed to check it. M 22 seems to have been formed in the Milky Way while NGC 5824 possibly was originated in a dwarf galaxy, although our results are inconclusive for NGC 5824. The Galactic bulge seems to have been formed fast i.e., probably the oldest globular cluster is there. In fact HP 1 has a bluer horizontal branch than expected for its metallicity and we interpret that as an age effect. We determine its distance using light curves of variable stars in order to constrain future age determinations via colour-magnitude diagram. Finally, we investigate interaction between Milky Way and its neighbour galaxy SMC. We find that some star clusters are being stripped out of the SMC main body, which is consistent with tidal stripping scenario for the interaction between the galaxies, instead of ram pressure that would only affect gas.
Aglomerados globulares são traçadores da formação e evolução de suas galáxias. Cinemática, abundâncias químicas, idades e posições dos aglomerados permitem traçar interações entre Via Láctea e galáxias vizinhas e suas histórias de enriquecimento químico. Nesta tese analisamos espectros de média resolução de mais de 800 estrelas gigantes vermelhas em 51 aglomerados globulares Galácticos. É a primeira vez que [Fe/H] and [Mg/Fe] determinados de modo consistente são publicados para uma amostra desse porte, ~1/3 dos objetos catalogados. Nossas metalicidades são mais precisas que trabalhos anteriores similares. Uma quebra em [Fe/H] ~ -1.0 é encontrada no gráfico [Fe/H] vs. [Mg/Fe] para o bojo e halo, embora bojo parece ter uma quebra em [Fe/H] maior, i.e, bojo tem formaçãao mais eficiente que o halo. Comparando abundâncias com idade, a escala de tempo para SNIa ficar importante é 1Gano. [Fe/H] vs. idade corrobora diferentes eficiências de formação do bojo e halo, mas [Mg/Fe] vs. idade não mostra isso. O halo foi formado em mini halos ou galáxias anãs, e dois aglomerados com dispersão em [Fe/H] tiveram suas origens analisadas. M 22 parece ter sido formado na Via Láctea e NGC 5824 possivelmente foi originado em uma galáxia anã, embora os resultados são inconclusivos para NGC 5824. O bojo parece ter sido formado rapidamente e deve possuir o aglomerado mais velho. De fato, HP 1 tem um ramo horizontal mais azul que o esperado para sua metalicidade e vemos isso como um efeito da idade. Determinamos sua distância usando curvas de luz de RR Lyrae de maneira a restringir futuras determinações de idade via diagrama cor-magnitude. Finalmente, investigamos a interação entre Via Láctea e sua galáxia vizinha SMC. Encontramos aglomerados sendo removidos do corpo central da SMC, consistente com cenário de remoção por força de maré para a interação entre as galáxias, em vez de ``ram pressure\'\' que afeta só gás.

Due to the finite speed of light and a vast, expanding universe, telescopes are just now receiving the light emitted by galaxies as they were forming in the very early universe. The light from these galaxies has been redshifted (stretched to longer, redder wavelengths) as a result of its journey through expanding space. Using sophisticated techniques and exceptional multi-wavelength optical and infrared data, we isolate a population of 378 galaxies in the process of formation when the Universe was only two billion years old. By matching the distinctive properties of the light spectra of these galaxies to models, the redshift, age, dust content, star formation rate and total stellar mass of each galaxy are determined. Comparing our results to similar surveys of galaxy populations at other redshifts, a picture emerges of the growth and evolution of massive, star-forming galaxies over the course of billions of years.

The theory of stellar evolution and stellar structure relies on the observation of stars in di erent phases of their evolutionary cycle. The relation between observations and theory can be strengthened by obtaining observational data of a large sample of stars in a particular evolutionary phase. The search for Cephei stars, as conducted in this study, can contribute to the sample of known Cephei stars, where these interesting stars are massive non-supergiant early B-type stars, displaying pulsating behaviour which is not well understood. Stars tend to form in clusters where it can therefore be expected that young massive stars can be found in open clusters. For this reason two young southern open clusters were observed in order to search for B-type pulsating stars. The region of NGC 6204 and Hogg 22 was observed over a period of thirteen nights in Johnson B, V and I bands. NGC 6204 is believed to be the oldest cluster of the two at a distance of 0.8 kpc while the much younger Hogg 22 is more distant at 2.8 kpc. These two open clusters are located 6 arcminutes apart which made it possible to observe them simultaneously with a 12.8 12.8 arcminute eld of view. The observations were done with the newly installed 1600 telescope of the North-West University, South Africa. In order to do a variability search, periodic stars need to be identi ed from the cluster data, where a typical data set may contain thousands of scienti c images. In addition to the main motivation for this study, a pipeline was created in order to automate the photometry and data reduction processes. A Lomb-Scargle transform was applied to the stellar light curves in order to identify periodic sources. 354 signi cantly periodic stars were identi ed from the 3182 observed stars. Amongst them, two new possible Cephei stars were found together with a possible slowly pulsating B star (SPB), and numerous eclipsing binary systems. By using photometry of this region obtained by Forbes & Short (1996), instrumental magnitudes were transformed to a standard system in order to compare photometry results. From the constructed colour magnitude diagram of the two clusters, it could be seen that some stars, indicated by Forbes & Short (1996) to be cluster members, were in fact eld stars belonging to neither cluster. The reduction and photometry pipeline was implemented successfully on the data set, which also highlighted the importance of instrumentation and correct data analysis procedures. Possible improvements were identi ed in order to overcome di culties experienced during this study.
Thesis (MSc (Space Physics))--North-West University, Potchefstroom Campus, 2013

This thesis concerns the evolution of language. A proliferation of theoretical models have been presented in recent years purporting to offer evolutionary accounts for various aspects of modern languages. These models rely heavily on abstract mechanistic models of the production and reception of language by modern humans, drawn from various approaches in linguistics which aim at such models. A very basic and ubiquitous assumption is that expressions have meaning in virtue of being associated with internal representations, and that therefore the evolution of language can be modelled on the basis of individuals trying to produce external manifestations of these internal “meanings”. I examine the role of this assumption in language evolution theorising, and review evidence from neuroscience and first language acquisition relevant to the validity of this assumption. The chaotic nature of the relationship between “meaning” and the brain undermines the supposition that the evolution of language was driven by spontaneous association between internal structures and external forms. I then turn to the philosophical basis of language evolution theorising, adopting a Wittgensteinian perspective on the cognitive interpretation of linguistic theories. I argue that the theoretical apparatus of such approaches is embedded in language games whose complicated rules relate to linguistic behaviour (and idealisations of that behaviour) but not to neural organisation. The reinterpretation of such descriptions of language as descriptions of the internal structures of language users is rejected as a grammatical confusion: if the rules for constructing linguistic theory descriptions do not mention neural structures, then theoretical descriptions of the linguistic abilities of an individual say nothing non-trivial about their internal brain structure. I do not deny that it would, in principle, be possible to reduce linguistic theories (reinterpreted as mechanistic descriptions) to neural structures, but claim that this possibility is guaranteed only by leaving the practice of re-describing physical brain descriptions entirely unconstrained. Thus the idea that we can reasonably infer the behaviour of humans and prehumans in more primitive communicative environments by manipulation of the models of linguistic theories is unfounded: we have no idea how such a manipulation would translate into statements about neural organisation, and so no idea how plausible such statements about earlier neural organisation (and the resultant behaviours) are. As such, cognitive interpretations of linguistic theories provide no better ground for statements about behaviour during earlier stages in the evolution of language than guessing. Rejecting internal-mechanism based accounts as unfounded leaves the evolution of language unexplained. In the latter parts of this thesis, I offer a more neutral approach which is sensitive to the limited possibilities available for making predictions about human (and pre-human) behaviour at earlier stages in the evolution of language. Rather than focusing on the individual and imputed internal language machinery, the account considers the communicative affordances available to individuals. The shifts in what individuals can learn to do in interaction with others, that result in turn from the learning of interactive practices by others, form the basis of this account. General trends in the development of communicative affordances are used to account for generalisations over attested semantic change, and to suggest how certain aspects of modern language use developed without simply assuming that it is “natural” for humans to (spontaneously) behave in these ways. The model is used in an account of the evolution and common structure of colour terms across different languages.

In this thesis, I explore the star formation histories of both spiral and elliptical galaxies. In Part 1,1 present an in-depth study of the star formation histories of spiral galaxies with a wide range of properties. Optical and near-infrared colours are used in conjunction with up-to-date stellar population synthesis models to constrain the ages and metallicities of my sample galaxies. I find that age and metallicity gradients are common in spiral galaxies of all types. The age of a spiral galaxy correlates mainly with its surface brightness, and its metallicity correlates strongly with both its surface brightness and absolute magnitude. Using simple models, I demonstrate that the correlations observed in this thesis show that the star formation history of a region within a galaxy depends primarily on its surface density, and possibly on the dynamical time. Metal- enriched outflow from low mass galaxies seems to be required to reproduce a reasonably strong metallicity-magnitude correlation. These variations in star formation history are a continuous function of the physical parameters: in particular, I find no evidence for a bimodal spiral galaxy surface brightness distribution. In Part 2, I present a short study on the formation epoch of early-type galaxies. I developed a photometric redshift estimator optimised for redshifts z ~ 1. The redshift estimator provides redshifts accurate to ~ 10 per cent. This redshift estimator is then applied to a sample of morphologically-selected early-type galaxies in the northern Hubble Deep Field. Comparison of their colour-magnitude relation with a passively evolved Coma cluster colour-magnitude relation indicates that over half of the sample must form at redshifts greater than two.

We present a detailed study of the colours of late-type galaxy discs for ten of the EDisCS galaxy clusters with 0.5 less than or similar to z less than or similar to 0.8. Our cluster sample contains 172 spiral galaxies, and our control sample is composed of 96 field disc galaxies. We deconvolved their ground-based V and I images obtained with FORS2 at the VLT with initial spatial resolutions between 0.4 and 0.8 arcsec to achieve a final resolution of 0.1 arcsec with 0.05 arcsec pixels, which is close to the resolution of the ACS at the HST. After removing the central region of each galaxy to avoid pollution by the bulges, we measured the V - I colours of the discs. We find that 50% of cluster spiral galaxies have disc V - I colours redder by more than 1 sigma of the mean colours of their field counterparts. This is well above the 16% expected for a normal distribution centred on the field disc properties. The prominence of galaxies with red discs depends neither on the mass of their parent cluster nor on the distance of the galaxies to the cluster cores. Passive spiral galaxies constitute 20% of our sample. These systems are not abnormally dusty. They are are made of old stars and are located on the cluster red sequences. Another 24% of our sample is composed of galaxies that are still active and star forming, but less so than galaxies with similar morphologies in the field. These galaxies are naturally located in the blue sequence of their parent cluster colour-magnitude diagrams. The reddest of the discs in clusters must have stopped forming stars more than similar to 5 Gyr ago. Some of them are found among infalling galaxies, suggesting preprocessing. Our results confirm that galaxies are able to continue forming stars for some significant period of time after being accreted into clusters, and suggest that star formation can decline on seemingly long (1 to 5 Gyr) timescales.

When do novel adaptations arise as rearrangements of ancestral components and when do they arise de novo? Answering this question requires direct study of the proximate mechanisms behind novel phenotypes that arise from diverse starting points along different historical contingencies. Here we capitalize on uniquely replicated historical sequences of population establishment in the house finch (Haemorphous mexicanus) to study the evolution of color-producing enzymatic pathways that underlie population divergence in color phenotypes. We first evaluated genetic diversity and differentiation in a neutral marker (the mitochondrial NADH II dehydrogenase gene) across 12 study populations, both in the ancestral range in Arizona and across the Continental Divide in Montana at the range edge. We uncovered 29 haplotypes in our samples, describing 17 new haplotypes for this species. We then examined the influence of inter-population differences (such as habitat, age, and genetic relationships) on variation in the network of enzymatic reactions that produce carotenoid-based coloration in this species. Placing these comparisons in the framework of historical sequence of population establishment allows us to elucidate likely evolutionary trajectories of novel feather color phenotypes in this species.

A revision and a phylogenetic analysis of the genera Zelomorpha Ashmead, 1900 and Hemichoma Enderlein, 1920 were conducted. Phylogenetic analyses used molecular and morphological data. A total of 39 sequences were obtained for COI (887 bases long) and 57 for 28S (1254 bases long). DNA sequences were aligned manually and also aligned with ClustalW (Thompson et al. 1997). Parsimony, Maximum Likelihood, and Bayesian approaches were applied to phylogenetic analyses with each gene region analyzed separately and in a combined analysis. The phylogenetic analysis analyses supported the monophyletic status of the genera Zelomorpha, as defined by Sharkey et al. (2006), and Hemichoma; they upholdseld the hypothesis that the the New World species formerly placed in Biroia belonged to Zelomorpha, and corroborated the synonomy ofgenus Dichelosus with Zelomorpha (Sarmiento and Sharkey, 2005). A total of 3,242 specimens of Hemichoma and Zelomorpha collected through the New World representing 113 species were examined. In addition to the 29 species of Zelomorpha described originally in diverse genera and now moved into the Zelomorpha, 74 new species are described. Seven new species are described for the genus Hemichoma for a total of 10 species. All species are fully redescribed. Fully illustrated keys to the species of Zelomorpha and Hemichoma are provided. The phylogenetic results based on maximum parsimony suggest that, despite the colorful nature of the sister group Hemichoma, species of Zelomorpha were nocturnal and became diurnal secondarily in one lineage. The change to diurnality is linked to a decrease in eye size, to an increase in body size, and to the emergence of colorful patterns. Palatability field tests using lizards as predators of Zelomorpha concinna, a common species with one of the more characteristic and bright color patterns, suggest that the coloration has a warning function and that this wasp is highly unpalatable. Evidence was found that the short ventrally curved ovipositor is an effective defensive structure. DISCLAIMER: The text of this dissertation does not constitute the publication of new species as defined by the International Code of Zoological Nomenclature. The newly estrablished species names in this work will be/have been recognized as valid upon their publication in a peer-reviewed journal.

Searching for active galactic nuclei (AGNs) in dwarf galaxies is important for our understanding of the seed black holes that formed in the early universe. Here, we test infrared selection methods for AGN activity at low galaxy masses. Our parent sample consists of similar to 18,000 nearby dwarf galaxies (M-* < 3 x 10(9) M-circle dot, z < 0.055) in the Sloan Digital Sky Survey with significant detections in the first three bands of the AllWISE data release from the Wide-field Infrared Survey Explorer (WISE). First, we demonstrate that the majority of optically selected AGNs in dwarf galaxies are not selected as AGNs using WISE infrared color diagnostics and that the infrared emission is dominated by the host galaxies. We then investigate the infrared properties of optically selected star-forming dwarf galaxies, finding that the galaxies with the reddest infrared colors are the most compact, with blue optical colors, young stellar ages, and large specific star formation rates. These results indicate that great care must be taken when selecting AGNs in dwarf galaxies using infrared colors, as star-forming dwarf galaxies are capable of heating dust in such a way that mimics the infrared colors of more luminous AGNs. In particular, a simple W1 - W2 color cut alone should not be used to select AGNs in dwarf galaxies. With these complications in mind, we present a sample of 41 dwarf galaxies that fall in the. WISE infrared color space typically occupied by more luminous AGNs and that are worthy of follow-up observations.

Many animals live in societies of varying degrees of organization. Some individuals in these societies seem to sacrifice their own fitness to increase the fitness of some others. Understanding the forces that mould the evolution of such altruistic behaviour has become a dominant theme in modern evolutionary biology. Primitively eusocial polistine wasps provide excellent model systems to study the evolution of altruism as they show high degrees of plasticity in their behaviour. Different individuals in the same population pursue different social strategies such as nesting alpne or nesting in groups. When wasps nest in groups, usually only one individual becomes the egg layer, while die rest assume the role of sterile workers. Why do the workers not become solitary foundresses and rear their own offspring instead of working to rear the brood of another individual? Here I have used the tropical primitively eusocial wasp Ropalidia marginata to explore some factors that might potentially favour the worker strategy over the solitary founding strategy. Workers in multiple foundress nests may benefit by rearing brood more closely related to them than their own offspring would be. However, from previous work on this species it is known that relatedness between sisters is rather low and that workers therefore rear quite distantly related brood. Therefore, I have concentrated on factors other than genetic relatedness that might potentially favour the worker strategy. A total of 145 naturally initiated nests with different numbers of foundresses was monitored over a period of 16 months, and their productivities were compared. Although the total colony productivity increased, the per capita productivity did not increase with increasing foundress numbers. Colonies with larger foundress numbers did not produce significantly heavier progeny and did not produce them significantly faster than colonies with fewer individuals. The conspecific usurpers preferred to usurp single foundress colonies more often than multiple foundress colonies. Therefore, protection from conspecific usurpers might be an advantage of multiple foundress associations. About 10% of the multiple foundress nests experienced queen turnovers. This provides a finite chance to reproduce and gain some individual fitness for workers, at some future point of time. Wasps may not be similar in their reproductive abilities and those who are less fertile might be joining others who are more fertile. Testing such a hypothesis would require that individuals who have chosen to be subordinate cofoundresses in multiple foundress associations are forced to nest alone. During this study a total of 77 nests was monitored. Cofoundresses forced to nest alone had significantly lower productivity than natural solitary foundresses and also queens of multiple foundress nests who were forced to nest alone. This suggested that wasps are not similar either in their reproductive ability or brood rearing ability or both. To ascertain which of the factors was responsible for lower productivity in cofoundresses, productivity of wasps isolated into laboratory cages was compared. There was no significant difference in the productivity of isolated cofoundresses and isolated queens. This suggests that wasps are not subfertile per se but probably differ in their foraging and brood rearing abilities. The certainty with which resources are brought into the nest and therefore, the certainty with which the mean per capita productivity is attained, provides an automatic benefit of group living according to the central limit theorem. This prediction was also tested. The coefficient of variation of mean per capita productivity decreased significantly with increasing foundress numbers. Behavioural observations on another 36 colonies, with different number of adults, showed that the coefficient of variation of food brought to the nest and the rate at which larvae were fed, decreased significantly with increasing number of adults. A computer simulation was used to find out the effect of group size on the variance in feed larva. Assuming that larvae cannot be starved for too long and cannot utilize more than a certain amount of food at a time, the fitness of larvae was found to increase with an increase in the number of adults attending the nest. Previous work on R. marginata has been largely confined to postemergence colonies. An attempt was made to look at and compare social organization in preemergence colonies with that of postemergence colonies. It was found that the egg layer was not the most dominant animal in the well-established preemergence colonies. There were no detectable differences in the social organization of the preemergence colonies (of this study) with that of postemergence colonies of the earlier studies. Perhaps my conclusions drawn from studying preemergence colonies are therefore applicable more widely to the species. It can be concluded that the apparent increased fitness of the worker strategy over solitary foundress strategy does not come from any increase in per capita productivity, but comes instead from (i) the greater predictability with which the mean per capita productivity is attained in larger colonies, (ii) the lower probabilities of usurpation of larger colonies, (iii) queen turnovers that provide opportunities for workers in multiple foundress colonies to gain some direct individual fitness and (iv) the lower brood rearing abilities of workers in multiple foundress nests that make the worker strategy the best of a bad job.

There are several plausible explanations for the initial evolution of aposematism and warning signals but, since these all have support in the form of experimental evidence, it is unlikely that there is one single, simple evolutionary pathway. I investigated the influence of predator psychology on the design of aposematic signals and concentrated on the effects of (innate) colour preferences, learning and memory, using two species of avian predators: ('naYve') domestic chicks (Gallus domesticus) and wild (and therefore experienced) great tits (Paros major). I found that young chicks had innate preferences for some specific colours that were. more saturated and from the long-wavelength part of the spectrum. Furthermore, these preferences were not based on an effect of contrast with the viewing background. However, I did not observe any colour preferences in the great tits, perhaps because they are naturally a generalist species. Domestic chicks trained with two rewarded colours generalise between them to strongly prefer an intermediate colour. I used this phenomenon to further investigate the learning and memorability of colours in chicks. I found an interesting effect, where there is a delay between an encounter with novel prey and when this experience affects behaviour, which could potentially affect avoidance learning. I additionally investigated the relationship between attractiveness and memorability of coloured signals and found that these are potentially distinct features of warning patterns. Finally, observed how great tits learnt and remembered some typically-aposematic colours and compared this to my findings from the chicks. The great tits not only failed to show any colour preferences, but red, yellow and neutral grey stimuli were also equally well learnt in a discrimination task and remembered. The great tits did not show the same generalisation to an intermediate colour as the chicks, but generalised their learning to the novel colour more strongly when the trained colours were unpalatable than when they were palatable

Ornamental traits are considered honest advertisements of fitness, and their evolution is usually explained in terms of sexual selection. This explanation remains unsatisfactory in some instances, for example, juvenile birds whose plumage is molted prior to adulthood and breeding. I first evaluate whether juvenile plumage reflectance signals dominance status in the Federally Threatened Florida scrub-jay (Aphelocoma coerulescens) using a combination of observational and experimental methods. Then I estimate the heritability, non-genetic maternal and environmental effects, and strength of selection on juvenile plumage reflectance using archived feather samples and a pedigree constructed from historical nest records. Finally, I compare plumage reflectance and its use as a signal between a wildland and suburban population of scrub-jays. I conclude that plumage reflectance is a signal of dominance, and that social selection can also drive the evolution of sexually dimorphic traits. In this species, plumage reflectance is heritable and influenced by maternal effects, but environmental effects are inconsequential. Although this trait appears to have an important function, only mean brightness and female hue are associated with lifetime reproductive success. Plumage reflectance was more UV-shifted in the suburban birds, but there is no reason to believe that urbanization decreases the value of this plumage as a signal. However, these plumage differences may facilitate dispersal from suburban areas, contributing to the decline of suburban populations.
Ph.D.
Doctorate
Biology
Sciences
Conservation Biology; Ecology and Organismal Biology Track