An environmental model of self-compatibility transitions in the solanaceae plant family

Higher level selection processes such as species selection are not generally predicted to overpower individual selection on character traits. Goldberg et al. provide a model derived from collected life history data and argue that species selection is maintaining self-incompatibility in the Solanaceae plant family. This model applies only on the level of the species, not representing the underlying interactions between individuals and the environment. We propose a new model with environmental variation at the individual level that may explain the maintenance and frequency of loss of this character trait. We use individual based modelling techniques to explore our hypothesis, and compare it with that originally proposed. The results show alternative values required for the mutation rate to produce the species level transition frequency under the opposing models, given certain assumptions. Future work is suggested to refine the parameter relationships, test for robustness, and determine if individual models of higher complexity will exhibit similar outcomes

On the Evolutionary Modification of Self-Incompatibility: Implications of Partial Clonality for Allelic Diversity and Genealogical Structure

Experimental investigations of homomorphic self-incompatibility (SI) have revealed an unanticipated level of complexity in its expression, permitting fine regulation over the course of a lifetime or a range of environmental conditions. Many flowering plants express some level of clonal reproduction, and phylogenetic analyses suggest that clonality evolves in a correlated fashion with SI in Solanum (Solanaceae). Here, we use a diffusion approximation to explore the effects on the evolutionary dynamics of SI of vegetative propagation with SI restricted to reproduction through seed. While clonality reduces the strength of frequency-dependent selection maintaining S-allele diversity, much of the great depth typical of S-allele genealogies is preserved. Our results suggest that clonality can play an important role in the evolution of SI systems, and may afford insight into unexplained features of allele genealogies in the Solanaceae

Time and Chance Happen to Them All: A Macroevolutionary Examination of the Effects of Whole Genome Multiplications

Polyploidy, the state of having more than two complete sets of chromosomes, is common in plants and has been linked to several beneficial traits. On the macroevolutionary scale, the effects of polyploidy have been hotly debated for over one hundred years, being alternatively described as an “evolutionary dead end” and the most important discovery in evolutionary biology since Darwin and Wallace. This thesis aims to contribute to the debate by studying the diversification, biogeography, and ecophysiology of polyploid flowering plants with recently developed phylogenetic comparative methods. This dissertation has three chapters. In Chapter I, I review work on the so-called “dead-end hypothesis” in polyploid research, which I argue is in fact multiple hypotheses masquerading as one. I supplement the review with an analysis of tip diversification rates in Solanaceae, employing the MiSSE model. In Chapter II, I examine the “latitudinal polyploidy gradient,” in which polyploid plants comprise greater proportions of the flora at higher latitudes. To compare latitudinal movement and patterns of origination between diploids and polyploids across four flowering plant clades, I use the novel machuruku model to reconstruct ancestral ranges and develop a new function for ancestral state reconstruction within the corHMM package. In Chapter III, I perform the first systematic review and meta-analysis comparing pathogen resistance in diploid and polyploid plants, incorporating phylogenetic information at the family level. Across these three analyses, I do not find support for associations between polyploidy and increased diversification or the evolution of beneficial traits. It is thus possible that any beneficial effects resulting from polyploidy can be chalked up to the “luck of the draw.” Together, these chapters all present novel or under-utilized methods of studying the effects of polyploidy in phylogenetic context

Time and Chance Happen to Them All: A Macroevolutionary Examination of the Effects of Whole Genome Multiplications

Polyploidy, the state of having more than two complete sets of chromosomes, is common in plants and has been linked to several beneficial traits. On the macroevolutionary scale, the effects of polyploidy have been hotly debated for over one hundred years, being alternatively described as an “evolutionary dead end” and the most important discovery in evolutionary biology since Darwin and Wallace. This thesis aims to contribute to the debate by studying the diversification, biogeography, and ecophysiology of polyploid flowering plants with recently developed phylogenetic comparative methods. This dissertation has three chapters. In Chapter I, I review work on the so-called “dead-end hypothesis” in polyploid research, which I argue is in fact multiple hypotheses masquerading as one. I supplement the review with an analysis of tip diversification rates in Solanaceae, employing the MiSSE model. In Chapter II, I examine the “latitudinal polyploidy gradient,” in which polyploid plants comprise greater proportions of the flora at higher latitudes. To compare latitudinal movement and patterns of origination between diploids and polyploids across four flowering plant clades, I use the novel machuruku model to reconstruct ancestral ranges and develop a new function for ancestral state reconstruction within the corHMM package. In Chapter III, I perform the first systematic review and meta-analysis comparing pathogen resistance in diploid and polyploid plants, incorporating phylogenetic information at the family level. Across these three analyses, I do not find support for associations between polyploidy and increased diversification or the evolution of beneficial traits. It is thus possible that any beneficial effects resulting from polyploidy can be chalked up to the “luck of the draw.” Together, these chapters all present novel or under-utilized methods of studying the effects of polyploidy in phylogenetic context

The evolution of group traits: modelling natural selection on trait prevalence within and between groups

One of evolution's greatest innovations was group living; indeed, it is fundamental to our daily lives as humans. Yet despite intense theoretical and empirical work, the details of how group living arose and is maintained are poorly understood. A central question in this area concerns the strength of natural selection operating between groups of organisms (group selection) because some think this is key to the evolution of group behaviour. It is, however, challenging to measure natural selection occurring between groups and between the individuals within those groups simultaneously. Consequently, a number of contentious theoretical issues have plagued group selection research for a number of decades, and empirical work on this topic is often misinterpreted. In this thesis, I investigate three biological systems that are candidates for group selection where empirical data is readily available. Using techniques from theoretical and computational biology - simulations, game theory and population genetics - I model evolution occurring at multiple levels simultaneously (multi-level selection), shedding light on the evolution and maintenance of group traits. First, I consider the evolution of a trait - lateralization - at the population- and colony-level in eusocial organisms, which have a reproductive structure that promotes group organisation and cooperation. I provide an evolutionary explanation for the strength of lateralization in colonies of the red wood ant, Formica rufa, as a compromise between intraspecific and predatory interactions. After extending the analysis to involve predators targeting multiple colonies simultaneously, I show that populations should tend towards an equal distribution of left- and right- lateralized colonies, resulting in zero population-level lateralization. This contradicts the established view that sociality should produce strong levels of lateralization at the population level. Second, I study a sub-social spider, Anelosimus studiosus, which is a group-living species that has recently been claimed to exhibit group-level adaptation. I use evolutionary game theory to explain the evolution of colony aggression with individual costs and benefits, providing an alternative to the existing group-level interpretation. The model generates a striking fit to the data without any between-group interactions. Therefore, I conclude that more evidence is needed to infer group-level adaptation in this colonial spider. Third, I study the Solanaceae, a plant family whose breeding system is reported to have undergone species selection - group selection acting on whole species. I investigate the evolution of self-fertilization over the family's phylogenetic history. By integrating an existing phylogeny with models of breeding system evolution at the individual level, I find the average selection pressure - and attendant properties of populations - expected to have characterised the Solanaceae over ~36 million years. In conclusion, I have shown the power of modelling approaches to clarify evolutionary explanations, to question existing interpretations, and to identify experiments that can help researchers identify the true causes of trait evolution

Polyploidy before and after domestication of crop species

Recent advances in the genomics of polyploid species answer some of the long-standing questions about the role of polyploidy in crop species. Here, we summarize the current literature to reexamine scenarios in which polyploidy played a role both before and after domestication. The prevalence of polyploidy can help to explain environmental robustness in agroecosystems. This review also clarifies the molecular basis of some agriculturally advantageous traits of polyploid crops, including yield increments in polyploid cotton via subfunctionalization, modification of a separated sexuality to selfing in polyploid persimmon via neofunctionalization, and transition to a selfing system via nonfunctionalization combined with epistatic interaction between duplicated S-loci. The rapid progress in genomics and genetics is discussed along with how this will facilitate functional studies of understudied polyploid crop species

The Evolution And Reproductive Ecology Of Oenothera (Onagraceae)

This dissertation describes the role of pollination in the floral diversification of Oenothera with an integration of both ecological and phylogenetic approaches. Oenothera: Onagraceae) is a model system for studying plant reproductive biology. It provides excellent examples of shifts in reproductive traits such as pollination and breeding system, features that have been important in angiosperm diversification. These systems are evolutionarily labile; they easily shift between different states. These different reproductive traits may shift in a concerted fashion; therefore, a more comprehensive approach to understanding the evolution of these plant systems simultaneously addresses shifts in pollination and breeding system. Using 54 species of Oenothera, I first collected detailed data describing the pollination systems, breeding systems, and floral traits associated with pollinator rewards; and second I determined the phylogenetic structure, evolutionary history and relationships among these species. Finally, in that phylogenetic context, I examined the timing and position of transitions in reproductive traits and consider how these traits are associated with pollination and breeding systems. My results offer new insights regarding the specialization of pollination systems and the predictive power of pollination syndromes. I find that specialization in pollination is not accurately characterized by visitation rates alone, and that considering functional groups of visitors to the flowers provides the most informative characterization of pollination systems. I also find that pollination syndromes do not sufficiently or accurately describe these pollination systems. My results also clarify phylogenetic relationships in the genus Oenothera, determine that there have been 13 independent transitions to self-compatibity, and provide the first phylogenetic tree for subsection Kneiffia. I find that pollination and breeding system do not correlate consistently with floral traits, and do not show an association with each other. Finally, I find that the transitions in the reproductive traits reveal a complex and diverse pattern in which shifts in floral traits occur prior and post a transition in pollination system. I also document an example of a rare transition from a generalized pollination system to a specialized pollination system. The placement of floral trait transitions with regards to pollinator shifts suggests selective pressures in floral traits that are predictable and follow transitions to novel dominant pollinator groups, rather than changes in pollination system

Multiple independent origins of auto-pollination in tropical orchids (Bulbophyllum) in light of the hypothesis of selfing as an evolutionary dead end

Background: The transition from outcrossing to selfing has long been portrayed as an ‘evolutionary dead end because, first, reversals are unlikely and, second, selfing lineages suffer from higher rates of extinction owing to a reduced potential for adaptation and the accumulation of deleterious mutations. We tested these two predictions in a clade of Madagascan Bulbophyllum orchids (30 spp.), including eight species where auto-pollinating morphs (i.e., selfers, without a ‘rostellum) co-exist with their pollinator-dependent conspecifics (i.e., outcrossers, possessing a rostellum). Specifically, we addressed this issue on the basis of a time-calibrated phylogeny by means of ancestral character reconstructions and within the state-dependent evolution framework of BiSSE (Binary State Speciation and Extinction), which allowed jointly estimating rates of transition, speciation, and extinction between outcrossing and selfing. Results: The eight species capable of selfing occurred in scattered positions across the phylogeny, with two likely originating in the Pliocene (ca. 4.43.1 Ma), one in the Early Pleistocene (ca. 2.4 Ma), and five since the mid-Pleistocene (ca. 1.3 Ma). We infer that this scattered phylogenetic distribution of selfing is best described by models including up to eight independent outcrossing-to-selfing transitions and very low rates of speciation (and either moderate or zero rates of extinction) associated with selfing. Conclusions: The frequent and irreversible outcrossing-to-selfing transitions in Madagascan Bulbophyllum are clearly congruent with the first prediction of the dead end hypothesis. The inability of our study to conclusively reject or support the likewise predicted higher extinction rate in selfing lineages might be explained by a combination of methodological limitations (low statistical power of our BiSSE approach to reliably estimate extinction in small-sized trees) and evolutionary processes (insufficient time elapsed for selfers to go extinct). We suggest that, in these tropical orchids, a simple genetic basis of selfing (via loss of the ‘rostellum) is needed to explain the strikingly recurrent transitions to selfing, perhaps reflecting rapid response to parallel and novel selective environments over Late Quaternary ( 1.3 Ma) time scales.P20726-B03P17124-B0(VLID)243455

Interactions between breeding system and ploidy affect niche breadth in Solanum

Understanding the factors driving ecological and evolutionary interactions of economically important plant species is important for agricultural sustainability. The geography of crop wild relatives, including wild potatoes (Solanum section Petota), have received attention; however, such information has not been analysed in combination with phylogenetic histories, genomic composition and reproductive systems to identify potential species for use in breeding for abiotic stress tolerance. We used a combination of ordinary least-squares (OLS) and phylogenetic generalized least-squares (PGLM) analyses to identify the discrete climate classes that make up the climate niche that wild potato species inhabit in the context of breeding system and ploidy. Self-incompatible diploid or self-compatible polyploid species significantly increase the number of discrete climate classes within a climate niche inhabited. This result was sustained when correcting for phylogenetic non-independence in the linear model. Our results support the idea that specific breeding system and ploidy combinations increase niche breadth through the decoupling of geographical range and niche diversity, and therefore, these species may be of particular interest for crop adaptation to a changing climate