A critical examination of Popper’s falsificationism as a methodological criterion of demarcation led to the development o f a supplementary means of distinguishing science from pseudo- science The discipline is made the unit of appraisal and its pattern o f historical development b used as the indicator of demarcation. Results of a test of this indicator against astrology and physical optics accord with our basic judgm ents of these disciplines. The indicator effectively reveals that scientific creationism is pseudo-science, and that evolutionary biology is genuine science. Three fundam ental approaches to scientific investigation, viz. v erificationism , falsificationism and m ulti-cornered testing (M CT) are contrasted. MCT is distinguished by competition between hypotheses, which makes it more informative than at least the naive versions of the other two approaches. While competition does not produce immediate victors, it does make demands on theories, which can be augmented by prescribing a series of independent tests. The comparative method implies the existence of two types of evidence. Common evidence is that which io predicted or explained by two or more rival hypotheses. Discriminatory evidence favours one rival over the others. It is argued that in both the fields of species biology and speciation there have been instances o f over-relying on common evidence, o f indistinctly defining alternative hypotheses, of ro t following their logical consequences and of not using exisiing discriminatory evidence to adjudicate between these hypotheses. Species concepts and definitions of modes o f speciation are evaluated. Normative principles are suggested for defining species and other important terms in evolutionary biology, and for testing species concepts and modes of speciation. The advantages and limitations o f a historical indicator of demarcation and the merits and principles of the comparative approach to method are discussed and illustrated using the analoev of a mathematical game. Scientific crcanomsni is shown to have a coating of scientific method, but to have systematically violated fundamental methodological principles. D arn in ’* method in contrast, had a comparative structure, and distinguished between common *nd discriminatory evidence. While there are methodological problems sn evolutionary biology, these are shown to be minor in comparison to that four*! in to c n o fk ciratxxiiun.

Thesis advisor: Brian Robinette / Thesis advisor: Dominic Doyle / Thesis (STL) — Boston College, 2016. / Submitted to: Boston College. School of Theology and Ministry. / Discipline: Sacred Theology.

Thesis (Ph.D.)--University of the Witwatersrand, Faculty of Science (Anatomical Sciences),1998.

Naturally evolving proteins must navigate a vast set of possible sequences to evolve new functions. This process depends on the genotype-phenotype map. Much effort has been directed at measuring protein genotype phenotype maps to uncover evolutionary trajectories that lead to new functions. Often, these maps are too large to comprehensively measure. Sparsely measured maps, however, are prone to missing key evolutionary trajectories. Many groups turn to computational models to infer missing phenotypes. These models treat mutations as independent perturbations to the genotype-phenotype map. A key question is how to handle non-independent effects known as epistasis. In this dissertation, we address two sources of epistasis: 1) global and 2) local epistasis. We find that incorporating global epistasis improves our predictive power, while local epistasis does not. We use our model to infer unknown phenotypes in the Plasmodium falciparum chloroquine transporter (PfCRT) genotype-phenotype map, a protein responsible for conferring drug resistance in malaria. From these predictions, we uncover key evolutionary trajectories that led high resistance. This dissertation includes previously published and unpublished co-authored material. / 2020-01-11

The Neogene geologic processes and climatic changes had tremendous impact on evolution of biota in different regions of Northern Hemisphere (NH). The Qinghai- Tibetan Plateau (QTP) was a central part of these processes. Migrations from the QTP to other temperate regions represent one of the main biogeographic patterns for Northern Hemisphere. However, this 'out-of-QTP' hypothesis has never been tested through a phylogeographic analysis of a widely distributed species and the ages and routs of these migrations are largely not resolved. On the other hand, climate change played an important role in shaping the amount and structure of intraspecific genetic diversity, which provide the main basic substrate for any evolutionary change. Therefore, a detailed understanding of the effects of historic climate alterations on intraspecific genetic diversity can provide valuable insights into the evolutionary consequences of past climate changes and predicting the likely direction of global warming effects on sustainability of extant populations and species. In this thesis, I first studied the phylogeography of Hippophae rhamnoides to test the 'out-of-QTP' hypothesis (Chapter II). Then, I performed phylogenetic, dating and biogeographic analyses of the genus Hippophae (Chapter III). Finally, I studied the...

Understanding the evolution of cooperative behaviors is a major goal of evolutionary biology, but the majority of research in this field has focused on why helpers assist others. Helpers’ reproductive costs introduce a clear paradox to our understanding of natural selection as helpers in cooperative systems apparently sacrifice reproductive opportunities to increase others’ fitness. This puzzle in cooperative behaviors has led to significant advances in our understanding of indirect and delayed fitness benefits for helpers. However, as cooperation results from the interaction of individuals that may have very different incentives for participation it is equally important to understand whether and how cooperation benefits the dominant recipients of this help. There has been relatively little attention paid to why the recipient of the apparent help participates in the cooperative relationship, in part because the advantage to the dominant individual seems apparent in many systems. Existing work reveals a variety of potential benefits for dominant individuals and that the benefits for dominants may be less obvious than assumed. To date investigations into costs and benefits of cooperation to dominant individuals have been largely limited to cooperative breeding behavior. My dissertation research investigates the fitness consequences of cooperative courtship display for dominant individuals, in the White-ruffed Manakin, Corapipo altera. Manakins (Aves: Pipridae) are small, primarily lekking passerines, and, in some species, males cooperate in their courtship displays. Previous work on manakin cooperative display behavior has focused on benefits to subordinate males. The fitness consequences of cooperation for dominant individuals has not yet addressed in a system with variation in cooperative strategies. I found strong evidence of cooperation among male C. altera. I also found that, within a single population of C. altera on the Atlantic slope of Costa Rica, some males participate in coordinated display with other males (45.4±20% were classified as cooperative in any given year), while other males appear to only display singly. My dissertation research investigated the causes and consequences of cooperation by dominant C. altera males by quantifying aspects of the males' fitness including how inclusive fitness benefits may facilitate the maintenance of cooperative display coalitions and the consequences of cooperative display coalitions for males’ annual reproductive success, survival, and social status — important parts of lifetime fitness for long-lived, iteroparous species including C. altera. I found that cooperative males were not more closely related than expected at random from the population. Males that cooperated did not have higher annual reproductive success than males that displayed solo nor was there a significant difference in the frequency of copulations after a solo courtship display and a courtship display by multiple males. In a survival analysis, cooperation did not significantly affect the survival of dominant males. There was no consistent pattern of cooperation (or non-cooperation) among males across their tenure as dominant male: some were always cooperative, some always non-cooperative, but many males with multi-year tenures switched between cooperative and non-cooperative statuses. However, more males than expected employed strictly solo strategies across their tenure as dominant individuals, given the population-wide rates of survival and cooperation. The degree to which males cooperated, defined as the proportion of tenure classified as cooperative, was unrelated to variation in lifespan or length of tenure as a dominant male. Additionally, the proportion of total tenure classified as cooperative did not explain the patterns of lifetime reproductive success. Together, these results reject the hypotheses that dominant males in cooperative partnerships gain indirect or direct fitness benefits from their associations with subordinate males. Seeking to understand processes underlying patterns of fitness consequences from cooperative behaviors, I conducted three experiments to determine if males at sites where the dominant male was cooperative were faster or more intense in their response to an experimental stimulus. Cooperative males were not faster to respond to a female at the display site nor were they faster to respond to the vocalization of an unknown male conspecific at the display site. Cooperative males were not significantly more likely to respond to a predator model, however, they were significantly more likely to spend time near the snake and lizard models. There could be benefit of sociality in the detection of terrestrial predators. This research addresses previously unexplored aspects of cooperative courtship display, and therefore represents a significant contribution to the more general understanding of the costs and benefits of cooperation. The variation in the amount of cooperation expressed by different individuals of this species offers a unique opportunity to separate the fitness consequences of cooperation by comparing differences in success not only among individuals, but also those among displays in different cooperative contexts by the same individual. / A Dissertation submitted to the Department of Biological Science in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Summer Semester 2017. / July 17, 2017. / cooperation, Corapipo altera, lek, Pipridae / Includes bibliographical references. / Emily H. DuVal, Professor Directing Dissertation; Mike Mesterton-Gibbons, University Representative; Kimberly H. Hughes, Committee Member; David Houle, Committee Member; Scott J. Steppan, Committee Member.

Clonality is the general term that encompasses all manner of pinching, splitting, budding, and fragmenting behaviors by which organisms divide their somatic body tissues into more or less independent units. It can be as straight forward as fragments of a sponge surviving after being rent apart by a hurricane or as convoluted as the telescoping generations of parthenogenic aphids. Clonality is a widespread feature of animal life cycles and the degree of clonal investment is expected to affect everything from spatial genotypic and genetic structure to evolutionary dynamics and ecology interactions. Yet, the shear diversity and complexity of clonal behavior has hampered efforts to develop a general understanding of how and why clonality evolves as the adaptive benefits of these behaviors may be as idiosyncratic as the mechanisms by which cloning occurs. Contrary to some past formulations of the problem, the production of clonal progeny is not typically an alternative to sexual reproduction, as most clonal organisms also reproduce sexually. While there is often an immediate tradeoff where a unit of energy can either be invested in gametes or clonal progeny at any given time, there is not inherently a tradeoff between asexual and sexual reproduction over the span of a lifetime. Dividing somatic tissue in to separate units can be a way of increasing total lifetime fecundity by increasing total biomass, more efficiently colonizing open space or promoting longevity by spreading the risk of mortality over spatially-separated somatic units. With this perspective, understanding the adaptive value of clonality becomes a matter of analyzing the holistic suite of fitness effects that arise from variation in allocating energy among unitary growth, clonal propagation and gametogenesis. The amount of energy available and the fitness value of a particular investment strategy are governed in large part by the environment and so understanding the environmental context is key to understanding the forces shaping life cycle evolution. Temperature, in particular, affects the metabolic cost of maintaining body tissues and is key in determining the energetically optimal body size for a unitary animal. Where temperatures fluctuate seasonally or where clonal replicates may spread across a heterogeneous landscape, the reaction norm of fission rate, body size or traits associated with gamete production may be an important target of selection, influencing which life cycle patterns can evolve. In this dissertation I examine the influence of seasonal and geographic temperature variation on fission rate, body size and gamete production of the clonal sea anemone, Diadumene lineata (Verrill 1869), to better understand the constraints and tradeoffs that govern the evolution of resource allocation strategy; and ultimately, the factors that drive the evolution of clonality in this species. Through a combination of laboratory experiments, field observations, optimality modeling and genetic tools I demonstrate that (1) fission rates are strongly temperature dependent, resulting in seasonal and geographic variation in clonal behavior, (2) the production of gametes is closely tied to body size and shows an inverse latitudinal pattern with fission rate, (3) the observed reaction norm of fission rate with temperature is consistent with selection to maximize gamete production across the locally experienced range of temperatures, as opposed to selection for maximum clonal proliferation, per se, and (4) there is a latitudinal decrease in genotypic richness and diversity that corresponds with changes in fission rate, suggesting that variation in fission rate leads to changes in the spatial structure of genetic variation among sites. Together, these results are consistent with the hypothesis that clonality is adaptive under conditions where individual body size is constrained by the environment. Under these conditions more gametes may be produced over a lifetime by genets dividing somatic tissue into multiple small units rather than remaining a single large unit. In this species, there is an immediate cost to dividing a large body into two pieces as the number of gametes produced by two small individuals sums to less than those produced by a large individual, yet, the lost reproductive potential may be able to be compensated for over time by an increased growth rate at a smaller body size. Additional costs and benefits imposed by changes in mortality rate, competitive ability or mate choice as fission rate changes remain to be investigated and may be equally important in understanding and predicting the evolution of clonal behavior in this and other species. / A Dissertation submitted to the Department of Biological Science in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Summer Semester 2017. / June 19, 2017. / asexual reproduction, clonality, Diadumene lineata, life cycle, phenotypic plasticity, sea anemone / Includes bibliographical references. / Thomas E. Miller, Professor Directing Dissertation; Markus Huettel, University Representative; Kim Hughes, Committee Member; Don Levitan, Committee Member; Janie Wulff, Committee Member.

Non-random mating is presumed to be an important mechanism that allows for the maintenance of genetic variation. Assortative mating has been studied extensively in organisms that possess defined ways in which sperm is transferred to eggs (e.g. via copulation, courtship or vector assisted pollination in plants), but rarely in broadcast spawners. Broadcast spawning is perceived as a mating event that allows for mixing of gametes and promotes random mating. However, there are multiple pathways in which spawning adults can affect fertilization of gametes in non-random ways. For example, positive assortative mating can occur in broadcast spawners if similar phenotypes spawn closer together in space or time, or possess similar gamete recognition proteins that expedite fertilization. Here, I propose to examine assortative fertilization, patterns of aggregation and gamete recognition protein genotype of the sperm bindin gene as a function of spine color in the sea urchin Lytechinus variegatus as well as evaluating deviations from Hardy-Weinberg Equilibrium (HWE) based on color. Results indicate that laboratory crosses of urchins within color morphs yielded higher fertilization success than crosses between color morphs. Field surveys determined that these sea urchins are aggregating by color at times of their reproductive season when they are more likely to spawn. Tests for HWE using field data of urchin phenotypes suggest strong deviations from HWE. However, DNA sequences of regions of the sperm bindin gene for sea urchins of different color do not show evidence of genetic structure of the population. Paternal success in broadcast spawners is largely determined by the proximity of males to spawning females and the compatibility between them at the time they release their gametes. Selection is predicted to favor traits and behaviors that increase the likelihood of spawning near a more compatible neighbor. These results provide strong evidence for assortative mating and an explanation for the maintenance of color variation in this species. / A Thesis submitted to the Department of Biological Science in partial fulfillment of the requirements for the degree of Master of Science. / Summer Semester 2017. / July 18, 2017. / assortative mating, broadcast spawning, color variation, fertilization success, genetic variation / Includes bibliographical references. / Don R. Levitan, Professor Directing Thesis; Kimberly A. Hughes, Committee Member; Scott Burgess, Committee Member.

Understanding how environmental forces, genetic variation, and developmental process combine to mold adaptations remains a core challenge in evolutionary biology. Our research is answering this challenge. More specifically we focused on how these three drivers of adaptation have shaped the evolution of body morphology in poeciliid fish. The body morphology of poeciliid fish has been shown to be under strong ecological selection and sexual selection. In the poecilid fish Poecilia reticulata, body morphology can evolve rapidly, over a span of four to five years. These attributes makes it an ideal system to study the processes leading to adaptive evolution. Here we studied this adaptive evolution in poeciliid fish at two scales: among populations of a single species and within populations of a single species. At the broadest scale, we investigated local adaptation among populations of a single poeciliid species, Heterandria formosa. We quantified patterns in morphological variation among populations and tested for associations between this variation and ecological data, which are derived from long term population censuses. Results from this study illustrate the complicated construction of multivariate phenotypic variation and suggest that different agents of selection have acted on different components of body morphology. These patterns in inter-population phenotypic variation can be evidence of local adaptation; however, they can also be reflective of patterns in phenotypic plasticity induced by environmental or maternal effects. The role of maternal effects are especially relevant in H. formosa as females are live bearing and provide nutrients to developing embryos via a placenta. We used a common garden experiment and a large factorial breeding experiment to explicitly test for genetically based differences among populations in their responses to environmental variation (norms of reaction). This laboratory work allowed a definitive diagnosis of which features actually represented local adaptations among populations of Heterandria formosa. Results showed that male body morphology has a significant genetic component and signs of population specific response to both the environment during post-parturition development and in response to the maternal environment during embyronic development. The narrowest scope of our work focuses on the evolution of body morphology within an experimental population of the Trinidadian guppy. Interestingly, the strength and direction of selection on phenotypic variation is not the same among all individuals within a population. In particular, genetic correlations between the sexes can produce intralocus sexual conflicts (ISC) when selection favors different trait values in the genders. This form of sexual conflict can inhibit the evolution of males and females so that neither sex can reach its optimal trait value. Theory suggests that ISC will have a minimal effect in populations off there adaptive peak such as those in a novel or variable environment. However, ISC is likely to have an inhibitory effect in populations in a stable environment near their adaptive, thereby limiting adaptive evolution. Here we used an experimental population of Trinidadian guppies in a novel environment to unravel the emergence of sexual conflict as populations adapt to novel environments. Guppies from a high predation environment were translocated to a drainage with minimal predation. The phenotypic evolution of the population was tracked monthly. This work incorporates mark-recapture methods, complete pedigree reconstruction using high throughput sequencing, and geometric morphometric shape analysis. Results indicate that there are fitness differences among individuals and different optimal values in males and females but the role of sexual conflict within this population is currently negligible. To conclude, our work investigated the environmental and genetic factors influencing the evolution of body morphology in poeciliid fish. We demonstrate the complicated nature of selection with different selective agents acting on different aspects of body morphology. We found that populations of fish have unique environmental maternal effects which may ultimately be adaptive. We also conclude that while there are optimal trait value differences in males and female guppies but being off the adaptive peak limits the influence of ISC on morphological evolution. / A Dissertation submitted to the Department of Biological Science in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Summer Semester 2018. / July 13, 2018. / Local Adaptation, Morphometric, Poeciliid, Sexual Conflict / Includes bibliographical references. / Joseph Travis, Professor Directing Dissertation; Dennis Slice, University Representative; Emily DuVal, Committee Member; Gregory Erickson, Committee Member; Kimberly Hughes, Committee Member.

Species interactions can regulate a population’s density and therefore can act as a selective force on that population. Such evolutionary responses have the potential to feedback and change ecological interactions between species. For species that compete for resources, the interaction between ecological and evolutionary dynamics will regulate the stability of the species interactions, determining whether competing species can coexist. The outcome of competition between species is determined by two factors: (1) niche overlap, or the similarity in how species use resources and are affected by their environment, and (2) fitness differences, or differences in how efficiently each species uses resources in their environment. Decreasing niche overlap will decrease competitive interactions, thereby stabilizing coexistence. Decreasing fitness differences makes species more equal in their competitive abilities, facilitating coexistence. In the absence of evolutionary constraints, both niche overlap and fitness differences among species are subject to change as a consequence of evolution among competitors, and thus ecological dynamics between two species will also change. In this dissertation, I develop a broader understanding of (1) how niche overlap and fitness differences between species change after evolution in response to competition, (2) how changes in niche overlap and fitness differences are mediated through changes in resource use of protists, and (3) what role evolutionary history plays in shaping ecological and evolutionary dynamics. I address these goals with a suite of approaches including theoretical models, an experimental lab system, and comparative methods. I constructed a quantitative genetic model of trait evolution, where the trait of a species determined its resource use, and found that species are prone to change in their niche overlap as well as their fitness differences as a result of trait evolution. However, the magnitude of changes in niche overlap and fitness differences were determined by the resource availability within the environments. When resources were broadly available, species changed more in their niche overlap, whereas when resources were narrowly available, species changed more in their fitness difference. To test these predictions, I developed a system in the laboratory where protists competed for a bacterial resource. Species were allowed to evolve in either monoculture or a two-species mixture; the effects of evolution on competition, niche overlap and fitness differences were quantified using parameterized models. In general I found that species tended to converge in their niche as a result of evolution, however, changes in fitness differences between species were larger and more influential on coexistence than changes in niche differences. Both increases in niche overlap, and increases in fitness differences decreased coexistence among species pairs. By describing the bacterial communities associated with these protists before and after selection I determined that protists tended to converge or not change in which bacteria they were consuming as a result of selection. Additionally, for eleven protist species, I determined whether traits or relatedness predicted competitive ability by placing species on a molecular phylogeny and conducting pairwise competition experiments for all pairs. I found no correlations, suggesting neither traits, nor evolutionary history was informative for explaining current ecological and evolutionary interactions in this deeply divergent clade. There are two major conclusions from this dissertation: (1) when species evolve in response to competition, changes in fitness differences may often be more important than changes in niche overlap, (2) evolution can, and may be likely to, decrease the ability of species to coexist through increases in niche overlap and increases in fitness differences. This work suggests that one must simultaneously consider the role of evolutionary and ecological processes to understand community processes. Specifically, when researchers are attempting to explain mechanisms of coexistence between species, they must consider how evolutionary dynamics may change the ecological interactions within communities of competitors. / A Dissertation submitted to the Department of Biological Science in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Summer Semester 2017. / August 4, 2017. / Coexistence, Competition, Evolution, Fitness Difference, Niche Overlap, Selection / Includes bibliographical references. / Thomas Miller, Professor Directing Dissertation; Richard Bertram, University Representative; Brian Inouye, Committee Member; Scott Steppan, Committee Member; Alice Winn, Committee Member.