Dissertations / Theses on the topic 'Evolutionary biology'

My aIm In this thesis is to analyse the 'evolutionary analogy', a particular form. of evolutionary epistemology which claims that scientific change is governed by the same mechanisms, or by mechanisms analogous to those at work in organic evolution, mainly natural selection. In tenns of research questions, the overall aim of this thesis is to answer 'Is the process of scientific change analogous to or even the same as organic change?' Many philosophers proposed evolutionary theories of scientific change - evolutionary analogies. By drawing analogies or even equating the mechanisms of organic and scientific evolution they described the process underlying the latter but also justified its value, implicitly or explicitly, by a simple analogy: better theories are those which survive old ones, as better species are those which survive previous ones. The results of these philosophers, however, have not been satisfactory and a novel approach is needed. In this thesis I am interested in a purely descriptive philosophy of science and my position will be based on the critique of the most recent and comprehensive attempt to defend the evolutionary analogy, made by David Hull. In order to answer the research question I have formulated above, the following issues will be addressed: what is organic evolution;. what is meant by 'evolutionary analogy'; how analogy/identity can be evaluated; how evolutionary analogy/identity has been defended by philosophers; how these defences perform; what is the best defence available; whether it passes the evaluation and, if not, whether it can be improved; if all the positions fail, whether it is possible to conceive alternative analogies between other relevant processes which do not incur the same problems. By addressing these issues, I will be able to conclude that the process of scientific change is different from organic change and that only loose analogies can be defended.

Echinoderms are a highly diverse phylum of marine invertebrates with a good fossil record that extends back 550 million years. The work presented here is a contribution towards documenting their long history both in terms of phylogenetic branching pattern and evolutionary biology. Taxonomy is the primary means by which evolutionary processes can be studied because it is through taxonomy that species are recognised and their relationships to one another established. Taxonomy at various levels thus forms a major part of the thesis. Species are documented and described both for specific time intervals and within monophyletic groups. Relationships above species level are derived employing cladistic methodology and used to investigate various evolutionary concepts (e.g. the molecular clock; periodicity of extinction). Much of this work deals with the phylogenetic relationships of echinoids at various taxonomic levels, but the relationships of major groups within the phylum are also investigated cladistically. Class relationships have been clarified and revised. By combining data on phylogenetic relationships with those on stratigraphical occurrence, evolutionary trees are constructed which are then used to investigate current ideas on evolutionary processes. Topics investigated include punctuated versus gradualistic evolution, periodicity of extinction, the nature of the Cambrian radiation and the 'Red Queen hypothesis'. Artefact produced by taxonomic convention is recognised as a serious problem in many palaeobiological studies. The evolving relationship between echinoderms and their environment is investigated from a functional morphological point of view. Work of Recent faunas provides the key to understanding morphological variation in the fossil record. Evolutionary changes are documented through time and interpreted in biological terms for specific topics, such as tooth ultrastructure, ambulacral arrangement and trace fossil morphology. The relationship of fossil biotas to tectonic events and their application to palaeogeographical reconstruction is investigated quantitatively, both for echinoids and other groups.

Proefschrift Universiteit van Amsterdam.
Omslagtitel: Brunellia : evolutionary biology of Brunellia Ruiz & Pavón (Brunelliaceae, Oxalidales) Met lit. opg. - Met samenvatting in het Nederlands en Spaans.

The sheer complexity of evolutionary systems biology requires us to develop more sophisticated tools for analysis, as well as more probing and biologically relevant representations of the data. My research has focused on three aspects of evolutionary systems biology. I ask whether a gene’s position in the human metabolic network affects the degree to which natural selection prunes variation in that gene. Using a novel orthology inference tool that uses both sequence similarity and gene synteny, I inferred orthologous groups of genes for the full genomes of 8 mammals. With these orthologs, I estimated the selective constraint (the ratio of non-synonymous to synonymous nucleotide substitutions) on 1190 (or 80.2%) of the genes in the metabolic network using a maximum likelihood model of codon evolution and compared this value to the betweenness centrality of each enzyme (a measure of that enzyme’s relative global position in the network). Second, I have focused on the evolution of metabolic systems in the presence of gene and genome duplication. I show that increases in a particular gene’s copy number are correlated with limiting metabolic flux in the reaction associated with that gene. Finally, I have investigated the proliferative cell programs present in 6 different cancers (breast, colorectal, gastrointestinal, lung, oral squamous and prostate cancers). I found an overabundance of genes that share expression between cancer and embryonic tissue and that these genes form modular units within regulatory, proteininteraction, and metabolic networks. This despite the fact that these genes, as well as the proteins they encode and reactions they catalyze show little overlap among cancers, suggesting parallel independent reversion to an embryonic pattern of gene expression.

Fusarium oxysporum Schlecht. is a cosmopolitan species complex that consists of both pathogenic and non-pathogenic members. The pathogenic members are subdivided into formae speciales, based on virulence to specific host species. More than 150 formae speciales have been described, of which F. oxysporum f.sp. cubense (E.F.Smith) Snyder and Hansen (Foc), causal agent of Fusarium wilt of banana, is regarded as one of the economically most important and destructive. According to phenotypic and genotypic markers, Foc has been classified into three races and 24 vegetative compatibility groups, and can be divided into a number of clonal lineages that roughly correspond with VCG groupings. In this thesis, we investigated the evolutionary relationships among VCGs using multi-gene sequencing and MAT genotyping. A PCR-RFLP fingerprint discriminating the Foc lineages and a PCR primer that identified Foc ‘subtropical’ race 4 isolates, was developed. Nine microsatellite markers (SSRs) were applied to a global population of Foc in order to investigate diversity not always detectable using sequencing data. Phylogenetic analysis of isolates representing Foc, various other formae speciales of F. oxysporum and non-pathogenic F. oxysporum of the genes encoding the translation elongation factor-1á (TEF), the mitochondrial small subunit (MtSSU), ribosomal RNA (rRNA), the repeated region encoded on the mitochondrion (MtR) and the intergenic spacer (IGS) gene regions separated these isolates into four clades, two of which included Foc. Within these two clades, Foc separated into six lineages that broadly corresponded to VCGs, while the non-pathogenic isolates of F. oxysporum grouped together in only one of the two clades, with an unknown Foc VCG isolate. The mating type of all isolates was determined and crosses were attempted between isolates harbouring MAT-1 and MAT-2 genes, without success. Cultural, morphological and pathogenic variation among isolates of Foc was unable to identify lineages as species. The separation of Foc isolates into two clades suggested that the banana pathogen evolved during two unrelated events. Factors such as horizontal gene transfer, however, might also have played a part in the pathogen’s evolution, as was evident from the divergent placement of some VCGs and lineages within the phylogenetic trees constructed. The inclusion of other formae speciales of F. oxysporum and non-pathogenic F. oxysporum isolates illustrated the great diversity that exists within the F. oxysporum complex. The inclusion of the Foc isolate of an unknown VCG suggests that the genetic diversity of Foc might be far greater than what is known and what was revealed in this study. The opposite mating types found in the respective lineages indicate a sexual origin for the Fusarium wilt fungus that could account for its polyphyletic nature. Within South Africa, Foc ‘subtropical’ race 4 is regarded the most important constrain to banana production. Conventional control practices for Fusarium wilt of banana are ineffective, and disease management relies heavily on the use of clean planting material and the early detection and isolation of the pathogen, in order to restrict spread to unaffected areas. Identification of Foc typically involves vegetative compatibility assays and pathogenicity testing using a set of differential host cultivars. The development of a PCR-based method for the rapid and accurate identification of Foc ‘subtropical’ race 4 will, therefore, be of great importance. The lack of morphological variation between lineages of Foc, and between pathogenic and non-pathogenic members, as well as the unreliability in race identification in Foc, makes the use of molecular tools a viable alternative. Following DNA isolation, PCR and sequencing of the MtR, the DNA sequence data revealed an 8-bp insertion that was subsequently targeted for the design of a Foc ‘subtropical’ race 4-specific primer. Isolates were positively identified as Foc ‘subtropical’ race 4 with the amplification of an 800-pb fragment. The development of the Foc ‘subtropical’ race 4 primer will aid in rapid and accurate detection of the Fusarium wilt pathogen of banana. The population structure defined according to SSR data of a global population of 239 Foc isolates resembled the structure defined according to multi-gene phylogeny, with some exceptions. Measures of gene and genotypic diversity unequivocally supported the opinion that Asia is the centre of origin of Foc. The presence of unique genotypes in all geographically-defined Foc populations could potentially indicate their evolution outside the centre of origin, although this is highly unlikely. The absence of certain genotypes from the Asian population was either due to insufficient and selective sampling, or it demonstrated the effects of clonal selection in combination with adaptation to the forces of geographic isolation and environmental changes over time. The worldwide collection of Foc mostly consisted of six over represented genotypes, thereby providing support for a clonal genetic structure. It was, however, not possible to reject the hypothesis of a recombining population for the populations representing isolates of Lineage V. The implication of recombination within some Foc lineages may be due to unobserved sexual reproduction in nature or the historical association with a sexual ancestor. When one considers diversity within and among genotypes, a specific genotype was mostly associated with only one or two Foc VCGs, therefore indicating that vegetative compatibility determination, in combination with phylogenetic analyses, is a powerful tool for characterizing isolates causing Fusarium wilt of banana. Results from this study, in combination with the multi-gene phylogeny, clearly indicated the presence of unrelated lineages that most probably represent cryptic species. Copyright 2008, University of Pretoria. All rights reserved. The copyright in this work vests in the University of Pretoria. No part of this work may be reproduced or transmitted in any form or by any means, without the prior written permission of the University of Pretoria. Please cite as follows: Fourie, G 2008, Evolutionary biology of Fusarium oxysporum f.s.p. cubense, MSc dissertation, University of Pretoria, Pretoria, viewed yymmdd < http://upetd.up.ac.za/thesis/available/etd-11192008-094622/> E1216/gm
Dissertation (MSc)--University of Pretoria, 2008.
Microbiology and Plant Pathology
unrestricted

This thesis identifies and explores the meanings of different concepts of fitness currently used in evolutionary biology. Fourteen distinct definitions are described in detail. Understanding of the role of fitness in evolutionary biology requires that historical and cultural factors be appraised. Particular focus is given to the interdisciplinary structure of evolutionary biology. Relative merits of different kinds of theories for representing evolutionary phenomena are examined. A comparison is drawn between hypothetical-deductive explanations, semantic models, schematic arguments and schematic abstractions. The schematic abstraction of Darden and Cain (1989) is concluded to be most appropriate for representing the process of natural selection, when the role of fitness in that process requires clarification. Evolutionary explanations are also analysed from a causal perspective. Although quantum physics casts doubt on whether the world can be described as causal, all explanations identify relevant causes. Hence, a causal analysis of evolutionary processes is used as an "heuristic device" for identifying confusing and contradicting aspects of processes in which fitness features. Inquiry into what constitutes fitness clarifies the relationship of fitness to concepts of adaptation, adaptedness and adaptability. A vital aspect is the unique and complex relationship of adaptive traits to the organism’s life history. Because certain traits are traded off at the level of the life history, and because the life history forms a constraining matrix for organismic selection, natural selection must be regarded as acting on organisms and their life history. Bock and von Wahlert’s (1965) classification of adaptive traits is utilised for characterising the relationship between fitness-bearing traits and the environment. Fitness, as the sum of all fitness-bearing traits, is not causal in determining survival and reproductive success. Causal processes operate at the level of individual traits: in certain situations some traits may, on their own, determine survival and reproductive success and others may not be utilised at all. Since fitness is a potential for traits to realise survival and reproductive success - a potential unique for each organism and, in a wider comparison, unique for each species - it must be regarded as a supervenient property. This enables it to be related to other supervenient properties, invalidating the contention that relevant generalisation can only be drawn from the consequences of fitness, i.e. from relative survival and reproductive success. Particular focus is placed on the process of which fitness is part: natural selection. An analysis of fitness in the Darden and Cain (1989) scheme concludes fitness must incorporate three attributes which are difficult to reconcile: interaction, unit of selection and replication. It clarifies the essential reason many different interpretations of the concept exist: more weight is often given to one attribute in favour of another, or sometimes two attributes combine, leaving the third under-represented. Different interactors and units of selection are found at different levels of selection. The concept of the interactive plane is developed to designate the state-space for a selection process where unit(s) of selection, interactors and environmental factor(s) interact. Discussion of Wimsatt’s (1981) context-independence criterion and Lloyd’s (1988) additivity standard further specifies how levels of selection can be identified. It is followed by an investigation of the role of fitness in selection processes occurring at different levels of biological organisation. When the role of fitness in natural selection is analysed, the central premise of the thesis becomes apparent: procurement, by the interactor, of an ecological benefit as a necessary prerequisite to survival and reproductive success. This recognised, it becomes possible to "map" several complex routes through which benefit can be translated into survival and reproductive success. Fitness can be maximised by other processes operative within the wider parameters of natural selection. Two processes are identified: niche construction and phenocopy. Similar to natural selection, both have a benefit occurring as a prerequisite for differential survival and reproductive success. Since niche construction and phenocopy processes only occur at the organismal level, they reassert the central role of the organism in microevolution. In addition, these processes broaden the perspective on the definition of a selective environment. The role of fitness in microevolution is dissimilar to that in macroevolution. Fitness’s of different evolutionary entities are non-transitive, so the fitness of a species cannot be extrapolated from the fitness’s of its constituent organisms and populations. It is argued that genealogical entities only possess fitness if they can be placed in a relevant ecological context. As genealogical entities above the species have no coherent ecological role to play, they cannot be allocated a fitness value. The role of fitness in the process of species selection is explored. It is concluded that fitness-bearing traits of species in the macroevolutionary context must be regarded as predispositions for fitness bearing traits in microevolution. When the concept of fitness as regards adaptation, natural selection and macroevolutionary processes is clarified, the fourteen biological fitness definitions are re-evaluated in this expanded frame of reference. Such a reappraisal leads to the conclusion that the concept of fitness embodies two incompatible roles of interaction and replication, either in a micro- or macroevolutionary context. In the last chapter, a further analysis of different forms of reasoning in evolutionary biology concludes that the predominant focus on replication can be attributed to the demand in genetics to explain hereditary patterns, resulting in the utilisation of compositional forms of reasoning. These stand in contrast to evolutionary forms for which a temporal and directional element is a necessary part of the explanation. A proper assessment of interaction requires evolutionary forms of reasoning, whereas replication is best suited to compositional ones. This distinction underpins the subsequent proposal that the role of fitness can best be represented by a two-stage model. The first stage would investigate causes for fitness differences and how these causes translate into ecological benefits for interactors. The second stage would focus on evolutionary consequences of fitness: how benefits obtained by interactors translate into the survival and reproductive success of evolutionary replicators. Of central importance to this two-stage model is the ability to translate ecological benefits obtained by individual interactors in a contingent ecological setting into a measure of longer-term survival of less individual replicators in the wider evolutionary context.

Understanding the diversity of life is one of the main aims of evolutionary biology, and requires knowledge of the occurrence and causes of adaptive genetic differentiation among geographically distinct populations. Environmental stress caused by acidity may cause strong directional selection in natural populations, but is little explored from an evolutionary perspective. In this thesis, a series of laboratory experiments and field data was used to study evolutionary and ecological responses of amphibians to environmental acidity.

Local adaptation to acid stress was studied in the moor frog (Rana arvalis).The results show that acid origin populations have higher acid stress tolerance during the embryonic stages than neutral origin populations, and that acid and neutral origin populations have diverged in embryonic and larval life-histories. The mechanisms underlying adaptive differentiation are partially mediated by maternal effects related to extra-embryonic membranes and egg size. Acid origin females invest in larger eggs and have a stronger egg size-fecundity trade-off than females from neutral areas, likely reflecting adaptive differentiation in maternal investment patterns.

Potential carry-over effects of low pH, and the effects of UV-b/pH interaction were investigated in the common frog (R. temporaria). The results suggest that amphibian larvae are able to compensate for the negative effects of acidity experienced early in life, if conditions later turn beneficial. R. temporaria populations differed in their sensitivity to synergistic effects of low pH/UV-B, indicating variation in population responses to environmental stress.

In conclusion, these results suggest rapid evolution in response to human induced environmental change, much of which may be mediated via adaptive maternal effects. Acidification may be a powerful selective force shaping life-history evolution.

DNA-DNA hybridization experiments were used to examine the genetic variation that has accumulated with the North American Biological Species (NABS) of Armillaria. Forty strains including nine of the ten NABS and A. tabescens were used in this study. The normalized percent hybridization values ranged from 80%-100% similarity within a given biological species and ranged from 30%-85% among the biological species, The NPH data was summarized with UPGMA clustering analysis to give four main clustering groups, two were homogeneous and two were heterogeneous, The first included A. tabescens; the second included A. mellea; the third included A. calvescens, A. gallica, A. sinapina, NABS IX, and NABS X; the fourth included A. gemina and A. ostoyae. One cluster of two A. gallica strains shared greater similarity with NABS X than it had to four other conspecific strains, The NPH data and estimates of genome size (genetic complexity) was analyzed using a stoichiometric approach to calculate equivalents of homologous DNA and low copy repetition frequencies. Reciprocal NPH values did not predict relative genome size as expected, However, as the relative genome size increases, the equivalents of homologous DNA increases in the same proportion. This suggests that as an Armillaria genome increases in total complexity (novel sequences), certain ancestral sequences are duplicated in proportion the increase in total genetic complexity, This interpretation of the data is discussed with respect to interspecific hybridization, diploidy, and chromosomal evolution including alloploidy, aneuploidy, and chromosomal length polymorphisms.
Ph. D.

Part A studies the optimal strategies of seed germination problems where the population has a class structure under a fluctuating environment . In particular, a multidimensional age-class model is studied using a dynamical programming method. Numerical results about the so-called optimal stochastic strategy which consists of information about previous environmental states are computed. Comparing the optimal stochastic strategy with the optimal population-based strategy shows that the optimal stochastic strategy is highly effective in genera.l. A potentially useful diffusion approximation for the seed germination problem is also derived with numerical results. For part B, a multi-dimensional Moran model is studied using a diffusion approximation approach. The scaling limit and corresponding governing stochastic partial differential equations (SDEs) are derived. An expansion method is used to approximate the stationary distribution of the SDEs. An approximation formula for the effective migration rate is then derived.

The Negativicutes are a class of bacteria within the predominantly Grampositive phylum Firmicutes that possess a diderm Gram-negative cell envelope along with lipopolysaccharides. Remarkably, some members of this class of Gram-negative bacteria can form endospores. The evolutionary origins of this enigmatic class were investigated through bioinformatics analyses, which defined and characterised their Gram-negative and Gram-positive toolkits, while analyses of Gram-negative signature proteins provided insights into the origins of the Gram-negative toolkit. The genome of Sporomusa sphaeroides, a sporulating species from the Negativicutes, was sequenced and annotated for the first time. In addition, the transcriptional landscapes of Veillonella parvula and Sporomusa sphaeroides during logarithmic and stationary phase growth were investigated using RNA-Seq, expanding the repertoire of known genome features, including non-coding RNAs within these species.

The potential restriction to effective dispersal and gene flow caused by habitat fragmentation can apply to multiple levels of evolutionary scale; from the fragmentation of ancient supercontinents driving diversification and speciation on disjunct landmasses, to the isolation of proximate populations as a result of their inability to cross intervening unsuitable habitat. Investigating the role of habitat fragmentation in driving diversity within and among taxa can thus include inferences of phylogenetic relationships among taxa, assessments of intraspecific phylogeographic structure and analyses of gene flow among neighbouring populations. The proposed Gondwanan clade within the chironomid (non-biting midge) subfamily Orthocladiinae (Diptera: Chironomidae) represents a model system for investigating the role that population fragmentation and isolation has played at different evolutionary scales. A pilot study by Krosch et al (2009) indentified several highly divergent lineages restricted to ancient rainforest refugia and limited gene flow among proximate sites within a refuge for one member of this clade, Echinocladius martini Cranston. This study provided a framework for investigating the evolutionary history of this taxon and its relatives more thoroughly. Populations of E. martini were sampled in the Paluma bioregion of northeast Queensland to investigate patterns of fine-scale within- and among-stream dispersal and gene flow within a refuge more rigorously. Data was incorporated from Krosch et al (2009) and additional sites were sampled up- and downstream of the original sites. Analyses of genetic structure revealed strong natal site fidelity and high genetic structure among geographically proximate streams. Little evidence was found for regular headwater exchange among upstream sites, but there was distinct evidence for rare adult flight among sites on separate stream reaches. Overall, however, the distribution of shared haplotypes implied that both larval and adult dispersal was largely limited to the natal stream channel. Patterns of regional phylogeographic structure were examined in two related austral orthoclad taxa – Naonella forsythi Boothroyd from New Zealand and Ferringtonia patagonica Sæther and Andersen from southern South America – to provide a comparison with patterns revealed in their close relative E. martini. Both taxa inhabit tectonically active areas of the southern hemisphere that have also experienced several glaciation events throughout the Plio-Pleistocene that are thought to have affected population structure dramatically in many taxa. Four highly divergent lineages estimated to have diverged since the late Miocene were revealed in each taxon, mirroring patterns in E. martini; however, there was no evidence for local geographical endemism, implying substantial range expansion post-diversification. The differences in pattern evident among the three related taxa were suggested to have been influenced by variation in the responses of closed forest habitat to climatic fluctuations during interglacial periods across the three landmasses. Phylogeographic structure in E. martini was resolved at a continental scale by expanding upon the sampling design of Krosch et al (2009) to encompass populations in southeast Queensland, New South Wales and Victoria. Patterns of phylogeographic structure were consistent with expectations and several previously unrecognised lineages were revealed from central- and southern Australia that were geographically endemic to closed forest refugia. Estimated divergence times were congruent with the timing of Plio-Pleistocene rainforest contractions across the east coast of Australia. This suggested that dispersal and gene flow of E. martini among isolated refugia was highly restricted and that this taxon was susceptible to the impacts of habitat change. Broader phylogenetic relationships among taxa considered to be members of this Gondwanan orthoclad group were resolved in order to test expected patterns of evolutionary affinities across the austral continents. The inferred phylogeny and estimated divergence times did not accord with expected patterns based on the geological sequence of break-up of the Gondwanan supercontinent and implied instead several transoceanic dispersal events post-vicariance. Difficulties in appropriate taxonomic sampling and accurate calibration of molecular phylogenies notwithstanding, the sampling regime implemented in the current study has been the most intensive yet performed for austral members of the Orthocladiinae and unsurprisingly has revealed both novel taxa and phylogenetic relationships within and among described genera. Several novel associations between life stages are made here for both described and previously unknown taxa. Investigating evolutionary relationships within and among members of this clade of proposed Gondwanan orthoclad taxa has demonstrated that a complex interaction between historical population fragmentation and dispersal at several levels of evolutionary scale has been important in driving diversification in this group. While interruptions to migration, colonisation and gene flow driven by population fragmentation have clearly contributed to the development and maintenance of much of the diversity present in this group, long-distance dispersal has also played a role in influencing diversification of continental biotas and facilitating gene flow among disjunct populations.

Antechinus is an Australian genus of small carnivorous marsupials. Since 2012, the number of described species in the genus has increased by 50% from ten to fifteen. The systematic relationships of these new species and others in the genus have not been well resolved and a broad phylogeographic study of the genus is lacking. Moreover, little ecological information is known about these new species. Therefore, the present thesis examined the evolutionary biology of Antechinus in two complimentary components. The first component aimed to resolve the systematics and phylogeography of the genus Antechinus. The second component, at a finer spatiotemporal scale, aimed to improve understanding of the autecology, habitat use and risk of extinction within the group, with a focus on the recently named buff-footed antechinus, A. mysticus and a partially sympatric congener, A. subtropicus.

Previous work has demonstrated that coflowering plant species (those that flower simultaneously in the same place) can potentially compete for pollination services. Competition for pollination among plant species can negatively impact their reproductive success. To minimise competition, plants can partition the activity of shared pollinators through releasing their floral resources at different times. Resource partitioning has been studied in several individual plant species, and some guilds of plants (e.g. African acacias), but little is known about temporal changes in resources at a community level. This thesis examines the spatiotemporal changes of floral resources at a community level and its implications for pollinator activity patterns. The temporal patterns of nectar and pollen provision of 70 plant species in two different plots were investigated at Mpala, in north central Kenya between 2004 and 2006. The communities studied showed that seasonal and daily microclimatic fluctuations significantly affect flowering patterns, times of flower opening, dehiscence and nectar production; and consequently the overall amount of pollen mass and nectar volume available at different times. I explored the effects of daily temporal changes in floral resource availability on pollinator activity patterns both in a guild of Malvaceae plant species, and at the community level through pollination webs. Detailed observations of daily patterns of resource provision and floral visitation in six Malvaceae plant species showed that plants can effectively avoid competition through attracting different pollinators, and via resource partition. Examination of daily changes in resource availability and the links portrayed in plant-visitor webs revealed that visitors move from one plant species to another, actively tracking changes in floral resource provision. These results suggest that in combination with physiological limitations imposed to the pollinators by temperature, bottom-up influences are a main force shaping daily pollinator activity patterns at a community level. Competition for pollination can only occur if plant species flower simultaneously and share pollinators within the same geographic area. Competition for pollination has been investigated in at least two African communities, but none of these studies have assessed the geographic spatial scale over which competition among coflowering species might happen. With the aim of measuring the geographic distance that pollinators visiting African acacias fly whilst foraging, I used molecular techniques to conduct paternity analysis as a proxy of how far pollen is carried away from particular trees within a population of Senegalia (Acacia) mellifera. The paternity analysis showed that pollinators move on average a maximum of 60 metres from the sampled trees, and that trees producing more flowers (resources) receive more visits, confirming that if sufficient resources are available pollinators can stay within relatively small geographic areas. Pollen movement only provides a partial measurement of the genetic neighbourhood of individual plants, because genes via seed dispersal can travel longer distances than those encompassed by the pollinators foraging areas. To investigate patterns of genetic variability in S. mellifera, I used microsatellites to conduct landscape genetic analyses including 25 adult populations and 9 seedling populations. Fourteen distinctive genetic clusters separated by four main geographic barriers were identified in the analyses. Significantly higher inbreeding was found in the seedling populations than in the adult populations. I discuss the possibility that this situation has been caused by anthropogenic exploitation and fragmentation of the adult stands.

In this thesis I explore the co-evolutionary dynamics of defences and counter-defences in a predator-prey interaction. I hypothesize that the cost of defences and counter-defences result in the cycling of these traits under all circumstances: directional selection alternate between increasing and decreasing trait values (defense of the prey and counter-defense of the predator). Using Taricha granulosa and Thamnophis sirtalis as an example of a predator-dangerous prey system, I modeled the ecological and evolutionary dynamics of predator-prey interactions and analyzed the results from equations and simulations. The cost of counter-defence influenced evolutionary dynamics most: high or low values of cost stabilized the evolutionary dynamics to constant phenotypes; intermediate values of cost destabilized the equilibrium causing cycling or diversification. Contrary to what I hypothesized, under most parameter values the predator-prey system does not cycle. My study shows predator-dangerous prey coevolutionary dynamics are always mostly influenced by predator parameters.
Dans cette thèse, j'explore les dynamiques évolutives de défense et contre-défense dans un système de prédateurs et proies. Je fais l'hypothèse que les coûts associés aux traits de défense et contre-défense ont pour conséquence des cycles évolutifs de ces traits dans tous les environnements : la sélection directionnelle fluctue pour augmenter et diminuer les valeurs de traits (défense de la proie et contre-défense du prédateur). En utilisant Taricha granulosa et Thamnophis sirtalis comme exemple de système des prédateurs-proies, j'ai modélisé leur dynamiques écologiques et évolutives et j'ai étudié le système de façon analytique et par des simulations. Le coût des contre-défenses est le facteur le plus important pour déterminer les dynamiques évolutives : des valeurs fortes ou faibles du coût stabilisent les dynamiques évolutives sur des phénotypes constants; des valeurs intermédiaires du coût déstabilisent l'équilibre en engendrant des cycles ou de la diversification. Contrairement à mon hypothèse de départ, le système de prédateurs et proies ne produit pas de cycle évolutif pour la plupart des valeurs de paramètres. Mon étude montre que les interactions entre les prédateurs et les proies dangereuses sont toujours surtout influencées par les paramètres du prédateur.

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Biology, 2019
Cataloged from PDF version of thesis.
Includes bibliographical references (pages 156-168).
The composite members of the human gut microbiome encounter a myriad of selective pressures from the host environment and other microbial members in the ecosystem. Understanding the evolutionary dynamics of microbial species in the gut microbiome requires sequencing information that differentiates strains and even single cells. In this thesis, I present efforts that investigate the evolution of bacterial strains in their complex natural environments. In the first project, I discover that a commensal species, Bacteroides fragilis, undergoes within-person adaptive evolution in the absence of antibiotics. Combining culture-based whole genome sequencing with metagenomes, I uncover genes important to B. fragilis survival in the human gut microbiome and describe evolutionary dynamics within individuals and across populations. In the second project, I developed a strain-tracking method that predicts personal microbiomes. Using this method to track closely-related strains, I discover signals of adaptive evolution for Bacteroidetes strains, potentially over decades of colonization in adult twins. In the final project, this strain-tracking method is applied to advance the analysis of microbial transmission within social networks of Fiji islanders. These projects demonstrate the power of genome-resolved and strain-resolved methods in revealing insights of evolutionary dynamics of the gut microbiome. Future studies are expected to further investigate other taxonomical groups in depth and technical breakthroughs are needed to improve the throughput of evolutionary studies of complex systems like the gut microbiome.
by Shijie Zhao.
Ph. D.
Ph.D. Massachusetts Institute of Technology, Department of Biology

Krüppel-related zinc finger proteins constitute the largest single class of transcription factors within the human genome. Members of this protein family have the ability to either activate or repress transcription depending on the presence of specific activator or repressor domains within the protein. Approximately one third of the Krüppel-related zinc finger proteins contain an evolutionarily well-conserved repressor domain termed the KRAB domain. This domain acts as a potent repressor of transcription by interacting with the co-repressor protein, TIF1β. TIF1β then, in turn, recruits HP1 proteins, HDACs and probably other proteins involved in gene silencing. In order to identify novel KRAB-containing zinc finger proteins, one mouse monocytic cDNA library and two testis cDNA libraries were screened for novel members of this multigene family. Six novel KRAB-ZNF cDNAs, four mouse and two human, were isolated. The corresponding proteins were all shown to contain N-terminally located KRAB domains as well as varying numbers of C-terminally located zinc finger motifs. An extensive comparative sequence analysis of the KRAB domains of these proteins together with KRAB domains from a large number of previously identified KRAB-ZNF proteins resulted in a clear subdivision into three different subfamilies, A+B, A+b and A. Later, we also isolated a fourth KRAB box, which is present downstream of the KRAB A box in a few proteins of the KRAB A family. This module was named KRAB C. Potential functional differences between these different subfamilies were investigated. In line with previous observations, the KRAB A box was shown to repress transcription, an activity which was enhanced by the presence of the KRAB B box. However, addition of neither the KRAB b box nor the KRAB C box had any effect on repression. Moreover, all KRAB A motifs had the ability to bind TIF1β, and this binding was increased both by the presence of the KRAB B box and by the KRAB C box. The KRAB b box, however, did not seem to contribute to TIF1β-binding. One of the novel human cDNAs, HKr19, was found to be a member of the large ZNF91 family of KRAB zinc finger genes. Interestingly, the expression of HKr19 and a number of other closely related genes were restricted to lymphoid cells, indicating that these genes may be involved in regulating lineage commitment. The effect of HKr19 on cell viability was investigated by transfection into human embryonic kidney cells (HEK 293). The results indicated that HKr19, or its zinc finger domain in isolation, were toxic to these cells when expressed at high levels. The MZF6D protein, on the other hand, showed a testis-specific expression. In situ hybridization analysis located this expression to meiotic germ cells, suggesting a role for this protein in spermatogenesis. Further, the evolutionary perspectives of this large gene family were addressed, and its enormous expansion throughout evolution probably includes numerous duplication events. The results from two extensive sequence analyses give clues to how the repetitive nature of the ZNF motif has given rise to both internal duplications of single motifs as well as duplications of entire genes resulting in gene clusters.

The characteristics of space and the movement of agents are intrinsic elements which are fundamental to any class of biological problems. From the diffusion properties of small and macromolecules in the cytoplasm, to the migration patterns of populations in a macroecological perspective, it is now clear that a full understanding of the different phenomena requires further insights not only on how the different elements interact, but on the different ways they are distributed in space, according to the proper spatial scales for each problem. This work analyzes three different classes of biological problems, focusing on the role played by space in understanding the phenomena from a theoretical perspective. First, we investigate the clustering of mechanosensitive channels on bacterial membranes and how their spatial distribution can lead to collective behaviour, significantly altering their functions. Second, we study protein production, trying to understand how particular properties on ribosomes' diffusion are linked with specific features of the translation process. Finally, on a very different scale, we explore spatial patterns' formation on a coevolutionary problem, where the interaction between two species is site-dependent. We approach these problems with different analytical and numerical techniques, revealing new biological aspects and providing novel views on current discussions in each field. We believe our results reinforce the importance of theoretical approaches to Biology and how space can significantly change many of these models.

Evolutionary novelty, the origin of new characters such as the turtle shell or the flower, is a fundamental problem for an evolutionary view of life. Accordingly, it is a central research topic in contemporary biology involving input from several biological disciplines and explanations at several levels of organization. As such it raises questions relative to scientific collaboration and multi-level explanations. Novelty is also involved in theoretical debates in evolutionary biology. It has been appropriated by evo-devo, a scientific synthesis linking research on evolution and development. Thanks to its focus on development, evo-devo claims to explain the mechanistic origin of novelties as new forms, while the Modern Synthesis can only provide statistical explanation of evolutionary change. The origin of an evolutionary novelty is a historical emergence of a new character involving form and function. I focus on three neglected dimensions of the problem of novelty, the functional-historical approach to the problem, research on novelty in the Modern Synthesis era and novelty in plants. I compare the evo-devo approach to novelty to a functional-historical approach of novelty. I focus on its origin in Darwin and its presence in the Modern Synthesis. The comparison of the two approaches reveals distance between conceptual frameworks and proximity in explanatory practices. This is partly related to unwarranted conceptual opposition. In particular, I list several ways of distinguishing novelty and adaptation, some of which are not conceptually sound. I then focus on the relation between novelty and adaptation in the Modern Synthesis era, and on the relation of novelty to other fundamental biological problems (speciation, origin of higher taxa, complexity). Pushing this approach further, I challenge the view that the Modern Synthesis excluded development and reached a hardened consensus. Finally, I analyse how Günter Wagner's developmental theory of novelty applies to novelties in plant.

In this thesis I analyze the evolutionary ethics and propose a new perspective that develops on the notion of altruism. The view of evolutionary ethics, especially the sociobiological account, has some problems. The most important philosophical problem is the &ldquo
is-ought&rdquo
problem which refers to the question as to whether moral propositions can be inferred from factual statements. In order to overcome this problem I suggest a different reading of the notion of altruism namely &ldquo
altruistic behavior practice&rdquo
that refers to norms, habits and repeated actions that provide the sustainability of society. The notion of altruistic behavior practice is presented and evaluated with the help of Alasdair MacIntyre&rsquo
s and John Dewey&rsquo
s moral philosophy. The moral views of these two philosophers are based on human practices and habitual formations in society. In this respect, evolutionary ethics and the notion of altruism are re-established on the basis of human practices and habitual modes of socialization.

Long-range regulatory regions play important functions in the regulation of transcription and are particularly involved in the precise spatio-temporal expression of target genes. Such regions have specific characteristics, among which is their ability to regulate many target genes that can be located up to 1Mb from the transcription start site. The prediction and functional characterization of such regions remains an open problem. Evolutionary approaches have been developed to detect regulatory regions that are under purifying selection. However, little has been done with regards to the impact of long-range regulation on genome evolution.
This thesis focuses on three different aspects of long-range regulation: i/ First we develop a method that predicts regions particularly prone to the fixation of evolutionary breakpoints. We discuss the results obtained in the context of long-range regulation and show that this type of regulation is a major factor shaping vertebrate genomes in evolution. ii/ The second project aims at predicting functional interactions between regulatory regions and target genes based on the observation of evolutionary rearrangements in various vertebrate species. We show how this approach produces a biologically meaningful prediction dataset that will be useful to researchers working on regulation. iii/ Third, we focus on the in vivo characterization of regulatory regions. We present a powerful and reliable enhancer detection pipeline composed of an in silico approach to predict putative enhancers and an in vivo method to functionally characterize the expression specificity of predicted regions in the developing medaka fish.
The results presented in this thesis contribute to different areas of research such as a better understanding of evolutionary dynamics related to evolutionary rearrangements and to a better in silico and in vivo characterization of cis-regulatory regions.
La régulation longue distance a d'importantes fonctions dans la régulation de la transcription et est particulièrement impliquée dans la régulation spatiale et temporelle des gènes cibles. Ces régions ont des caractèristiques spécifiques telles que la capacité de contrôler different gènes à des distances jusqu'a 1Mb du site d'initiation de la transcription. La prédiction et la caractérisation fonctionelle de ces regions restent un problème d'actualité. Des approches évolutionaires ont été d´eveloppées pour détecter les régions sous pression de sélection. En revanche, peu a été fait en rapport avec l'impact de la régulation de longue distance sur l'évolution du génome.
Cette thèse se concentre sur trois differents aspects de la régulation longue distance: i/ Premièrement, nous developpons une méthode de prédiction des regions particulièrement sujettes à la fixation des réarrangements de l'évolution. Nous étudions les résultats obtenus dans le contexte de la régulation longue distance et nous montrons que ce type de régulation est un composant majeur dans le façonnement du génome au cours de l'évolution. ii/ Le second projet à pour but de prédire les interactions fonctionnelles entre les régions de régulation et leur gènes cible à partir de l'observation de réarrangements de l'évolution dans differentes espèces. Nous montrons comment une telle approche produit des resultants biologiquement significatifs qui seront particulièrement utiles aux chercheurs travaillant dans le domaine de la régulation. iii/ Troisièmement, nous nous concentrons sur la caractérisation fonctionnelle in vivo des regions régulatrices. Nous présentons une méthode fiable de détection des enhancers composée d'une approche informatique pour la prédiction de ces régions et d'une approche biologique pour caractériser fonctionnellement les spécificités d'expression de ces régions dans le poisson medaka.
Les résultats présentés dans cette thèse contribuent à une meilleure comprehension des dynamiques d'évolution en relation avec la régulation longue distance et une meilleure prédiction et caractérisation fonctionnelle de ces régions régulatrices.

Populations exposed to changing environments often decline in abundance and may therefore find themselves at risk of extinction. Safe abundances can be regained, and persistence secured, when populations can adapt fast enough. Here I ask how population and environmental factors determine a population's ability to persist in changing environments by adapting genetically. In Chapter 2 I investigate the response to a gradual, directional change in the environment and in Chapter 3 I investigate the response to a sudden, sustained shift. Chapter 3 also discusses the effects of interspecific competition. In both chapters I use the canonical equation of adaptive dynamics, which allows me to derive analytical expressions while including ecological process neglected in previous theory; in particular, I consider logistic population growth, frequency-dependent intraspecific competition, and interspecific competition. I use computer simulations to examine the accuracy of my analytical results when the simplifying assumptions of adaptive dynamics are relaxed. Chapter 2 derives the trait lag which maximizes the rate of evolution and also computes this maximum. Populations with higher mutational input experiencing stronger selection have the ability to adapt faster. Computer simulations show that the derived maximum rate of evolution is a good predictor of extinction across a wide range of parameter values, including those that deviate from the assumptions of adaptive dynamics. Chapter 3 first uncovers an expression for the population trait value across time and then uses this expression to calculate the time a population is below a threshold abundance, the 'time at risk'. The population trait value approaches the fitness peak quickly at first, and the rate declines exponentially. Populations with greater mutational input and maximum abundance, and those which are initially better adapted spend less time at risk. The time at risk is maximized at intermediate selection strengths, as strong selection lowers abundance and weak selection slows adaptation. Simulations show good alignment when mutations are rare and population sizes small. Interspecific competition lowers the abundance of the focal population, generally increasing the time at risk, but this can be compensated for under particular scenarios by increased selection pressure. Interspecific competition can sometimes speed adaptation and foster persistence. The ecological and evolutionary response of natural populations to environmental change depends on complex ecological interactions. Theory and experiments which include such interactions are needed for accurate descriptions of genetic adaptation to environmental change, in both the lab and in the wild.
Les populations exposées à des environnements changeants déclinent souvent en abondance et peuvent ainsi être confrontées à un risque d'extinction. Des abondances suffisantes peuvent être retrouvées, ainsi qu'une persistance durable, quand les populations peuvent s'adapter suffisamment vite. Dans cette étude, je me demande comment les facteurs des populations et de l'environnement déterminent la capacité des populations à persister dans des environnements changeants grâce à une adaptation génétique. Dans le chapitre 2, j'étudie la réponse à un changement graduel et directionnel de l'environnement, et dans le chapitre 3, j'étudie la réponse à un changement soudain et soutenu. Le chapitre 3 discute également les effets de la compétition interspécifique. Dans les deux chapitres, j'utilise l'équation canonique des dynamiques adaptatives, ce qui me permet d'en dériver des expressions analytiques ainsi que d'y inclure des processus écologiques négligés dans les théories précédentes; en particulier, je considère la croissance logistique des populations, la compétition intraspécifique fréquence-dépendante, et la compétition interspécifique. J'utilise des simulations informatiques pour examiner l'exactitude de mes résultats analytiques lorsque les hypothèses simplificatrices des dynamiques sont relâchées. Le chapitre 2 dérive le retard de trait, ce qui maximise le taux d'évolution, et aussi calcule ce maximum. Les populations avec le plus grand apport de mutation rencontrant une sélection plus forte ont la capacité de s'adapter plus vite. Les simulations informatiques montrent que le taux maximal d'évolution est un bon prédicteur de l'extinction pour une large gamme de valeur de paramètres, incluant ceux qui dévient des hypothèses de dynamiques adaptatives. Le chapitre 3 dérive, tout d'abord, une expression pour la valeur de trait de population au cours du temps et, ensuite, utilise cette expression pour calculer le temps durant lequel une population se trouve sous le seuil d'abondance, le « temps du risque ». La valeur de trait de population s'approche, tout d'abord, du pic de fitness, puis le taux décline de manière exponentielle. Les populations avec un plus grand apport de mutation et une abondance maximale, et celles qui sont initialement mieux adaptées passent moins de temps dans la zone à risque. Le temps du risque est maximal à des intensités de sélection intermédiaires, puisque de fortes sélections diminuent l'abondance et de faibles sélections ralentissent l'adaptation. Les simulations montrent un bon alignement quand les mutations sont rares et les tailles des populations sont petites. La compétition interspécifique diminue l'abondance de la population focale, en accroissant généralement le temps du risque, mais cela peut être compensé pour des scénarios particuliers par un accroissement de la pression de sélection. La réponse écologique et évolutive des populations naturelles à un changement environnemental dépend de phénomènes écologiques complexes. Les théories et les expériences qui incluent de tels phénomènes sont nécessaires pour des descriptions précises de l'adaptation génétique à un changement environnemental, à la fois en laboratoire et dans la nature.

Whole-genome duplication (WGD), which leads to polyploidy, has been implicated in speciation and biological novelty. In plants, many species have experienced historical bouts of WGD or exhibit extant ploidy variation, which is likely representative of an early stage in the evolution of new polyploid lineages. To elucidate the evolutionary dynamics of autopolyploids and species with multiple ploidy levels, I develop population genetic theory in Chapter 2 that I use in Chapter 4 to extract information about the evolutionary history of Arabidopsis arenosa, a European wildflower that has diploid and autotetraploid populations. Chapter 3 involves a separate project exploring the ascertainment bias in restriction site associated DNA sequencing (RADseq). In Chapter 2, I develop coalescent models for autotetraploid species with tetrasomic inheritance and show that the ancestral genetic process in a large population without recombination may be approximated using Kingman’s standard coalescent, with a coalescent effective population size 4N. Using this result, I was able to use existing coalescent simulation programs to show in Chapter 4 that, in A. arenosa, a widespread autotetraploid race arose from a single ancestral population. This autopolyploidization event was not accompanied by immediate reproductive isolation between diploids and tetraploids in this species, as I find evidence of extensive interploidy admixture between diploid and tetraploid populations that are geographically close. To draw these conclusions about population history in Chapter 4, I used a reduced representation genome-sequencing approach based on restriction digestion. However, I was bothered by the possibility that sampling chromosomes based on restriction digestion may introduce a bias in allele frequency estimation due to polymorphisms in restriction sites. To explore the effects of this nonrandom sampling and its sensitivity to different evolutionary parameters, we developed a coalescent-simulation framework in Chapter 3 to mimic the biased recovery of chromosomes in RAdseq experiments. We show that loci with missing haplotypes have estimated diversity statistic values that can deviate dramatically from true values and are also enriched for particular genealogical histories. These results urge caution when applying this technique to make population genetic inferences and helped me tailor analyses in Chapter 4 to accommodate for this particular method of DNA sequencing.
Biology, Organismic and Evolutionary

I investigated patterns of genetic variation in the North American gall-forming aphid, Pemphigus obesinymphae. In Chapters 2a and 2b, I developed and then implemented clone-specific molecular markers to investigate clonal mixing in P. obesinymphae . During its gall-forming phase, P. obesinymphae clones produce aggressive larval "soldiers", which altruistically defend their colonies from natural enemies. I showed that movement occurs between galls, indicating that P. obesinymphae colonies are not pure clones. I also showed that intruders behave selfishly, by not defending unrelated clones, and by accelerating development into reproductive adults. These results reveal a greater degree of complexity and conflict in aphid social groups than previously known. In Chapter 2c, I surveyed molecular variation in P. obesinymphae and its bacterial endosymbiont, Buchnera aphidicola. I found levels of variation at two Buchnera loci to be similar to those estimated from a previous study on a distantly-related aphid, Uroleucon ambrosiae. In the western US, P. obesinymphae and B. aphidicola were nearly monomorphic, and in the eastern US, estimates of synonymous divergence ranged from 0.08 to 0.16%. Most polymorphisms in sub-populations at low frequencies, indicating a recent purge of ancestral polymorphism. These results emphasize the importance of aphid population biology in shaping evolutionary patterns in B. aphidicola. In Chapter 2d, I explored the role of life cycle variation in speciation between Pemphigus aphids. P. obesinymphae and P. populi-transversus are closely-related and sympatric on the cottonwood, Populus deltoides (Salicaceae), but they have distinctly different life cycles. P. populi-transversus has a sexual stage that occurs in the fall, while P. obesinymphae produces sexuales in late spring. Field evidence indicates that intermediate phenotypes rarely occur, and mitochondrial and bacterial endosymbiont DNA sequences show no maternal gene flow between the two species. I considered the possibility of an initial allopatric phase in the divergence, and discuss the sequence of evolutionary changes that likely led to the sympatric divergence of P. populi-transversus and P. obesinymphae. The most plausible interpretation of available data is that a shift in timing of the life cycle in an ancestral population spurred divergence between the species pair.

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Biology, 2015.
This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.
Cataloged from student-submitted PDF version of thesis.
Includes bibliographical references (pages 92-96).
One of the most interesting discoveries of the last decade is the surprising degree of phenotypic variability between individual cells in clonal microbial populations, even in identical environments. While some variation is an inevitable consequence of low numbers of regulatory molecules in cells, the magnitude of the variability is nevertheless an evolvable trait whose quantitative parameters can be "tuned" by the biochemical characteristics and architecture of the underlying gene network. This raises the question of what adaptive advantage might be conferred to cells that implement high variation in their decision-making. Currently, the predominant answer in the field is that stochastic gene expression allows cells to "hedge their bets" against unpredictable and potentially catastrophic environmental shifts. We proposed and experimentally demonstrated an alternative solution: that heterogeneity implements the evolutionarily stable mixed strategy (or mixed ESS), from the field of evolutionary game theory. In a mixed ESS, phenotypic heterogeneity is a result of competitive interactions between cells in the population rather than a response to uncertain environments, so unlike with bet-hedging, in a mixed ESS the evolutionary fitness of different phenotypes is frequency dependent. Each phenotype can invade the other when rare, and the resulting equilibrium-the stable mix of the two-is not necessarily the one that maximizes the population's fitness. We demonstrated these and other predictions of the mixed ESS using engineered "pure strategist" strains of the yeast GAL network. We demonstrated also that the wild type mixed strategist can invade both pure strategists and is uninvasible by either. Taken together, our results provide experimental evidence that evolutionary hawk-dove games between identical cells can explain the phenotypic heterogeneity found in clonal microbial populations.
by David W. Healey.
Ph. D.

Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Biology, 2006.
"September 2006."
Includes bibliographical references (leaves 37-38).
I have researched the effect that selection for the function of the High Osmolarity Glycerol (HOG) pathway has on the evolutionary stability of the pheromone response pathway in the yeast Saccharomyces cerevisiae. I first set out to demonstrate that, because the pheromone and HOG response pathways share protein components, selection for HOG function will enrich a population for cells capable of pheromone response. I performed experiments in both continuous and batch culture to demonstrate this effect. I then characterized the decay of the pheromone response pathway first, by measuring its mutation rate and second, by measuring the fitness of a series of strains with pheromone response gene deletions. I conclude with thoughts on possible experiments that may be used to further this research.
by Jeffrey S. Gritton.
S.M.

Thesis (Ph.D.)--Indiana University, Dept. of Biology 2009.
Title from home page (viewed on Jul 8, 2010). Source: Dissertation Abstracts International, Volume: 70-10, Section: B, page: 5957. Advisers: Loren H. Rieseberg; Scott D. Michaels.

In this thesis, I used the filamentous ascomycete genus Neurospora as a model to test theoretical predictions on the evolutionary consequences of different reproductive strategies and reproductive gene evolution. The genus Neurospora contains taxa representing a diversity of reproductive strategies, and here I constructed a phylogeny by which I was able to show that several independent transitions in reproductive mode have occurred in the evolutionary history of the genus. This feature makes Neurospora a suitable model for the evolution of reproductive modes. Molecular evolutionary analysis of housekeeping genes revealed an accelerated protein evolution in the highly inbreeding homothallic taxa, in accordance with theory predictions of lower efficiency of selection in asexual and highly inbreeding taxa. Furthermore, self-sterile (heterothallic) taxa capable of asexual propagation was found to be associated with a three-fold higher neutral substitution rate, indicative of a higher mutation accumulation due to elevated number of cell divisions per unit time in these taxa. Further, I have shown a general pattern of rapid evolution of genes involved in reproduction in Neurospora, thus extending the pattern of general high divergence of reproductive genes previously well known in animals, to fungi. Two rapidly evolving reproductive genes: the pheromone receptor genes pre-1 and pre-2 involved in mate recognition were studied in detail. For the gene pre-1 the rapid divergence was found to be driven by positive selection in both heterothallic and homothallic taxa. The rapid divergence of the pheromone receptor gene pre-2 cannot be explained by positive selection and for this gene a subtle differences in evolutionary constraints between heterothallic and homothallic taxa were found. The general similarity in evolutionary constraints of pre-genes in taxa of both mating-systems indicates that these genes serve other functions beside mate recognition.

Despite the important role spatial processes play in natural communities, far too little theoretical work has been devoted to exploring how complex food web communities may be assembled in space, and how the spatial structure of trophic interactions may provide a stabilizing mechanism for complex food web networks. In this thesis I develop a food web metacommunity model based on a classic Levins-type patch-dynamic model which views trophic interactions between species as occurring in a spatially subdivided habitat. I then use this model to explore both simple and complex trophic networks in an ecological and evolutionary context. I first review and evaluate previous attempts at defining a patch-dynamic metacommunity model of trophic interactions. After correcting the flaws in previously published models I develop a corrected model and apply it to simple trophic configurations. I show how the stability of simple trophic interactions, like omnivory loops, depends upon the interacting effects of space and network configuration. I then use the model to study the evolution of dispersal in a simple predator-prey system. Specifically, I investigate how both predator and prey dispersal rates will evolve in response to increasing patch extinction rates caused by locally strong top-down predator effects. I show how the predator's evolutionarily stable (ESS) dispersal rate will increase, as expected, in response to increasing local extinction, while the prey's ESS dispersal rate exhibits a counterintuitive nonmonotonic response – actually decreasing for some ranges of extinction. I explain how the prey's counterintuitive response arises because of the way trophic interactions between species play out at different spatial scales. After applying the model to simple networks I then explore the assembly of complex food webs. I show that, under very simple assumptions, diverse and complex food web networks can be assembled through the creation of network branches which provide opportunities for the build-up species and multiple food chain paths in the food web. I also show how these network branches can emerge simply as the result of the spatial distribution of trophic interactions, and the structural support provided by omnivory and generalist feeding links. I then attempt to determine if natural food webs show a relationship between biodiversity and network branching. To this end I examine a set of empirical food webs and observe a striking linear scaling relationship between food web size and the degree of branching in the minimum spanning tree of a food web. This empirical corroboration of the theory suggests that the theory reported here may be of value as a guide to how space and dispersal interact to structure natural food webs at large scales.
Malgré l'importance des processus spatiaux dans les communautés écologiques naturelles, peu de théories examinent le rôle de l'espace dans l'assemblage et la stabilisation des réseaux trophiques complexes. Dans cette thèse, je développe un modèle de réseau trophique spatial (métacommunauté) fondé sur un model dynamique de métapopulation du type Levins, où les interactions trophiques entres les espèces ont lieu au sein d'une série de populations locales. Ce modèle de métacommunauté me permet d'examiner les réseaux trophiques simples et complexes dans un contexte écologique et évolutif.Dans le premier chapitre, je résume et critique les modèles actuels de métacommunauté du type Levins incorporant les interactions trophiques dans un contexte spatial. Après avoir identifié les erreurs de ces modèles, je développe un modèle corrigé afin d'examiner des réseaux trophiques simples. Je montre que la stabilité des interactions trophiques simples (telles que les boucles omnivores) dépend de l'interaction entre la structure spatiale et la topologie du réseau trophique. Dans le deuxième chapitre, j'utilise ce modèle afin de déterminer l'évolution du taux de dispersion du prédateur et de sa proie lorsque la prédation favorise l'extinction des populations locales. Je montre que face à une augmentation du taux d'extinction, le taux de dispersion évolutivement stable du prédateur augmente de façon monotone alors que celui de la proie varie de façon non-monotone et diminue pour certains niveaux d'extinction. Je démontre que cette réponse contre-intuitive de la proie est due à la structure spatiale des interactions trophiques entre les espèces.Dans le troisième chapitre, j'utilise le modèle afin d'étudier l'assemblage de réseaux trophiques complexes dans l'espace. Je montre que l'addition de branches dans le réseau trophique (ramification) permet l'accumulation d'espèces dans des chaînes alimentaires distinctes et la création de réseaux trophiques complexes. Je démontre que cette ramification du réseau trophique est due à la distribution spatiale des interactions trophiques ainsi que le support structurel apporté par les boucles omnivores et généralistes.Dans le quatrième chapitre, j'essaye de déterminer si la relation entre la biodiversité et la ramification des réseaux trophiques observée dans le modèle est applicable aux réseaux trophiques naturels. Je montre qu'il existe une forte relation linéaire entre la taille des réseaux trophiques naturels et le nombre de branches qui caractérise leur arbre couvrant minimum. Cette vérification empirique du modèle indique que la théorie développée dans cette thèse pourrait permettre de mieux comprendre les rôles que jouent l'espace et de la dispersion dans l'assemblage et la structure des réseaux trophiques naturels à grandes échelles.

I conducted a series of studies which looked at influences on avian clutch size. Firstly I examined the traditional view that the demands of rearing chicks create a bottleneck at which clutch size is shaped by natural selection. I considered whether instead other stages such as incubation might also be important. I proposed that reproductive demands at each stage of the breeding season may be interdependent, and by developing a mathematical model, I formalised the argument and showed that data on the relationship between the number of offspring and the expenditure of resources at many stages of the season could reveal the importance of natural selection on clutch size at each stage. I then reviewed the literature on the importance of incubation for clutch size determination. Results indicated that metabolic demands of incubation were appreciable and that the incubation of enlarged clutches imposed penalties on the adults. In a field study of kittiwakes I found that breeding success was depressed during incubation and chick rearing by enlargement of clutches and broods respectively. I measured metabolic rates of kittiwakes during incubation and found them to be comparable with those during chick-rearing. Secondly, I examined whether individual adults within populations differed in their reproductive capacities (i.e. whether there was a range of 'adult quality') and whether this could then affect clutch size. In a study of kittiwakes I found clusters of birds with similar breeding performance, but found that these clusters did not persist between years. In a study of swifts, I found that some individuals were consistently good breeders but that this had negligible effects on the distribution of lifetime reproductive success between individuals. I then examined whether the low clutch sizes and high survival of swifts might reflect a bet-hedging strategy in a fluctuating environment, but found little evidence of this. I looked at whether differences in the amount of space available at the nest site could account for differences in clutch sizes of kittiwakes, but could find no such evidence. Lastly I developed a theoretical model to look at how clutch size might be affected by changes in reproductive effort with age. I examined whether the predictions of optimality models were borne out by the more appropriate population genetics approach and found that in birds the optimality models are robust.

Production of mutant biological molecules for understanding biological principles or as therapeutic agents has gained considerable interest recently. Synthetic genes are today being widely used for production of such molecules due to the substantial decrease in the costs associated with gene synthesis technology. Along one such line, we have engineered tRNA genes in order to dissect the effects of G:U base-pairs on the accuracy of the protein translation machinery. Our results provide greater detail into the thermodynamic interactions between tRNA molecules and an Elongation Factor protein (termed EF-Tu in bacteria and eEF1A in eukaryotes) and how these interactions influence the delivery of aminoacylated tRNAs to the ribosome. We anticipate that our studies not only shed light on the basic mechanisms of molecular machines but may also help us to develop therapeutic or novel proteins that contain unnatural amino acids. Further, the manipulation of the translation machinery holds promise for the development of new methods to understand the origins of life. Along another line, we have used the power of synthetic biology to experimentally validate an evolutionary model. We exploited the functional diversity contained within the EF-Tu/eEF1A gene family to experimentally validate the model of evolution termed ‘heterotachy’. Heterotachy refers to a switch in a site’s mutational rate class. For instance, a site in a protein sequence may be invariant across all bacterial homologs while that same site may be highly variable across eukaryotic homologs. Such patterns imply that the selective constraints acting on this site differs between bacteria and eukaryotes. Despite intense efforts and large interest in understanding these patterns, no studies have experimentally validated these concepts until now. In the present study, we analyzed EF-Tu/eEF1A gene family members between bacteria and eukaryotes to identify heterotachous patterns (also called Type-I functional divergence). We applied statistical tests to identify sites possibly responsible for biomolecular functional divergence between EF-Tu and eEF1A. We then synthesized protein variants in the laboratory to validate our computational predictions. The results demonstrate for the first time that the identification of heterotachous sites can be specifically implicated in functional divergence among homologous proteins. In total, this work supports an evolutionary synthetic biology paradigm that in one direction uses synthetic molecules to better understand the mechanisms and constraints governing biomolecular behavior while in another direction uses principles of molecular sequence evolution to generate novel biomolecules that have utility for industry and/or biomedicine.

The unique nature of island ecosystems have fascinated generations of naturalists, ecologists, and evolutionary biologists. Studying island systems led to the development of keystone biological theories including: Darwin and Wallace's theories of natural selection, Carlquist's insights into the biology of adaptive radiations, MacArthur and Wilson's theory of island biogeography, and many others. Utilizing islands as natural laboratories allows us to discover the underlying fabric of ecology and evolutionary biology. This dissertation represents my attempt to contribute to this long and storied scientific history by thoroughly investigating two aspects of island biology: 1. the role of island climate in shaping drought tolerance of woody plants, and 2. the absence of mammalian herbivores from insular environments and its effects on woody plant defenses.

These goals were accomplished by quantifying functional trait patterns, seasonal water relations, and plant defenses among closely-related species pairs of chaparral shrubs from matched field sites on Santa Catalina Island and the adjacent Santa Ana Mountains in southern California. This experimental design allowed me to test for repeated evolutionary divergences across island and mainland environments and to examine the evolutionary trade-offs between traits.

Chapter 1 focuses on differences in dry season water availability and hydraulic safety between island and mainland chaparral shrubs by measuring seasonal water relations and cavitation resistance. My results suggest that island plants are more buffered than mainland relatives from the harsh summer drought conditions that characterize the Mediterranean type climate region of California. Furthermore, island plants exhibit increased hydraulic safety margins that suggest island plants may fare better than mainland relatives during episodes of increasing aridity.

Chapter 2 examines an exhaustive suite of 12 functional traits that characterize the drought-related functional strategies of island and mainland chaparral shrubs. Island plants have more mesomorphic leaf and canopy traits than mainland relatives. However, stem hydraulic traits are surprisingly similar between the island and mainland environments despite large differences in seasonal water relations. The differences between patterns at the leaf and stem levels may be related to the existence of evolutionary correlations for leaf traits but not for stem traits. Multivariate principal component analyses suggest that island plants are employing a very different suite of functional traits than their mainland relatives that allows them to take advantage of the more moderate conditions that characterize the island environment without sacrificing increased vulnerability to drought at the stem level.

Chapter 3 tests the hypothesis that the absence of mammalian herbivores throughout most of Santa Catalina Island's history has selected for plants that are less defended and more palatable than mainland relatives that have experienced more consistent browsing pressure. My results confirm that island plants have fewer morphological defenses and are more preferred by mammalian herbivores compared to close relatives from the mainland. These findings also suggest that island plants are more vulnerable to browsing by introduced mammalian herbivores. This vulnerability should be taken into account when making management decisions concerning introduced herbivores on islands.

In conclusion, chaparral shrubs on Santa Catalina Island have different levels of drought tolerance and herbivore defenses compared to mainland relatives that affect how they are likely to be impacted by climate change and other anthropogenic alterations of the insular environment. Furthermore, the pattern of evolutionary divergences between island and mainland plants reported in this dissertation offer new insights into how drought tolerance and herbivore defenses are shaped by environmental factors.

The purpose of this dissertation was to explore the status of and relationships among the variables of teacher acceptance of evolutionary theory, teacher understanding of evolutionary theory, and teacher understanding of the nature of science among Indiana public high school biology teachers. The relationships between these variables and the emphasis evolution receives in the classroom and teacher academic variables were investigated. Teacher knowledge structure of the concept of evolution was also explored.To answer the questions and hypotheses delineated in the study, a 68-item questionnaire and concept mapping activity was administered to the population of 989 teachers. The response rate was 53%.The teachers exhibited only a moderate level of acceptance and a marginal level of understanding of evolutionary theory. Teacher understanding of the nature of science was moderately high. Evolution played only a minor role in the curriculum. While the teachers had completed considerable course work in biology, the vast majority lacked specific course work in evolution and the nature of science.The data revealed a significant relationship between teacher acceptance and teacher understanding of evolutionary theory and between teacher acceptance of evolutionary theory and teacher understanding of the nature of science. The data also revealed significant associations between teacher allocation of instructional time to evolution and teacher level of acceptance of evolutionary theory, teacher level of understanding of evolutionary theory, teacher level of understanding of the nature of science, and teacher completion of a course in evolution. Additionally, the data revealed significant associations between teacher level of understanding of evolutionary theory and teacher completion of a course in evolution and teacher academic background in biology. Significant associations were revealed between teacher level of acceptance of evolutionary theory and both teacher completion of a course in evolution and teacher completion of a course in the nature of science.A significant amount of the variance in teacher acceptance of evolutionary theory was explained by the other variables delineated. The concept mapping activity revealed that teacher acceptance and understanding of evolutionary theory was reflected in teacher knowledge structure of evolution and that teachers' knowledge structures were characterized by an unsophisticated organizational framework.
Department of Biology

Thesis: Ph. D. in Microbiology Graduate Program, Massachusetts Institute of Technology, Department of Biology, 2019
Cataloged from PDF version of thesis.
Includes bibliographical references.
Microbes have adapted to life in complex microbial communities in a large variety of ways, and they are continually evolving to better compete in their changing environments. But identifying the conditions that a particular microbe thrives under, and how they have become adapted to those condition can be exceedingly difficult. For instance, Clostridium difficile became widely known for being the world's leading cause of hospital associated diarrhea, but people can also have C. difficile in their gut without developing diarrhea. Although these asymptomatic carriers are now thought to be the largest source of infection, we know very little about how these people become colonized. In the first chapter of my thesis I use publicly available microbiome survey data and a mouse model of colonization to show that C. difficile colonizes people immediately after diarrheal illnesses, suggesting C. difficile is a disturbance adapted opportunist.
However, the differences between very recently diverged microbial populations that are adapted for growth in different conditions can be very difficult to detect. To address this limitation, I developed a method of identifying regions that have undergone recent selective sweeps in these populations as a means of distinguishing them, and specifically quantifying their abundance in complex environments. But part of what makes microbial evolution so difficult to interpret is the vast diversity of genes that are only shared by a fraction of all the members in a population. To better understand how these flexible regions are structured, I systematically extracted all contiguous flexible regions in nine marine Vibrio populations and compared their organization and evolutionary histories.
I found that horizontal gene transfer and social interactions have led to the evolution of modular gene clusters that mediate forms of social cooperation, metabolic tradeoffs, and make up a substantial portion of these flexible genomic regions. The observations made in these studies help us understand how microbes are organized into socially and ecologically cohesive groups, and how they have evolved to interact with complex and changing environments.
by David VanInsberghe.
Ph. D. in Microbiology Graduate Program
Ph.D.inMicrobiologyGraduateProgram Massachusetts Institute of Technology, Department of Biology